bims-skolko Biomed News
on Scholarly communication
Issue of 2021–11–07
twenty-one papers selected by
Thomas Krichel, Open Library Society
  1. For NGOs, article-processing charges sap conservation funds.
  2. Editorial: preventing the publication of falsified research.
  3. Editors between Support and Control by the Digital Infrastructure - Tracing the Peer Review Process with Data from an Editorial Management System.
  4. The Peer Review Process During the COVID-19 Pandemic.
  5. Medical Journal Content Continues Rapid Growth.
  6. Open Data Practices among Users of Primary Biodiversity Data.
  7. ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures.
  8. Colour blindness: journals should enable image redisplay.
  9. The importance of adherence to international standards for depositing open data in public repositories.
  10. An analysis of invitations for article submission received via e-mails.
  11. Article categories, treatment cohort studied, and countries publishing in Journal of Renal Care 2019-2021.
  12. Providing English and native language quotes in qualitative research: A call to action.
  13. How Your Writing Can Succeed: Getting a Manuscript Accepted by The American Journal of Gastroenterology.
  14. Comparing dream to reality: an assessment of adherence of the first generation of preregistered studies.
  15. Software review: The JATSdecoder package-extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed central's open access database.
  16. Science communication skills as an asset across disciplines: A 10-year case study of students' motivation patterns at Université Laval.
  17. Transparent Peer Review: A Look Inside the Peer Review Process.
  18. The Revista Ştiinţifică "Vasile Adamachi" and its role in forming national and international scientific awareness of Greater Romania, 1910-1933.
  19. Inclusion, Exclusion and Equity in Academic Credentials in Relation to The Review Process in Scholarly Publications.
  20. Advancing Diversity, Equity, and Inclusion in Scientific Publishing.
  21. [How-to case report].
  1. Nature. 2021 Nov;599(7883): 32
    For NGOs, article-processing charges sap conservation funds.
    Kevin A Wood, Julia L Newth, Geoff M Hilton.
      
    Keywords:  Conservation biology; Environmental sciences; Publishing
    DOI:  https://doi.org/10.1038/d41586-021-02979-5
  2. Toxicol Res (Camb). 2021 Oct;10(5): 961
    Editorial: preventing the publication of falsified research.
      
    DOI:  https://doi.org/10.1093/toxres/tfab090
  3. Front Res Metr Anal. 2021 ;6 747562
    Editors between Support and Control by the Digital Infrastructure - Tracing the Peer Review Process with Data from an Editorial Management System.
    Judith Hartstein, Clemens Blümel.
      Many journals now rely on editorial management systems, which are supposed to support the administration and decision making of editors, while aiming at making the process of communication faster and more transparent to both reviewers and authors. Yet, little is known about how these infrastructures support, stabilize, transform or change existing editorial practices. Research suggests that editorial management systems as digital infrastructures are adapted to the local needs at scholarly journals and reflect main realms of activities. Recently, it has been established that in a minimal case, the peer review process is comprised of postulation, consultation, decision and administration. By exploring process generated data from a publisher's editorial management system, we investigate the ways by which the digital infrastructure is used and how it represents the different realms of the process of peer review. How does the infrastructure support, strengthen or restrain editorial agency for administrating the process? In our study, we investigate editorial processes and practices with their data traces captured by an editorial management system. We do so by making use of the internal representation of manuscript life cycles from submission to decision for 14,000 manuscripts submitted to a biomedical publisher. Reconstructing the processes applying social network analysis, we found that the individual steps in the process have no strict order, other than could be expected with regard to the software patent. However, patterns can be observed, as to which stages manuscripts are most likely to go through in an ordered fashion. We also found the different realms of the peer review process represented in the system, some events, however, indicate that the infrastructure offers more control and observation of the peer review process, thereby strengthening the editorial role in the governance of peer review while at the same time the infrastructure oversees the editors' performance.
    Keywords:  digital infrastructure; digital transformation of scholarly publishing; editorial management systems; peer review; process generated data
    DOI:  https://doi.org/10.3389/frma.2021.747562
  4. Fed Pract. 2021 Jul;38(7): 298-299
    The Peer Review Process During the COVID-19 Pandemic.
    Reid A Paul, Joyce Brody, Cynthia M A Geppert.
      
    DOI:  https://doi.org/10.12788/fp.0157
  5. Arthroscopy. 2021 Nov;pii: S0749-8063(21)00822-7. [Epub ahead of print]37(11): 3221-3222
    Medical Journal Content Continues Rapid Growth.
    James H Lubowitz, Jefferson C Brand, Michael J Rossi.
      Medical journal content continues to expand at a rapid rate. This is promising for the future of innovation and patient care but challenging for clinicians and scientists. We feature new journals, new social media platforms, educational advertisements, illuminating Letters to the Editor and enlightening Author Replies, Podcasts, Visual Abstracts, and Infographics. This is a developmental time for medical journal publication.
    DOI:  https://doi.org/10.1016/j.arthro.2021.09.006
  6. Bioscience. 2021 Nov;71(11): 1128-1147
    Open Data Practices among Users of Primary Biodiversity Data.
    Caitlin P Mandeville, Wouter Koch, Erlend B Nilsen, Anders G Finstad.
      Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.
    Keywords:  applied ecology; biodiversity; informatics; monitoring and mapping; publication practices
    DOI:  https://doi.org/10.1093/biosci/biab072
  7. Microbiol Resour Announc. 2021 Nov 04. 10(44): e0087121
    ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures.
    Jacob L Steenwyk, Antonis Rokas.
      Clear and effective figures are central to successfully communicating scientific data. Here, we present ggpubfigs, an R package with colorblind-friendly color palettes and extensions of the ggplot2 graphic system, which helps make publication-quality scientific figures from quantitative data; ggpubfigs is an open-source and user-friendly tool that is available from https://github.com/JLSteenwyk/ggpubfigs.
    DOI:  https://doi.org/10.1128/MRA.00871-21
  8. Nature. 2021 Nov;599(7883): 32
    Colour blindness: journals should enable image redisplay.
    Jeremy Adler.
      
    Keywords:  Communication; Publishing
    DOI:  https://doi.org/10.1038/d41586-021-02982-w
  9. BMC Res Notes. 2021 Nov 02. 14(1): 405
    The importance of adherence to international standards for depositing open data in public repositories.
    Diego A Forero, Walter H Curioso, George P Patrinos.
      There has been an important global interest in Open Science, which include open data and methods, in addition to open access publications. It has been proposed that public availability of raw data increases the value and the possibility of confirmation of scientific findings, in addition to the potential of reducing research waste. Availability of raw data in open repositories facilitates the adequate development of meta-analysis and the cumulative evaluation of evidence for specific topics. In this commentary, we discuss key elements about data sharing in open repositories and we invite researchers around the world to deposit their data in them.
    Keywords:  Data repositories; Data reuse; Open data; Open science
    DOI:  https://doi.org/10.1186/s13104-021-05817-z
  10. Indian J Med Ethics. 2021 Aug 10. -(-): 1-5
    An analysis of invitations for article submission received via e-mails.
    Sandeep B Bavdekar, Shruti Saha, Urmila M Thatte, Nithya J Gogtay.
      Predatory journals charge publication fees from authors and publish without an adequate peer review, and often do not provide editorial and/or publishing services. Our objective was to evaluate e-mail solicitations received by authors in a defined time period to identify attributes of these solicitations as a metric to identify legitimacy of the journal. All e-mails seeking article submission received between January 1 and September 30, 2019, were evaluated. Each e-mail along with its respective webpage was evaluated for the journal's and publisher's names, mention of peer review, any assurance of publication, a mention of article processing charges (APC), composite invites [in the e-mail] and mention of peer review, the presence and functionality of archives, presence of manuscript management tab, mention of APC [on the webpage]. Descriptive statistics were used for the analysis. Of the 135 e-mails screened, 100 were finally included in the analysis. We found that 72% of the journals and/ or publishers were included in Beall's list. According to our criteria, a total of 85% of the solicitations were from journals that we identified as "presumed predatory". Our study has identified assurance of publication, rapid turnaround time, ambiguous information in the email and webpage, false claims of indexing as some descriptors which may help young authors and researchers assess a journal's legitimacy.
    DOI:  https://doi.org/10.20529/IJME.2021.060
  11. J Ren Care. 2021 Dec;47(4): 220
    Article categories, treatment cohort studied, and countries publishing in Journal of Renal Care 2019-2021.
    Magnus Lindberg.
      
    DOI:  https://doi.org/10.1111/jorc.12402
  12. Nurs Open. 2021 Nov 01.
    Providing English and native language quotes in qualitative research: A call to action.
    Ahtisham Younas, Sergi Fàbregues, Angela Durante, Parveen Ali.
       BACKGROUND: When publishing qualitative research in international journals, researchers studying non-English-speaking participants provide quotes in English language. This is an issue of increasing concern given the need to be rigorous to represent a diversity of participants within their context, beyond how language (alone) situates them.
    AIM: To argue for providing English and native language quotes in qualitative research reports.
    DESIGN: Discussion.
    METHODS: This paper is based on the literature on use of quotes and translation in qualitative research and authors' experiences of publishing qualitative research.
    RESULTS: Provision of native and English language quotes may allow for greater transparency of findings, thereby reflecting that the researchers adequately captured the socially and culturally dependent experiences of participants.
    CONCLUSIONS: Presentation of findings with eloquent quotes serves as the gateway into the sociocultural experiences of individuals. We argued against the norm of providing translated quotes in qualitative reports and build a case for the provision of native as well as English language quotes to promote cross-cultural understanding.
    Keywords:  methodology; qualitative research; quotation; research methods; research reporting
    DOI:  https://doi.org/10.1002/nop2.1115
  13. Am J Gastroenterol. 2021 Nov 05.
    How Your Writing Can Succeed: Getting a Manuscript Accepted by The American Journal of Gastroenterology.
    George F Longstreth, Heather M Patton, Brian E Lacy.
      
    DOI:  https://doi.org/10.14309/ajg.0000000000001552
  14. R Soc Open Sci. 2021 Oct;8(10): 211037
    Comparing dream to reality: an assessment of adherence of the first generation of preregistered studies.
    Aline Claesen, Sara Gomes, Francis Tuerlinckx, Wolf Vanpaemel.
      Preregistration is a method to increase research transparency by documenting research decisions on a public, third-party repository prior to any influence by data. It is becoming increasingly popular in all subfields of psychology and beyond. Adherence to the preregistration plan may not always be feasible and even is not necessarily desirable, but without disclosure of deviations, readers who do not carefully consult the preregistration plan might get the incorrect impression that the study was exactly conducted and reported as planned. In this paper, we have investigated adherence and disclosure of deviations for all articles published with the Preregistered badge in Psychological Science between February 2015 and November 2017 and shared our findings with the corresponding authors for feedback. Two out of 27 preregistered studies contained no deviations from the preregistration plan. In one study, all deviations were disclosed. Nine studies disclosed none of the deviations. We mainly observed (un)disclosed deviations from the plan regarding the reported sample size, exclusion criteria and statistical analysis. This closer look at preregistrations of the first generation reveals possible hurdles for reporting preregistered studies and provides input for future reporting guidelines. We discuss the results and possible explanations, and provide recommendations for preregistered research.
    Keywords:  open science; preregistration; psychological science; researcher degrees of freedom; transparency
    DOI:  https://doi.org/10.1098/rsos.211037
  15. Scientometrics. 2021 Oct 24. 1-17
    Software review: The JATSdecoder package-extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed central's open access database.
    Ingmar Böschen.
      JATSdecoder is a general toolbox which facilitates text extraction and analytical tasks on NISO-JATS coded XML documents. Its function JATSdecoder() outputs metadata, the abstract, the sectioned text and reference list as easy selectable elements. One of the biggest repositories for open access full texts covering biology and the medical and health sciences is PubMed Central (PMC), with more than 3.2 million files. This report provides an overview of the PMC document collection processed with JATSdecoder(). The development of extracted tags is displayed for the full corpus over time and in greater detail for some meta tags. Possibilities and limitations for text miners working with scientific literature are outlined. The NISO-JATS-tags are used quite consistently nowadays and allow a reliable extraction of metadata and text elements. International collaborations are more present than ever. There are obvious errors in the date stamps of some documents. Only about half of all articles from 2020 contain at least one author listed with an author identification code. Since many authors share the same name, the identification of person-related content is problematic, especially for authors with Asian names. JATSdecoder() reliably extracts key metadata and text elements from NISO-JATS coded XML files. When combined with the rich, publicly available content within PMCs database, new monitoring and text mining approaches can be carried out easily. Any selection of article subsets should be carefully performed with in- and exclusion criteria on several NISO-JATS tags, as both the subject and keyword tags are used quite inconsistently.
    Keywords:  Meta-research; PubMed central; Software; Text extraction; Text mining
    DOI:  https://doi.org/10.1007/s11192-021-04162-z
  16. Public Underst Sci. 2021 Nov 05. 9636625211051970
    Science communication skills as an asset across disciplines: A 10-year case study of students' motivation patterns at Université Laval.
    Amélie Daoust-Boisvert.
      As the demand for science communication proficiency is growing and post-secondary science communication courses and programs are launched or redesigned, it is paramount to understand who takes these courses and why. Based on a convergent mixed methods approach, this article explores the characteristics and self-reported motivations of students enrolled in an online science communication course at Université Laval, Canada, from 2009 to 2018. Results show that the typical science communication student is a woman with a career-orientated motivation pattern, mostly seeing science communication skills as an asset for a career in communication, science, or health. Be it career-driven, interest-driven, or online education-driven, motivation pattern differences emerge depending on the students' gender or field of study. Those patterns offer new paths of research, such as exploring the impact of science communication program design or of advertising strategies on enrollment.
    Keywords:  gender and science; science communication; science education; science journalism
    DOI:  https://doi.org/10.1177/09636625211051970
  17. J Phys Chem Lett. 2021 Nov 03. 10861-10862
    Transparent Peer Review: A Look Inside the Peer Review Process.
    Sofia Garakyaraghi, William Aumiller, Carolyn R Bertozzi, Gregory Scholes.
      
    DOI:  https://doi.org/10.1021/acs.jpclett.1c03308
  18. Hist Sci. 2021 Nov 01. 732753211054979
    The Revista Ştiinţifică "Vasile Adamachi" and its role in forming national and international scientific awareness of Greater Romania, 1910-1933.
    Alexandra Chiriac.
      The Revista Ştiinţifică "Vasile Adamachi" (1910-1948) had aimed since its first edition to disseminate the newest achievements of science to the interested general public with the explicit intention of building national consciousness and solidarity that would forward Romania's natural powers through science. Even though the editors of the journal had complained constantly that their efforts to promote the national scientific movement were making slow progress, they maintained their openness toward the international state of research by publishing notes and reviews of the main scientific developments worldwide. Caught between those two ideals (that of a Romanian science and of keeping up with the international scientific scene), the journal reflects the struggles, the difficulties, but also the successes of the individual researchers, acting as a two-way communication channel between science producers and consumers. It provides us with a valuable insight into the Self versus Other perception in a time when contact between the Romanian and Western European cultures was beginning to consciously evolve from mere imitation of a dominant power to the incorporation of fragmented foreign categories. It is a perfect example of 'patchwork', in which the native and foreign elements coexisted in a continuous process of redefining and reshaping the newly formed national identity.
    Keywords:  Greater Romania (1910–1933); Science journal; dissemination of science; interested public; knowledge transfer; scientific communication
    DOI:  https://doi.org/10.1177/00732753211054979
  19. J Craniofac Surg. 2021 Nov-Dec 01;32(8):32(8): 2571-2572
    Inclusion, Exclusion and Equity in Academic Credentials in Relation to The Review Process in Scholarly Publications.
    Mutaz B Habal.
      
    DOI:  https://doi.org/10.1097/SCS.0000000000008263
  20. Gastroenterology. 2021 Nov 02. pii: S0016-5085(21)03715-X. [Epub ahead of print]
    Advancing Diversity, Equity, and Inclusion in Scientific Publishing.
    Chyke A Doubeni, Douglas A Corley, Richard M Pee.
      
    DOI:  https://doi.org/10.1053/j.gastro.2021.10.043
  21. Herzschrittmacherther Elektrophysiol. 2021 Nov 04.
    [How-to case report].
    Harilaos Bogossian, Carsten W Israel.
      Case reports are often the first step of innovations and new techniques in science and thus are fundamental for some later established procedures. In addition, they have a great educational effect and offer young scientists the opportunity to gain their first experiences in writing manuscripts. In addition to an interesting detail (e.g. figure), a clear message is essential for a good case report.
    Keywords:  Didactics; Figure; Innovation; Manuscript; Message
    DOI:  https://doi.org/10.1007/s00399-021-00829-5
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.