bims-librar Biomed News
on Biomedical librarianship
Issue of 2022‒04‒03
fourteen papers selected by
Thomas Krichel
Open Library Society

  1. J Clin Epidemiol. 2022 Mar 24. pii: S0895-4356(22)00067-1. [Epub ahead of print]
      OBJECTIVE: Several specialized collections of COVID-19 literature have been developed during the global health emergency. These include the WHO COVID-19 Global Literature Database, Cochrane COVID-19 Study Register, CAMRADES COVID-19 SOLES, Epistemonikos' COVID-19 L-OVE and LitCovid. Our objective was to evaluate the completeness of these collections and to measure the time from when COVID-19 articles are posted to when they appear in the collections.STUDY DESIGN AND SETTING: We tested each selected collection for the presence of 440 included studies from 25 COVID-19 systematic reviews. We sampled 112 journals and prospectively monitored their websites until a new COVID-19 article appeared. We then monitored for two weeks to see when the new articles appeared in each collection. PubMed served as a comparator.
    RESULTS: Every collection provided at least one record not found in PubMed. Four records (1%) were not in any of the sources studied. Collections contained between 83% and 93% of the primary studies with the WHO database being most complete. By two weeks, between 60% and 78% of tracked articles had appeared.
    CONCLUSIONS: Our findings support the use of the best performing Covid-19 collections by systematic reviews to replace paywalled databases.
    Keywords:  Completeness; Covid-19 Publication; Currency; Database; Evaluation; PubMed
  2. Appl Clin Inform. 2022 Mar;13(2): 363-369
      BACKGROUND:  Molecular tumor boards (MTBs) cope with the complexity of an increased usage of genome sequencing data in cancer treatment. As for most of these patients, guideline-based therapy options are exhausted, finding matching clinical trials is crucial. This search process is often performed manually and therefore time consuming and complex due to the heterogeneous and challenging dataset.OBJECTIVES:  In this study, a prototype for a search tool was developed to demonstrate how cBioPortal as a clinical and genomic patient data source can be integrated with, a database of clinical studies to simplify the search for trials based on genetic and clinical data of a patient. The design of this tool should rest on the specific needs of MTB participants and the architecture of the integration should be as lightweight as possible and should not require manual curation of trial data in advance with the goal of quickly and easily finding a matching study.
    METHODS:  Based on a requirements analysis, interviewing MTB experts, a prototype was developed. It was further refined using a user-centered development process with multiple feedback loops. Finally, the usability of the application was evaluated with user interviews including the thinking-aloud protocol and the system usability scale (SUS) questionnaire.
    RESULTS:  The integration of in cBioPortal is achieved by a new tab in the patient view where the genomic profile for the search is prefilled and additional parameters can be adjusted. These parameters are then used to query the application programming interface (API) of The returned search results subsequently are ranked and presented to the user. The evaluation of the application resulted in an SUS score of 83.5.
    CONCLUSION:  This work demonstrates the integration of cBioPortal with to use clinical and genomic patient data to search for appropriate trials within an MTB.
  3. JMIR Med Inform. 2022 Mar 29. 10(3): e26511
      BACKGROUND: Health kiosks are publicly accessible computing devices that provide access to services, including health information provision, clinical measurement collection, patient self-check-in, telemonitoring, and teleconsultation. Although the increase in internet access and ownership of smart personal devices could make kiosks redundant, recent reports have predicted that the market will continue to grow.OBJECTIVE: We seek to clarify the current and future roles of health kiosks by investigating the settings, roles, and clinical domains in which kiosks are used; whether usability evaluations of health kiosks are being reported, and if so, what methods are being used; and what the barriers and facilitators are for the deployment of kiosks.
    METHODS: We conducted a scoping review using a bibliographic search of Google Scholar, PubMed, and Web of Science databases for studies and other publications between January 2009 and June 2020. Eligible papers described the implementation as primary studies, systematic reviews, or news and feature articles. Additional reports were obtained by manual searching and querying the key informants. For each article, we abstracted settings, purposes, health domains, whether the kiosk was opportunistic or integrated with a clinical pathway, and whether the kiosk included usability testing. We then summarized the data in frequency tables.
    RESULTS: A total of 141 articles were included, of which 134 (95%) were primary studies, and 7 (5%) were reviews. Approximately 47% (63/134) of the primary studies described kiosks in secondary care settings. Other settings included community (32/134, 23.9%), primary care (24/134, 17.9%), and pharmacies (8/134, 6%). The most common roles of the health kiosks were providing health information (47/134, 35.1%), taking clinical measurements (28/134, 20.9%), screening (17/134, 12.7%), telehealth (11/134, 8.2%), and patient registration (8/134, 6.0%). The 5 most frequent health domains were multiple conditions (33/134, 24.6%), HIV (10/134, 7.5%), hypertension (10/134, 7.5%), pediatric injuries (7/134, 5.2%), health and well-being (6/134, 4.5%), and drug monitoring (6/134, 4.5%). Kiosks were integrated into the clinical pathway in 70.1% (94/134) of studies, opportunistic kiosks accounted for 23.9% (32/134) of studies, and in 6% (8/134) of studies, kiosks were used in both. Usability evaluations of kiosks were reported in 20.1% (27/134) of papers. Barriers (e.g., use of expensive proprietary software) and enablers (e.g., handling of on-demand consultations) of deploying health kiosks were identified.
    CONCLUSIONS: Health kiosks still play a vital role in the health care system, including collecting clinical measurements and providing access to web-based health services and information to those with little or no digital literacy skills and others without personal internet access. We identified research gaps, such as training needs for teleconsultations and scant reporting on usability evaluation methods.
    Keywords:  barrier; behavior; consultation; facilitator; health service; health systems; internet; kiosk; mobile phone; online health information; promotion; remote consultation; review; teleconsultation; telemedicine; telemonitoring; user experience
  4. J Chem Inf Model. 2022 Mar 29.
      The layout of portable document format (PDF) files is constant to any screen, and the metadata therein are latent, compared to mark-up languages such as HTML and XML. No semantic tags are usually provided, and a PDF file is not designed to be edited or its data interpreted by software. However, data held in PDF files need to be extracted in order to comply with open-source data requirements that are now government-regulated. In the chemical domain, related chemical and property data also need to be found, and their correlations need to be exploited to enable data science in areas such as data-driven materials discovery. Such relationships may be realized using text-mining software such as the "chemistry-aware" natural-language-processing tool, ChemDataExtractor; however, this tool has limited data-extraction capabilities from PDF files. This study presents the PDFDataExtractor tool, which can act as a plug-in to ChemDataExtractor. It outperforms other PDF-extraction tools for the chemical literature by coupling its functionalities to the chemical-named entity-recognition capabilities of ChemDataExtractor. The intrinsic PDF-reading abilities of ChemDataExtractor are much improved. The system features a template-based architecture. This enables semantic information to be extracted from the PDF files of scientific articles in order to reconstruct the logical structure of articles. While other existing PDF-extracting tools focus on quantity mining, this template-based system is more focused on quality mining on different layouts. PDFDataExtractor outputs information in JSON and plain text, including the metadata of a PDF file, such as paper title, authors, affiliation, email, abstract, keywords, journal, year, document object identifier (DOI), reference, and issue number. With a self-created evaluation article set, PDFDataExtractor achieved promising precision for all key assessed metadata areas of the document text.
  5. Database (Oxford). 2022 Mar 28. pii: baac019. [Epub ahead of print]2022
      The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease-gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the text-mined associations, which have increased by at least 9-fold at all confidence cutoffs. We show that this dramatic increase is primarily due to adding full-text articles to the text corpus, secondarily due to improvements to both the disease and gene dictionaries used for named entity recognition, and only to a very small extent due to the growth in number of PubMed abstracts. DISEASES now also makes use of a new GWAS database, Target Illumination by GWAS Analytics, which considerably increased the number of GWAS-derived disease-gene associations. DISEASES itself is also integrated into several other databases and resources, including GeneCards/MalaCards, Pharos/Target Central Resource Database and the Cytoscape stringApp. All data in DISEASES are updated on a weekly basis and is available via a web interface at, from where it can also be downloaded under open licenses. Database URL:
  6. Hernia. 2022 Mar 27.
      BACKGROUND: Health literacy is considered the single best predictor of health status. Organizations including the American Medical Association (AMA) and the National Institutes of Health (NIH) have recommended that the readability of patient education materials not exceed the sixth-grade level. Our study focuses on the readability of self-designated hernia centers websites at both academic and community organizations across the United States to determine their ability to dispense patient information at an appropriate reading level.METHODS: A search was conducted utilizing the Google search engine. The key words "Hernia Center" and "University Hernia Center" were used to identify links to surgical programs within the United States. The following readability tests were conducted via the program: Flesch-Kincaid Grade Level (FKGL), Gunning Fox Index (GFI), Coleman-Liau Index (CLI), Simple Measure of Gobbledygook (SMOG), and Flesch Reading Ease (FRE) score.
    RESULTS: Of 96 websites, zero (0%) had fulfilled the recommended reading level in all four tests. The mean test scores for all non-academic centers (n = 50) were as follows: FKGL (11.14 ± 2.68), GFI (14.39 ± 3.07), CLI (9.29 ± 2.48) and SMOG (13.38 ± 2.03). The mean test scores [SK1] for all academic programs (n = 46) were as follows: FKGL (11.7 ± 2.66), GFI (15.01 ± 2.99), CLI (9.34 ± 1.91) and SMOG (13.71 ± 2.02). A one-sample t test was performed to compare the FKGL, GFI, CLI, and SMOG scores for each hernia center to a value of 6.9 (6.9 or less is considered an acceptable reading level) and a p value of 0.001 for all four tests were noted demonstrating statistical significance. The Academic and Community readability scores for both groups were compared to each other with a two-sample t test with a p value of > 0.05 for all four tests and there were no statistically significant differences.
    CONCLUSION: Neither Academic nor Community hernia centers met the appropriate reading level of sixth-grade or less. Steps moving forward to improve patient comprehension and/or involving with their care should include appropriate reading level material, identification of a patient with a low literacy level with intervention or additional counseling when appropriate, and the addition of adjunct learning materials such as videos.
    Keywords:  Health Literacy and Academic Hernia Centers; Health literac and hernia repairs; Health literacy and Community Hernia Centers; Readability and Hernia centers
  7. Orthopade. 2022 Mar 29.
      INTRODUCTION: The advance of the digital revolution in medicine and health is called "e-health". The Internet serves as a digital health information platform and is indispensable as a source of medical information. The aim of this work was to examine the behavior of orthopedic patients with respect to finding information on their illnesses. The role and the importance of the Internet as an informative health application for these patients are highlighted.MATERIALS AND METHODS: The basis of this prospective cross-sectional study was a patient survey in Germany of orthopedic patients from July 2019 to July 2020. Descriptive statistics were calculated, and regression analyses were carried out to show coherent results.
    RESULTS: We analyzed the responses of 1262 orthopedic patients. Most of them used the Internet as a digital health information platform. Patients rated their Internet skills as good to very good, regardless of age or educational level. Most respondents said that they currently use the Internet at least once a week to find out about their orthopedic illnesses. Patients reported a positive change in attitude towards the Internet as a digital source of medical information, and its use has increased in the past 12 months.
    CONCLUSION: The Internet as an informative digital health application in orthopedics is used intensively and is widely accepted by patients. While mistrust of orthopedic health information from the Internet has decreased, patient confidence in meaningful digital health information platforms has increased. The Internet is seen as a useful health information platform alongside medical advice.
    Keywords:  COVID-19; Health education; Orthopedics; Survey; Web use
  8. World Neurosurg. 2022 Mar 24. pii: S1878-8750(22)00384-9. [Epub ahead of print]
      OBJECTIVES: To assess the readability of spine-related patient education materials on professional society websites and determine if this has improved since last studied. Also, to compare the readability of these materials to a more patient-centered source, such as WebMD.METHODS: Patient education pages from the AANS, NASS, and spine-related pages from the AAOS and WebMD were reviewed. Readability was evaluated using Flesch Kincaid Grade Level (FKGL) and Flesch Reading Ease (FRE) formulas. Mean FKGL and FRE scores of the societies were compared using one-way ANOVA. The rate of reading level at/below an eighth-grade level was compared with chi-square testing.
    RESULTS: A total of 156 sites were analyzed. The mean FKGL of professional society sites was 11.4. The mean FRE for professional societies was 45.8 with a rate of 14.4% written at/below an 8th grade reading level. There was a significant difference in FKGL scores and materials at/below 8th grade level between AAOS and AANS and AAOS and NASS. The mean FKGL and FRE for WebMD were 7.57 and 68.1, respectively; a significant difference compared to AAOS, NASS, and AANS. 80% of WebMD materials were written at or below the 8th grade reading level; a significant difference when compared to AANS and NASS (p<0.0001), but not AAOS (p= 0.059) CONCLUSIONS: The average readability of spine-related topics exceeded the 8th-grade reading level. AAOS resources had better readability compared to NASS and AANS. There was no improvement in readability since last studied. Readability of professional societies' materials was significantly worse than from WebMD.
    Keywords:  Online Resources; Patient Education; Readability; Spine
  9. Cornea. 2022 Mar 24.
      PURPOSE: The purpose of this study was to assess the quality, reliability, readability, and technical quality of web sites relating to dry eye disease.METHODS: A cross-sectional study was conducted that evaluated the first 75 web sites on a Google Search by using the keyword "dry eyes." Each web site was evaluated by 2 independent reviewers using the DISCERN, HONcode, and JAMA criteria to assess quality and reliability. Interrater reliability was also analyzed. Readability was assessed using the Flesch-Kincaid readability tests and the Gunning fog, Simple Measure of Gobbledygook, Coleman-Liau, and automated readability indices. Technical quality was determined by the presence of 10 specific features. Web sites were further categorized into institutional (academic centers, medical associations, and government institutions) and private (private practices) categories.
    RESULTS: There was no significant difference in scoring observed between the 2 reviewers. The overall mean DISCERN score ± standard error (SE) was 3.2 ± 0.1, the mean HONcode score (±SE) was 9.3 ± 0.3, and the mean JAMA score (±SE) was 1.9 ± 0.1. Institutional web sites had a higher DISCERN score (3.4 ± 0.1 vs. 3.1 ± 0.1; P < 0.05) and HONcode score (10.3 ± 0.5 vs. 8.8 ± 0.4; P < 0.05) than private sites. Technical quality was higher in institutional web sites compared with private web sites (P < 0.05). Readability was poor among all web sites, with most web sites not achieving below a ninth grade reading level.
    CONCLUSIONS: Quality, reliability, and readability scores were low for most web sites. Although institutional web sites achieved higher scores than private web sites, revision is warranted to improve their overall quality of information and readability profile.
  10. J Pediatr Orthop B. 2022 Mar 31. pii: BPB.0000000000000972. [Epub ahead of print]
      YouTube is an increasingly accessible platform for families to obtain health information from; however, it is unregulated. The aim of this article was to assess the quality, reliability and accuracy of YouTube videos related to three common pediatric hip conditions: development dysplasia of the hip (DDH), slipped capital femoral epiphysis (SCFE) and Legg-Calve-Perthes disease. YouTube was searched using a variety of keyword combinations. Videos were analysed using Journal of the American Medical Association, Global Quality Score and condition-specific scores created specifically for this study. Video duration and the number of views were also recorded. In total 120 videos were analysed, 40 for each of DDH, SCFE and Perthes disease. YouTube videos from physicians and academic institutions/hospitals are of significantly higher quality, reliability and accuracy than videos from patients, nonphysicians and commercial outlets. The higher quality for physician videos is associated with significantly longer video. Differences between the three pediatric orthopaedic conditions were not statistically significant. Videos of higher quality may be used as an adjunctive tool to strengthen clinical consultation. Parents and caregivers should be guided to videos from academic institutions or hospitals as a way of improving health literacy.
  11. Asian Pac J Cancer Prev. 2022 Mar 01. pii: 90038. [Epub ahead of print]23(3): 1023-1029
      INTRODUCTION: In the internet era we live in, it is very easy to access information. While this situation has positive effects for patients using the internet, it also brings some negative effects. The effects of the quality of YouTube™ videos on nasopharyngeal cancer were examined.METHODS: "Nasopharyngeal Cancer" as search term was used to conduct a search on YouTube™. The 'Sort by' search filter was set at 'relevance', which is the default for YouTube™ searches. The first 250 results were reviewed and analyzed. After the videos were eliminated according to the exclusion criteria, 45 videos were evaluated by two authors. Video materials were categorized according to "video type" and "source of content". According to "video type" and "source of content" the videos were categorized into  two as educational and testimonial and three as medical institution, medical website, and individual users. After recording the features of all evaluated videos, accuracy score, audiovisual score, modified discern score, patient education materials assessment tool for audiovisual materials (PEMAT) score and usefulness score were determined for each video to evaluate the accuracy, reliability, and understandability of the videos.
    RESULTS: The usefulness score, modified discern score, and accuracy score of the educational videos were significantly higher than testimonial videos (p<0.001 for all). Educational videos provided more useful and accurate video content than testimonial videos. In addition, it was also determined that the median PEMAT actionability score and audiovisual score of the individual group were statistically significantly lower than medical institutions and medical websites (p=0.001 and p<0.001, respectively). The videos provided by medical institutions, including universities, did not have a significant advantage over other groups in terms of accuracy, reliability, and usefulness.
    CONCLUSION: Healthcare videos concerning nasopharyngeal cancer on YouTube™ are heterogeneous and are not peer reviewed. Therefore, medical professions on nasopharyngeal cancer need to upload more accurate, reliable and easy to understand videos onto online platforms such as YouTube™.
    Keywords:  Internet; Nasopharyngeal cancer; Patient information; Youtube; accuracy
  12. Arch Ital Urol Androl. 2022 Mar 29. 94(1): 57-61
      OBJECTIVE: The Internet is an important and easily accessible source of information. The aim of the current study was to investigate the quality of YouTube videos on cystoscopy and to establish if they can be used as a reliable information tool for internet users.MATERIALS AND METHODS: The search term "cystoscopy" was used on YouTube platform and the first 120 YouTube videos were analyzed. To assess the video quality Patient Education Materials Assessment Tool (PEMAT) for Audiovisual (A/V) Materials (Understandability and Actionability sections), Misinformation score and Global Quality Score (GQS) were used.
    RESULTS: Of all 120 videos, 72 were included in the analyses. Of all videos, 59.7% (n = 43), and 40.3% (n = 29) were targeted to General Public and Healthcare Workers. Moreover, "technical aspects" was the main topic addressed (n = 29, 40.3%). The median PEMAT A/V Understandability and Actionability scores were 50.0% (IQR: 39.1-70.0) and 66.7% (IQR: 33.3- 100.0), respectively. The median Misinformation score ranged from 1.0 to 3.0. According to GQS, 22 (30.6%), 26 (36.1%), 16 (22.2%), 8 (11.1%) videos were poor, generally poor, moderate, and good, respectively. No video was evaluated as excellent.
    CONCLUSIONS: Today, YouTube videos on cystoscopy are more frequently uploaded by healthcare workers, who share information about specific aspects of this procedure. However, the quality of YouTube contents on cystoscopy is still poor. Therefore, currently users interested in cystoscopy cannot rely on YouTube to get good informative material on this topic. In consequence, future authors should focus on improving the quality of video contents on cystoscopy.
  13. Prim Care Diabetes. 2022 Mar 26. pii: S1751-9918(22)00071-7. [Epub ahead of print]
      OBJECTIVE: In this study, the content of Turkish YouTube videos as a source of information on diabetic foot care training and the presence of nurses in these videos were examined.METHODS: A search was performed in the video sharing platform YouTube with the keyword "diabetic foot care" on 09.12.2020. From 200 videos, 87 were included in the study, and they were independently evaluated by two investigators for their usefulness, reliability, and quality.
    RESULTS: Of the videos, 8% were categorized as very useful, 33.3% moderately useful, 51.7% somewhat useful, and 6.9% not useful, while 4.6% contained misleading information. It was also found that the instructor was a nurse in only 12.6% of these videos.
    CONCLUSION: There is useful information about diabetic foot care on YouTube; however, there are also videos with misleading information. In addition, it has been observed that very few of these videos were prepared by nurses. In order to improve the foot care behaviors of individuals with diabetes, it may be suggested that professional groups, especially nurses who are primarily responsible for training and care, should create original, detailed, and interesting videos on appropriate diabetic foot care.
    Keywords:  Diabetic foot care; Nurse; YouTube