Ensemble Algorithm for Risk Prediction of Clinical Failure After Anterior Cruciate Ligament Reconstruction.

Background: Patient-specific risk profiles of clinical failure after anterior cruciate ligament reconstruction (ACLR) are meaningful for preoperative surgical planning and postoperative rehabilitation guidance. Purpose: To create an ensemble algorithm machine learning (ML) model and ML-based web-based tool that can predict the patient-specific risk of clinical failure after ACLR. Study Design: Cohort study; Level of evidence, 3. Methods: Included were 432 patients (mean age, 26.8 ± 8.4 years; 74.1% male) who underwent anatomic double-bundle ACLR with hamstring tendon autograft between January 2010 and February 2019. The primary outcome was the probability of clinical failure at a minimum 2-year follow-up. The authors included 24 independent variables for feature selection and model development. The data set was split randomly into training sets (75%) and test sets (25%). Models were built using 4 ML algorithms: extreme gradient boosting, random forest, light gradient boosting machine, and adaptive boosting. In addition, a weighted-average voting (WAV) ensemble model was constructed using the ensemble-voting technique to predict clinical failure after ACLR. Concordance (area under the receiver operating characteristic curve [AUC]), calibration, and decision curve analysis were used to evaluate predictive performances of the 5 models. Results: Clinical failure occurred in 73 of the 432 patients (16.9%). The 8 most important predictors for clinical failure were follow-up period, high-grade preoperative knee laxity, time from injury to ACLR, participation in competitive sports, posterior tibial slope, graft diameter, age at surgery, and medial meniscus resection. The WAV ensemble algorithm achieved the best predictive performance based on concordance (AUC, 0.9139), calibration (calibration intercept, -0.1806; calibration slope, 1.2794; Brier score, 0.0888), and decision curve analysis (greatest net benefits) and was used to develop an web-based application to predict a patient's clinical failure risk of ACLR. Conclusion: The WAV ensemble algorithm was able to accurately predict patient-specific risk of clinical failure after ACLR. Clinicians and patients can use the web-based application during preoperative consultation to understand individual prediction outcomes.

Integrating open education practices with data analysis of open science in an undergraduate course.

The open science movement produces vast quantities of openly published data connected to journal articles, creating an enormous resource for educators to engage students in current topics and analyses. However, educators face challenges using these materials to meet course objectives. I present a case study using open science (published articles and corresponding datasets) and open educational practices in a capstone course. While engaging in current topics of conservation, students trace connections in the research process, learn statistical analyses, and recreate analyses using the programming language R. I assessed the presence of best practices in open articles and datasets, examined student selection in the open grading policy, surveyed students on their perceived learning gains, and conducted a thematic analysis on student reflections. First, articles and datasets met just over half of the assessed fairness practices, which increased with the publication date. There was a marginal difference in how assessment categories were weighted by students, with reflections highlighting appreciation for student agency. In course content, students reported the greatest learning gains in describing variables, while collaborative activities (e.g., interacting with peers and instructor) were the most effective support. The most effective tasks to facilitate these learning gains included coding exercises and team-led assignments. Autocoding of student reflections identified 16 themes, and positive sentiments were written nearly 4x more often than negative sentiments. Students positively reflected on their growth in statistical analyses, and negative sentiments focused on how limited prior experience with statistics and coding made them feel nervous. As a group, we encountered several challenges and opportunities in using open science materials. I present key recommendations, based on student experiences, for scientists to consider when publishing open data to provide additional educational benefits to the open science community.

Gender and Geographical Representation on Editorial Board Members of Medical Informatics Journals.

Previous work has suggested that gender and geographical distribution (affiliation) of Editors-in-Chief (EiC) and Editorial Board (EB) members are inequitable in representation of scientific communities, and could benefit from increasing diversity of representation. Specifically, previous studies suggest that male and ethnically white (or non-minoritized groups) are overrepresented. Such differences in representation may potentially influence the scientific and scholarly record. This paper aims to build on pre-existing literature by examining the diversity of representation among EiCs and EB members in the top (Q1) journals in the "Medicine-Health Informatics" category (ranked by SCImago Journal and Country Rank, or SJR) in terms of gender as assessed by genderize.io) and geographical distribution of affiliations. Preliminary findings are consistent with those of previous work on the topic: only 25% (8/32) of the EiCs in the selected journals are female, while females only represent 32.7% (426/1303) of the EB members across journals. Furthermore, the US is highly represented in EBs, with more than half of the members, i.e., 52.2% (698/1337), being US-affiliated. Present results suggest the need for an intentional approach to diversifying representation on editorial boards of medical informatics journals. Such intention can be seen as part of a call to action from important stakeholders, including medical informatics leaders and programs, journal management and publishers, and the medical informatics and scientific community more generally.

Public Availability of Data Management and Analysis Scripts of Studies Conducted on Open-Access Intensive Care Databases.

Intensive care units (ICUs) provide care for critical patients at high risk of morbidity and mortality, and require continuous monitoring of clinical, biological and, imaging parameters. Collaborative ventures have enabled the emergence of large open access databases for the secondary use of Electronic Health Records (EHRs). The objective of this work was to evaluate the availability of scripts and datasets in publications based on ICU open-access databases. We included 910 original articles based on four ICU open-access databases (Amsterdam University Medical Centers Database, eICU Collaborative Research Database, High time resolution ICU dataset, and Medical Information Mart for Intensive Care). The majority of the studies did not provide their data management scripts (n=839, 92.9%), neither the analysis script (n=843, 93.4%) in the article. Attempts to contact the 845 corresponding authors in question resulted in 89.11% (n=753) of our e-mail requests going unanswered over a two-month period. We received 51 automated messages (55.43%) indicating that emails have not been delivered, while 6 messages (6.52%) redirected to alternative email addresses. Only 20 corresponding authors (18.18%) answered, finally providing the requested materials. Despite scientific journals recommendations to share materials, our study unveils the absence of crucial components for the replication of studies by other research teams.

The societal impact of Open Science: a scoping review.

Open Science (OS) aims, in part, to drive greater societal impact of academic research. Government, funder and institutional policies state that it should further democratize research and increase learning and awareness, evidence-based policy-making, the relevance of research to society's problems, and public trust in research. Yet, measuring the societal impact of OS has proven challenging and synthesized evidence of it is lacking. This study fills this gap by systematically scoping the existing evidence of societal impact driven by OS and its various aspects, including Citizen Science (CS), Open Access (OA), Open/FAIR Data (OFD), Open Code/Software and others. Using the PRISMA Extension for Scoping Reviews and searches conducted in Web of Science, Scopus and relevant grey literature, we identified 196 studies that contain evidence of societal impact. The majority concern CS, with some focused on OA, and only a few addressing other aspects. Key areas of impact found are education and awareness, climate and environment, and social engagement. We found no literature documenting evidence of the societal impact of OFD and limited evidence of societal impact in terms of policy, health, and trust in academic research. Our findings demonstrate a critical need for additional evidence and suggest practical and policy implications.

The Peer Review Process: Past, Present, and Future.

The peer review process is a fundamental aspect of modern scientific paper publishing, underpinning essential quality control. First conceptualised in the 1700s, it is an iterative process that aims to elevate scientific literature to the highest standards whilst preventing publication of scientifically unsound, potentially misleading, and even plagiarised information. It is widely accepted that the peer review of scientific papers is an irreplaceable and fundamental aspect of the research process. However, the rapid growth of research and technology has led to a huge increase in the number of publications. This has led to increased pressure on the peer review system. There are several established peer review methodologies, ranging from single and double blind to open and transparent review, but their implementation across journals and research fields varies greatly. Some journals are testing entirely novel approaches (such as collaborative reviews), whilst others are piloting changes to established methods. Given the unprecedented growth in publication numbers, and the ensuing burden on journals, editors, and reviewers, it is imperative to improve the quality and efficiency of the peer review process. Herein we evaluate the peer review process, from its historical origins to current practice and future directions.

Testing the Digital Atlas of Ancient Rare Diseases (DAARD) using a new case of Legg-Calvé-Perthes disease from Early Byzantine (500-700 CE) Olympia, Greece.

OBJECTIVE: The first case of Legg-Calvé-Perthes disease (LCPD) in Greece is presented. LCPD, a rare disease, is discussed using the Digital Atlas of Ancient Rare Diseases (DAARD), which tests the benefits of the database for diagnosing and contextualizing the new case with 42 archaeological cases of LCPD recorded in the DAARD. MATERIALS: A 30-40-year-old, probable male individual was found at the archaeological site of Olympia, Greece, dating to 500-700 CE. METHODS: Biological sex, age-at-death and pathological changes were investigated using macroscopic and osteometric methods. The DAARD provided the typical characteristics of LCPD. RESULTS: Pathological changes in both hip joints without any other related changes in the skeleton corresponded to the skeletal features of LCPD. The DAARD produced 42 cases of LCPD, most of which from Europe, with a preference for male sex and unilateral involvement of the hip joint. CONCLUSIONS: The DAARD aids in diagnosing rare diseases and interpreting new cases in the context of already known studies. SIGNIFICANCE: This study shows that the DAARD has the potential to help researchers move beyond the level of single case studies and create a broader picture of the history of rare diseases. LIMITATIONS: This paper focuses on the benefits of the DAARD in relation to LCPD but not all rare diseases have been included in the database. SUGGESTIONS FOR FURTHER RESEARCH: More rare diseases from archaeological contexts should be added to the DAARD to create a base for the interpretation of their history and expand our understanding of rare diseases in the past.

Title, abstract and keywords: a practical guide to maximize the visibility and impact of academic papers.

In a growing digital landscape, enhancing the discoverability and resonance of scientific articles is essential. Here, we offer 10 recommendations to amplify the discoverability of studies in search engines and databases. Particularly, we argue that the strategic use and placement of key terms in the title, abstract and keyword sections can boost indexing and appeal. By surveying 230 journals in ecology and evolutionary biology, we found that current author guidelines may unintentionally limit article findability. Our survey of 5323 studies revealed that authors frequently exhaust abstract word limits-particularly those capped under 250 words. This suggests that current guidelines may be overly restrictive and not optimized to increase the dissemination and discoverability of digital publications. Additionally, 92% of studies used redundant keywords in the title or abstract, undermining optimal indexing in databases. We encourage adopting structured abstracts to maximize the incorporation of key terms in titles, abstracts and keywords. In addition, we encourage the relaxation of abstract and keyword limitations in journals with strict guidelines, and the inclusion of multilingual abstracts to broaden global accessibility. These recommendations to editors are designed to improve article engagement and facilitate evidence synthesis, thereby aligning scientific publishing with the modern needs of academic research.

Pooled Cohort Profile: ReCoDID Consortium's Harmonized Acute Febrile Illness Arbovirus Meta-Cohort.

Infectious disease (ID) cohorts are key to advancing public health surveillance, public policies, and pandemic responses. Unfortunately, ID cohorts often lack funding to store and share clinical-epidemiological (CE) data and high-dimensional laboratory (HDL) data long term, which is evident when the link between these data elements is not kept up to date. This becomes particularly apparent when smaller cohorts fail to successfully address the initial scientific objectives due to limited case numbers, which also limits the potential to pool these studies to monitor long-term cross-disease interactions within and across populations. CE data from 9 arbovirus (arthropod-borne viruses) cohorts in Latin America were retrospectively harmonized using the Maelstrom Research methodology and standardized to Clinical Data Interchange Standards Consortium (CDISC). We created a harmonized and standardized meta-cohort that contains CE and HDL data from 9 arbovirus studies from Latin America. To facilitate advancements in cross-population inference and reuse of cohort data, the Reconciliation of Cohort Data for Infectious Diseases (ReCoDID) Consortium harmonized and standardized CE and HDL from 9 arbovirus cohorts into 1 meta-cohort. Interested parties will be able to access data dictionaries that include information on variables across the data sets via Bio Studies. After consultation with each cohort, linked harmonized and curated human cohort data (CE and HDL) will be made accessible through the European Genome-phenome Archive platform to data users after their requests are evaluated by the ReCoDID Data Access Committee. This meta-cohort can facilitate various joint research projects (eg, on immunological interactions between sequential flavivirus infections and for the evaluation of potential biomarkers for severe arboviral disease).

Knowledge, Attitudes, and Practices of Health Sciences Faculty Towards Scholarly Open Access and Predatory Publishing.

Health sciences librarians often lack knowledge of the motivations behind faculty publishing behavior. This study establishes some understanding of their choices through interviews with academic health sciences faculty members. Knowledge of the concepts of open access was lacking, as was the differences between open access and predatory publishing. Faculty had varied opinions on publication without robust peer review, its ethical implications, manuscript quality, and trust in scientific publishing. Evidence from this study suggests that librarians must take an active role in shaping the future of scholarly communication through education, advocacy, and a commitment to moving science forward equitably and ethically.

Update on IJTLD OPEN: the future is open.

The launch of IJTLD OPEN, which is fully compliant with Plan S, has extended our author base and allowed readers worldwide to access the content for free. PubMed Central (PMC) has recently approved the journal for indexing (including indexing by PubMed), which will further improve visibility and access. Because authors retain copyright they can use their articles without restriction (e.g., to post on free digital repositories), helping to further disseminate their research. All these factors help to ensure that IJTLD OPEN has maximum reach and impact. However, we recognise that fees for open access may present a barrier for authors based in low- to middle-income countries. We call on the international community to ensure funding support for open access is broadly available, with equal opportunity for researchers worldwide.

Bridging Gaps: A Quality Improvement Project for the Continuing Medical Education on Stick (CMES) Program.

BACKGROUND: Aimed at bridging the gap in continuing medical education (CME) resource availability in low- and middle-income countries (LMICs), the "Continuing Medical Education on Stick" (CMES) program introduces two technological solutions: a universal serial bus (USB) drive and the CMES-Pi computer facilitating access to monthly updated CME content without data cost. Feedback from users suggests a lack of content on tropical infectious diseases (IDs) and content from a Western perspective, which may be less relevant in LMIC settings. METHODS: This quality improvement project was intended to identify areas for improvement of the CMES database to better meet the educational needs of users. We compared the CMES content with the American Board of Emergency Medicine (ABEM) Exam content outline to identify gaps. The curriculum map of the CMES library, encompassing content from 2019 to 2024, was reviewed. An anonymous survey was conducted among 47 global users to gather feedback on unmet educational needs and suggestions for content improvements. All healthcare workers who were members of the CMES WhatsApp group were eligible to participate in the survey. RESULTS: The curriculum map included 2,572 items categorized into 23 areas. The comparison with the ABEM outline identified gaps in several clinical areas, including procedures, traumatic disorders, and geriatrics, which were represented -5%, -5%, and -4% in the CMES library compared with the ABEM outline, respectively. Free responses from users highlighted a lack of content on practical skills, such as electrocardiogram (ECG) interpretation and management of tropical diseases. Respondents identified emergency medical services (EMS)/prehospital care (81%), diagnostic imaging (62%), and toxicology/pharmacology (40%) as the most beneficial areas for clinical practice. In response to feedback from users, new content was added to the CMES platform on the management of sickle cell disease and dermatologic conditions in darkly pigmented skin. Furthermore, a targeted podcast series called "ID for Users of the CMES Program (ID4U)" has been launched, focusing on tropical and locally relevant ID, with episodes now being integrated into the CMES platform. CONCLUSIONS: The project pinpointed critical gaps in emergency medicine (EM) content pertinent to LMICs and led to targeted enhancements in the CMES library. Ongoing updates will focus on including more prehospital medicine, diagnostic imaging, and toxicology content. Further engagement with users and education on utilizing the CMES platform will be implemented to maximize its educational impact. Future adaptations will consider local relevance over the ABEM curriculum to better serve the diverse needs of global users.

Evaluation of no-show rate in outpatient clinics with open access scheduling system: A systematic review.

Background: Patients' missed appointments can cause interference in the functions of the clinics and the visit of other patients. One of the most effective strategies to solve the problem of no-show rate is the use of an open access scheduling system (OA). This systematic review was conducted with the aim of investigating the impact of OA on the rate of no-show of patients in outpatient clinics. Methods: Relevant articles in English were investigated based on the keywords in title and abstract using PubMed, Scopus, and Web of Science databases and Google Scholar search engine (July 23, 2023). The articles using OA and reporting the no-show rate were included. Exclusion criteria were as follows: (1) review articles, opinion, and letters, (2) inpatient scheduling system articles, and (3) modeling or simulating OA articles. Data were extracted from the selected articles about such issues as study design, outcome measures, interventions, results, and quality score. Findings: From a total of 23,403 studies, 16 articles were selected. The specialized fields included family medicine (62.5%, 10), pediatrics (25%, four), ophthalmology, podiatric, geriatrics, internal medicine, and primary care (6.25%, one). Of 16 articles, 10 papers (62.5%) showed a significant decrease in the no-show rate. In four articles (25%), the no-show rate was not significantly reduced. In two papers (12.5%), there were no significant changes. Conclusions: According to this study results, it seems that in most outpatient clinics, the use of OA by considering some conditions such as conducting needs assessment and system design based on the patients' and providers' actual needs, and cooperating of all system stakeholders through consistent training caused a significant decrease in the no-show rate.

Analytical code sharing practices in biomedical research.

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

De Novo Design of Inhibitors of DNA Methyltransferase 1: A Critical Comparison of Ligand- and Structure-Based Approaches.

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub.

Opening science to society: how to progress societal engagement into (open) science policies.

A broad understanding of the aims and objectives of the international open science movement was recently adopted with the 2021 UNESCO Recommendation on Open Science, expanding the focus of open science to include scientific knowledge, infrastructures, knowledge systems and the open engagement of societal actors. In response, recent discussions on science policy practice are shifting to the implementation of open science via national policies. While policy instruments to support some aspects of open science are well-studied, guidance on the emerging 'social' aspects of open science has lagged, prompting UNESCO to generate guidance. In this paper, several authors of the UNESCO Open Science Toolkit guidance document on 'Engaging societal actors in Open Science' synthesize the scholarly underpinnings behind its recommendations. This work draws upon a targeted search from academic, policy, and grey literature in the fields of open science and community engagement, with a special focus on citizen science, to derive guidance on how to overcome barriers to the uptake of societal engagement approaches. The results present building blocks of what an enabling environment for the open engagement of societal actors could look like, identifying key considerations and reflecting on opportunities and challenges for progressing and evaluating sound open engagement of societal actors into regional & national (open) science policies.

BIOMX-DB: A web application for the BIOFACQUIM natural product database.

Natural product databases are an integral part of chemoinformatics and computer-aided drug design. Despite their pivotal role, a distinct scarcity of projects in Latin America, particularly in Mexico, provides accessible tools of this nature. Herein, we introduce BIOMX-DB, an open and freely accessible web-based database designed to address this gap. BIOMX-DB enhances the features of the existing Mexican natural product database, BIOFACQUIM, by incorporating advanced search, filtering, and download capabilities. The user-friendly interface of BIOMX-DB aims to provide an intuitive experience for researchers. For seamless access, BIOMX-DB is freely available at www.biomx-db.com.

Monitoring Open Science as transformative change: Towards a systemic framework.

Following a flurry of policies for Open Science (OS), there is now a wave of initiatives to monitor its adoption. However, the great diversity of understandings and activities related to Open Science makes monitoring very challenging. There is a danger that by focusing on what can be readily observed (e.g. publications) many other OS activities are overlooked (e.g. participation), with a potential narrowing of OS scope, streetlight effects, and deviation from the values of OS. Since Open Science can be understood as a systemic transformation of the research system, we have borrowed concepts from Transformative Innovation Policies frameworks which aim at evaluating socio-technical transitions. In accordance with this view of OS as a systemic transformation, we propose that the new monitoring efforts should shift towards: (i) systemic perspectives which considers the various actions related to OS, including policies and outputs (e.g. datasets) but also processes (e.g. participatory events), outcomes (e.g. citizen interest in science) and expected impacts (e.g. better scientific contributions to addressing societal problems); (ii) implementation of monitoring as reflexive learning (rather than accountability or benchmarking); (iii) mapping the directionality of the activities and the values associated with the choices in directions. In summary, a monitoring framework for OS requires a profound change in conventional monitoring practices. The scope should broaden from current focus on outputs (such as publications) towards the processes of connection that make science 'open' (usage, co-creation and dialogue), as well as towards outcomes (changes in practices) and the longer-term impacts that reflect the values and normative commitments of OS.