bims-librar Biomed news
on Biomedical librarianship
Issue of 2018‒11‒18
thirteen papers selected by
Thomas Krichel
Open Library Society


  1. F1000Res. 2018 ;7 1655
    Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M.
      Publishing peer review materials alongside research articles promises to make the peer review process more transparent as well as making it easier to recognise these contributions and give credit to peer reviewers. Traditionally, the peer review reports, editors letters and author responses are only shared between the small number of people in those roles prior to publication, but there is a growing interest in making some or all of these materials available. A small number of journals have been publishing peer review materials for some time, others have begun this practice more recently, and significantly more are now considering how they might begin. This article outlines the outcomes from a recent workshop among journals with experience in publishing peer review materials, in which the specific operation of these workflows, and the challenges, were discussed. Here, we provide a draft as to how to represent these materials in the JATS and Crossref data models to facilitate the coordination and discoverability of peer review materials, and seek feedback on these initial recommendations.
    Keywords:  Crossref; JATS; JATS4R; peer review; scholarly publishing
    DOI:  https://doi.org/10.12688/f1000research.16460.1
  2. Eur Radiol. 2018 Nov 15.
    Frank RA, Sharifabadi AD, Salameh JP, McGrath TA, Kraaijpoel N, Dang W, Li N, Gauthier ID, Wu MZ, Bossuyt PM, Levine D, McInnes MDF.
      OBJECTIVES: To assess the risk of citation bias in imaging diagnostic accuracy research by evaluating whether studies with higher accuracy estimates are cited more frequently than those with lower accuracy estimates.METHODS: We searched Medline for diagnostic accuracy meta-analyses published in imaging journals from January 2005 to April 2016. Primary studies from the meta-analyses were screened; those assessing the diagnostic accuracy of an imaging test and reporting sensitivity and specificity were eligible for inclusion. Studies not indexed in Web of Science, duplicates, and inaccessible articles were excluded. Topic (modality/subspecialty), study design, sample size, journal impact factor, publication date, times cited, sensitivity, and specificity were extracted for each study. Negative binomial regression was performed to evaluate the association of citation rate (times cited per month since publication) with Youden's index (sensitivity + specificity -1), highest sensitivity, and highest specificity, controlling for the potential confounding effects of modality, subspecialty, impact factor, study design, sample size, and source meta-analysis.
    RESULTS: There were 1016 primary studies included. A positive association between Youden's index and citation rate was present, with a regression coefficient of 0.33 (p = 0.016). The regression coefficient for sensitivity was 0.41 (p = 0.034), and for specificity, 0.32 (p = 0.15).
    CONCLUSION: A positive association exists between diagnostic accuracy estimates and citation rates, indicating that there is evidence of citation bias in imaging diagnostic accuracy literature. Overestimation of imaging test accuracy may contribute to patient harm from incorrect interpretation of test results.
    KEY POINTS: • Studies with higher accuracy estimates may be cited more frequently than those with lower accuracy estimates. • This citation bias could lead clinicians, reviews, and clinical practice guidelines to overestimate the accuracy of imaging tests, contributing to patient harm from incorrect interpretation of test results.
    Keywords:  Bibliometrics; Diagnostic test; Publication bias; Routine; Sensitivity and specificity
    DOI:  https://doi.org/10.1007/s00330-018-5801-8
  3. Clin Pharmacol Ther. 2018 Nov 11.
    Schmith VD, Reynolds KS, Brouwer KLR, Vicini P.
      Many articles in clinical pharmacology may highly influence drug development and regulatory decision making, far beyond the measure conveyed by the Journal Impact Factor. Quantifying impact from the grey content (e.g., nonpublished information) remains an evolving dilemma. A collaboration is proposed with library scientists and bioinformaticians to develop methods to measure the impact of grey content on drug development and regulatory decision making. Mechanisms to reward this impact are discussed.
    DOI:  https://doi.org/10.1002/cpt.1236
  4. BMC Med Res Methodol. 2018 Nov 13. 18(1): 130
    Ćurković M, Košec A.
      BACKGROUND: Using internet search engines (such as Google search) in systematic literature reviews is increasingly becoming a ubiquitous part of search methodology. In order to integrate the vast quantity of available knowledge, literature mostly focuses on systematic reviews, considered to be principal sources of scientific evidence at all practical levels. Any possible individual methodological flaws present in these systematic reviews have the potential to become systemic.MAIN TEXT: This particular bias, that could be referred to as (re)search bubble effect, is introduced because of inherent, personalized nature of internet search engines that tailors results according to derived user preferences based on unreproducible criteria. In other words, internet search engines adjust their user's beliefs and attitudes, leading to the creation of a personalized (re)search bubble, including entries that have not been subjected to rigorous peer review process. The internet search engine algorithms are in a state of constant flux, producing differing results at any given moment, even if the query remains identical. There are many more subtle ways of introducing unwanted variations and synonyms of search queries that are used autonomously, detached from user insight and intent. Even the most well-known and respected systematic literature reviews do not seem immune to the negative implications of the search bubble effect, affecting reproducibility.
    CONCLUSION: Although immensely useful and justified by the need for encompassing the entirety of knowledge, the practice of including internet search engines in systematic literature reviews is fundamentally irreconcilable with recent emphasis on scientific reproducibility and rigor, having a profound impact on the discussion of the limits of scientific epistemology. Scientific research that is not reproducible, may still be called science, but represents one that should be avoided. Our recommendation is to use internet search engines as an additional literature source, primarily in order to validate initial search strategies centered on bibliographic databases.
    Keywords:  Literature searches; Reporting; Research ethics; Scientific rigor; Web searching
    DOI:  https://doi.org/10.1186/s12874-018-0599-2
  5. Health Info Libr J. 2018 Nov 14.
    Ibegbulam IJ, Akpom CC, Enem FN, Onyam DI.
      BACKGROUND: Adolescent female students should be provided opportunities to access reproductive health information to navigate this period of development successfully. Examining the use of the Internet for accessing reproductive health information by this group will provide useful information on their information needs and seeking behaviour.OBJECTIVE: The aim of this study was to investigate the use of the Internet for reproductive health information among adolescent female students in secondary schools in Enugu, Nigeria.
    METHOD: This descriptive study was conducted on adolescent female students in six secondary schools in Enugu urban. Data were collected using a self-administered questionnaire. A total of 120 adolescent female students participated in the study.
    FINDINGS: The adolescent female students use the Internet to seek for information on general see education (n = 120, 100%), sexual hygiene (n = 71, 59%), abstinence from premarital sex (n = 68, 57%), avoidance of sexual abuse (n = 67, 56%). Their preference for the Internet include its privacy (n = 115, 96%) and wealth of information (n = 111, 92%).
    CONCLUSIONS: Adolescent female students use the Internet to meet their reproductive health information needs. Access to the Internet should be enhanced for this group.
    Keywords:  Africa, west; Internet; Internet access; access to information; health information needs; information need; information seeking behaviour; information sources; questionnaires; women's health
    DOI:  https://doi.org/10.1111/hir.12242
  6. Bull Exp Biol Med. 2018 Nov 12.
    Suvorov RE, Kim YS, Gisina AM, Chiang JH, Yarygin KN, Lupatov AY.
      The data on cancer stem cell surface molecular markers of 27 most common cancer diseases were analyzed using natural language processing and data mining techniques. As a source, 8933 full-text open-access English-language scientific articles available on the Internet were used. Text mining was based on searching for three entities within one sentence, namely a tumor name, a phrase "cancer stem cells" or its synonym, and a name of differentiation cluster molecule. As a result, a list of surface molecular markers was formed that included markers most frequently mentioned in the context of certain tumor diseases and used in studies of human and animal tumor cells. Based on similarity of the associated markers, the tumors were divided into five groups.
    Keywords:  cancer stem cells; data mining; information extraction; natural language processing; surface molecular markers
    DOI:  https://doi.org/10.1007/s10517-018-4302-8
  7. J Affect Disord. 2018 Nov 05. pii: S0165-0327(18)31577-5. [Epub ahead of print]245 270-278
    McMullan RD, Berle D, Arnáez S, Starcevic V.
      BACKGROUND: Cyberchondria refers to an abnormal behavioral pattern in which excessive or repeated online searches for health-related information are distressing or anxiety-provoking. Health anxiety has been found to be associated with both online health information seeking and cyberchondria. The aims of the present systematic review and meta-analysis were to examine the magnitude of these associations and identify any moderator variables.METHODS: A systematic literature search was performed across several databases (PsycINFO, PubMed, Embase) and reference lists of included studies.
    RESULTS: Twenty studies were included across two independent meta-analyses, with 7373 participants. Random effects meta-analyses showed that there was a positive correlation between health anxiety and online health information seeking [r = 0.34, 95% CI (0.20, 0.48), p < .0001], and between health anxiety and cyberchondria [r = 0.62, 95% CI (0.52, 0.71), p < .0001]. A meta-regression indicated that the age of study participants [Q(1) = 4.58, p = .03] was partly responsible for the heterogeneity found for the relationship between health anxiety and cyberchondria.
    LIMITATIONS: The generalizability and validity of our findings are restricted by the methodological limitations of the primary studies, namely, an over-reliance on a single measure of cyberchondria, the Cyberchondria Severity Scale.
    CONCLUSIONS: Our review found a positive correlation between health anxiety and online health information seeking, and between health anxiety and cyberchondria. Further research should aim to explore the contexts for these associations as well as address the identified limitations of the extant literature.
    Keywords:  Cyberchondria; Health anxiety; Internet; Meta-analysis; Online seeking; Systematic review
    DOI:  https://doi.org/10.1016/j.jad.2018.11.037
  8. J Clin Epidemiol. 2018 Nov 10. pii: S0895-4356(18)30537-7. [Epub ahead of print]
    Sharp MK, Tokalić R, Gómez G, Wager E, Altman DG, Hren D.
      OBJECTIVE: The STrengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement provides guidance on reporting observational studies. Many extensions have been created for specialized methods or fields. We determined endorsement prevalence and typology by journals in extension-related fields.STUDY DESIGN AND SETTING: A published protocol defined search strategies to identify journals publishing observational studies (2007 - 2017) across seven fields relating to STROBE extensions. We extracted text regarding STROBE, 7 STROBE extensions, reporting guidelines CONSORT and PRISMA, and transparent reporting documents/groups: ICMJE, COPE, and the EQUATOR Network. Relationships between endorsing STROBE, endorsing other guidelines and journal impact factor were tested using Chi-square and Mann-Whitney.
    RESULTS: Of 257 unique journals, 12 (5%) required STROBE on submission, 22 (9%) suggested use, 12 (5%) recommended a "relevant guideline", 72 (28%) mentioned it indirectly (via editorial policies or ICMJE Recommendations), and 139 (54%) did not mention STROBE. The relevant extension was required by 2 (<1%) journals; 4 (1%) suggested use. STROBE endorsement was not associated with journal impact indices but was with CONSORT and PRISMA endorsement.
    CONCLUSION: Reporting guideline endorsement rates are low; information is vague and scattered. Unambiguous language is needed to improve adherence to reporting guidelines and increase the quality of reporting.
    Keywords:  STROBE; epidemiologic research design; guidelines as topic; information dissemination/methods; observational studies
    DOI:  https://doi.org/10.1016/j.jclinepi.2018.11.006
  9. FEMS Microbiol Lett. 2018 Nov 12.
    Romano S, Ansorge R.
      Over the last decades, the world of communication underwent drastic changes, and Internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people, and institutions. We conducted an on-line survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that > 80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them, and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.
    DOI:  https://doi.org/10.1093/femsle/fny264
  10. Int J Oral Maxillofac Implants. 2018 Nov/Dec;33(6):33(6): 1240-1246
    Yeung AWK, Leung WK.
      PURPOSE: This bibliometric study analyzed English language dental implant literature from 2007 to 2016 to evaluate and identify the terms, authors, and journals concerning dental implant articles with high citation count and the structure of their bibliometric networks.MATERIALS AND METHODS: The Web of Science database was searched to identify articles on the topic of dental implants published under the Web of Science category of Dentistry, Oral Surgery & Medicine from 2007 to 2016. The articles were first assessed using descriptive analysis concerning the authors, organizations, countries/territories, and journals. Afterward, VOSviewer was used to visualize the term map, author network, and journal network consisting of the most highly cited entities. CiteSpace II was used with default settings to identify keywords that experienced a large increase in citations received within the surveyed period of time.
    RESULTS: The citation analyses were based on 12,114 dental implant articles published during the survey period. The top five highly cited terms with > 500 publication counts were peri-implantitis (a mean of 20.17 citations per surveyed article [CPA]), survival rate (19.02 CPA), survival (18.74 CPA), implant failure (16.58 CPA), and success rate (16.53 CPA). The top five authors with highest average citations authored 80 papers (80/12,114 = 0.7%) that received 5,962 citations (5,962/151,404 = 3.9%) among the highly cited authors' network. Clinical Oral Implants Research had the largest total number of citation links (19,283), and hence, was in the center of the journal network, with a mean of 21.47 citations per surveyed article.
    CONCLUSION: The terms with high impact were related to implant success, survival, failure, and peri-implantitis. Clinical Oral Implants Research and The International Journal of Oral & Maxillofacial Implants were in the center of the journal citation network.
    DOI:  https://doi.org/10.11607/jomi.6727
  11. WOSP 2017 (2017). 2017 Dec;2017 40-45
    Guan Y, Du J, Torvik VI.
      We analyze nearly 20 million geocoded PubMed articles with author affiliations. Using K-means clustering for the lower 48 US states and mainland China, we find that the average published paper is within a relatively short distance of a few centroids. These centroids have shifted very little over the past 30 years, and the distribution of distances to these centroids has not changed much either. The overall country centroids have gradually shifted south (about 0.2° for the USA and 1.7° for China), while the longitude has not moved significantly. These findings indicate that there are few large scientific hubs in the USA and China and the typical investigator is within geographical reach of one such hub. This sets the stage to study centralization of biomedical research at national and regional levels across the globe, and over time.
    Keywords:  Geocoding; author affiliation; bibliographic databases; clustering
    DOI:  https://doi.org/10.1145/3127526.3127534
  12. Tunis Med. 2018 Jul;96(7): 411-416
    Zemni I, Safer M, Horrigue I, Ben Abdelaziz A, Hammami S, Ben Abdelaziz A.
      BACKGROUND: English is becoming nowadays the universal language of science. Rresearch published in English can be considered as a bibliometric indicator of the scientific productivity.AIM: We sought to describe the evolution of the Tunisian medical publications written in English over the period from 2004 to 2014.
    METHODS: Medline's database was consulted using a research query associating the names of the country and the main university cities both in French and in English. The articles with a Tunisian health affiliation were retained but the articles of dentistry, pharmacy and non-medical fields were not included.
    RESULTS: We counted 979 English language Tunisian medical articles published during the three tracer years of the study: 2004, 2009 and 2014. The increase rate was about 38% between 2004 and 2014. The contribution of medical fields in English language publications was important but showed a clear decrease over time. The retrieved articles did not have the same distribution according to the specialties and the institutions. The distribution according to the journals showed that these articles were mainly published by foreign journals with an increasing impact factors between 2004 and 2014.
    CONCLUSION: The English language Tunisian medical productivity had shown an important increase over time but many specialties and institutions still not enough implicated in this production.Therefore, increasing research funding, improving the physicians' research methodology and English writing capacities are likely needed to improve the Tunisian medical output.