bims-librar Biomed News
on Biomedical librarianship
Issue of 2022‒04‒17
seventeen papers selected by
Thomas Krichel
Open Library Society

  1. BMC Med Res Methodol. 2022 Apr 10. 22(1): 107
      BACKGROUND: Systematic reviews (SRs) are valuable resources as they address specific clinical questions by summarizing all existing relevant studies. However, finding all information to include in systematic reviews can be challenging. Methodological search filters have been developed to find articles related to specific clinical questions. To our knowledge, no filter exists for finding studies on the role of prognostic factor (PF). We aimed to develop and evaluate a search filter to identify PF studies in Ovid MEDLINE that has maximum sensitivity.METHODS: We followed current recommendations for the development of a search filter by first identifying a reference set of PF studies included in relevant systematic reviews on the topic, and by selecting search terms using a word frequency analysis complemented with an expert panel discussion. We evaluated filter performance using the relative recall methodology.
    RESULTS: We constructed a reference set of 73 studies included in six systematic reviews from a larger sample. After completing a word frequency analysis using the reference set studies, we compiled a list of 80 of the frequent methodological terms. This list of terms was evaluated by the Delphi panel for inclusion in the filter, resulting in a final set of 8 appropriate terms. The consecutive connection of these terms with the Boolean operator OR produced the filter. We then evaluated the filter using the relative recall method against the reference set, comparing the references included in the SRs with our new search using the filter. The overall sensitivity of the filter was calculated to be 95%, while the overall specificity was 41%. The precision of the filter varied considerably, ranging from 0.36 to 17%. The NNR (number needed to read) value varied largely from 6 to 278. The time saved by using the filter ranged from 13-70%.
    CONCLUSIONS: We developed a search filter for OVID-Medline with acceptable performance that could be used in systematic reviews of PF studies. Using this filter could save as much as 40% of the title and abstract screening task. The specificity of the filter could be improved by defining additional terms to be included, although it is important to evaluate any modification to guarantee the filter is still highly sensitive.
    Keywords:  Prognostic factor; Search filter; Systematic review
  2. J Evid Based Med. 2022 Mar;15(1): 39-54
      AIM: The aim of this overview is to identify and collate evidence from existing published systematic review (SR) articles evaluating various methodological approaches used at each stage of an SR.METHODS: The search was conducted in five electronic databases from inception to November 2020 and updated in February 2022: MEDLINE, Embase, Web of Science Core Collection, Cochrane Database of Systematic Reviews, and APA PsycINFO. Title and abstract screening were performed in two stages by one reviewer, supported by a second reviewer. Full-text screening, data extraction, and quality appraisal were performed by two reviewers independently. The quality of the included SRs was assessed using the AMSTAR 2 checklist.
    RESULTS: The search retrieved 41,556 unique citations, of which 9 SRs were deemed eligible for inclusion in final synthesis. Included SRs evaluated 24 unique methodological approaches used for defining the review scope and eligibility, literature search, screening, data extraction, and quality appraisal in the SR process. Limited evidence supports the following (a) searching multiple resources (electronic databases, handsearching, and reference lists) to identify relevant literature; (b) excluding non-English, gray, and unpublished literature, and (c) use of text-mining approaches during title and abstract screening.
    CONCLUSION: The overview identified limited SR-level evidence on various methodological approaches currently employed during five of the seven fundamental steps in the SR process, as well as some methodological modifications currently used in expedited SRs. Overall, findings of this overview highlight the dearth of published SRs focused on SR methodologies and this warrants future work in this area.
    Keywords:  knowledge synthesis; methodology; overview; systematic reviews
  3. Med Sci Educ. 2022 Apr 05. 1-5
      To provide an online service learning opportunity for medical students during the COVID-19 pandemic, medical faculty and librarians developed and implemented a "Debunking Medical Myths" module in which students learned to search for emerging medical literature, evaluate evidence, and use that evidence to create an infographics debunking a COVID-19-related myth for a non-medical audience. The resultant infographics are visually appealing and designed to make complex health information easy to understand. The module was well-received by students, who demonstrated a nuanced understanding of the use of infographics to convey health information, and students' work was evaluated highly by community members.Supplementary Information: The online version contains supplementary material available at 10.1007/s40670-022-01541-w.
    Keywords:  Evidence-based medicine; Health communication; Infographics; Medical students; Public health; Undergraduate medical education
  4. BMC Bioinformatics. 2022 Apr 15. 23(1): 135
      BACKGROUND: Long non-coding RNA (LncRNA) plays important roles in physiological and pathological processes. Identifying LncRNA-protein interactions (LPIs) is essential to understand the molecular mechanism and infer the functions of lncRNAs. With the overwhelming size of the biomedical literature, extracting LPIs directly from the biomedical literature is essential, promising and challenging. However, there is no webserver of LPIs relationship extraction from literature.RESULTS: LPInsider is developed as the first webserver for extracting LPIs from biomedical literature texts based on multiple text features (semantic word vectors, syntactic structure vectors, distance vectors, and part of speech vectors) and logistic regression. LPInsider allows researchers to extract LPIs by uploading PMID, PMCID, PMID List, or biomedical text. A manually filtered and highly reliable LPI corpus is integrated in LPInsider. The performance of LPInsider is optimal by comprehensive experiment on different combinations of different feature and machine learning models.
    CONCLUSIONS: LPInsider is an efficient analytical tool for LPIs that helps researchers to enhance their comprehension of lncRNAs from text mining, and also saving their time. In addition, LPInsider is freely accessible from with no login requirement. The source code and LPIs corpus can be downloaded from .
    Keywords:  Corpus; Logistic regression; Multiple text features; Named entity recognition; lncRNA–protein interaction
  5. Nucleic Acids Res. 2022 Apr 12. pii: gkac240. [Epub ahead of print]
      The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search ( provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework ( enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.
  6. Database (Oxford). 2022 Apr 12. pii: baac026. [Epub ahead of print]2022
      SwissBioPics ( is a freely available resource of interactive, high-resolution cell images designed for the visualization of subcellular location data. SwissBioPics provides images describing cell types from all kingdoms of life-from the specialized muscle, neuronal and epithelial cells of animals, to the rods, cocci, clubs and spirals of prokaryotes. All cell images in SwissBioPics are drawn in Scalable Vector Graphics (SVG), with each subcellular location tagged with a unique identifier from the controlled vocabulary of subcellular locations and organelles of UniProt ( Users can search and explore SwissBioPics cell images through our website, which provides a platform for users to learn more about how cells are organized. A web component allows developers to embed SwissBioPics images in their own websites, using the associated JavaScript and a styling template, and to highlight subcellular locations and organelles by simply providing the web component with the appropriate identifier(s) from the UniProt-controlled vocabulary or the 'Cellular Component' branch of the Gene Ontology (, as well as an organism identifier from the National Center for Biotechnology Information taxonomy ( The UniProt website now uses SwissBioPics to visualize the subcellular locations and organelles where proteins function. SwissBioPics is freely available for anyone to use under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.DATABASE URL:
  7. Health Promot Chronic Dis Prev Can. 2022 Mar 16. 42(5):
      INTRODUCTION: With the rapid spread of online coronavirus-related health information, it is important to ensure that this information is reliable and effectively communicated. This study observes the dissemination of COVID-19 health literacy information by Canadian postsecondary institutions aimed at university students as compared to provincial and federal government COVID-19 guidelines.METHODS: We conducted a systematic scan of web pages from Canadian provincial and federal governments and from selected Canadian universities to identify how health information is presented to university students. We used our previously implemented health literacy survey with Canadian postsecondary students as a sampling frame to determine which academic institutions to include. We then used specific search terms to identify relevant web pages using Google and integrated search functions on government websites, and compared the information available on pandemic measures categorized by university response strategies, sources of expertise and branding approaches.
    RESULTS: Our scan of Canadian government and university web pages found that universities similarly created one main page for COVID-19 updates and information and linked to public sector agencies as a main resource, and mainly differed in their provincial and local sources for obtaining information. They also differed in their strategies for communicating and displaying this information to their respective students.
    CONCLUSION: The universities in our sample outlined similar policies for their students, aligning with Canadian government public health recommendations and their respective provincial or regional health authorities. Maintaining the accuracy of these information sources is important to ensure student health literacy and counter misinformation about COVID-19.
    Keywords:  COVID-19; Canada; health literacy; online information; postsecondary students; public health; university
  8. Health Commun. 2022 Apr 11. 1-10
      The COVID-19 outbreak was declared a pandemic by the World Health Organization and claimed hundreds of thousands of lives in the U.S. However, the adoption of protective behaviors in response to COVID-19 varies among sociodemographic groups. To better understand the disparities in U.S. adults' adoption of protective behaviors in relation to sociodemographic factors, we conducted a two-wave panel survey in the U.S. Although sociodemographic factors were not found to be significant predictors in lagged regression analysis, results from a cross-sectional analysis showed that the White, younger, and higher educated individuals were more likely to take protective behaviors. Furthermore, based on the structural equation modeling, indirect effects were observed. Specifically, online COVID-19 information seeking mediated the effects of age and education on performance of protective behaviors, and subjective norms and online COVID-19 information seeking were found to be significant serial mediators of these relationships. The study not only extends the health disparities and health information seeking literature, but also offers practical insights to health campaigns and interventions promoting protective behaviors during a pandemic and reducing health disparities.
  9. PLoS One. 2022 ;17(4): e0266276
      During the COVID-19 pandemic, there is a growing interest in online information about coronavirus worldwide. This study aimed to investigate the digital health literacy (DHL) level, information-seeking behaviour, and satisfaction of information on COVID-19 among East and South-East Asia university students. This cross-sectional web-based study was conducted between April to June 2020 by recruiting students from universities in China, Malaysia, and the Philippines. University students who have Internet access were invited to participate in the study. Items on sociodemographic variables, DHL, information-seeking behaviour, and information satisfaction were included in the questionnaire. Descriptive statistics and logistic regression analysis were conducted. A total of 5302 university students responded to the survey. The overall mean score across the four DHL subscales was 2.89 (SD: 0.42). Search engines (e.g., Google, Bing, Yahoo) (92.0%) and social media (88.4%) were highly utilized by the students, whereas Websites of doctors or health insurance companies were of lower utilization (64.7%). Across the domains (i.e., adding self-generated content, determining relevance, evaluating reliability, and protecting privacy) higher DHL was positively associated with higher usage of trustworthy resources. Providing online information on COVID-19 at official university websites and conducting health talks or web-based information dissemination about the strategies for mental health challenges during pandemic could be beneficial to the students. Strengthening DHL among university students will enhance their critical thinking and evaluation of online resources, which could direct them to the quality and trustworthy information sources on COVID-19.
  10. J Biomed Inform. 2022 Apr 09. pii: S1532-0464(22)00078-8. [Epub ahead of print] 104062
      MOTIVATION: Training domain-specific named entity recognition (NER) models requires high quality hand curated gold standard datasets which are time-consuming and expensive to create. Furthermore, the storage and memory required to deploy NLP models can be prohibitive when the number of tasks is large. In this work, we explore utilizing multi-task learning to reduce the amount of training data needed to train new domain-specific models. We evaluate our system across 22 distinct biomedical NER datasets and evaluate the extent to which transfer learning helps task performance using two forms of ablation.RESULTS: We found that multitasking models generally do not improve performance, but in many cases perform on par compared to single-task models. However, we show that in some cases, new unseen tasks can be trained as a single model using less data by starting with weights from a multitask model and improve performance.
    AVAILABILITY: The software underlying this article are available in: CONTACT:
    Keywords:  Biomedical Text Processing; Deep Learning; Named entity recognition; Natural language processing; machine learning
  11. J Hand Surg Glob Online. 2022 Jan;4(1): 3-7
      Purpose: Our purpose was to analyze the content and quality of YouTube videos related to distal biceps tendon (DBT) ruptures and repair. We aimed to compare differences between academic and nonacademic video sources.Methods: The most popular YouTube videos related to DBT injuries were compiled and analyzed according to source. Viewing characteristics were determined for each video. Video content and quality were assessed by 2 reviewers and analyzed according to the Journal of the American Medical Association benchmark criteria, DISCERN criteria, and a Distal Biceps Content Score. Cohen's kappa was used to measure interrater reliability.
    Results: A total of 59 DBT YouTube videos were included. The intraclass correlation coefficients ranged from moderate to excellent for the content scores. The mean DISCERN score was 29, and no videos were rated as either "good" or "excellent" for content quality. With the exception of the mean Journal of the American Medical Association criteria score (1.5 vs 0.5), videos from academic sources did not demonstrate significantly higher levels of content quality. Only 4/59 videos (7%) discussed the natural history of nonsurgically treated DBT ruptures. Of the 32 videos that discussed surgical techniques, only 3/32 (9%) had a preference for 2-incision techniques. No videos discussed the association between spontaneous DBT ruptures and cardiac amyloidosis.
    Conclusions: The overall content, quality, and reliability of DBT videos on YouTube are poor. Videos from academic sources do not provide higher-quality information than videos from nonacademic sources. Videos related to operative treatment of DBT ruptures more frequently discuss single-incision techniques.
    Clinical relevance: Social media videos can function as direct-to-consumer marketing materials, and surgeons should be prepared to address misconceptions regarding the management of DBT tears. Patients are increasingly seeking health information online, and surgeons should direct patients toward more reliable and vetted sources of information.
    Keywords:  Distal biceps repair; Distal biceps rupture; Patient education; Social media; YouTube
  12. BMJ Open Ophthalmol. 2022 ;7(1): e000966
      Objective: Patient adherence to glaucoma medications is poor, and is linked to low literacy levels. Patients commonly use the internet to access health information, and it is recommended that patient information is written at an 11-year-old reading level. The aim of this study is to assess the readability and quality of online patient education materials for the medical management of open angle glaucoma.Methods and analysis: The top 10 relevant Google searches for nine glaucoma medications (timolol, brimonidine, apraclonidine, dorzolamide, latanoprost, bimatoprost, travoprost, tafluprost and brinzolamide) and three generic searches were analysed for readability and accountability. Readability was assessed using Flesch Reading Ease Score (FRES), Flesch-Kincaid Grade Level (FKGL), Gunning Fog Index (GFI) and Simple Measure of Gobbledygook Index (SMOG). Webpages were classified by source and assessed using Journal of the American Medical Association (JAMA) benchmarks of accountability.
    Results: 111 articles were included in the analysis. Mean readability scores were: FRES 55.5 (95% CI 53.4 to 57.5); FKGL 9.7 (95% CI 9.3 to 10.0); GFI 12 (95% CI 11.6 to 12.4) and SMOG 9.3 (95% CI 8.9 to 9.6). One-way analysis of variance demonstrated no significant difference in readability score between source type. 9% of the webpages satisfied all 4 JAMA benchmarks. Pearson's correlation coefficient showed a correlation between the FRES and accountability score (r=0.19, p=0.045).
    Conclusion: The majority of online patient education materials for the medical treatment of glaucoma are written at a level too difficult for the general population and fail to meet accountability standards.
    Keywords:  Glaucoma; Treatment Medical
  13. J Healthc Inform Res. 2020 Dec;4(4): 395-410
      In this pilot study, we explore the feasibility and accuracy of using a query in a commercial natural language processing engine in a named entity recognition and normalization task to extract a wide spectrum of clinical concepts from free text clinical letters. Editorial guidance developed by two independent clinicians was used to annotate sixty anonymized clinic letters to create the gold standard. Concepts were categorized by semantic type, and labels were applied to indicate contextual attributes such as negation. The natural language processing (NLP) engine was Linguamatics I2E version 5.3.1, equipped with an algorithm for contextualizing words and phrases and an ontology of terms from Intelligent Medical Objects to which those tokens were mapped. Performance of the engine was assessed on a training set of the documents using precision, recall, and the F1 score, with subset analysis for semantic type, accurate negation, exact versus partial conceptual matching, and discontinuous text. The engine underwent tuning, and the final performance was determined for a test set. The test set showed an F1 score of 0.81 and 0.84 using strict and relaxed criteria respectively when appropriate negation was not required and 0.75 and 0.77 when it was. F1 scores were higher when concepts were derived from continuous text only. This pilot study showed that a commercially available NLP engine delivered good overall results for identifying a wide spectrum of structured clinical concepts. Such a system holds promise for extracting concepts from free text to populate problem lists or for data mining projects.
    Keywords:  Annotation; Clinical letters; Gold standard; Named entity recognition; Natural language processing; Text mining
  14. Cleft Palate Craniofac J. 2022 Apr 11. 10556656221093292
      INTRODUCTION: The internet has improved access to knowledge, with a reported 72% of internet users accessing health information online. YouTube is the most popular video-sharing website and is a frequently accessed source for health information. There are concerns, however, that patients and carers may be unable to identify and filter for trustworthy sources of information on these platforms. This study aimed to assess the quality of videos that are likely to be accessed when families search YouTube for transcranial procedures for the management of craniosynostosis.METHODOLOGY: This was a cross-sectional, observational study that evaluated YouTube videos when searching for "fronto-orbital advancement" or "cranial vault remodeling." The first 25 videos for each term were included. Videos were assessed for quality using the previously validated JAMA and DISCERN scoring tools.
    RESULTS: There was low interobserver variability for the scoring tools used. There was no statistically significant correlation between the video quality and any video characteristics assessed. Videos published by organizations had higher mean quality scores for both the JAMA and DISCERN tools when compared to surgeon, patient, or medical device company-produced videos.
    CONCLUSION: This study showed that searching YouTube for fronto-orbital advancement and cranial vault remodeling yields videos of low quality and therefore patients and carers should be discouraged from "YouTube-ing" these procedures. Platforms such as YouTube may provide an opportunity for craniofacial units to create and disseminate high-quality educational videos to complement routine perioperative education.
    Keywords:  pediatrics; social support; synostosis
  15. Acta Orthop Traumatol Turc. 2022 Mar;56(2): 88-93
      OBJECTIVE: This study aimed to evaluate the contents and readability levels of informative texts about anterior cruciate ligament (ACL) on Turkish websites.METHODS: In this cross-sectional study, online searches were performed using the Google, Yandex, and Yahoo search engines on 16, 17, and 18 November 2020, respectively. In these three search engines, 'anterior cruciate ligament', 'anterior cruciate ligament surgery', 'ACL', and 'ACL surgery' were entered in Turkish. The first 10 pages from each search on the websites were collected. The websites were divided into 3 groups according to their sources. Group 1 was classified as websites prepared by private hospitals or medical centers; group 2, as individual websites of orthopedics and traumatology physicians; and group 3, as non-profit websites providing general health information that does not fall into these two groups. The websites were analyzed based on both the website interface and a specific content scoring guide by two reviewers. The Flesch Kincaid (FK) grade level and the Flesch reading ease (FRE) score were used to determine the readability of information on the websites.
    RESULTS: Eighty-five unique websites were evaluated. The mean quality score of all the websites was 10.4 ± 4.5 with a maximum score of 25 (range=3-21). No significant difference in quality score was found between the groups. The mean FK grade score of all the websites was 11.2 ± 1.7 (range=7.9-15.3). The mean FRE score of all the websites was 46.8 ± 7.7 (range=24.1-63.7). No statistically significant differences in FK grade and FRE score were found between the groups. Although 59 websites (69%) had a third-party seal indicating the certification of one of the organizations established to provide a standard of health information on the Internet, only 21 websites (25%) were updated in the year before the search.
    CONCLUSION: The readability level of the informative texts about the ACL on the Turkish websites was above the educational level in Turkey. In addition, the quality score of the Turkish websites related to ACL was low. The content of the informative texts should be organized while taking into account the patients' literacy level.
  16. BMJ Open. 2022 Apr 15. 12(4): e059239
      OBJECTIVES: With the increasing popularity of searches for medical information on YouTube, the availability of videos concerning carpal tunnel syndrome (CTS) is increasing. This study aimed to evaluate the quality and reliability of YouTube videos on CTS.SETTING AND PARTICIPANTS: No participants were included.
    PRIMARY AND SECONDARY OUTCOME MEASURES: We searched YouTube on 1 April 2021 using the keywords "carpal tunnel syndrome" and "carpal tunnel release" and evaluated the first 55 retrieved videos. We summarised the video characteristics including Video Power Index (VPI), which was designed to evaluate video popularity based on the number of likes and views. We categorised them based on source and content. Video quality and reliability were evaluated using the Journal of the American Medical Association (JAMA) benchmark criteria, the Global Quality Score (GQS) and the Carpal Tunnel Syndrome-Specific Score (CTS-ss) .
    RESULTS: The mean (range: minimum-maximum) of JAMA scores, GQS and CTS-ss were 2.13 (1-4), 2.69 (1-5), and 5.0 (1-15), respectively. The most common source of video was from allied health workers, and academically sourced videos had the highest JAMA score and GQS. Three scores were significantly correlated with each other. Multiple linear regression analysis showed that a higher JAMA score was associated with a higher likes ratio, and a higher GQS was associated with a longer video running time and greater number of comments. However, a higher VPI was not associated with higher video quality or reliability represented by the three scores.
    CONCLUSIONS: YouTube videos on CTS have low quality and reliability. Video popularity was not significantly correlated with quality or reliability. Our findings suggest that expert groups should provide and promote high-quality video content to YouTube users and patients.
    Keywords:  EDUCATION & TRAINING (see Medical Education & Training); Hand & wrist; NEUROLOGY; Neurological pain; REHABILITATION MEDICINE
  17. Female Pelvic Med Reconstr Surg. 2022 Apr 15.
      IMPORTANCE: Apical pelvic organ prolapse is a common condition that affects women. Currently, sacrocolpopexy is considered the criterion standard surgical treatment, with an increasing preference for minimally invasive techniques.OBJECTIVE: In this study, the content and readability of select internet pages describing robotic and laparoscopic sacrocolpopexy were evaluated.
    STUDY DESIGN: Using an online key word planner, the phrases "robotic sacrocolpopexy" and "laparoscopic sacrocolpopexy" were determined to be the most popular search terms. These terms were systematically browsed in incognito mode in 3 of the most popular web search engines: Google, Yahoo, and Bing. Links that were nontext primary, duplicate, irrelevant, and non-English were excluded. The Flesch-Kincaid Grade Level and Flesch-Kincaid Reading Ease indices were used to assess readability.
    RESULTS: The average readability of all sites was 12.9, requiring at least a 12th-grade reading level, which is significantly higher than the recommended American Medical Association/National Institutes of Health (AMA/NIH) level of sixth-grade or below. One hundred percent of all analyzed sites were above this recommended sixth-grade reading level. There was no significant difference between mean grade level or reading ease score from the type of web source (P = 0.32 and 0.34, respectively), approach of surgery (P = 0.91, 0.70), or specialty (P = 0.48, 0.36).
    CONCLUSIONS: Almost all websites require at least a high school education to properly comprehend, regardless of source or specialty. It is important that health care providers be aware of available information, so they may direct patients to specific resources that are personally validated or provide in-office materials at an appropriate reading level.