bims-librar Biomed News
on Biomedical librarianship
Issue of 2019‒06‒16
twenty papers selected by
Thomas Krichel
Open Library Society


  1. Bull Emerg Trauma. 2019 Apr;7(2): 93-98
    Rastegarfar B, Ardalan A, Nejat S, Keshtkar A, Moradian MJ.
      Objective: To find a proper search strategy to do a systematic review related to preparedness for disasters.Methods: MeSH and Emtree terms were searched to detect synonyms for two main search terms "disaster" and "preparedness". Expert opinion on the synonyms was examined applying a Google form. The adopted syntax was searched in PubMed and results were sifted. Hand searching in two top key journals was done and sensitivity was calculated.
    Results: Out of 1120 articles, 122 were included. In PDM journal, 10 articles were included by hand searching, out of which 5 were not spotted in PubMed search with the proposed syntax. In DMPHP journal, 13 publications were included, with 5 not found in PubMed search. Because of human error in hand searching 2 articles were added.
    Conclusion: The proposed syntax in this study achieves a sensitivity of search of 0.6 in PubMed which could be quite applicable for researchers. Moreover, in case only MeSH or Emtree terms were applied in search strategy or where hand searching was not performed, there were a number of articles missed.
    Keywords:  Disaster; Health; Preparedness
    DOI:  https://doi.org/10.29252/beat-070201.
  2. Lancet. 2019 Jun 08. pii: S0140-6736(19)31206-1. [Epub ahead of print]393(10188): 2294-2295
    Gunter J.
      
    DOI:  https://doi.org/10.1016/S0140-6736(19)31206-1
  3. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 181-186
    Pomputius A.
      Maintaining regular engagement with audiences through various forms of social media is becoming more important as library users and the general public increasingly rely on social media for news, updates, and feedback. While large corporations have been monitoring social media for more than a decade, libraries have recently begun to use social listening to stay abreast of trends and assess user needs as voiced directly by their communities. This column will explain what social listening is, explore concerns over its widespread application, consider examples of social media listening software currently available, and offer an overview of its application in library settings.
    Keywords:  Emerging technology; libraries; social listening; social media
    DOI:  https://doi.org/10.1080/02763869.2019.1588042
  4. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 113-130
    Glotfelty-Scheuering OA.
      Hospitals are increasingly implementing Nurse Residency Programs (NRPs), but medical librarians are often left out of their institution's respective programs. Librarians possess a unique, knowledge-based skill set that is a natural fit for the content and goals of a NRP and should be more frequently considered and used by such programs. This article identifies and explores several roles for librarians in NRPs and discusses the impact and results of including librarians.
    Keywords:  Escape room; Nurse Residency Program; evidence-based nursing; evidence-based practice; hospital library; medical librarian
    DOI:  https://doi.org/10.1080/02763869.2019.1588043
  5. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 131-142
    Inman M, Blevins AE, Ketterman E, Young KL.
      Over the years, library collections have vastly changed due to an ever-growing presence of resources available online. Many libraries have experienced a dramatic decrease in the circulation of physical materials with the shift to online availability of materials. It is of great value to ensure libraries are meeting the needs of their users, and this can be accomplished by identifying their information-seeking patterns. The aim of this article is to examine how faculty use the library and to identify what services and resources are of value to their work.
    Keywords:  Electronic resources; information seeking; library services; survey
    DOI:  https://doi.org/10.1080/02763869.2019.1588046
  6. J Biomed Inform. 2019 Jun 11. pii: S1532-0464(19)30143-1. [Epub ahead of print] 103224
    Milliken LK, Motomarry SK, Kulkarni A.
      BACKGROUND: Information curation and literature surveillance efforts that synthesize the current knowledge about the impact of genetic variability on disease states and drug responses are vitally important for the practise of evidence-based precision medicine. For these efforts, finding the relevant and comprehensive set of articles from the ever growing scientific literature is a challenge.METHODS: We have designed and developed Article Retrieval for Precision Medicine (ARtPM), an end-to-end article retrieval system that employs multi-stage architecture to retrieve and rank relevant articles for a given medical case summary (genetic variants, disease, demographic, and other medical conditions). We compared ARtPM with five baselines, including PubMed Best Match, the improved search functionality recently introduced by PubMed.
    RESULTS: The differences in the performance of ARtPM and five baselines were statistically significant for four metrics that quantify different aspects of search effectiveness (P-values for P@10, R-prec, infNDCG, Recall@1000 were <.001, <.001, .003, .009, respectively). Pairwise systems' comparisons show that ARtPM is comparable or better than the best performing baseline on three metrics (R-prec: 0.324 vs 0.299, P-value=.06; infNDCG: 0.556 vs 0.465, P-value=.08; R@1000: 0.665 vs 0.572, P-value=.007), but performance in P@10 (0.603 vs 0.630, P-value:.64) needs to improve.
    CONCLUSION: The recall-focused phase of the ARtPM is effective at retrieving more relevant articles. The precision-focused ranking phase performs well at deeper ranks but needs further work on early ranks (e.g., richer feature set). Overall, the ARtPM system effectively facilitates evidence-based precision medicine practice, and provides a robust search framework for further work in this direction.
    Keywords:  Biomedical Information Retrieval; Biomedical Knowledge Curation; Document Retrieval; Learning to Rank; Precision Medicine; Query Expansion
    DOI:  https://doi.org/10.1016/j.jbi.2019.103224
  7. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 156-162
    Britton RM, Robertson J.
      Changing patron demands, coupled with significant repurposing of library space, led the library to experience a marked decline in the usage of the print reference collection. Such a significant decrease challenged librarians to find new methods for promoting this still viable collection. It was decided to integrate the print reference books into the general library collection. After a year, circulation data demonstrated that by integrating collections, reference titles were now used more frequently.
    Keywords:  Academic libraries; collection management; library space; medical libraries; reference collection; reference service
    DOI:  https://doi.org/10.1080/02763869.2019.1589864
  8. Data Brief. 2019 Aug;25 104048
    Khan SUR, Islam MA.
      Recently, Temporal Information Retrieval (TIR) has grabbed the major attention of the information retrieval community. TIR exploits the temporal dynamics in the information retrieval process and harnesses both textual relevance and temporal relevance to fulfill the temporal information requirements of a user Ur Rehman Khan et al., 2018. The focus time of document is an important temporal aspect which is defined as the time to which the content of the document refers Jatowt et al., 2015; Jatowt et al., 2013; Morbidoni et al., 2018, Khan et al., 2018. To the best of our knowledge, there does not exist any standard benchmark data set (publicly available) that holds the potential to comprehensively evaluate the performance of focus time assessment strategies. Considering these aspects, we have produced the Event-dataset, which is comprised of 35 queries and set of news articles for each query. Such that, C = { Q s , D s } , where C represents the dataset, Q s is query set Q s = { q 1 , q 2 , q 3 , … … . , q 35 } and for each q i there is a set of news articles q i = { d r , d n r } . d r , d n r are sets of relevant documents and non-relevant documents respectively. Each query in the dataset represents a popular event. To annotate these articles into relevant and non-relevant, we have employed a user-study based evaluation method wherein a group of postgraduate students manually annotate the articles into the aforementioned categories. We believe that the generation of such dataset can provide an opportunity for the information retrieval researchers to use it as a benchmark to evaluate focus time assessment methods specifically and information retrieval methods generically.
    Keywords:  Focus time assessment; Information retrieval; Temporal; Text classification
    DOI:  https://doi.org/10.1016/j.dib.2019.104048
  9. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 163-170
    Rios DM.
      Health profession students benefit academically, clinically, and professionally when they acquire the writing skills necessary for scholarly communication. The purpose of this article is to discuss how a solo, embedded health science librarian spearheaded collaborative efforts and contributed to the creation of a scaffolded writing program within the existing optometry curriculum. The article includes a discussion of the opportunities, challenges, and outcomes of this writing endeavor.
    Keywords:  Health profession students; scholarly communication; student success; writing skills
    DOI:  https://doi.org/10.1080/02763869.2019.1588038
  10. Health Commun. 2019 Jun 10. 1-8
    Ahn J, Kahlor LA.
      Research suggests that a search for health information from diverse sources is crucial for obtaining accurate and quality information. As a result, this study examines motivators of intentions to use multiple information sources. Our guiding framework is the planned risk information seeking model, which poses a direct relationship between seeking-related subjective norms and information seeking intentions, and an indirect relationship between those two variables through information insufficiency (or perceived need for more information). To further explore these relationships, we integrate a novel variable, anticipated regret, as an additional mediator of both relationships. The information seeking behavior of interest in this study is intention to seek information through multiple sources. Survey results from 379 undergraduate students show that seeking-related subjective norms are positively related with information insufficiency through regret, and positively related with seeking intent through regret and information insufficiency. The implications of these findings are discussed.
    DOI:  https://doi.org/10.1080/10410236.2019.1626535
  11. Gen Dent. 2019 May-Jun;67(3):67(3): 38-46
    Hicks D, Melkers M, Barna J, Isett KR, Gilbert GH.
      Accessible sources of clinical information have proliferated over the past decade. Although these new sources that contextualize information for practice are user friendly, there are questions about their accuracy because much of the material is not peer reviewed. On the other hand, traditional peer-reviewed material can be somewhat removed from the needs of practicing dentists, and recently questions have been raised about the accuracy of journals. This study assessed the accuracy of cone beam computed tomography (CBCT) radiation safety information in both professional media and peer-reviewed journals. Articles introducing CBCT technology to dentists and published in peer-reviewed journals were compared to articles appearing in professional magazines, clinically oriented news sites, and blogs written by clinicians for clinicians. The reported radiation doses of CBCT and conventional dental radiographs were recorded, as were conclusions about the comparative doses of these 2 imaging modalities. The proportion of articles reporting CBCT dose to be greater than, equal to, or less than that of conventional dental radiographs was not different between the peer-reviewed and professional media articles during the period 2003-2016. There is weak evidence that the conclusions of peer-reviewed journal articles, but not professional media sources, became more conservative after the 2010 publication of an article in The New York Times that was critical of misinformation concerning the safety and efficacy of CBCT in dentistry. Professional media articles that were not peer reviewed were as accurate as peer-reviewed journals for this topic and during the time period assessed. However, the method used here necessitated a narrow focus, and more studies are needed to broaden understanding.
  12. J Med Internet Res. 2019 Jun 13. 21(6): e12876
    Foufi V, Timakum T, Gaudet-Blavignac C, Lovis C, Song M.
      BACKGROUND: Social media platforms constitute a rich data source for natural language processing tasks such as named entity recognition, relation extraction, and sentiment analysis. In particular, social media platforms about health provide a different insight into patient's experiences with diseases and treatment than those found in the scientific literature.OBJECTIVE: This paper aimed to report a study of entities related to chronic diseases and their relation in user-generated text posts. The major focus of our research is the study of biomedical entities found in health social media platforms and their relations and the way people suffering from chronic diseases express themselves.
    METHODS: We collected a corpus of 17,624 text posts from disease-specific subreddits of the social news and discussion website Reddit. For entity and relation extraction from this corpus, we employed the PKDE4J tool developed by Song et al (2015). PKDE4J is a text mining system that integrates dictionary-based entity extraction and rule-based relation extraction in a highly flexible and extensible framework.
    RESULTS: Using PKDE4J, we extracted 2 types of entities and relations: biomedical entities and relations and subject-predicate-object entity relations. In total, 82,138 entities and 30,341 relation pairs were extracted from the Reddit dataset. The most highly mentioned entities were those related to oncological disease (2884 occurrences of cancer) and asthma (2180 occurrences). The relation pair anatomy-disease was the most frequent (5550 occurrences), the highest frequent entities in this pair being cancer and lymph. The manual validation of the extracted entities showed a very good performance of the system at the entity extraction task (3682/5151, 71.48% extracted entities were correctly labeled).
    CONCLUSIONS: This study showed that people are eager to share their personal experience with chronic diseases on social media platforms despite possible privacy and security issues. The results reported in this paper are promising and demonstrate the need for more in-depth studies on the way patients with chronic diseases express themselves on social media platforms.
    Keywords:  chronic disease; data mining; social media
    DOI:  https://doi.org/10.2196/12876
  13. HPB (Oxford). 2019 Jun 05. pii: S1365-182X(19)30476-9. [Epub ahead of print]
    Raptis DA, Sinanyan M, Ghani S, Soggiu F, Gilliland JJ, Imber C.
      INTRODUCTION: The internet has become a fundamental source of medical information for patients, however, little is known about the quality of patient information regarding the management of gallstone disease (GD).METHODS: A systematic review of information on GD in the internet was performed. The top 100 websites for every different search term and search engine were assessed using the validated EQIP tool (Score 0-36).
    RESULTS: A total of 2000 websites were identified and 212 (11%) were eligible for analysis. The overall median EQIP score of all websites was 15 (IQR 13-18). Of all websites, 63% originated from North America however, these represented the lowest median EQIP score of 15. Only 41% of the websites differentiated between clinical presentations and 19% provided emergency information. Only 3% of the websites reported complication rates, ranging from 3 to 36%.
    CONCLUSION: This is a comprehensive assessment of online patient information on GD using the EQIP tool. The assessment of the quality of websites concerning GD by the EQIP tool indicates that the majority of sites were of low-quality information. There is an immediate need for better informative and educational websites regarding GD that are compatible with international quality standards.
    DOI:  https://doi.org/10.1016/j.hpb.2019.03.355
  14. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 171-180
    Schiavo JH.
      PROSPERO is an international database of systematic review protocols produced by the University of York's Center for Research and Dissemination and funded by the National Institute for Health Research. It contains protocols of systematic reviews on health and social care, welfare, public health, education, crime, justice, and health-related international development. PROSPERO compiles a comprehensive listing of systematic review protocols in an attempt to avoid duplication of effort, reduce reporting bias, and promote transparency.
    Keywords:  Evidence-based practice; health sciences database; product evaluation; search engine
    DOI:  https://doi.org/10.1080/02763869.2019.1588072
  15. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 197-201
    Moreau E.
      This guest column details the experience of an early career academic librarian learning how to instruct and assist students in health sciences programs. It includes information on mentoring, peer coaching, formal and informal trainings, and proficiencies needed for reference and instruction services. The author shares sources of specific knowledge and skills that empowered her to transition to health sciences librarianship.
    Keywords:  Library instruction; health sciences librarianship; medical education
    DOI:  https://doi.org/10.1080/02763869.2019.1595281
  16. Health Info Libr J. 2019 Jun 11.
    Golder S, Farrah K, Mierzwinski-Urban M, Wright K, Loke YK.
      BACKGROUND: Objectively derived search filters for adverse drug effects and complications in surgery have been developed but not for medical device adverse effects.OBJECTIVE: To develop and validate search filters to retrieve evidence on medical device adverse effects from ovid medline and embase.
    METHODS: We identified systematic reviews from Epistemonikos and the Health Technology Assessment (hta) database. Included studies within these reviews that reported on medical device adverse effects were randomly divided into three test sets and one validation set of records. Using word frequency analysis from one test set, we constructed a sensitivity maximising search strategy. This strategy was refined using two other test sets, then validated.
    RESULTS: From 186 systematic reviews which met our inclusion criteria, 1984 unique included studies were available from medline and 1986 from embase. Generic adverse effects searches in medline and embase achieved 84% and 83% sensitivity. Recall was improved to over 90%, however, when specific adverse effects terms were added.
    CONCLUSION: We have derived and validated novel search filters that retrieve over 80% of records with medical device adverse effects data in medline and embase. The addition of specific adverse effects terms is required to achieve higher levels of sensitivity.
    Keywords:   embase ; medline ; information retrieval; literature searching; medical devices; medical subject headings (MeSH); meta-analysis; methodological filters; review; search strategies; searching
    DOI:  https://doi.org/10.1111/hir.12260
  17. J Med Internet Res. 2019 Jun 10. 21(6): e10980
    Eichenberg C, Schott M.
      BACKGROUND: An increasing number of people consult physicians because of distressing information found online. Cyberchondria refers to the phenomenon of health anxiety because of online health information.OBJECTIVE: This study aimed to examine online health research of individuals with and without symptoms of hypochondria and their impact on health anxiety as well as behavior.
    METHODS: An online survey was conducted. Demographic data, health-related internet use, and general health behavior were assessed. The illness attitude scale was used to record symptoms of hypochondria.
    RESULTS: The final sample consisted of N=471 participants. More than 40% (188/471) of participants showed at least some symptoms of hypochondria. Participants with symptoms of hypochondria used the internet more frequently for health-related purposes and also frequented more online services than individuals without symptoms. Most online health services were rated as more reliable by individuals with symptoms of hypochondria. Changes to behavior such as doctor hopping or ordering nonprescribed medicine online were considered more likely by individuals with symptoms of hypochondria.
    CONCLUSIONS: Results show that individuals with symptoms of hypochondria do not turn to online research as a result of lacking alternatives but rather consult health services on- as well as offline.
    Keywords:  anxiety; eHealth; hypochondria; survey
    DOI:  https://doi.org/10.2196/10980
  18. Biomed Tech (Berl). 2019 Jun 14. pii: /j/bmte.ahead-of-print/bmt-2018-0068/bmt-2018-0068.xml. [Epub ahead of print]
    Keyvanpour M, Serpush F.
      MEDLINE is a rapidly growing database; to utilize this resource, practitioners and biomedical researchers have dealt with tedious and time-consuming tasks such as discovering, searching, reading and evaluating of biomedical documents. However, making a label for a group of biomedical documents is expensive and needs a complicated operation. Otherwise, compound words, polysemous and synonymous problems can influence the search in MEDLINE. Therefore, designing an efficient way of sharing knowledge and information organization is essential so that information retrieval systems can provide ideal outcomes. For this purpose, different strategies are used in the retrieval of biomedical documents (RBD). However, still a number of unrelated results for the users' query are obtained in the RBD process. Studies have shown that well-defined clusters in the retrieval system exhibit a more efficient performance in contrast to the document-based retrieval. Accordingly, the present study proposes the Expanding Statistical Language Modeling and Thesaurus (ESLMT) for clustering and retrieving biomedical documents. The results showed that Clustering with ESLM Similarity and Thesaurus (CESLMST) in all those criteria in this study have a higher value than the other compared methods. The results indicated that the mean average precision (MAP) has improved in the Clusters' Retrieval Derived from ESLM Similarity-Query (CRDESLMS-QET) method in comparison to the previous methods with the Text REtrieval Conference (TREC) data set.
    Keywords:  MEDLINE; MeSH thesaurus; biomedical document retrieval; clustering; statistical language modeling
    DOI:  https://doi.org/10.1515/bmt-2018-0068
  19. Med Ref Serv Q. 2019 Apr-Jun;38(2):38(2): 143-155
    Knapp M, Risha Z, Gatewood R, Van Der Volgen J, Brown R, Kizilboga R.
      This article is a case study that discusses the development and implementation of an internal learning object repository (LOR) for a large national organization with a distributed working environment. It describes the organizational environment and why an internal LOR was needed. It describes technical considerations, including the various document management systems (DMS) available, and why an open source DMS was selected to use as an internal LOR. Lastly, this article weighs the benefits and challenges of implementing a LOR across a distributed working environment and reflects on challenges associated with implementation.
    Keywords:  Digital learning objects repository; document management systems; learning object repository
    DOI:  https://doi.org/10.1080/02763869.2019.1588049
  20. Ann Otol Rhinol Laryngol. 2019 Jun 13. 3489419856377
    Bailey CE, Kohler WJ, Makary C, Davis K, Sweet N, Carr M.
      OBJECTIVES: The aim of this study was to compare eHealth literacy-one's perception of one's ability to use the Internet for health care-among otolaryngology patients in 3 geographic settings of the same department.SETTING: An academic otolaryngology department.
    METHOD: Patients' opinions and perceptions of their eHealth literacy were assessed with a validated paper survey administered in the summer of 2017.
    RESULTS: Of 381 asked, 351 people completed the survey, 149 at a university town teaching hospital clinic (group A), 101 at a nearby rural clinic (group B), and 101 at a remote rural clinic (group C). Mean scores were 30.80, 28.97, and 29.03 for groups A, B, and C, respectively. The overall mean was 29.76 ± 5.97. Three surveys reported the minimum score of 8, and 26 reported the maximum score of 40. Results were statistically significantly different among all sites (P = .001), between groups A and B (P = .027), and between groups A and C (P = .0175). Women reported higher eHealth literacy (30.13 ± 6.27) than men (28.87 ± 5.11) (P = .045). Participant age and role (patient or parent of a patient) were statistically insignificant. Mean scores were similar to those previously reported in other patient populations.
    CONCLUSIONS: Otolaryngology patients in a university town had better eHealth literacy than patients in more rural settings, suggesting that online medical resources and access points are less likely to be useful in rural populations.
    Keywords:  eHEALS; eHealth; electronic; health literacy; self-assessment
    DOI:  https://doi.org/10.1177/0003489419856377