bims-skolko Biomed News
on Scholarly communication
Issue of 2020–11–01
twenty papers selected by
Thomas Krichel, Open Library Society
  1. fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community.
  2. Is open peer review, a growing trend in scholarly publishing, a double-edged sword?
  3. Edit reviews without permission? Some journal editors say it's OK.
  4. For how long and with what relevance do genetics articles retracted due to research misconduct remain active in the scientific literature.
  5. Is it still worth Publishing Case Reports? They are Part of our Lives.
  6. A Solution to Academic Radiology's Experience With Solicitation E-mails From Predatory Journals.
  7. Publishing ethics in the era of paper mills.
  8. Do journals instruct authors to address sex and gender in psychological science?
  9. Faults and Standards in Publishing on Race: A Commentary and Recommendation.
  10. Scholarly Publishing Experience of Postgraduate Students in Nigerian Universities.
  11. COVID-19 and Biomedical Publishing: Challenges and Prospects.
  12. Social Media and Science.
  13. Want a better h-index? - All you need to know about copyright and open access.
  14. Writing Your Next Medicinal Chemistry Article: Journal Bibliometrics and Guiding Principles for Industrial Authors.
  15. Are you passing along something true or false? Dissemination of social media messages about genetically modified organisms.
  16. Supercharge your research: a ten-week plan for open data science.
  17. Encouraging data sharing in Genome.
  18. Two years into the Brazilian Reproducibility Initiative: reflections on conducting a large-scale replication of Brazilian biomedical science.
  19. Evaluation of Iranian Medical Journals from the Perspective of Publication Ethics.
  20. The Thirty-First Year Journey, the Journal of the Korean Academy of Child and Adolescent Psychiatry.
  1. Clin Sci (Lond). 2020 Oct 30. 134(20): 2729-2739
    fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community.
    René Bernard, Tracey L Weissgerber, Evgeny Bobrov, Stacey J Winham, Ulrich Dirnagl, Nico Riedel.
      Statistically significant findings are more likely to be published than non-significant or null findings, leaving scientists and healthcare personnel to make decisions based on distorted scientific evidence. Continuously expanding ´file drawers' of unpublished data from well-designed experiments waste resources creates problems for researchers, the scientific community and the public. There is limited awareness of the negative impact that publication bias and selective reporting have on the scientific literature. Alternative publication formats have recently been introduced that make it easier to publish research that is difficult to publish in traditional peer reviewed journals. These include micropublications, data repositories, data journals, preprints, publishing platforms, and journals focusing on null or neutral results. While these alternative formats have the potential to reduce publication bias, many scientists are unaware that these formats exist and don't know how to use them. Our open source file drawer data liberation effort (fiddle) tool (RRID:SCR_017327 available at: http://s-quest.bihealth.org/fiddle/) is a match-making Shiny app designed to help biomedical researchers to identify the most appropriate publication format for their data. Users can search for a publication format that meets their needs, compare and contrast different publication formats, and find links to publishing platforms. This tool will assist scientists in getting otherwise inaccessible, hidden data out of the file drawer into the scientific community and literature. We briefly highlight essential details that should be included to ensure reporting quality, which will allow others to use and benefit from research published in these new formats.
    Keywords:  datasets; null results; publication bias; selective reporting; statistical significance
    DOI:  https://doi.org/10.1042/CS20201125
  2. J Korean Assoc Oral Maxillofac Surg. 2020 Oct 31. 46(5): 299-300
    Is open peer review, a growing trend in scholarly publishing, a double-edged sword?
    Joo-Young Park.
      
    DOI:  https://doi.org/10.5125/jkaoms.2020.46.5.299
  3. Science. 2020 Oct 30. 370(6516): 515-516
    Edit reviews without permission? Some journal editors say it's OK.
    Cathleen O'Grady.
      
    DOI:  https://doi.org/10.1126/science.370.6516.515
  4. Account Res. 2020 Oct 30. 1-17
    For how long and with what relevance do genetics articles retracted due to research misconduct remain active in the scientific literature.
    Rafael Dal-Ré, Carmen Ayuso.
      We aimed to quantify the number of pre- and post-retraction citations obtained by genetics articles retracted due to research misconduct. All retraction notices available in the Retraction Watch database for genetics articles published in 1970-2016 were assessed. The reasons for retraction were fabrication/falsification and plagiarism. The endpoints were the number of citations of retracted articles and when and how journals reported on retractions and whether this was published on PubMed. Four hundred and sixty retracted genetics articles were cited 34,487 times; 7,945 (23%) were post-retraction citations. Median time to retraction and time to last citation were 3.2 and 3 years, respectively. Most (96%) had a PubMed retraction notice, One percent of these were totally removed from journal websites altogether, and 4% had no information available on either the online or PDF versions. Ninety percent of citations were from articles retracted due to falsification/fabrication. The percentage of post-retraction citations was significantly higher in the case of plagiarism (42%) than in the case of fabrication/falsification (21.5%) (p<0.001). Median time to retraction was shorter (1.3 years) in the case of plagiarism than for fabrication/falsification (4.8 years, p<0.001). The retraction was more frequently reported in the PDFs (70%) for the fabrication/falsification cases than for the plagiarism cases (43%, p<0.001). The highest rate of retracted papers due to falsification/fabrication was among authors in the USA, and the highest rate for plagiarism was in China. Although most retractions were appropriately handled by journals, the gravest issue was that median time to retraction for articles retracted for falsification/fabrication was nearly 5 years, earning close to 6800 post-retraction citations. Journals should implement processes to speed-up the retraction process that will help to minimize post-retraction citations.
    Keywords:  Research misconduct; Retraction Watch database; citations; genetics; retraction notices
    DOI:  https://doi.org/10.1080/08989621.2020.1835479
  5. Braz J Cardiovasc Surg. 2020 Oct 29. 35(5): 851
    Is it still worth Publishing Case Reports? They are Part of our Lives.
    Carlos A Mestres.
      
    DOI:  https://doi.org/10.21470/1678-9741-2020-0131
  6. AJR Am J Roentgenol. 2020 Oct 28. 1-8
    A Solution to Academic Radiology's Experience With Solicitation E-mails From Predatory Journals.
    Ryan VanDenBerg, Nariman Nezami, Vi Nguyen, Jason K Sicklick, Clifford R Weiss.
      OBJECTIVE. The objective of our study was to help academic researchers avoid predatory publishers by characterizing the problem with respect to radiology and medical imaging and to test an intervention to address aggressive e-mail solicitation. MATERIALS AND METHODS. In total, 803 faculty from 10 U.S. academic radiology departments and 193 faculty in the senior author's department were surveyed about their experiences with soliciting journals. To document the characteristics of these journals and their publishers, we retrospectively reviewed the academic institutional e-mail box of one radiologist over 51 days. Journals' bibliometric parameters were compared with those of established medical imaging journals offering open access publishing. We tested filters for selected syntax to identify spam e-mails during two time periods. RESULTS. Of 996 faculty, 206 responded (16% nationally, 42% locally). Most (98%) received e-mails from soliciting publishers. Only 7% published articles with these publishers. Submission reasons were invitations, fee waivers, and difficulty publishing elsewhere. Overall, 94 publishers sent 257 e-mails in 51 days, 50 of which offered publishing opportunities in 76 imaging journals. Six journals were indexed in PubMed, and two had verifiable impact factors. The six PubMed-indexed journals had a lower mean publication fee ($824) than top medical imaging journals ($3034) (p < 0.001) and had a shorter mean duration of existence (9.5 vs 49.0 years, respectively; p = 0.005). The e-mail filters captured 71% of soliciting e-mails during the initial 51-day period and 85% during the same period 1 year later. CONCLUSION. Soliciting publishers have little impact on scientific literature. Academicians can avoid soliciting e-mails with customized e-mail filters.
    Keywords:  e-mail; imaging; predatory publishing; solicited publishing; soliciting journals
    DOI:  https://doi.org/10.2214/AJR.20.22923
  7. Biol Open. 2020 Oct 28. pii: bio056556. [Epub ahead of print]9(10):
    Publishing ethics in the era of paper mills.
    Rachel Hackett, Steven R Kelly.
      
    DOI:  https://doi.org/10.1242/bio.056556
  8. Res Integr Peer Rev. 2020 ;5 14
    Do journals instruct authors to address sex and gender in psychological science?
    Courtenay Cavanaugh, Yara Abu Hussein.
       Background: Sex and gender influence individuals' psychology, but are often overlooked in psychological science. The sex and gender equity in research (SAGER) guidelines provide instruction for addressing sex and gender within five sections of a manuscript (i.e., title/abstract, introduction, methods, results, and discussion) (Heidari et al., Res Integr Peer Rev 1:1-9, 2016).
    Methods: We examined whether the 89 journals published by the American Psychological Association provide explicit instruction for authors to address sex and gender within these five sections. Both authors reviewed the journal instructions to authors for the words "sex," and "gender," and noted explicit instruction pertaining to these five sections.
    Results: Only 8 journals (9.0%) instructed authors to address sex/gender within the abstract, introduction, and/or methods sections. No journals instructed authors to address sex and gender in the results or discussion sections.
    Conclusion: These journals could increase sex/gender equity and improve the reproducibility of psychological science by instructing authors to follow the SAGER guidelines.
    Keywords:  Equity; Gender; Journal instructions to authors; sex; Reproducibility; Research design and reporting
    DOI:  https://doi.org/10.1186/s41073-020-00100-4
  9. J Am Heart Assoc. 2020 Oct 28. e018848
    Faults and Standards in Publishing on Race: A Commentary and Recommendation.
    Zachary Obinna Enumah.
      
    Keywords:  peer‐review; quality; race and ethnicity; structural racism
    DOI:  https://doi.org/10.1161/JAHA.120.018848
  10. Account Res. 2020 Oct 29.
    Scholarly Publishing Experience of Postgraduate Students in Nigerian Universities.
    Adeyinka Tella, Bosire Onyancha.
      The study examined scholarly publishing experience among postgraduate students in Nigerian universities. A survey design was employed, using a questionnaire as an instrument for data collection from 919 postgraduate students selected from twelve universities in Southwest Nigeria. The findings revealed that scholarly publication means the procedure of generating, producing, and judging scholarly content, distributing and circulating it to the scholarly community and conserving it for future use, and writing and publishing novel academic ideas in scholarly communication outlets. A (23.7%) of research students had published academic papers and the majority of those research students had 0-2 years' experience. Knowledge of data analysis, literature search and review, development of relevant research questions, methodology, access to relevant materials, e-mail, phone, identification of relevant keywords, and ICT skills are considered necessary for scholarly publishing. Postgraduate students are aware of predatory journals and publishers. Challenges to scholarly publishing experience are inadequate mentorship and support, skills, knowledge; lack of funds, and limited access to available materials including journal articles, databases, and others. Also, universities in Nigeria should consider funding scholarly publications for any postgraduate students that put in the effort to get published; and mentorship, support, and collaboration with supervisors should be more emphasized.
    Keywords:   Postgraduate students ; Publication experience ; Publication output ; Scholarly communication ; Scholarly publishing
    DOI:  https://doi.org/10.1080/08989621.2020.1843444
  11. J Coll Physicians Surg Pak. 2020 Oct;30(10): 92-93
    COVID-19 and Biomedical Publishing: Challenges and Prospects.
    Muhammed Mubarak.
      Null.
    DOI:  https://doi.org/10.29271/jcpsp.2020.10.92
  12. Braz J Cardiovasc Surg. 2020 Oct 01. 35(5): IV-V
    Social Media and Science.
    Marcelo Luiz Peixoto Sobral.
      
    DOI:  https://doi.org/10.21470/1678-9741-2020-0384
  13. Orthop Traumatol Surg Res. 2020 Oct 24. pii: S1877-0568(20)30273-5. [Epub ahead of print]
    Want a better h-index? - All you need to know about copyright and open access.
    Janelise Favre, Tania Germond, Philippe Clavert, Philippe Collin, Aude Michelet, Alexandre Lädermann.
       INTRODUCTION: Physicians, whether in the public or private sector, are increasingly bound to "publish or perish". Although researchers have become aware of certain ethical concerns relating to the concept of authorship, clinicians still tend to neglect issues of copyright. The present study aims: 1) to explain to orthopedic surgeons what exactly is protected by copyright in a scientific article; 2) to assess the legal implications of publishing contracts; and 3) to specify the means of publication that best boost the author's h-index.
    MATERIAL AND METHODS: The study was based on intellectual property legislation and jurisprudence and the underlying principles. The European and American medical and legal literature was analyzed.
    RESULTS: It is vital to understand the basic principles of copyright and the legal implications of publishing contracts. A scientific article is protected by copyright as soon as it has been written. This confers both moral and property rights. "Moral" rights protect the person of the author and are inalienable; unlike property rights, they cannot be transferred. Publishing contracts can only concern property and other derivative rights. Most scientific articles are published in open access via Creative Commons (CC) licenses. The greater the freedom of use provided for in the CC license, the more easily other authors can use the article, adding to it or altering it. As all CC licenses include an attribution clause, authors publishing under a relatively unrestrictive CC license increase the chances of boosting their h-index.
    CONCLUSION: Forewarned is forearmed. Mastering the means of publication enables authors to make the most of their publications in boosting their h-index, and also to contribute to the new Open Science paradigm: abandoning some intellectual property in favor of innovation and knowledge sharing rather than clinging to data protection.
    LEVEL OF EVIDENCE: IV.
    Keywords:  Authorship; Citation; Copyright protection; Creative commons; H-index; Open Access; Plagiarism; Publication; Research; Science; Scientific work
    DOI:  https://doi.org/10.1016/j.otsr.2020.05.015
  14. J Med Chem. 2020 Oct 26.
    Writing Your Next Medicinal Chemistry Article: Journal Bibliometrics and Guiding Principles for Industrial Authors.
    Richard J D Hatley, Panayiotis A Procopiou, Steven P McLachlan, Laura E Westendorf, Nicholas A Meanwell, William R Ewing, Simon J F Macdonald.
      Writing scientific articles is immensely rewarding but challenging. This Perspective provides the medicinal chemist with background and advice on the art and process of writing manuscripts and complements the instructions to authors provided by journals. Included are many tips that we wish we had known when we first started writing. Bibliometric data from seven medicinal chemistry journals between 2000 and 2019 are collated including Bioorganic and Medicinal Chemistry Letters and the Journal of Medicinal Chemistry. Although the overall number of articles has doubled, the output from 23 large pharma companies in the past decade has dropped significantly. Commentary is given on the entire process of writing original scientific articles, opinion articles, and reviews. Examples from our own papers and experience are shared including what typically motivates the writer, challenges commonly encountered, and how we find time to write. Finally, the benefits derived from much wider publishing of industrial medicinal chemistry are described.
    DOI:  https://doi.org/10.1021/acs.jmedchem.0c01159
  15. Public Underst Sci. 2020 Oct 24. 963662520966745
    Are you passing along something true or false? Dissemination of social media messages about genetically modified organisms.
    Qian Xu, Yunya Song, Nan Yu, Shi Chen.
      Using network analysis, this study investigates how information veracity and account verification influence the dissemination of information in the context of discourse about genetically modified organisms on social media. We discovered that misinformation and true information about genetically modified organisms demonstrated different dissemination patterns on social media. In general, the dissemination networks of misinformation about genetically modified organisms were found to have higher structural stability than those of true information about genetically modified organisms, as shown by the denser network structure with fewer distinct subgroups residing within the dissemination networks. More importantly, unverified account status significantly boosted the dissemination of misinformation by increasing network density. In addition, we found that the posts about genetically modified organisms from unverified accounts received more reposts and had more layers of information relay than those from the verified accounts. Theoretical and practical implications of these findings on combating misinformation are discussed in the article.
    Keywords:  account verification status; genetically modified organisms; information dissemination; information veracity; social media
    DOI:  https://doi.org/10.1177/0963662520966745
  16. Nature. 2019 Oct 31.
    Supercharge your research: a ten-week plan for open data science.
    Julia S Stewart Lowndes, Halley E Froehlich, Allison Horst, Nishad Jayasundara, Malin L Pinsky, Adrian C Stier, Nina O Therkildsen, Chelsea L Wood.
      
    Keywords:  Careers; Lab life; Research data; Research management
    DOI:  https://doi.org/10.1038/d41586-019-03335-4
  17. Genome. 2020 Nov;63(11): iii
    Encouraging data sharing in Genome.
    Melania E Cristescu, Lewis Lukens.
      
    DOI:  https://doi.org/10.1139/gen-2020-0075
  18. Mem Inst Oswaldo Cruz. 2020 ;pii: S0074-02762020000100853. [Epub ahead of print]115 e200328
    Two years into the Brazilian Reproducibility Initiative: reflections on conducting a large-scale replication of Brazilian biomedical science.
    Kleber Neves, Clarissa Fd Carneiro, Ana Paula Wasilewska-Sampaio, Mariana Abreu, Bruna Valério-Gomes, Pedro B Tan, Olavo B Amaral.
      Scientists have increasingly recognised that low methodological and analytical rigour combined with publish-or-perish incentives can make the published scientific literature unreliable. As a response to this, large-scale systematic replications of the literature have emerged as a way to assess the problem empirically. The Brazilian Reproducibility Initiative is one such effort, aimed at estimating the reproducibility of Brazilian biomedical research. Its goal is to perform multicentre replications of a quasi-random sample of at least 60 experiments from Brazilian articles published over a 20-year period, using a set of common laboratory methods. In this article, we describe the challenges of managing a multicentre project with collaborating teams across the country, as well as its successes and failures over the first two years. We end with a brief discussion of the Initiative's current status and its possible future contributions after the project is concluded in 2021.
    DOI:  https://doi.org/10.1590/0074-02760200328
  19. Arch Iran Med. 2020 Oct 01. 23(10): 697-703
    Evaluation of Iranian Medical Journals from the Perspective of Publication Ethics.
    Ehsan Shamsi-Gooshki, Hasan Bagheri, Mahmood Salesi.
       BACKGROUND: Scientific journals will gain real credit when they meet publication ethics standards. This study seeks to evaluate the current status of medical journals' adherence to some ethical standards.
    METHODS: The 412 scientific journals approved by the Ministry of Health and Medical Education were included in this study. The process of downloading articles and data extraction for seven general and specific indicators related to publication ethics was conducted by trained researchers. Different methods were implemented by the team of colleagues to prevent possible errors in data extraction. After data integration, data analysis was performed using SPSS version 23.
    RESULTS: Overall, 408 journals and 3948 articles met the inclusion criteria. The distribution of journals according to the highest journal index was 5.4%, 13.7%, 8.3%, 8.1% and 64.5% for ISI, ESCI, PubMed, Scopus and Other indexes, respectively. In 27.7% of the articles, the review process took over 6 months. According to the results, 6.6% and 31.7% of the articles belonged to the journals' editors and owner universities, respectively. Journal self-citation was seen in 19.2% of articles and in fewer than half of the articles (45.5%), the status of conflict of interest was declared. In 36.9% of the articles, the code of ethics or university ethics committee approval, and in 36.5% of clinical trial articles, the clinical trial registration code was reported.
    CONCLUSION: Modifying processes or introducing new rules for indicators of publication ethics by trustee organizations can improve the current status. These seven indicators can also be used to rank journals.
    Keywords:  Ethics; Indicators; Medical journals; Publications
    DOI:  https://doi.org/10.34172/aim.2020.88
  20. Soa Chongsonyon Chongsin Uihak. 2020 Oct 01. 31(4): 201-206
    The Thirty-First Year Journey, the Journal of the Korean Academy of Child and Adolescent Psychiatry.
    Hee Jeong Yoo, Min-Hyeon Park, Jae Hyun Yoo, Minha Hong, Geon Ho Bahn.
       Objectives: The Journal of the Korean Academy of Child and Adolescent Psychiatry (JKACAP) has had a 31 year-long history, sharing research and reviews of children and adolescents' mental health to promote voluntary participation and communication of the members of this society. Here, we have reviewed the detailed history of the journal from the perspective of developmental progression of JKACAP and discussed the direction of further development.
    Methods & Results: We reviewed the journey of the journal by focusing on the effort it took to take the journal to a global standard, and discussed the future direction of progress of JKACAP, based on the opinions raised at the Editor-in-Chiefs' reunion.
    Conclusion: JKACAP has just stepped on the path to globalization by being indexed in Emerging Sources Citation Index, PubMed Central, and Scopus. It is time to progress to another dimension, by acknowledging and overcoming more complicated issues, such as augmenting impact of the journal, expanding domains of interdisciplinary collaboration, and more global cooperation.
    Keywords:  Adolescent; Child; Journal; Korean; Perspective; Psychiatry; Trajectory
    DOI:  https://doi.org/10.5765/jkacap.200035
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.