bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒11‒13
seventeen papers selected by
Thomas Krichel
Open Library Society
  1. Top 10 reasons your manuscript may be rejected without review.
  2. How often do cancer researchers make their data and code available and what factors are associated with sharing?
  3. Choices of immediate open access and the relationship to journal ranking and publish-and-read deals.
  4. Political impartiality of medical journals is needed.
  5. "Researchers' Perceptions and awareness of predatory publishing: A Survey".
  6. Beyond Covid-19, why AI is revolutionizing the scientific ecosystem.
  7. COVID-19-Related manuscripts: lag from preprint to publication.
  8. Publication delays and associated factors in ophthalmology journals.
  9. Role and importance of journal reader: Scientific contribution of letter to editor.
  10. Compliance with International Committee of Medical Journal Editors policy on individual participant data sharing in clinical trial registries: An audit.
  11. Write a Scientific Paper course - Utility or otherwise?
  12. The Measurable Impact of a Diversity, Equity, and Inclusion Editor on Diversifying Content, Authorship, and Peer Review Participation in the Journal of Vascular Surgery.
  13. Finding our voice-Scholarship in peer review.
  14. Left in the dark: the importance of publicly available clinical trial protocols.
  15. Pragmatic and open science-based solution to a current problem in the reporting of living systematic reviews.
  16. All journals should include a correspondence section.
  17. Predictors of Dissertation Publication in Clinical and Counseling Psychology.
  1. Parasit Vectors. 2022 Nov 10. 15(1): 418
    Top 10 reasons your manuscript may be rejected without review.
    Filipe Dantas-Torres.
      
    DOI:  https://doi.org/10.1186/s13071-022-05543-w
  2. BMC Med. 2022 Nov 09. 20(1): 438
    How often do cancer researchers make their data and code available and what factors are associated with sharing?
    Daniel G Hamilton, Matthew J Page, Sue Finch, Sarah Everitt, Fiona Fidler.
      BACKGROUND: Various stakeholders are calling for increased availability of data and code from cancer research. However, it is unclear how commonly these products are shared, and what factors are associated with sharing. Our objective was to evaluate how frequently oncology researchers make data and code available and explore factors associated with sharing.METHODS: A cross-sectional analysis of a random sample of 306 cancer-related articles indexed in PubMed in 2019 which studied research subjects with a cancer diagnosis was performed. All articles were independently screened for eligibility by two authors. Outcomes of interest included the prevalence of affirmative sharing declarations and the rate with which declarations connected to data complying with key FAIR principles (e.g. posted to a recognised repository, assigned an identifier, data license outlined, non-proprietary formatting). We also investigated associations between sharing rates and several journal characteristics (e.g. sharing policies, publication models), study characteristics (e.g. cancer rarity, study design), open science practices (e.g. pre-registration, pre-printing) and subsequent citation rates between 2020 and 2021.
    RESULTS: One in five studies declared data were publicly available (59/306, 19%, 95% CI: 15-24%). However, when data availability was investigated this percentage dropped to 16% (49/306, 95% CI: 12-20%), and then to less than 1% (1/306, 95% CI: 0-2%) when data were checked for compliance with key FAIR principles. While only 4% of articles that used inferential statistics reported code to be available (10/274, 95% CI: 2-6%), the odds of reporting code to be available were 5.6 times higher for researchers who shared data. Compliance with mandatory data and code sharing policies was observed in 48% (14/29) and 0% (0/6) of articles, respectively. However, 88% of articles (45/51) included data availability statements when required. Policies that encouraged data sharing did not appear to be any more effective than not having a policy at all. The only factors associated with higher rates of data sharing were studying rare cancers and using publicly available data to complement original research.
    CONCLUSIONS: Data and code sharing in oncology occurs infrequently, and at a lower rate than would be expected given the prevalence of mandatory sharing policies. There is also a large gap between those declaring data to be available, and those archiving data in a way that facilitates its reuse. We encourage journals to actively check compliance with sharing policies, and researchers consult community-accepted guidelines when archiving the products of their research.
    Keywords:  Cancer; Code sharing; Data sharing; FAIR principles; Oncology
    DOI:  https://doi.org/10.1186/s12916-022-02644-2
  3. Front Res Metr Anal. 2022 ;7 943932
    Choices of immediate open access and the relationship to journal ranking and publish-and-read deals.
    Lars Wenaas.
      The role of academic journals is significant in the reward system of science, which makes their rank important for the researcher's choice in deciding where to submit. The study asks how choices of immediate gold and hybrid open access are related to journal ranking and how the uptake of immediate open access is affected by transformative publish-and-read deals, pushed by recent science policy. Data consists of 186,621 articles published with a Norwegian affiliation in the period 2013-2021, all of which were published in journals ranked in a National specific ranking, on one of two levels according to their importance, prestige, and perceived quality within a discipline. The results are that researchers chose to have their articles published as hybrid two times as often in journals on the most prestigious level compared with journals on the normal level. The opposite effect was found with gold open access where publishing on the normal level was chosen three times more than on the high level. This can be explained by the absence of highly ranked gold open access journals in many disciplines. With the introduction of publish-and-read deals, hybrid open access has boosted and become a popular choice enabling the researcher to publish open access in legacy journals. The results confirm the position of journals in the reward system of science and should inform policymakers about the effects of transformative arrangements and their costs against the overall level of open access.
    Keywords:  gold; hybrid; incentives; journal ranking; open access; transformative agreements
    DOI:  https://doi.org/10.3389/frma.2022.943932
  4. Lancet. 2022 Nov 12. pii: S0140-6736(22)01850-5. [Epub ahead of print]400(10364): 1679
    Political impartiality of medical journals is needed.
    Marcos Roberto Tovani-Palone.
      
    DOI:  https://doi.org/10.1016/S0140-6736(22)01850-5
  5. Account Res. 2022 Nov 09.
    "Researchers' Perceptions and awareness of predatory publishing: A Survey".
    Sweety Angelirie Kharumnuid, Poonam Singh Deo.
      The term "Predatory" alludes to the assumption that these organizations prey on academics for financial gain by charging article processing charges (APC) while failing to meet scholarly publishing standards. Predatory publishing is a growing threat to the academic society. As a result, the University Grants Commission (UGC), India's premier educational institution, has responded by launching the University Grants Commission - Consortium for Academic Research and Ethics (UGC-CARE) list, which attempts to promote research quality, integration, and publication ethics. An online survey was undertaken to determine the perception and awareness of North Eastern Hill University's researchers concerning predatory journals. A total of 160 respondents were recorded. The research scholar's awareness of predatory journals was the basis of the study. The survey reveals that while the majority of participants (58.75%) were aware of predatory publications, a significant portion (41.25%) were not. It was found that the most crucial factor when submitting an original manuscript for publication is if a journal is on the UGC-CARE list. Researchers, aware of the negative consequences of publishing in piracy-related publications, prefer not to submit their scientific work to such publishers as it risk tarnishing their reputation. As a result, research findings emphasize the necessity for awareness initiatives to educate researchers about predatory publications early in their academic careers. Research initiatives like the UGC-CARE list should be encouraged to minimize predatory publishing and promote quality research, integrity, and publication ethics.
    Keywords:  Ethical Publication; India; North-Eastern Hill University (NEHU); Predatory Journal; Predatory Publishing; UGC-CARE
    DOI:  https://doi.org/10.1080/08989621.2022.2145470
  6. Ethics Med Public Health. 2022 Nov 03. 100853
    Beyond Covid-19, why AI is revolutionizing the scientific ecosystem.
    C Bommier, J Haiech, P Charlier.
      
    Keywords:  AI; Artificial intelligence; Covid-19; Peer-review; Researchers assessment
    DOI:  https://doi.org/10.1016/j.jemep.2022.100853
  7. BMC Res Notes. 2022 Nov 05. 15(1): 340
    COVID-19-Related manuscripts: lag from preprint to publication.
    Emily Drzymalla, Wei Yu, Muin J Khoury, Marta Gwinn.
      OBJECTIVE: Preprints have had a prominent role in the swift scientific response to COVID-19. Two years into the pandemic, we investigated how much preprints had contributed to timely data sharing by analyzing the lag time from preprint posting to journal publication.RESULTS: To estimate the median number of days between the date a manuscript was posted as a preprint and the date of its publication in a scientific journal, we analyzed preprints posted from January 1, 2020, to December 31, 2021 in the NIH iSearch COVID-19 Portfolio database and performed a Kaplan-Meier (KM) survival analysis using a non-mixture parametric cure model. Of the 39,243 preprints in our analysis, 7712 (20%) were published in a journal, after a median lag of 178 days (95% CI: 175-181). Most of the published preprints were posted on the bioRxiv (29%) or medRxiv (65%) servers, which allow authors to choose a subject category when posting. Of the 20,698 preprints posted on these two servers, 7358 (36%) were published, including approximately half of those categorized as biochemistry, biophysics, and genomics, which became published articles within the study interval, compared with 29% categorized as epidemiology and 26% as bioinformatics.
    Keywords:  COVID-19; Data availability; Journal publication; Preprint; Publication time
    DOI:  https://doi.org/10.1186/s13104-022-06231-9
  8. PeerJ. 2022 ;10 e14331
    Publication delays and associated factors in ophthalmology journals.
    Yinglin Yu, Wei Li, Chaoqun Xu, Yuan Tan, Weining Zhu, Bowen Zhang, Yingshi Zou, Leyi Hu, Guangming Jin, Zhenzhen Liu.
      Introduction: This study aimed to evaluate the publication delays and correlative factors of peer-reviewed ophthalmology journals.Methods: The ophthalmology journals listed in the Journal Citation Report 2020 were retrieved from the Web of Science database. The first original research article of each journal issue from January to December 2020 was extracted, and its submission, final revision, acceptance, and publication dates were obtained. Information on impact factors, advance online publication (AOP) status, open access (OA) rate and acceptance rate in 2020 was also collected. The correlations between publication delays and potential associated factors were analyzed.
    Results: A total of 58 ophthalmology journals were included and information on 685 articles was collected. The median times from submission to acceptance, from acceptance to publication, and from submission to publication were 118.0 (IQR, 74.0-185.0) days, 31.0 (IQR, 15.0-64.0) days, and 161.0 (IQR, 111.0-232.0) days, respectively. A higher impact factor was correlated with shorter delays of acceptance and publication (P < 0.05). There was a positive correlation between acceptance rates and publication delays (r = 0.726, P = 0.007). Forty-seven (81.03%) journals provided AOP. There was no statistically significant difference for impact factors and publication delays between journal with and without AOP (all P > 0.05). No correlation between OA rate and publication delays or impact factors was detected (all P > 0.05).
    Conclusions: Journals with higher impact factors and lower acceptance rates tend to have quicker publication processes. No significant associations were detected between publication delays and AOP or OA rate.
    Keywords:  Bibliometrics; Impact factor; Ophthalmology journals; Publication delays
    DOI:  https://doi.org/10.7717/peerj.14331
  9. J Family Med Prim Care. 2022 Aug;11(8): 4117-4118
    Role and importance of journal reader: Scientific contribution of letter to editor.
    Raman Kumar.
      Letters to the editor are not often considered high in the publication hierarchy but they contribute immensely to the growth and development of any discipline and scientific examination. In many academic settings, letters to editors are not accounted for promotion and career advancement. However, letter to editor publications by active readers are no lesser contribution to science and they should be considered of equal stature and at par with other published manuscript types.
    Keywords:  Journal reader; letter to editor; peer review; scientific publication
    DOI:  https://doi.org/10.4103/jfmpc.jfmpc_1602_22
  10. Perspect Clin Res. 2022 Oct-Dec;13(4):13(4): 213-214
    Compliance with International Committee of Medical Journal Editors policy on individual participant data sharing in clinical trial registries: An audit.
    Ronak Borana, Soumyadeep Bhaumik.
      
    DOI:  https://doi.org/10.4103/picr.picr_85_22
  11. Saudi J Anaesth. 2022 Oct-Dec;16(4):16(4): 437-439
    Write a Scientific Paper course - Utility or otherwise?
    Victor Grech, Sarah Cuschieri, Abdelazeem A Eldawlatly.
      Background: Publish or perish is a cliched mantra but publishing requires the acquisition of a wide set of disparate skills that are typically learned in a completely ad-hoc manner in an early period of one's career. The Write a Scientific Paper (WASP) course is delivered online by an experienced, international faculty of academics, including several medical journal editors. This study retrospectively analyzed the attendees' perceptions of the usefulness and the utility of WASP.Methods: An email questionnaire of 11 questions was sent to all previous WASP attendees, 370 subjects, in May 2022. The questions included the geographical locations of the subjects as well as the number of published articles before and since WASP course. Besides a couple of questions on rating and recommending the WASP course, some other related questions were also asked.
    Results: There were 68 responses (18%) with high agreement (Cronbach α = 0.92). The WASP course fared well across the different research-oriented dimensions and expectations and is mostly welcomed by young career professionals. Following WASP, a 9% increase in scientific writing and published articles engagement was reported.
    Discussion: WASP is an international and unique course that emphasises presentation skills using newspaper media theory. It highlights to the delegates the importance of understanding the conflicting tripod of forces that govern publishing. Authors wish to publish more; readers are inundated, wishing to read less, whereas journal editors' primary aims are to elevate their journals' impact factors. WASP endorsements and the testimonials are invariably positive. The transition to online barely affected satisfaction rates with WASP while permitting the enrolment of a more international faculty that includes even more journal editors. WASP's ultimate objective is to impart the faculty's collective experience to the delegates in this crucial, early aspect of career progress.
    Keywords:  Manuscript; questionnaire; writing a scientific paper
    DOI:  https://doi.org/10.4103/sja.sja_512_22
  12. J Vasc Surg. 2022 Nov 08. pii: S0741-5214(22)02473-9. [Epub ahead of print]
    The Measurable Impact of a Diversity, Equity, and Inclusion Editor on Diversifying Content, Authorship, and Peer Review Participation in the Journal of Vascular Surgery.
    M Libby Weaver, Rebecca A Sorber, Courtenay M Holscher, Morgan L Cox, Brandon V Henry, Benjamin S Brooke, Michol A Cooper.
      OBJECTIVES: Women and minorities remain underrepresented in academic vascular surgery. This underrepresentation persists in the editorial peer review process which may contribute to publication bias. In 2020, the Journal of Vascular Surgery (JVS) addressed this by diversifying the editorial board and creating a new Editor of Diversity, Equity, and Inclusion (DEI). The impact of a DEI editor on modifying the output of JVS has not yet been examined. We sought to determine the measurable impact of a DEI editor on diversifying perspectives represented in the journal, and on contributing to changes in the presence of DEI subject matter across published journal content.METHODS: Authorship and content of published primary research manuscripts, editorials, and special articles in JVS were examined from November 2019 through July 2022. Publications were examined for the year prior to initiation of the DEI Editor ('pre'), the year following, ('post'), and from September 2021 to July 2022, accounting for the average 47-week time period from submission to publication in JVS ('lag'). Presence of DEI topics and women authorship were compared using Chi-squared tests.
    RESULTS: During the period examined, the number of editorials, guidelines, and other special articles dedicated to DEI topics in the vascular surgery workforce or patient population increased from 0 in the year prior to 4 (16.7%) in the 11-month lag period. The number of editorials, guidelines, and other special articles with women as first or senior authors nearly doubled (24% pre, 44.4% lag, p=0.31). Invited commentaries and discussions were increasingly written by women as the study period progressed (18.7% pre, 25.9% post, 42.6% lag, p=0.007). The number of primary research manuscripts dedicated to DEI topics increased (5.6% pre, 3.3% post, 8.1% lag, p=0.007). Primary research manuscripts written on DEI topics were more likely to have women first or senior authors than non-DEI specific primary research manuscripts (68.0% of all DEI vs 37.5% of a random sampling of non-DEI primary research manuscripts, p<0.001). The proportion of distinguished peer reviewers increased (2.8% in 2020 to 21.9% in 2021, p<0.001).
    CONCLUSION: The addition of a DEI Editor to JVS significantly impacted the diversification of topics, authorship of editorials, special articles, and invited commentaries, and peer review participation. Ongoing efforts are needed to diversify subject matter and perspective in the vascular surgery literature and reduce publication bias.
    Keywords:  Diversity; Equity; Health Disparities; Inclusion; Peer Review; Publication Bias
    DOI:  https://doi.org/10.1016/j.jvs.2022.10.052
  13. Clin Teach. 2022 Nov 06. e13551
    Finding our voice-Scholarship in peer review.
    Jennie C Ross, Amy Martin, Siew Ping Han.
      
    DOI:  https://doi.org/10.1111/tct.13551
  14. Med J Aust. 2022 Nov 21. 217(10): 519-520
    Left in the dark: the importance of publicly available clinical trial protocols.
    Sabine Braat, Katherine J Lee.
      
    Keywords:  Clinical trials as topic; Guidelines as topic; Publishing; Randomized controlled trial as topic
    DOI:  https://doi.org/10.5694/mja2.51773
  15. BMJ Evid Based Med. 2022 Nov 09. pii: bmjebm-2022-112019. [Epub ahead of print]
    Pragmatic and open science-based solution to a current problem in the reporting of living systematic reviews.
    Maria-Inti Metzendorf, Stephanie Weibel, Stefanie Reis, Steve McDonald.
      Living systematic reviews (LSRs) are an increasingly common approach to keeping reviews up to date, in which new relevant studies are incorporated as they become available, so as to inform healthcare policy and practice in a timely manner. While journal publishers have been exploring the publication of LSRs using different updating and publishing approaches, readers cannot currently assess if the evidence underpinning a published LSR is up to date, as neither the search details, the selection process, nor the list of identified studies is made available between the publication of updates. We describe a new method to transparently report the living evidence surveillance process that occurs between published LSR versions. We use the example of the living Cochrane Review on nirmatrelvir combined with ritonavir (Paxlovid) for preventing and treating COVID-19 to illustrate how this can work in practice. We created a publicly accessible spreadsheet on the Open Science Framework platform, linking to the living Cochrane Review, that details the search and study selection process, enabling readers to track the progress of eligible ongoing or completed studies. Further automation of the evidence surveillance process should be explored.
    Keywords:  COVID-19; Information Science; Methods; Systematic Reviews as Topic
    DOI:  https://doi.org/10.1136/bmjebm-2022-112019
  16. World J Gastroenterol. 2022 Oct 21. 28(39): 5731-5734
    All journals should include a correspondence section.
    Nikolaos Papanas, Dimitri P Mikhailidis, Debabrata Mukherjee.
      Letters to the editor can provide useful scientific information and evaluation of published work as well as acting as an additional level of peer review. Furthermore, letters are good reading material, especially if they involve a debate between authors. Finally, letters are relatively short. Therefore, inexperienced career researchers can use such an opportunity to practice putting together a cogent argument. However, it is far from an ideal situation if letters are the only (or main) type of article on which to base an academic career.
    Keywords:  Correspondence; Debate; Journals; Letters to the editor; Medical writing; Peer review
    DOI:  https://doi.org/10.3748/wjg.v28.i39.5731
  17. Train Educ Prof Psychol. 2022 Nov;16(4): 394-402
    Predictors of Dissertation Publication in Clinical and Counseling Psychology.
    Robyn S Herbert, Spencer C Evans, Jessy Guler, Michael C Roberts.
      A doctoral dissertation constitutes a student's original research and a novel contribution to scientific knowledge. Yet, few psychology dissertations, particularly in professional subfields, are published in the peer-reviewed literature, and the reasons for this are unclear. The present study investigated student, advisor, and doctoral program variables that might predict dissertation publication in professional psychology. Using a stratified random cohort sample of 169 Ph.D. dissertations in clinical and counseling psychology, we conducted exhaustive searches to determine whether dissertation studies were published in peer-reviewed journals within 0-7 years following their completion. Logistic regression models were estimated to test whether dissertation publication was predicted by student and advisor prior research productivity, dissertation length, and doctoral program's training emphasis, accreditation status, and subfield. Results indicated that dissertations that were supervised by more research-productive advisors and that were relatively brief (<180 pages) were significantly more likely to be published in peer-reviewed journals. No other predictors were significant. Results are discussed with regard to implications for training and mentorship. Faculty advisors who publish frequently might be more likely to attract research-oriented students, to mentor students in preparing a publishable dissertation, and/or to encourage students to publish their dissertation research. By systematically promoting research dissemination as part of doctoral research training, graduate programs and faculty mentors in clinical and counseling psychology could help facilitate students' sharing their dissertation findings with the scientific community.
    Keywords:  dissertation; education and training; productivity; publication; research
    DOI:  https://doi.org/10.1037/tep0000371
This page is being maintained by Thomas Krichel. It was last updated on 2022‒11‒14 at 02:19:55.