bims-skolko Biomed News
on Scholarly communication
Issue of 2021‒01‒03
thirty-two papers selected by
Thomas Krichel
Open Library Society
  1. Retraction of COVID-19 Pharmacoepidemiology Research Could Have Been Avoided by Effective Use of Reporting Guidelines.
  2. Inconclusive trial results regarding prophylactic negative pressure wound therapy for major pancreatic surgery: Mitigating publication bias and moving toward effective evidence synthesis.
  3. Systematic examination of preprint platforms for use in the medical and biomedical sciences setting.
  4. Ten simple rules for typographically appealing scientific texts.
  5. Editorial: Method and Data Sharing and Reproducibility of Scientific Results.
  6. Journal Retraction Rates and Citation Metrics: An Ouroboric Association?
  7. Global trends in open access publication and open data.
  8. Asteroid treasure, COVID vaccine and public peer review.
  9. Writing scientific case reports for top-line journals.
  10. Reviewers' Self-Awareness and Its Impact on the Peer Review Process.
  11. Open Science to Address COVID-19: Sharing Data to Make Our Research Investment Go Further.
  12. Scientific integrity: what a journal can and cannot do.
  13. Expert Communication and the Self-Defeating Codes of Scientific Ethics.
  14. Open access takes flight.
  15. The unexpected costs of publishing in plastics surgery journals.
  16. Is Peer Review a Hindrance to Good Science or a Gatekeeper Against Bad Science?
  17. Inspiring Diverse & Innovative Science.
  18. Living systematic review: new inputs and challenges.
  19. 10 Years of Open Access Society Publishing.
  20. Reporting and publishing quality improvement projects.
  21. What the editors are reading, basic science.
  22. Erratum to "What is open-access publishing and what it means for the forensic enterprise" [Forensic Sci. Int.: Synergy (2019) 290-293].
  23. Changing the philosophy, direction, and the governance of The Breast Journal as it moves towards becoming an "Open Access" journal in 2022.
  24. Microbiome Research: Open Communication Today, Microbiome Applications in the Future.
  25. A review of 2020 through Nature's editorials.
  26. Time to move to open access.
  27. PBJ ranks higher, enhances diversity and offers free global access.
  28. Biosciences Proposal Bootcamp: Structured peer and faculty feedback improves trainees' proposals and grantsmanship self-efficacy.
  29. Reflections as 2020 comes to an end: the editing and educational environment during the COVID-19 pandemic, the power of Scopus and Web of Science in scholarly publishing, journal statistics, and appreciation to reviewers and volunteers.
  30. Inside the USCAP Journals.
  31. A New Gold Standard in FPMRS Publishing.
  32. Farewell message from the Editor-in-Chief: editorial.
  1. Clin Epidemiol. 2020 ;12 1403-1420
    Retraction of COVID-19 Pharmacoepidemiology Research Could Have Been Avoided by Effective Use of Reporting Guidelines.
    Eric I Benchimol, David Moher, Vera Ehrenstein, Sinéad M Langan.
      Introduction: Two recent high-profile publications (and subsequent retractions) of pharmacoepidemiology studies reporting the effectiveness and risk of hydroxychloroquine in COVID-19 patients received international media attention. Transparent and complete reporting of these studies could have provided peer reviewers and editors with sufficient information to question the methods used and the validity of results. Since these studies used routinely collected health data, the guidelines for the REporting of studies Conducted using Observational Routinely collected health Data (RECORD) should have been applied to ensure complete reporting of the research.Methods: We evaluated the two retracted articles for completeness of reporting using the RECORD for Pharmacoepidemiology (RECORD-PE) checklist, which includes the checklists for the STengthening the Reporting of OBservational studies in Epidemiology (STROBE) and RECORD. We compared the proportion of STROBE, RECORD and RECORD-PE items adequately reported using Chi-squared statistics.
    Results: In the article published by The Lancet, 29 of 34 STROBE items (85.3%) were adequately reported, compared with 3.5 of 13 RECORD items (26.9%) and 9.5 of 15 RECORD-PE items (63.3%)(χ2 = 14.839, P <0.001). Similarly, the article published in NEJM reported 24 of 34 STROBE items (70.6%), two of 13 RECORD items (15.4%), and 7.5 of 15 RECORD-PE items (50.0%) (χ2 = 11.668, P = 0.003). Important aspects of the methods unique to research using routinely collected health data were not reported, including variables used to identify exposure, outcome and confounders, validation of the coding or algorithms, a description of the underlying database population and the accuracy of data linkage methods.
    Discussion: While STROBE items were generally adequately reported, RECORD and RECORD-PE items were not. Reporting guidelines should be effectively implemented in order for transparency and completeness of research manuscripts, allowing for adequate evaluation by editors and peer reviewers.
    Keywords:  COVID-19; journalology; peer review; pharmacoepidemiology; reporting guidelines; routinely collected health data
    DOI:  https://doi.org/10.2147/CLEP.S288677
  2. Surgery. 2020 Dec 19. pii: S0039-6060(20)30821-7. [Epub ahead of print]
    Inconclusive trial results regarding prophylactic negative pressure wound therapy for major pancreatic surgery: Mitigating publication bias and moving toward effective evidence synthesis.
    Jesse Zuckerman, Julie Hallet.
      
    DOI:  https://doi.org/10.1016/j.surg.2020.11.036
  3. BMJ Open. 2020 Dec 29. 10(12): e041849
    Systematic examination of preprint platforms for use in the medical and biomedical sciences setting.
    Jamie J Kirkham, Naomi C Penfold, Fiona Murphy, Isabelle Boutron, John P Ioannidis, Jessica Polka, David Moher.
      OBJECTIVES: The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms.STUDY DESIGN AND SETTING: Preprint platforms that were launched up to 25 June 2019 and have a biomedical and medical scope according to MEDLINE's journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot tested and used to collect data from each preprint platform's webpage(s).
    RESULTS: A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, 6 (14%) were provided by F1000 Research (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal's remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read access and most have a policy regarding reasons for retraction and the sustainability of the service.
    CONCLUSION: A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility.
    Keywords:  medical ethics; medical journalism; statistics & research methods
    DOI:  https://doi.org/10.1136/bmjopen-2020-041849
  4. PLoS Comput Biol. 2020 Dec;16(12): e1008458
    Ten simple rules for typographically appealing scientific texts.
    Lars Ole Schwen.
      
    DOI:  https://doi.org/10.1371/journal.pcbi.1008458
  5. J Chem Inf Model. 2020 Dec 28. 60(12): 5868-5869
    Editorial: Method and Data Sharing and Reproducibility of Scientific Results.
    Kenneth M Merz, Rommie Amaro, Zoe Cournia, Matthias Rarey, Thereza Soares, Alexander Tropsha, Habibah A Wahab, Renxiao Wang.
      
    DOI:  https://doi.org/10.1021/acs.jcim.0c01389
  6. Cureus. 2020 Nov 18. 12(11): e11542
    Journal Retraction Rates and Citation Metrics: An Ouroboric Association?
    Amrutha B Nagella, Venkatesh S Madhugiri.
      Introduction Retraction of published papers has a far-reaching impact on the scientific world, especially if the retracted papers were published in high-impact journals. Although it has been noted that the retraction rates of journals correlated with their citation metrics, no conclusive data were available for most clinical specialties. In this study, we determined the retraction rate for anesthesia and two comparison groups (neurosurgery and high impact clinical journals). We then studied the correlation of the retraction rate with citation metrics. Methods We generated a list of all anesthesia journals that were indexed in the National Library of Medicine database. We obtained the number of papers published in each journal as well as the number of papers retracted from each. We also collated the Impact Factor® and H-index of each journal. The same methodology was followed for neurosurgery and high impact clinical journals. We then studied the correlations between the retraction rate and citation metrics of each journal. Results The retraction index was 2.59 for anesthesiology, 0.66 for neurosurgery and 0.75 for the high-impact clinical journals group. The retraction rate did not correlate with the citation metrics. However, the number of papers published in each journal and the absolute number of retractions showed a positive correlation with the citation metrics. The H-index showed stronger correlations with these parameters than the Impact factor. Conclusions The number of retractions increased in proportion to both the number of papers published in a journal and the citation metrics of that journal.
    Keywords:  anesthesia; citation metrics; h-index; impact factor; neurosurgery; retraction; retraction index; retraction rate
    DOI:  https://doi.org/10.7759/cureus.11542
  7. J Appl Clin Med Phys. 2020 Dec;21(12): 4-5
    Global trends in open access publication and open data.
    Michael Mills.
      
    DOI:  https://doi.org/10.1002/acm2.13140
  8. Nature. 2020 Dec;588(7839): 543
    Asteroid treasure, COVID vaccine and public peer review.
      
    Keywords:  Astronomy and astrophysics; Publishing; Vaccines
    DOI:  https://doi.org/10.1038/d41586-020-03553-1
  9. J Clin Apher. 2020 Dec 29.
    Writing scientific case reports for top-line journals.
    Robert Weinstein.
      The venerable clinical case report has been largely reduced to the status of commodity in the present age of dedicated case report journals. Top-line clinical journals may discourage or even refuse to accept clinical case reports due to their potential adverse effect on the impact factor of the journal. But while the traditional clinical case report, that presents a case history and attempts to extrapolate a lesson from it, may have fallen out of favor, there remains a need for astute clinical observations that serve to stimulate the generation of hypotheses and may lead, ultimately, to medical breakthroughs. Clinicians are very much capable of employing scientific reasoning when approaching an unusual clinical situation. By remaining up to date with the literature, and determining, at the outset of the case, what lessons may be learned from it, they can formulate a scientific approach, using clinical methods, to result in meaningful contributions to the literature in top-line journals.
    Keywords:  McLeod criteria; academic medicine; clinical hypothesis; manuscript writing; publication
    DOI:  https://doi.org/10.1002/jca.21869
  10. Eur J Vasc Endovasc Surg. 2020 Dec 22. pii: S1078-5884(20)31055-8. [Epub ahead of print]
    Reviewers' Self-Awareness and Its Impact on the Peer Review Process.
    Francesco Torella, Stavros A Antoniou, George A Antoniou.
      
    DOI:  https://doi.org/10.1016/j.ejvs.2020.11.034
  11. Ther Innov Regul Sci. 2020 Dec 24.
    Open Science to Address COVID-19: Sharing Data to Make Our Research Investment Go Further.
    Névine Zariffa, Jonas Haggstrom, Frank Rockhold.
      
    DOI:  https://doi.org/10.1007/s43441-020-00250-z
  12. Eur Heart J. 2020 Dec 21. 41(48): 4552-4555
    Scientific integrity: what a journal can and cannot do.
    Thomas F Lüscher, Kim Fox, Christian Hamm, Rickey E Carter, Stefano Taddei, Maarten Simoons, Filippo Crea.
      
    DOI:  https://doi.org/10.1093/eurheartj/ehaa963
  13. Am J Bioeth. 2021 Jan;21(1): 24-26
    Expert Communication and the Self-Defeating Codes of Scientific Ethics.
    Hugh Desmond.
      
    DOI:  https://doi.org/10.1080/15265161.2020.1845862
  14. Science. 2021 Jan 01. 371(6524): 16-20
    Open access takes flight.
    Jeffrey Brainard.
      
    DOI:  https://doi.org/10.1126/science.371.6524.16
  15. J Plast Reconstr Aesthet Surg. 2020 Dec 19. pii: S1748-6815(20)30689-6. [Epub ahead of print]
    The unexpected costs of publishing in plastics surgery journals.
    Ardit Begaj, Keith P Allison.
      
    DOI:  https://doi.org/10.1016/j.bjps.2020.12.022
  16. J Oral Maxillofac Surg. 2020 Dec 05. pii: S0278-2391(20)31423-3. [Epub ahead of print]
    Is Peer Review a Hindrance to Good Science or a Gatekeeper Against Bad Science?
    Akilesh Ramasamy.
      
    DOI:  https://doi.org/10.1016/j.joms.2020.11.033
  17. Trends Ecol Evol. 2021 Jan;pii: S0169-5347(20)30344-X. [Epub ahead of print]36(1): 1
    Inspiring Diverse & Innovative Science.
      
    DOI:  https://doi.org/10.1016/j.tree.2020.11.011
  18. Medwave. 2020 Dec 23. 20(11): e8092
    Living systematic review: new inputs and challenges.
    Laura Vergara-Merino, Catalina Verdejo, Cynthia Carrasco, Manuel Vargas-Peirano.
      This is the second article from a collaborative methodological series of biostatistics and clinical epidemiology narrative reviews. This review aims to describe living systematic reviews relevance, the considerations that should be taken when producing one, and the challenges proper of this type of review. The living systematic review is a continuous update that maintains a systematic reviews rigor and methodological quality. The living format is appropriate when the review aims to answer a priority question in terms of health decision-making, the existent certainty of the evidence for this question is low or very low, and new evidence will likely appear soon. To carry out a successful living systematic review, researchers should consider different things, such as: having a continuous and automated search, having update criteria, evaluating how to update the meta-analysis and how to perform the editorial process, and publishing in a friendly format, among others. As living systematic reviews are a new proposal, they will likely change in the future to improve their performance, so we will have to keep an eye on its future updates.
    Keywords:   Review Literature as Topic; Systematic Reviews as Topic
    DOI:  https://doi.org/10.5867/medwave.2020.11.8092
  19. ChemistryOpen. 2020 Dec 30.
    10 Years of Open Access Society Publishing.
    Francesca Rita Novara.
      That was ten, this is now! The Editor-in-Chief of ChemistryOpen Francesca Novara discusses what 2020 meant for the development of open science and ChemistryOpen and what is the landscape in which ChemistryOpen will celebrate its 10th anniversary.
    DOI:  https://doi.org/10.1002/open.202000353
  20. Aust J Rural Health. 2020 Dec;28(6): 528-529
    Reporting and publishing quality improvement projects.
    Russell Roberts, Jan Radford.
      
    DOI:  https://doi.org/10.1111/ajr.12696
  21. J Pediatr Urol. 2020 Dec 10. pii: S1477-5131(20)30727-0. [Epub ahead of print]
    What the editors are reading, basic science.
    Hsi-Yang Wu, Oliver Wallacy, Magdalena Fossum.
      
    DOI:  https://doi.org/10.1016/j.jpurol.2020.12.010
  22. Forensic Sci Int. 2020 ;2 708
    Erratum to "What is open-access publishing and what it means for the forensic enterprise" [Forensic Sci. Int.: Synergy (2019) 290-293].
    M M Houck, G Horsman, G Sauzier, M Bidmos.
      [This corrects the article DOI: 10.1016/j.fsisyn.2019.06.045.].
    DOI:  https://doi.org/10.1016/j.fsisyn.2020.04.002
  23. Breast J. 2020 Dec 23.
    Changing the philosophy, direction, and the governance of The Breast Journal as it moves towards becoming an "Open Access" journal in 2022.
    Shahla Masood.
      
    DOI:  https://doi.org/10.1111/tbj.14145
  24. Microorganisms. 2020 Dec 10. pii: E1960. [Epub ahead of print]8(12):
    Microbiome Research: Open Communication Today, Microbiome Applications in the Future.
    Bettina Schelkle, Quentin Galland.
      Microbiome research has recently gained centre-stage in both basic science and translational applications, yet researchers often feel that public communication about its potential overpromises. This manuscript aims to share a perspective on how scientists can engage in more open, ethical and transparent communication using an ongoing research project on food systems microbiomes as a case study. Concrete examples of strategically planned communication efforts are outlined, which aim to inspire and empower other researchers. Finally, we conclude with a discussion on the benefits of open and transparent communication from early-on in innovation pathways, mainly increasing trust in scientific processes and thus paving the way to achieving societal milestones such as the UN Sustainable Development Goals and the EU Green Deal.
    Keywords:  communication; innovation; microbiome; trust
    DOI:  https://doi.org/10.3390/microorganisms8121960
  25. Nature. 2020 12;588(7839): 537-538
    A review of 2020 through Nature's editorials.
      
    Keywords:  Careers; Government; Policy; SARS-CoV-2; Vaccines
    DOI:  https://doi.org/10.1038/d41586-020-03560-2
  26. Eur J Public Health. 2020 Dec 24. pii: ckaa231. [Epub ahead of print]
    Time to move to open access.
    Peter Allebeck, Dineke Zeegers Paget, Iveta Nagyova.
      
    DOI:  https://doi.org/10.1093/eurpub/ckaa231
  27. Plant Biotechnol J. 2021 Jan;19(1): 3-4
    PBJ ranks higher, enhances diversity and offers free global access.
    Henry Daniell.
      
    DOI:  https://doi.org/10.1111/pbi.13528
  28. PLoS One. 2020 ;15(12): e0243973
    Biosciences Proposal Bootcamp: Structured peer and faculty feedback improves trainees' proposals and grantsmanship self-efficacy.
    Crystal M Botham, Shay Brawn, Latishya Steele, Cisco B Barrón, Sofie R Kleppner, Daniel Herschlag.
      Grant writing is an essential skill to develop for academic and other career success but providing individual feedback to large numbers of trainees is challenging. In 2014, we launched the Stanford Biosciences Grant Writing Academy to support graduate students and postdocs in writing research proposals. Its core program is a multi-week Proposal Bootcamp designed to increase the feedback writers receive as they develop and refine their proposals. The Proposal Bootcamp consisted of two-hour weekly meetings that included mini lectures and peer review. Bootcamp participants also attended faculty review workshops to obtain faculty feedback. Postdoctoral trainees were trained and hired as course teaching assistants and facilitated weekly meetings and review workshops. Over the last six years, the annual Bootcamp has provided 525 doctoral students and postdocs with multi-level feedback (peer and faculty). Proposals from Bootcamp participants were almost twice as likely to be funded than proposals from non-Bootcamp trainees. Overall, this structured program provided opportunities for feedback from multiple peer and faculty reviewers, increased the participants' confidence in developing and submitting research proposals, while accommodating a large number of participants.
    DOI:  https://doi.org/10.1371/journal.pone.0243973
  29. J Educ Eval Health Prof. 2020;17:17 44
    Reflections as 2020 comes to an end: the editing and educational environment during the COVID-19 pandemic, the power of Scopus and Web of Science in scholarly publishing, journal statistics, and appreciation to reviewers and volunteers.
    Sun Huh.
      
    DOI:  https://doi.org/10.3352/jeehp.2020.17.44
  30. Lab Invest. 2021 Jan;101(1): 2-3
    Inside the USCAP Journals.
      
    DOI:  https://doi.org/10.1038/s41374-020-00521-1
  31. Female Pelvic Med Reconstr Surg. 2021 Jan 01. 27(1): 1
    A New Gold Standard in FPMRS Publishing.
    Linda Brubaker.
      
    DOI:  https://doi.org/10.1097/SPV.0000000000001024
  32. Appl Opt. 2020 Dec 20. 59(36): ED4
    Farewell message from the Editor-in-Chief: editorial.
    Ron Driggers.
      Outgoing Editor-in-Chief Ron Driggers shares his parting thoughts and hopes for the Applied Optics community in the coming year.
    DOI:  https://doi.org/10.1364/AO.417398
This page is being maintained by Thomas Krichel. It was last updated on 2021‒07‒23 at 10:24:22.