bims-skolko Biomed News
on Scholarly communication
Issue of 2019‒09‒08
fifteen papers selected by
Thomas Krichel
Open Library Society


  1. PLoS One. 2019 ;14(9): e0222157
    Malički M, Aalbersberg IJ, Bouter L, Ter Riet G.
      In light of increasing calls for transparent reporting of research and prevention of detrimental research practices, we conducted a cross-sectional machine-assisted analysis of a representative sample of scientific journals' instructions to authors (ItAs) across all disciplines. We investigated addressing of 19 topics related to transparency in reporting and research integrity. Only three topics were addressed in more than one third of ItAs: conflicts of interest, plagiarism, and the type of peer review the journal employs. Health and Life Sciences journals, journals published by medium or large publishers, and journals registered in the Directory of Open Access Journals (DOAJ) were more likely to address many of the analysed topics, while Arts & Humanities journals were least likely to do so. Despite the recent calls for transparency and integrity in research, our analysis shows that most scientific journals need to update their ItAs to align them with practices which prevent detrimental research practices and ensure transparent reporting of research.
    DOI:  https://doi.org/10.1371/journal.pone.0222157
  2. J Biomed Inform. 2019 Aug 29. pii: S1532-0464(19)30194-7. [Epub ahead of print] 103275
    Rosemblat G, Fiszman M, Shin D, Kilicoglu H.
      BACKGROUND: With the substantial growth in the biomedical research literature, a larger number of claims are published daily, some of which seemingly disagree with or contradict prior claims on the same topics. Resolving such contradictions is critical to advancing our understanding of human disease and developing effective treatments. Automated text analysis techniques can facilitate such analysis by extracting claims from the literature, flagging those that are potentially contradictory, and identifying any study characteristics that may explain such contradictions.METHODS: Using SemMedDB, our own PubMed-scale repository of semantic predications (subject-relation-object triples), we identified apparent contradictions in the biomedical research literature and developed a categorization of contextual characteristics that explain such contradictions. Clinically relevant semantic predications relating to 20 diseases and involving opposing predicate pairs (e.g., an intervention treats or causes a disease) were retrieved from SemMedDB. After addressing inference, uncertainty, generic concepts, and NLP errors through automatic and manual filtering steps, a set of apparent contradictions were identified and characterized.
    RESULTS: We retrieved 117,676 predication instances from 62,360 PubMed abstracts (Jan 1980-Dec 2016). From these instances, automatic filtering steps generated 2,236 candidate contradictory pairs. Through manual analysis, we determined that 58 of these pairs (2.6%) were apparent contradictions. We identified five main categories of contextual characteristics that explain these contradictions: a) internal to the patient, b) external to the patient, c) endogenous/exogenous, d) known controversy, and (e) contradictions in literature. Categories (a) and (b) were subcategorized further (e.g., species, dosage) and accounted for the bulk of the contradictory information.
    CONCLUSIONS: Semantic predications, by accounting for lexical variability, and SemMedDB, owing to its literature scale, can support identification and elucidation of potentially contradictory claims across the biomedical domain. Further filtering and classification steps are needed to distinguish among them the true contradictory claims. The ability to detect contradictions automatically can facilitate important biomedical knowledge management tasks, such as tracking and verifying scientific claims, summarizing research on a given topic, identifying knowledge gaps, and assessing evidence for systematic reviews, with potential benefits to the scientific community. Future work will focus on automating these steps for fully automatic recognition of contradictions from the biomedical research literature.
    Keywords:  Contradictions; biomedical research literature; natural language processing; semantic relations
    DOI:  https://doi.org/10.1016/j.jbi.2019.103275
  3. Braz J Med Biol Res. 2019 ;pii: S0100-879X2019000900401. [Epub ahead of print]52(9): e8935
    Baptista MS, Alves MJM, Arantes GM, Armelin HA, Augusto O, Baldini RL, Basseres DS, Bechara EJH, Bruni-Cardoso A, Chaimovich H, Colepicolo Neto P, Colli W, Cuccovia IM, Da-Silva AM, Di Mascio P, Farah SC, Ferreira C, Forti FL, Giordano RJ, Gomes SL, Gueiros Filho FJ, Hoch NC, Hotta CT, Labriola L, Lameu C, Machini MT, Malnic B, Marana SR, Medeiros MHG, Meotti FC, Miyamoto S, Oliveira CC, Souza-Pinto NC, Reis EM, Ronsein GE, Salinas RK, Schechtman D, Schreier S, Setubal JC, Sogayar MC, Souza GM, Terra WR, Truzzi DR, Ulrich H, Verjovski-Almeida S, Winck FV, Zingales B, Kowaltowski AJ.
      The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.
    DOI:  https://doi.org/10.1590/1414-431X20198935
  4. Hist Philos Life Sci. 2019 Sep 04. 41(3): 34
    de Melo-Martín I.
      The growing commercialization of scientific research has raised important concerns about industry bias. According to some evidence, so-called industry bias can affect the integrity of the science as well as the direction of the research agenda. I argue that conceptualizing industry's influence in scientific research in terms of bias is unhelpful. Insofar as industry sponsorship negatively affects the integrity of the research, it does so through biasing mechanisms that can affect any research independently of the source of funding. Talk about industry bias thus offers no insight into the particular epistemic shortcomings at stake. If the concern is with the negative effects that industry funding can have on the research agenda, conceptualizing this influence as bias obscures the ways in which such impact is problematic and limits our ability to offer solutions that can successfully address the concerns raised by the growing role of private funding in science.
    Keywords:  Bias; Commercialization of science; Industry bias; Non-epistemic values in science; Research agenda
    DOI:  https://doi.org/10.1007/s40656-019-0274-x
  5. Andrologia. 2019 Sep 06. e13405
    Baskaran S, Agarwal A, Panner Selvam MK, Henkel R, Durairajanayagam D, Leisegang K, Majzoub A, Singh D, Khalafalla K.
      Plagiarism is a common form of academic misconduct that extensively jeopardises the quality of scientific publication. The purpose of this study is to determine the extent of plagiarism in the most influential andrology articles. A total of 77 highly cited andrology articles were analysed for their similarity index using iThenticate and Turnitin. The articles were categorised based on the year (before and on/after 2000) and type of publication (review and research articles), and the similarity indices were compared. Furthermore, the analysed articles were categorised based on the level of similarity using an arbitrary similarity index range (low: ≤10, moderate: 11-20, high: 21-50 and very high: >50) and average incidence rate (%) was determined. Our analysis revealed a higher percentage of the similarity indices for reviews than research articles. We noticed a higher similarity index for articles published on/after 2000 than those published before. The majority of the influential articles in the field of andrology showed a low similarity index, while some articles exhibited moderate to high levels of similarity. These findings support the need for the development of similarity index guidelines as a major pre-requisite for establishing a more transparent and efficient system to address plagiarism in scientific publications.
    Keywords:  andrology; plagiarism; plagiarism detection tool; scientific misconduct; similarity index
    DOI:  https://doi.org/10.1111/and.13405
  6. PLoS One. 2019 ;14(9): e0221933
    Bongelli R, Riccioni I, Burro R, Zuczkowski A.
      Distinguishing certain and uncertain information is of crucial importance both in the scientific field in the strict sense and in the popular scientific domain. In this paper, by adopting an epistemic stance perspective on certainty and uncertainty, and a mixed procedure of analysis, which combines a bottom-up and a top-down approach, we perform a comparative study (both qualitative and quantitative) of the uncertainty linguistic markers (verbs, non-verbs, modal verbs, conditional clauses, uncertain questions, epistemic future) and their scope in three different corpora: a historical corpus of 80 biomedical articles from the British Medical Journal (BMJ) 1840-2007; a corpus of 12 biomedical articles from BMJ 2013, and a contemporary corpus of 12 scientific popular articles from Discover 2013. The variables under observation are time, structure (IMRaD vs no-IMRaD) and genre (scientific vs popular articles). We apply the Generalized Linear Models analysis in order to test whether there are statistically significant differences (1) in the amount of uncertainty among the different corpora, and (2) in the categories of uncertainty markers used by writers. The results of our analysis reveal that (1) in all corpora, the percentages of uncertainty are always much lower than that of certainty; (2) uncertainty progressively diminishes over time in biomedical articles (in conjunction with their structural changes-IMRaD-and to the increase of the BMJ Impact Factor); and (3) uncertainty is slightly higher in scientific popular articles (Discover 2013) as compared to the contemporary corpus of scientific articles (BMJ 2013). Nevertheless, in all corpora, modal verbs are the most used uncertainty markers. These results suggest that not only do scientific writers prefer to communicate their uncertainty with markers of possibility rather than those of subjectivity but also that science journalists prefer using a third-person subject followed by modal verbs rather than a first-person subject followed by mental verbs such as think or believe.
    DOI:  https://doi.org/10.1371/journal.pone.0221933
  7. Int J Low Extrem Wounds. 2019 Sep 03. 1534734619865860
    Derraik JGB, Butler ÉM, Rerkasem K.
      Many researchers find writing a scientific manuscript a highly discouraging task. This problem may be partly responsible for the fact that approximately half of completed clinical studies worldwide remain unreported or unpublished. Therefore, we aimed to create a user-friendly guide with helpful recommendations, which are complementary to the many existing reporting guidelines for quantitative clinical data. This article has been prepared with clearly defined subheadings, to facilitate quick identification of any specific sections/topics. We encourage the use of the IMRaD model (ie, Introduction, Methods, Results, and Discussion), providing guidance on the key information required, as well as the dos and don'ts. We also comment briefly on feedback and rejection, proposing the I AM approach (Ignore, Address, and Move on).
    Keywords:  article; manuscript; publication; scientific; study; writing
    DOI:  https://doi.org/10.1177/1534734619865860
  8. JACC Cardiovasc Imaging. 2019 Sep;pii: S1936-878X(19)30722-3. [Epub ahead of print]12(9): 1899-1902
    Chandrashekhar Y, Shaw L.
      
    DOI:  https://doi.org/10.1016/j.jcmg.2019.08.001
  9. Nature. 2019 Sep;573(7772): 34
    Khan SA.
      
    Keywords:  Communication; Conferences and meetings; Developing world; Publishing
    DOI:  https://doi.org/10.1038/d41586-019-02626-0
  10. BMC Health Serv Res. 2019 Sep 05. 19(1): 638
    Sipilä R, Mäkelä M, Komulainen J.
      BACKGROUND: The Choosing Wisely campaign has spread to many countries. Methods for developing recommendations are inconsistent. We describe our process of developing such recommendations from a comprehensive national set of clinical practice guidelines (Current Care, CC) and the results of a one-year Choosing Wisely Finland project.METHODS: Two of the authors drafted the quality and process criteria for all the Choosing Wisely Finland recommendations. The quality criteria were relevance, feasibility, evidence-based and strength. These were discussed in editors' meetings and subsequently revised. Two different processes for developing recommendations within national clinical practice guidelines were designed and piloted (processes A and B). Process A was based on a published guideline. The recommendations are drafted by an editor and revised and approved by the guideline development group. In process B the development of the recommendations is integrated with guideline production or update. Choosing Wisely recommendations were then drafted for half of the published CC Guidelines. An additional process (process C) was designed for producing independent recommendations outside a guideline.
    RESULTS: At least one Choosing Wisely recommendation could be identified from 39 out of 52 reviewed guidelines. Of the 106 recommendations drafted, 62 (58%) were accepted for publication. The main reasons for rejection were inability to give a strong recommendation (n = 18, 41%) and insufficient relevance (n = 14, 32%). Two thirds (n = 41, 66%) of the published recommendations were based on high to moderate level of evidence, and 18% (n = 11) on low or very low level of evidence, whereas for the rest, the quality of evidence was not critically appraised.
    CONCLUSIONS: Choosing Wisely recommendations can be produced systematically from existing clinical practice guidelines. The rigorous methods of evidence-based medicine ensure high-quality recommendations. We welcome the use of our processes and methods describes in this article by other guideline-producing organizations.
    Keywords:  Choosing wisely; Clinical decision-making; Guidelines as topic; Medical overuse
    DOI:  https://doi.org/10.1186/s12913-019-4460-z
  11. Compr Psychiatry. 2019 Aug 21. pii: S0010-440X(19)30042-2. [Epub ahead of print]94 152119
    Hafeez DM, Waqas A, Majeed S, Naveed S, Afzal KI, Aftab Z, Zeshan M, Khosa F.
      Gender disparity has been documented in advanced doctoral degrees, research, and academic positions, and therefore, it can logically be deduced that the gender disparity would be found in journals' editorial boards. In this study, we sought to determine the gender distribution in editorial boards of psychiatry journals worldwide. We also studied the academic achievements of editorial board members by comparing professional background, education level, and research productivity indices. We analyzed the gender of editorial members of 119 psychiatry journals from Clarivate Analytics' Journal Citation Reports. Our data included 8423 editorial board members from which we randomly selected 10% editorial board members to represent the full sample for further analyses. Overall, women represented 30.4% of editorial board and approximately 30% in each category: (1) Editor-in-chief/deputies, (2) Associate/section editors, (3) Editorial board*, and (4) Advisory board. The majority (65%) of men were M.D. psychiatrists, and women (58%) were Ph.D. psychologists. Women in editorial leadership positions (Category 1 & 2) were correlated with fewer women in editorial or advisory boards. Women had half the mean number of publications than men while serving journals with approximately the same mean impact factor. Our study results show that, besides gender disparity, gender bias does not exist in the psychiatry journal editorial boards. Given the implication of the editorial board position on science, academic advancement, and networking, this disparity remains detrimental to achieving equity, diversity, and inclusion in academic psychiatry.
    Keywords:  Editorial board; Female; Gender disparity; Psychiatry
    DOI:  https://doi.org/10.1016/j.comppsych.2019.152119
  12. J Hum Lact. 2019 Sep 06. 890334419869912
    Strong G.
      Peer-review publishing has long been the gold standard for disseminating research. The peer-review process holds researchers accountable for their work and conveys confidence that the article is of value to the reader. Predatory journals and publishing pose a global threat to the quality of scientific literature, accuracy of educational resources, and safety of patient care. Predatory publishing uses an exploitative business model, substandard quality control measures, and deceptive publishing practices. Given the proliferation of these journals and the extreme measures utilized to disguise substandard publishing practices, avoiding them can prove difficult. Understanding the nature of predatory publishing and how to recognize the warning signs provide helpful measures to authors, researchers, students, and readers. Additional resources known to help avoid predatory publishers have been discussed in addition to reviewing the Journal of Human Lactation guidelines for publishing.
    Keywords:  breastfeeding; ethics; lactation; peer-review; predatory journals; research quality
    DOI:  https://doi.org/10.1177/0890334419869912