bims-librar Biomed News
on Biomedical librarianship
Issue of 2019‒11‒03
six papers selected by
Thomas Krichel
Open Library Society


  1. BMJ Open. 2019 Oct 30. 9(10): e032738
    Hall A, Furlong B, Pike A, Logan G, Lawrence R, Ryan A, Etchegary H, Hennessey T, Toomey E.
      INTRODUCTION: Substantial delays in translating evidence to practice mean that many beneficial and vital advances in medical care are not being used in a timely manner. Traditional knowledge translation (KT) strategies have tended to target academics by disseminating findings in academic journals and at scientific conferences. Alternative strategies, such as theatre-based KT, appear to be effective at targeting broader audiences. The purpose of this scoping review is to collate and understand the current state of science on the use of theatre as a KT strategy. This will allow us to identify gaps in literature, determine the need for a systematic review and develop additional research questions to advance the field.METHODS AND ANALYSIS: This review will follow established scoping review methods outlined by Arksey and O'Malley in conjunction with enhanced recommendations made by Levac et al. The search strategy, guided by an experienced librarian, will be conducted in PubMed, CINHAL and OVID. Study selection will consist of three stages: (1) initial title and abstract scan by one author to remove irrelevant articles and create a shortlist for double screening, (2) title and abstract scan by two authors, and (3) full-text review by two authors. Included studies will report specifically on the use of theatre as means of KT of health-related information to any target population. Two reviewers will independently extract and chart the data using a standardised data extraction form. Descriptive statistics will be used to produce numerical summaries related to study characteristics, KT strategy characteristics and evaluation characteristics. For those studies that included an evaluation of the theatre production as a KT strategy, we will synthesise the data according to outcome.
    ETHICS AND DISSEMINATION: Ethical approval was not required for this study. Results will be published in relevant journals, presented at conferences and distributed via social media.
    Keywords:  knowledge translation; research use; scoping review; theatre
    DOI:  https://doi.org/10.1136/bmjopen-2019-032738
  2. Health Promot Int. 2019 Oct 30. pii: daz108. [Epub ahead of print]
    Mohamad Shakir SM, Wong LP, Lim Abdullah K, Adam P.
      The Internet has opened pathways for youth to find sexual health information which was not easily available to them in the past. Studies have shown that seeking sexual health information online may potentially influence an individuals' decision-making to change their sexual health behaviours. However, there is a gap in research on the associations of seeking online sexually transmitted infection (STI) information with STI prevention among young people, particularly in Malaysia. This study investigated the associations of seeking STI information online with the intentions of condom use among young adult online users in Malaysia. A cross-sectional online survey was conducted among Malaysian youth aged 18-25 years old who were recruited through Facebook. In total, 1530 respondents completed the survey, identifying 874 respondents who had sought STI information online. The majority of respondents had intentions to use condoms as protection against STI. Respondents who sought online STI information were significantly more likely to have the intention to use condoms compared to respondents who did not seek online STI information (OR = 1.33, 95% CI = 1.01-1.76, p = 0.040). Online STI information has the potential to increase access to STI information among young online users in Malaysia amid the stigma surrounding sex-related issues. Providing accurate STI information online from reliable sources may equip young people who have Internet access with awareness of sexual health protective behaviours such as condom use. It is recommended to facilitate Internet access to reach sectors of the population that currently do not have access, as the Internet is useful in STI prevention.
    Keywords:  Internet; STIs; condom use; health promotion; youth
    DOI:  https://doi.org/10.1093/heapro/daz108
  3. J Biomed Inform. 2019 Oct 29. pii: S1532-0464(19)30240-0. [Epub ahead of print] 103321
    Hassanzadeh H, Nguyen A, Verspoor K.
      OBJECTIVE: Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evidence used for synthesizing systematic reviews or practicing Evidence Based Medicine (EBM). Finding all relevant published evidence for a particular medical case is a time and labour intensive task, given the breadth of the biomedical literature. Automatic quantification of conceptual relationships between key clinical evidence within and across publications, despite variations in the expression of clinically-relevant concepts, can help to facilitate synthesis of evidence. In this study, we aim to provide an approach towards expediting evidence synthesis by quantifying semantic similarity of key evidence as expressed in the form of individual sentences. Such semantic textual similarity can be applied as a key approach for supporting selection of related studies.MATERIAL AND METHODS: We propose a generalisable approach for quantifying semantic similarity of clinical evidence in the biomedical literature, specifically considering the similarity of sentences corresponding to a given type of evidence, such as clinical interventions, population information, clinical findings, etc. We develop three sets of generic, ontology-based, and vector-space models of similarity measures that make use of a variety of lexical, conceptual, and contextual information to quantify the similarity of full sentences containing clinical evidence. To understand the impact of different similarity measures on the overall evidence semantic similarity quantification, we provide a comparative analysis of these measures when used as input to an unsupervised linear interpolation and a supervised regression ensemble. In order to provide a reliable test-bed for this experiment, we generate a dataset of 1,000 pairs of sentences from biomedical publications that are annotated by ten human experts. We also extend the experiments on an external dataset for further generalisability testing.
    RESULTS: The combination of all diverse similarity measures showed stronger correlations with the gold standard similarity scores in the dataset than any individual kind of measure. Our approach reached near 0.80 average Pearson correlation across different clinical evidence types using the devised similarity measures. Although they were more effective when combined together, individual generic and vector-space measures also resulted in strong similarity quantification when used in both unsupervised and supervised models. On the external dataset, our similarity measures were highly competitive with the state-of-the-art approaches developed and trained specifically on that dataset for predicting semantic similarity.
    CONCLUSION: Experimental results showed that the proposed semantic similarity quantification approach can effectively identify related clinical evidence that is reported in the literature. The comparison with a state-of-the-art method demonstrated the effectiveness of the approach, and experiments with an external dataset support its generalisability.
    Keywords:  Clinical Evidence; Clinical Semantic Similarity; Evidence Based Medicine; Systematic Review
    DOI:  https://doi.org/10.1016/j.jbi.2019.103321
  4. Wilderness Environ Med. 2019 Oct 28. pii: S1080-6032(19)30153-X. [Epub ahead of print]
    Strickland BM, Kanaan NC.
      INTRODUCTION: Educational materials are important tools in the prevention of altitude illness among individuals traveling to high altitude destinations. Travelers obtain information about altitude illness from many different educational resources. Our objective was to determine which educational resources for altitude illness prevention were used by trekkers on the Everest Base Camp trek and Annapurna Circuit. We also sought to compare which resources were used by individuals from different geographic areas.METHODS: A survey was administered to trekkers attending an altitude illness information lecture at the Himalayan Rescue Association clinic. Trekkers provided their basic demographic information and educational resources they used while preparing for the trek. Comparisons were made between trekkers based on the resources they used, as well as their age and country of origin.
    RESULTS: Of 1075 surveys administered, 906 were completed. Internet sources were most commonly used by trekkers (49%), followed by friends or family (22%), and healthcare providers (18%). The age of participants using Internet sources was 36±12 y (mean±SD), lower than those who did not use Internet sources (39±14 y, P<0.01). Participants came from 8 geographic areas; Europe (55%), North America (24%), and Oceania (11%) made up the vast majority. Compared to the overall cohort, participants from Oceania demonstrated more Internet reliance at 65% (χ2(1, n=102)=9.7, P<0.01).
    CONCLUSIONS: In this group of trekkers in the Himalayas, the Internet was the most common source of information on altitude illness prevention and management. Trekkers using Internet sources were slightly younger than non-Internet users.
    Keywords:  age; education; internet; prevention; resources
    DOI:  https://doi.org/10.1016/j.wem.2019.07.003
  5. BMC Bioinformatics. 2019 Oct 29. 20(1): 534
    Lamurias A, Ruas P, Couto FM.
      BACKGROUND: Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain.RESULTS: We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies. Our method is based on Personalized PageRank (PPR), using the relations of the ontology to generate a graph of candidate concepts for the mentioned entities. We demonstrate how the knowledge encoded in a domain-specific ontology can be used to calculate the coherence of a set of candidate concepts, improving the accuracy of entity linking. Furthermore, we explore weighting the edges between candidate concepts using semantic similarity measures (SSM). We show how PPR-SSM can be used to effectively link named entities to biomedical ontologies, namely chemical compounds, phenotypes, and gene-product localization and processes.
    CONCLUSIONS: We demonstrated that PPR-SSM outperforms state-of-the-art entity linking methods in four distinct gold standards, by taking advantage of the semantic information contained in ontologies. Moreover, PPR-SSM is a graph-based method that does not require training data. Our method improved the entity linking accuracy of chemical compounds by 0.1385 when compared to a method that does not use SSMs.
    Keywords:  Biomedical literature; ChEBI; Entity linking; GO; HPO; Ontologies; Text mining
    DOI:  https://doi.org/10.1186/s12859-019-3157-y
  6. Cleft Palate Craniofac J. 2019 Oct 30. 1055665619884447
    Adekunle AA, James O, Adeyemo WL.
      OBJECTIVE: To ascertain the level of utilization of social media platforms and search engines by parents of children with orofacial cleft presenting to our clinic, with respect to information seeking about the condition and its treatment.MATERIALS AND METHODS: All consenting parents of children attending the cleft outpatient clinic of the Department of Oral and Maxillofacial Surgery, Lagos University Teaching Hospital, Idi-Araba, Lagos, within the study period were included in the sample population. Data collection was done using a 17-item interviewer-administered questionnaire.
    RESULTS: A total of 50 parents participated in the study. Eighty-eight percent first sought information about their child's condition from hospital medical staff. Sixty-eight percent of the parents are active users of social media for general purposes, with Facebook being the most used platform (62%). Forty percent of the total respondents have used search engines/social media to seek information on their child's condition, with majority of those (80%) using Google to search for such information, 35% of the search was in relation to diagnosis, and 75% of the parents considered the information obtained very useful. Only 3 parents reported being part of a social media support group based on their child's condition.
    CONCLUSION: The use of Internet resources for information seeking among the population studied is low. There is need to leverage on social media to provide support groups for families with children who have cleft.
    Keywords:  Internet; cleft lip; cleft palate; orofacial cleft; social media
    DOI:  https://doi.org/10.1177/1055665619884447