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reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints.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.

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.

A prospective comparison of evidence synthesis search strategies developed with and without text-mining tools.

OBJECTIVE: We compared the process of developing searches with and without using text-mining tools (TMTs) for evidence synthesis products. STUDY DESIGN: This descriptive comparative analysis included seven systematic reviews, classified as simple or complex. Two librarians created MEDLINE strategies for each review, using either usual practice (UP) or TMTs. For each search we calculated sensitivity, number-needed-to-read (NNR) and time spent developing the search strategy. RESULTS: We found UP searches were more sensitive (UP 92% (95% CI, 85-99); TMT 84.9% (95% CI, 74.4-95.4)), with lower NNR (UP 83 (SD 34); TMT 90 (SD 68)). UP librarians spent an average of 12 h (SD 8) developing search strategies, compared to TMT librarians' 5 hours (SD 2). CONCLUSION: Across all reviews, TMT searches were less sensitive than UP searches, but confidence intervals overlapped. For simple SR topics, TMT searches were faster and slightly less sensitive than UP. For complex SR topics, TMT searches were faster and less sensitive than UP searches but identified unique eligible citations not found by the UP searches.

Search methods for prognostic factor systematic reviews: a methodologic investigation.

OBJECTIVE: This study retroactively investigated the search used in a 2019 review by Hayden et al., one of the first systematic reviews of prognostic factors that was published in the Cochrane Library. The review was designed to address recognized weaknesses in reviews of prognosis by using multiple supplementary search methods in addition to traditional electronic database searching. METHODS: The authors used four approaches to comprehensively assess aspects of systematic review literature searching for prognostic factor studies: (1) comparison of search recall of broad versus focused electronic search strategies, (2) linking of search methods of origin for eligible studies, (3) analysis of impact of supplementary search methods on meta-analysis conclusions, and (4) analysis of prognosis filter performance. RESULTS: The review's focused electronic search strategy resulted in a 91% reduction in recall, compared to a broader version. Had the team relied on the focused search strategy without using supplementary search methods, they would have missed 23 of 58 eligible studies that were indexed in MEDLINE; additionally, the number of included studies in 2 of the review's primary outcome meta-analyses would have changed. Using a broader strategy without supplementary searches would still have missed 5 studies. The prognosis filter used in the review demonstrated the highest sensitivity of any of the filters tested. CONCLUSIONS: Our study results support recommendations for supplementary search methods made by prominent systematic review methodologists. Leaving out any supplemental search methods would have resulted in missed studies, and these omissions would not have been prevented by using a broader search strategy or any of the other prognosis filters tested.

Gene-Centric Database Reveals Environmental and Lifestyle Relationships for Potential Risk Modification and Prevention.

The database at Nutrigenetics.net has been under development since 2007 to facilitate the identification and classification of PubMed articles relevant to human genetics. A controlled vocabulary (i.e., standardized terminology) is used to index these records, with links back to PubMed for every article title. This enables the display of indexes (alphabetical subtopic listings) for any given topic, or for any given combination of topics, including for genes and specific genetic variants. Stepwise use of such indexes (first for one topic, then for combinations of topics) can reveal relationships that are otherwise easily overlooked. These relationships include environmental and lifestyle variables with potential relevance to risk modification (both beneficial and detrimental), and to prevention, or at least to the potential delay of symptom onset for health conditions like Alzheimer disease among many others. Thirty-four specific genetic variants have each been mentioned in at least ≥1,000 PubMed titles/abstracts, and these numbers are steadily increasing. The benefits of indexing with standardized terminology are illustrated for genetic variants like MTHFR 677C-T and its various synonyms (e.g., rs1801133 or Ala222Val). Such use of a controlled vocabulary is also helpful for numerous health conditions, and for potential risk modifiers (i.e., potential risk/effect modifiers).

Machine learning reduced workload with minimal risk of missing studies: development and evaluation of a randomized controlled trial classifier for Cochrane Reviews.

OBJECTIVES: This study developed, calibrated, and evaluated a machine learning classifier designed to reduce study identification workload in Cochrane for producing systematic reviews. METHODS: A machine learning classifier for retrieving randomized controlled trials (RCTs) was developed (the "Cochrane RCT Classifier"), with the algorithm trained using a data set of title-abstract records from Embase, manually labeled by the Cochrane Crowd. The classifier was then calibrated using a further data set of similar records manually labeled by the Clinical Hedges team, aiming for 99% recall. Finally, the recall of the calibrated classifier was evaluated using records of RCTs included in Cochrane Reviews that had abstracts of sufficient length to allow machine classification. RESULTS: The Cochrane RCT Classifier was trained using 280,620 records (20,454 of which reported RCTs). A classification threshold was set using 49,025 calibration records (1,587 of which reported RCTs), and our bootstrap validation found the classifier had recall of 0.99 (95% confidence interval 0.98-0.99) and precision of 0.08 (95% confidence interval 0.06-0.12) in this data set. The final, calibrated RCT classifier correctly retrieved 43,783 (99.5%) of 44,007 RCTs included in Cochrane Reviews but missed 224 (0.5%). Older records were more likely to be missed than those more recently published. CONCLUSIONS: The Cochrane RCT Classifier can reduce manual study identification workload for Cochrane Reviews, with a very low and acceptable risk of missing eligible RCTs. This classifier now forms part of the Evidence Pipeline, an integrated workflow deployed within Cochrane to help improve the efficiency of the study identification processes that support systematic review production.

Quality assessment of randomized controlled trial abstracts on drug therapy of periodontal disease from the abstracts published in dental Science Citation Indexed journals in the last ten years

BACKGROUND: Randomized controlled trials (RCTs) provide the highest level of evidence and are likely to influence clinical decision-making. This study evaluated the reporting quality of RCT abstracts on drug therapy of periodontal disease and assessed the associated factors. MATERIAL AND METHODS: The Pubmed database was searched for periodontal RCTs published in Science Citation Indexed (SCI) dental journals from 2010/01/01 to 2019/07/17. Information was extracted from the abstracts according to a modified Consolidated Standards of Reporting Trials (CONSORT) guideline checklist. The data was analyzed using descriptive statistical analysis and the statistical associations were examined using the linear regression analysis (P < 0.05). RESULTS: This study retrieved 1715 articles and 249 of them were finally included. The average overall CONSORT score was 15.6 ± 3.4, which represented 40.9% (±0.6) of CONSORT criteria filling. The reporting rate of some items (trial design, numbers analyzed, confidence intervals, intention-to-treat analysis or per-protocol analysis, harms, registration) was less than 30%. The adequate reporting rate of some items (participants, randomization, numbers analyzed, confidence intervals, intention-to-treat analysis or per protocol analysis) was no more than 4%. None of the abstracts reported funding. According to the multivariable linear regression results, number of authors (P = 0.030), word count (P < 0.001), continent (P = 0.003), structured format (P < 0.001), type of periodontal disease (P < 0.001) and international collaboration (P = 0.023) have a significant association with reporting quality. CONCLUSIONS: The quality of RCT abstracts on drug therapy of periodontal disease in SCI dental journals remained suboptimal. More efforts should be made to improve RCT abstracts reporting quality

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Assessment of Language and Indexing Biases Among Chinese-Sponsored Randomized Clinical Trials.

Importance: Language and indexing biases may exist among Chinese-sponsored randomized clinical trials (CS-RCTs). Such biases may threaten the validity of systematic reviews. Objective: To evaluate the existence of language and indexing biases among CS-RCTs on drug interventions. Design, Setting, and Participants: In this retrospective cohort study, eligible CS-RCTs were retrieved from trial registries, and bibliographic databases were searched to determine their publication status. Eligible CS-RCTs were for drug interventions conducted from January 1, 2008, to December 31, 2014. The search and analysis were conducted from March 1 to August 31, 2019. Primary trial registries were recognized by the World Health Organization and the Drug Clinical Trial Registry Platform sponsored by the China Food and Drug Administration. Exposures: Individual CS-RCTs with positive vs negative results (positive vs negative CS-RCTs). Main Outcomes and Measures: For assessing language bias, the main outcome was the language of the journal in which CS-RCTs were published (English vs Chinese). For indexing bias, the main outcome was the language of the bibliographic database where the CS-RCTs were indexed (English vs Chinese). Results: The search identified 891 eligible CS-RCTs. Four hundred seventy CS-RCTs were published by August 31, 2019, of which 368 (78.3%) were published in English. Among CS-RCTs registered in the Chinese Clinical Trial Registry (ChiCTR), positive CS-RCTs were 3.92 (95% CI, 2.20-7.00) times more likely to be published in English than negative CS-RCTs; among CS-RCTs in English-language registries, positive CS-RCTs were 3.22 (95% CI, 1.34-7.78) times more likely to be published in English than negative CS-RCTs. These findings suggest the existence of language bias. Among CS-RCTs registered in ChiCTR, positive CS-RCTs were 2.89 (95% CI, 1.55-5.40) times more likely to be indexed in English bibliographic databases than negative CS-RCTs; among CS-RCTs in English-language registries, positive CS-RCTs were 2.19 (95% CI, 0.82-5.82) times more likely to be indexed in English bibliographic databases than negative CS-RCTs. These findings support the existence of indexing bias. Conclusions and Relevance: This study suggests the existence of language and indexing biases among registered CS-RCTs on drug interventions. These biases may distort evidence synthesis toward more positive results of drug interventions.

More systematic reviews were registered in PROSPERO each year, but few records' status was up-to-date.

OBJECTIVES: To determine the proportion of systematic reviews (SRs) registered in PROSPERO and explore differences between publication years, review focus, and country. Secondary objectives were (1) to compare the characteristics of registered and nonregistered SRs and (2) to assess the up-to-dateness of the PROSPERO records' status. STUDY DESIGN AND SETTING: In November 2018, we searched PubMed for SRs that were eligible for registration in PROSPERO. We included a random sample of n = 500 SRs. Data were analyzed descriptively. RESULTS: Overall, 76 (15.2%) of the included SRs had been registered in PROSPERO. This proportion has increased with each year, up to 31.6% (36/114) in 2018. It did not notably differ depending on the reviews' focus. SRs from the United States or China were generally registered less frequently and SRs from Australia or Canada more frequently. Registered and nonregistered SRs did not differ regarding the number of authors or the time from submission to publication or from search to submission and publication. We could analyze 75 PROSPERO records, of which 63 (84.0%) were not up-to-date. Most SRs (49/75; 65.3%) were still listed as "ongoing." CONCLUSION: More SRs were registered in PROSPERO each year, but only few records' status was up-to-date.

Building the Systematic Review Core in an academic health sciences library.

BACKGROUND: The authors present efforts to build capacity at our institution for conducting systematic reviews and other forms of evidence synthesis through partnerships and a recharge model. This report describes how we successfully created and launched a for-fee systematic review core at our library. CASE PRESENTATION: Throughout 2014 and 2015, library leadership proposed different models for getting institutional and financial support for librarians and staff to better support university researchers conducting systematic reviews. Though well received, initial requests for financial support were not funded. The executive director of the Health Sciences Library released two years' worth of salary and benefits to fund an evidence synthesis and retrieval librarian position. With this new position, the team formed a charge-back core facility in partnership with our university's Clinical Translation and Science Award hub. A series of procedural decisions and operational changes helped the group achieve success. Within eighteen months after launching the Systematic Review Core, we reached maximum capacity with more than twenty ongoing reviews. DISCUSSION: Assigning a dollar value to our expertise put us on par with other subject matter experts on campus and actually drove demand. We could act as paid consultants in research projects and shifted the perception of librarians from service providers to research partners. Affiliating with our partners was key to our success and boosted our ability to strengthen our campus' research infrastructure.

PubMed coverage varied across specialties and over time: a large-scale study of included studies in Cochrane reviews.

OBJECTIVE: PubMed is one of the most commonly used search tools in biomedical and life sciences. Existing studies of database coverage generally conclude that searching PubMed may not be sufficient although some find that the contributions from other databases are modest at best. However, generalizability of the studies of the coverage of PubMed is typically restricted. The objective of this study is to analyze the coverage of PubMed across specialties and over time. STUDY DESIGN AND SETTING: We use the more than 50,000 included studies in all Cochrane reviews published from 2012 to 2016 as our population and examine if the studies and resulting publications can be identified in PubMed. RESULTS: The results show that PubMed has a coverage of 70.9, 95% confidence interval (CI) (68.40, 73.30) of all the included publications and 82.8%, 95% CI (80.9, 84.7) of the included studies. There are huge differences in coverage across and within specialties. In addition, coverage varies within groups over time. CONCLUSION: Databases used for searching topics within the groups with highly varying or low coverage should be chosen with care as PubMed may have a relatively low coverage.

A new approach and gold standard toward author disambiguation in MEDLINE.

OBJECTIVE: Author-centric analyses of fast-growing biomedical reference databases are challenging due to author ambiguity. This problem has been mainly addressed through author disambiguation using supervised machine-learning algorithms. Such algorithms, however, require adequately designed gold standards that reflect the reference database properly. In this study we used MEDLINE to build the first unbiased gold standard in a reference database and improve over the existing state of the art in author disambiguation. MATERIALS AND METHODS: Following a new corpus design method, publication pairs randomly picked from MEDLINE were evaluated by both crowdsourcing and expert curators. Because the latter showed higher accuracy than crowdsourcing, expert curators were tasked to create a full corpus. The corpus was then used to explore new features that could improve state-of-the-art author disambiguation algorithms that would not have been discoverable with previously existing gold standards. RESULTS: We created a gold standard based on 1900 publication pairs that shows close similarity to MEDLINE in terms of chronological distribution and information completeness. A machine-learning algorithm that includes new features related to the ethnic origin of authors showed significant improvements over the current state of the art and demonstrates the necessity of realistic gold standards to further develop effective author disambiguation algorithms. DISCUSSION AND CONCLUSION: An unbiased gold standard can give a more accurate picture of the status of author disambiguation research and help in the discovery of new features for machine learning. The principles and methods shown here can be applied to other reference databases beyond MEDLINE. The gold standard and code used for this study are available at the following repository: https://github.com/amorgani/AND/.

Developing a Cancer-Focused Library Survey - Assessing the Current Environment and Planning for the Future.

The primary goal of this project is to understand how each National Cancer Institute-designated cancer center library, and all libraries that support cancer research, function within their institutions. Through an in-depth survey focused on three major areas (staff, content and tools procurement, and user services), the research team hopes to determine how a cancer-centric library can be successful in supporting quality patient care, research excellence, and education. Additionally, the survey will examine the necessary minimum staffing levels for librarians and information professionals based on organizational size and degree of research focus. The survey will seek out the new skills librarians will need to deliver optimal services. The survey will also explore how content libraries purchase reflects and maps to constituents' current medical and research activities. Libraries within a research intense environment have a responsibility to align with researchers and health care professionals to provide resources and services that support their workflows. Cancer libraries need to be attuned to their institutions' missions, whether that includes excellent patient care, research endeavors, or cutting-edge educational programs. The information gathered from the survey will provide data for this research team to define the vision and standards of excellence for a cancer specialized research library.

An Introduction to RA21: Taking Authentication Beyond IP Addresses.

Providing access to electronic resources is a core service for most libraries, and for more than two decades librarians have used Internet Protocol (IP) addresses as a way to authenticate users and prove they should have access to their institution's licensed materials. But in recent years, IP addresses have become a less accurate method of determining whether a user is affiliated with a particular library. Key players in the publishing industry and academia are working together on a new set of protocols to replace IP authentication called Resource Access for the 21st Century, or RA21. This column will briefly explore what RA21 is, what problems it purports to solve, and what problems it may create. A list of resources for further reading on RA21 is provided.

Fracturas del complejo cigomático / Fractures of the zygomatic complex

Introducción: El complejo cigomático maxilar con su convexidad prominente, es muy vulnerable a las lesiones. Objetivo: Abordar elementos actuales sobre el diagnóstico, clasificación, tratamiento y complicaciones de las fracturas del complejo cigomático. Métodos: Se realizó una revisión bibliográfica en septiembre de 2016. Se evaluaron revistas de impacto de Web of Sciencies (29 revistas) y 2 libros. Se consultaron las bases de datos de MEDLINE, PubMed y SciELO con los descriptores: zygomatic fracture, treatment, epidemiology. Se incluyeron artículos en idioma inglés, preferentemente de los últimos 5 años. Se obtuvieron 109 artículos. El estudio se circunscribió a 41. Análisis e integración de la información: El correcto diagnóstico basado en los hallazgos clínicos y medios auxiliares de diagnóstico, permite clasificar la fractura. La clasificación más empleada en nuestro medio es la de las Guías Prácticas de Estomatología. Las modalidades terapéuticas pueden incluir el tratamiento quirúrgico con el uso de métodos de fijación que permiten mayor o menor estabilidad. Las complicaciones pueden aparecer. Conclusiones: La proyección anatómica de los huesos malares justifica la incidencia de estas fracturas. El diagnóstico debe basarse en el interrogatorio, examen físico y los medios auxiliares de diagnóstico imaginológicos. La radiografía Waters es una buena opción de imagen. Al clasificar la fractura se establece un plan de tratamiento basado en la valoración individual de cada caso con el objetivo de evitar complicaciones posteriores(AU)

Introduction: Due to its prominent convexity, the zygomaticomaxillary complex is very vulnerable to injuries. Objective: Address current notions about the diagnosis, classification, treatment and complications of fractures of the zygomatic complex. Methods: A literature review was conducted in September 2016. The evaluation included high impact journals from the Web of Science (29 journals) and 2 books. The databases MEDLINE, PubMed and SciELO were consulted, using the search terms zygomatic fracture, treatment, epidemiology. Papers written in English were included, preferably from the last five years. Of the 109 papers obtained, the study considered 41. Data analysis and integration: Appropriate diagnosis based on clinical findings and the use of diagnostic aids allows classification of the fracture. The classification most commonly used in our environment is that of the Dental Practice Guidelines. Therapy modes may include surgery with fixation methods allowing greater or lesser stability. Complications may appear. Conclusions: The anatomical protrusion of malar bones accounts for the incidence of these fractures. Diagnosis should be based on interrogation, physical examination and the use of auxiliary diagnostic imaging. Waters radiography is a good imaging option. Upon classification of the fracture, a treatment plan is devised based on individual assessment of each case so as to prevent future complications(AU)