Europe PMC in 2023.

Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.

LitCovid in 2022: an information resource for the COVID-19 literature.

LitCovid (https://www.ncbi.nlm.nih.gov/research/coronavirus/)-first launched in February 2020-is a first-of-its-kind literature hub for tracking up-to-date published research on COVID-19. The number of articles in LitCovid has increased from 55 000 to ∼300 000 over the past 2.5 years, with a consistent growth rate of ∼10 000 articles per month. In addition to the rapid literature growth, the COVID-19 pandemic has evolved dramatically. For instance, the Omicron variant has now accounted for over 98% of new infections in the United States. In response to the continuing evolution of the COVID-19 pandemic, this article describes significant updates to LitCovid over the last 2 years. First, we introduced the long Covid collection consisting of the articles on COVID-19 survivors experiencing ongoing multisystemic symptoms, including respiratory issues, cardiovascular disease, cognitive impairment, and profound fatigue. Second, we provided new annotations on the latest COVID-19 strains and vaccines mentioned in the literature. Third, we improved several existing features with more accurate machine learning algorithms for annotating topics and classifying articles relevant to COVID-19. LitCovid has been widely used with millions of accesses by users worldwide on various information needs and continues to play a critical role in collecting, curating and standardizing the latest knowledge on the COVID-19 literature.

The methodological quality of 176,620 randomized controlled trials published between 1966 and 2018 reveals a positive trend but also an urgent need for improvement.

Many randomized controlled trials (RCTs) are biased and difficult to reproduce due to methodological flaws and poor reporting. There is increasing attention for responsible research practices and implementation of reporting guidelines, but whether these efforts have improved the methodological quality of RCTs (e.g., lower risk of bias) is unknown. We, therefore, mapped risk-of-bias trends over time in RCT publications in relation to journal and author characteristics. Meta-information of 176,620 RCTs published between 1966 and 2018 was extracted. The risk-of-bias probability (random sequence generation, allocation concealment, blinding of patients/personnel, and blinding of outcome assessment) was assessed using a risk-of-bias machine learning tool. This tool was simultaneously validated using 63,327 human risk-of-bias assessments obtained from 17,394 RCTs evaluated in the Cochrane Database of Systematic Reviews (CDSR). Moreover, RCT registration and CONSORT Statement reporting were assessed using automated searches. Publication characteristics included the number of authors, journal impact factor (JIF), and medical discipline. The annual number of published RCTs substantially increased over 4 decades, accompanied by increases in authors (5.2 to 7.8) and institutions (2.9 to 4.8). The risk of bias remained present in most RCTs but decreased over time for allocation concealment (63% to 51%), random sequence generation (57% to 36%), and blinding of outcome assessment (58% to 52%). Trial registration (37% to 47%) and the use of the CONSORT Statement (1% to 20%) also rapidly increased. In journals with a higher impact factor (>10), the risk of bias was consistently lower with higher levels of RCT registration and the use of the CONSORT Statement. Automated risk-of-bias predictions had accuracies above 70% for allocation concealment (70.7%), random sequence generation (72.1%), and blinding of patients/personnel (79.8%), but not for blinding of outcome assessment (62.7%). In conclusion, the likelihood of bias in RCTs has generally decreased over the last decades. This optimistic trend may be driven by increased knowledge augmented by mandatory trial registration and more stringent reporting guidelines and journal requirements. Nevertheless, relatively high probabilities of bias remain, particularly in journals with lower impact factors. This emphasizes that further improvement of RCT registration, conduct, and reporting is still urgently needed.

The NICE search filters for treating and managing COVID-19: validation in MEDLINE and Embase (Ovid).

Objective: In this paper we report how the United Kingdom's National Institute for Health and Care Excellence (NICE) search filters for treating and managing COVID-19 were validated for use in MEDLINE (Ovid) and Embase (Ovid). The objective was to achieve at least 98.9% for recall and 64% for precision. Methods: We did two tests of recall to finalize the draft search filters. We updated the data from an earlier peer-reviewed publication for the first recall test. For the second test, we collated a set of systematic reviews from Epistemonikos COVID-19 L.OVE and extracted their primary studies. We calculated precision by screening all the results retrieved by the draft search filters from a targeted sample covering 2020-23. We developed a gold-standard set to validate the search filter by using all articles available from the "Treatment and Management" subject filter in the Cochrane COVID-19 Study Register. Results: In the first recall test, both filters had 99.5% recall. In the second test, recall was 99.7% and 99.8% in MEDLINE and Embase respectively. Precision was 91.1% in a deduplicated sample of records. In validation, we found the MEDLINE filter had recall of 99.86% of the 14,625 records in the gold-standard set. The Embase filter had 99.88% recall of 19,371 records. Conclusion: We have validated search filters to identify records on treating and managing COVID-19. The filters may require subsequent updates, if new SARS-CoV-2 variants of concern or interest are discussed in future literature.

Librarians' Electronic Resource Reviews Network (LERRN): a free citation database for resource reviews.

Electronic resource reviews written by librarians are a valuable way to identify potential content platforms and stay current on new resources. Resource-focused articles can also assist with learning about useful features, training others, and marketing to potential user groups. However, articles evaluating or highlighting innovative uses of resources may be published in disparate journals or online platforms and are not collocated. Small or solo-staffed libraries may not subscribe to library and information sciences databases or journals that contain reviews of electronic resources. And many of these reviews or other useful articles are open access. With this in mind, the main aim of the LERRN citation database was to create a freely available citation database that brings together electronic resource reviews and other content that can assist librarians in appraising and using electronic resources.

Centers for Disease Control and Prevention Science Clips.

The Centers for Disease Control and Prevention (CDC) Science Clips is an online weekly bibliographical digest showcasing over 46,000 scientific articles and publications from 2009 to present. The digest is curated by the Stephen B. Thacker CDC Library to bring awareness to relevant and quality public health literature. This overview describes how users can access and navigate the database, and evaluates the database usability and relevance in public health.

searchRxiv: A Resource for Sharing Database Search Strategies.

Medical librarians can increase their work visibility and highlight their unique role on evidence synthesis teams with searchRxiv, an open access repository that makes librarian's efforts easily citable and resolves longstanding challenges pertaining to reproducing full search strategies within literature review articles. This column will discuss how to navigate searchRxiv to find, reuse, and cite published search strategies, as well as the process of depositing search strategies.

Search strategies (filters) to identify systematic reviews in MEDLINE and Embase.

BACKGROUND: Bibliographic databases provide access to an international body of scientific literature in health and medical sciences. Systematic reviews are an important source of evidence for clinicians, researchers, consumers, and policymakers as they address a specific health-related question and use explicit methods to identify, appraise and synthesize evidence from which conclusions can be drawn and decisions made. Methodological search filters help database end-users search the literature effectively with different levels of sensitivity and specificity. These filters have been developed for various study designs and have been found to be particularly useful for intervention studies. Other filters have been developed for finding systematic reviews. Considering the variety and number of available search filters for systematic reviews, there is a need for a review of them in order to provide evidence about their retrieval properties at the time they were developed. OBJECTIVES: To review systematically empirical studies that report the development, evaluation, or comparison of search filters to retrieve reports of systematic reviews in MEDLINE and Embase. SEARCH METHODS: We searched the following databases from inception to January 2023: MEDLINE, Embase, PsycINFO; Library, Information Science & Technology Abstracts (LISTA) and Science Citation Index (Web of Science). SELECTION CRITERIA: We included studies if one of their primary objectives is the development, evaluation, or comparison of a search filter that could be used to retrieve systematic reviews on MEDLINE, Embase, or both. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data using a pre-specified and piloted data extraction form using InterTASC Information Specialist Subgroup (ISSG) Search Filter Evaluation Checklist. MAIN RESULTS: We identified eight studies that developed filters for MEDLINE and three studies that developed filters for Embase. Most studies are very old and some were limited to systematic reviews in specific clinical areas. Six included studies reported the sensitivity of their developed filter. Seven studies reported precision and six studies reported specificity. Only one study reported the number needed to read and positive predictive value. None of the filters were designed to differentiate systematic reviews on the basis of their methodological quality. For MEDLINE, all filters showed similar sensitivity and precision, and one filter showed higher levels of specificity. For Embase, filters showed variable sensitivity and precision, with limited study reports that may affect accuracy assessments. The report of these studies had some limitations, and the assessments of their accuracy may suffer from indirectness, considering that they were mostly developed before the release of the PRISMA 2009 statement or due to their limited scope in the selection of systematic review topics. Search filters for MEDLINE Three studies produced filters with sensitivity > 90% with variable degrees of precision, and only one of them was developed and validated in a gold-standard database, which allowed the calculation of specificity. The other two search filters had lower levels of sensitivity. One of these produced a filter with higher levels of specificity (> 90%). All filters showed similar sensitivity and precision in the external validation, except for one which was not externally validated and another one which was conceptually derived and only externally validated. Search filters for Embase We identified three studies that developed filters for this database. One of these studies developed filters with variable sensitivity and precision, including highly sensitive strategies (> 90%); however, it was not externally validated. The other study produced a filter with a lower sensitivity (72.7%) but high specificity (99.1%) with a similar performance in the external validation. AUTHORS' CONCLUSIONS: Studies reporting the development, evaluation, or comparison of search filters to retrieve reports of systematic reviews in MEDLINE showed similar sensitivity and precision, with one filter showing higher levels of specificity. For Embase, filters showed variable sensitivity and precision, with limited information about how the filter was produced, which leaves us uncertain about their performance assessments. Newer filters had limitations in their methods or scope, including very focused subject topics for their gold standards, limiting their applicability across other topics. Our findings highlight that consensus guidance on the conduct of search filters and standardized reporting of search filters are needed, as we found highly heterogeneous development methods, accuracy assessments and outcome selection. New strategies adaptable across interfaces could enhance their usability. Moreover, the performance of existing filters needs to be evaluated in light of the impact of reporting guidelines, including the PRISMA 2009, on how systematic reviews are reported. Finally, future filter developments should also consider comparing the filters against a common reference set to establish comparative performance and assess the quality of systematic reviews retrieved by strategies.

Mental Health First Aid as a tool for improving mental health and well-being.

BACKGROUND: The prevalence of mental health problems is high, and they have a wide-ranging and deleterious effect on many sectors in society. As well as the impact on individuals and families, mental health problems in the workplace negatively affect productivity. One of the factors that may exacerbate the impact of mental health problems is a lack of 'mental health literacy' in the general population. This has been defined as 'knowledge and beliefs about mental disorders, which aid their recognition, management, or prevention'. Mental Health First Aid (MHFA) is a brief training programme developed in Australia in 2000; its aim is to improve mental health literacy and teach mental health first aid strategies. The course has been adapted for various contexts, but essentially covers the symptoms of various mental health disorders, along with associated mental health crisis situations. The programmes also teach trainees how to provide immediate help to people experiencing mental health difficulties, as well as how to signpost to professional services. It is theorised that improved knowledge will encourage the trainees to provide support, and encourage people to actively seek help, thereby leading to improvements in mental health. This review focuses on the effects of MHFA on the mental health and mental well-being of individuals and communities in which MHFA training has been provided. We also examine the impact on mental health literacy. This information is essential for decision-makers considering the role of MHFA training in their organisations. OBJECTIVES: To examine mental health and well-being, mental health service usage, and adverse effects of MHFA training on individuals in the communities in which MHFA training is delivered. SEARCH METHODS: We developed a sensitive search strategy to identify randomised controlled trials (RCTs) of MHFA training. This approach used bibliographic databases searching, using a search strategy developed for Ovid MEDLINE (1946 -), and translated across to Ovid Embase (1974 -), Ovid PsycINFO (1967 -), the Cochrane Central Register of Controlled Trials (CENTRAL) and the Cochrane Common Mental Disorders Group's Specialised Register (CCMDCTR). We also searched online clinical trial registries (ClinicalTrials.gov and WHO ICTRP), grey literature and reference lists of included studies, and contacted researchers in the field to identify additional and ongoing studies. Searches are current to 13th June 2023. SELECTION CRITERIA: We included RCTs and cluster-RCTs comparing any type of MHFA-trademarked course to no intervention, active or attention control (such as first aid courses), waiting list control, or alternative mental health literacy interventions. Participants were individuals in the communities in which MHFA training is delivered and MHFA trainees. Primary outcomes included mental health and well-being of individuals, mental health service usage and adverse effects of MHFA training. Secondary outcomes related to individuals, MHFA trainees, and communities or organisations in which MHFA training has been delivered DATA COLLECTION AND ANALYSIS: We used standard Cochrane methods. We analysed categorical outcomes as risk ratios (RRs) and odds ratios (ORs), and continuous outcomes as mean differences (MDs) or standardised mean differences (SMDs), with 95% confidence intervals (CIs). We pooled data using a random-effects model. Two review authors independently assessed the key results using the Risk of Bias 2 tool and applied the GRADE criteria to assess the certainty of evidence MAIN RESULTS: Twenty-one studies involving a total of 22,604 participants were included in the review. Fifteen studies compared MHFA training with no intervention/waiting list, two studies compared MHFA training with an alternative mental health literacy intervention, and four studies compared MHFA training with an active or an attention control intervention. Our primary time point was between six and 12 months. When MHFA training was compared with no intervention, it may have little to no effect on the mental health of individuals at six to 12 months, but the evidence is very uncertain (OR 0.88, 95% CI 0.61 to 1.28; 3 studies; 3939 participants). We judged all the results that contributed to this outcome as being at high risk of bias. No study measured mental health service usage at six to 12 months. We did not find published data on adverse effects. Only one study with usable data compared MHFA training with an alternative mental health literacy intervention. The study did not measure outcomes in individuals in the community. It also did not measure outcomes at our primary time point of six to 12 months. Four studies with usable data compared MHFA training to an active or attention control. None of the studies measured outcomes at our primary time point of six to 12 months. AUTHORS' CONCLUSIONS: We cannot draw conclusions about the effects of MHFA training on our primary outcomes due to the lack of good quality evidence. This is the case whether it is compared to no intervention, to an alternative mental health literacy intervention, or to an active control. Studies are at high risk of bias and often not sufficiently large to be able to detect differences.

Improving academic and public health impact of Cochrane public health reviews: what can we learn from bibliographic metrics and author dissemination strategies? A cross-sectional study.

BACKGROUND: To facilitate the development of impactful research dissemination strategies, this study aimed to: (i) survey authors of trials included in a sample of Cochrane reviews to describe strategies to disseminate trial findings, and examine their association with academic and policy impacts and (ii) audit academic and policy impact of CPH reviews. METHODS: Authors of 104 trials within identified Cochrane reviews completed survey items assessing the dissemination strategies. Field weighted citation (FWCI) data extracted from bibliographic databases served as a measure of academic impact of trials and CPH reviews. Policy and practice impacts of trials were assessed during the survey of trial authors using items based on the Payback Framework, and for CPH reviews using 'policy mention' data collected via Altmetric Explorer. RESULTS: Among the included trials, univariate (but not multivariable) regression models revealed significant associations between the use of dissemination strategies (i.e. posts on social media; workshops with end-users; media-releases) and policy or practice impacts. No significant associations were reported between dissemination strategies and trial FWCI. The mean FWCI of CPH reviews suggest that they are cited 220% more than other reviews in their field. CONCLUSIONS: Comprehensive dissemination strategies are likely required to maximize the potential the potential impacts of public health research.

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.

Discrepancies among Scopus and Web of Science, coverage of funding information in medical journal articles: a follow-up study.

Objective: This follow-up study aims to determine if and how the coverage of funding information in Web of Science Core Collection (WoS) and Scopus changed from 2015 to 2021. Methods: The number of all funded articles published in 2021 was identified in WoS and Scopus bibliographic databases using bibliometric analysis on a sample of 52 prestigious medical journals. Results: The analysis of the number of funded articles with funding information showed statistically significant differences between Scopus and WoS due to substantial differences in the number of funded articles between some single journals. Conclusion: Due to significant differences in the number of funded articles indexed in WoS and Scopus, which might be attributed to the different protocols for handling funding data in WoS and Scopus, we would still advise using both databases to obtain and analyze funding information.

Comparison of Databases for Complex Evidence Syntheses on Education for the Health Professions.

Increased requests for assistance with literature searches on educational topics within the health professions motivated two health science librarians to analyze search function and results in eleven bibliographic databases on questions representing three allied health instructional target populations (patient, caregiver, and future health professionals). Results overlap and relevance were estimated and useful functions and subject headings were examined, as evidence for future search and database recommendations. This research confirmed the authors' hypothesis that PubMed and CINAHL overlapped significantly yet yielded sufficient unique citations to recommend searching both, plus at least one education-specific database. For the six questions researched, psychology and sports medicine databases were less productive.

Application of text mining to the development and validation of a geographic search filter to facilitate evidence retrieval in Ovid MEDLINE: An example from the United States.

BACKGROUND: Given the increasing volume of published research in bibliographic databases, efficient retrieval of evidence is crucial and represents an opportunity to integrate novel techniques such as text mining. OBJECTIVES: To develop and validate a geographic search filter for identifying research from the United States (US) in Ovid MEDLINE. METHODS: US and non-US citations were collected from bibliographies of evidence-based reviews. Citations were partitioned by US/non-US status and randomly divided to a training and testing set. Using text mining, common one- and two-word terms in title/abstract fields were identified, and frequencies compared between US/non-US citations. RESULTS: Common US-related terms included (as ratio of frequency in US/non-US citations) US populations and geographic terms [e.g., 'Americans' (15.5), 'Baltimore' (20.0)]. Common non-US terms were non-US geographic terms [e.g., 'Japan' (0.04), 'French' (0.05)]. A search filter was developed with 98.3% sensitivity and 82.7% specificity. DISCUSSION: This search filter will streamline the identification of evidence from the US. Periodic updates may be necessary to reflect changes in MEDLINE's controlled vocabulary. CONCLUSION: Text mining was instrumental to the development of this search filter. A novel technique generated a gold standard set comprising >20,000 citations. This method may be adapted to develop subsequent geographic search filters.

Updated generic search filters for finding studies of adverse drug effects in Ovid medline and Embase may retrieve up to 90% of relevant studies.

BACKGROUND: The most current objectively derived search filters for adverse drug effects are 15 years old and other strategies have not been developed and tested empirically. OBJECTIVE: To develop and validate search filters to retrieve evidence on adverse drug effects from Ovid medline and Ovid Embase. METHODS: We identified systematic reviews of adverse drug effects in Epistemonikos. From these reviews, we collated their included studies which we then randomly divided into three tests and one validation set of records. We constructed a search strategy to maximise relative recall using word frequency analysis with test set one. This search strategy was then refined using test sets two and three and validated on the final set of records. RESULTS: Of 107 systematic reviews which met our inclusion criteria, 1948 unique included studies were available from medline and 1980 from Embase. Generic adverse drug effects searches in medline and Embase achieved 90% and 89% relative recall, respectively. When specific adverse effects terms were added recall was improved. CONCLUSION: We have derived and validated search filters that retrieve around 90% of records with adverse drug effects data in medline and Embase. The addition of specific adverse effects terms is required to achieve higher recall.

Detection performance of PCR for Legionella pneumophila in environmental samples: a systematic review and meta-analysis.

BACKGROUND: Legionellosis remains a public health problem. The most common diagnostic method to detect Legionella pneumophila (L. pneumophila) is culture. Polymerase chain reaction (PCR) is a fast and accurate method for this detection in environmental samples. METHODS: Four databases were searched for studies that evaluated the detection efficiency of PCR in L. pneumophila. The quality evaluation was conducted using Review Manager 5.3. We used Meta-DiSc 1.4 software and the Stata 15.0 software to create forest plots, a meta-regression, a bivariate boxplot and a Deeks' funnel plot. RESULTS: A total of 18 four-fold tables from 16 studies were analysed. The overall pooled sensitivity and specificity of PCR was 94% and 72%, respectively. The positive likelihood ratio (RLR) and negative likelihood ratio (NLR) was 2.73 and 0.12, respectively. The result of the diagnostic odds ratio (DOR) was 22.85 and the area under the curve (AUC) was 0.7884. CONCLUSION: Establishing a laboratory diagnostic tool for L. pneumophila detection is important for epidemiological studies. In this work, PCR demonstrated a promising diagnostic accuracy for L. pneumophila.

Context Analysis of Continued Citation of Retracted Manuscripts Published in Anesthesiology Journals.

The continued citation of retracted publications from the medical literature is a well-known and persistent problem. We describe the contexts of ongoing citations to manuscripts that have been retracted from a selection of anesthesiology journals. We also examine how bibliographic databases and publisher websites document the retracted status of these manuscripts. The authors performed an analysis of retracted publications from anesthesiology journals using the Retraction Watch database. We then examined how the retraction information was displayed on bibliographic databases, search engines, and publisher websites. The primary outcome was the context of continued citation after retraction of flawed publications within the specialty of anesthesiology. Secondary outcomes included comparison of the documentation, bibliographic databases, search engines, and publisher websites used in identifying the retracted status of these publications and provision of access to the respective retraction notices. A total of 245 original publications were retracted over a 28-year period from 9 anesthesiology journals. PubMed, compared to the other databases and search engines, was the most consistent (98.8%) in documenting the retracted status of the publications examined, as well as providing a direct link to the retraction notice. From the 211 publications retracted before January 2020, there were 1307 postretraction citations accessed from Scopus. The median number of postretraction citations was 3.5 (range, 0-88, with at least 1 citation in 164 publications) in Scopus. Of the postretraction citations, 80% affirmed the validity of the retracted publications, while only 5.2% of citations acknowledged the retraction or misconduct. In 10.2% of the citations from original research studies, retracted manuscripts appeared to influence the decision to pursue or the methods used in subsequent original research studies. The frequency of citation of the 15 most cited retracted publications declined in a similar pattern during the 10 years after retraction. Citation of manuscripts retracted from anesthesiology journals remains a common occurrence. Technological innovations and application of standards for handling retracted publications, as suggested by coalitions of researchers across the spectrum of scientific investigation, may serve to reduce the persistence of this error.