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.

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.

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.

Novel Compound MMV1804559 from the Global Health Priority Box Exhibits In Vitro and In Vivo Activity against Madurella mycetomatis.

OBJECTIVES: Eumycetoma is a neglected tropical disease (NTD) characterized by subcutaneous lesions and the formation of grains. Attempts to treat eumycetoma involve a combination of antifungal treatment and surgery, although the outcome is frequently disappointing. Therefore, there is a need to identify novel antifungal drugs to treat eumycetoma. In this respect, Medicines for Malaria Venture (MMV) has assembled libraries of compounds for researchers to use in drug discovery research against NTD. Therefore, we screened two MMVOpen compound libraries to identify novel leads for eumycetoma. METHODS: A total of 400 compounds from the COVID Box and the Global Health Priority Box were screened in vitro at 100 µM and 25 µM against the most common causative agents of eumycetoma, namely Madurella mycetomatis and Falciformispora senegalensis, and the resulting IC50 and MIC50 values were obtained. Compounds with an IC50 < 8 µM were identified for possible in vivo efficacy studies using an M. mycetomatis grain model in Galleria mellonella larvae. RESULTS: Out of the 400 compounds, 22 were able to inhibit both M. mycetomatis and F. senegalensis growth at 100 µM and 25 µM, with compounds MMV1593278, MMV020335, and MMV1804559 being selected for in vivo testing. Of these three, only the pyrazolopyrimidine derivative MMV1804559 was able to prolong the survival of M. mycetomatis-infected G. mellonella larvae. Furthermore, the grains in MMV1804559-treated larvae were significantly smaller compared to the PBS-treated group. CONCLUSION: MMV1804559 shows promising in vitro and in vivo activity against M. mycetomatis.

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.

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.

Open Access Publication in Total Ankle Arthroplasty Literature Is Associated With Increased Social Media Attention, but Not Increased Citations.

Background: Open access (OA) publications are increasingly common in orthopaedic literature. However, whether OA publications are associated with increased readership or citations among total ankle arthroplasty (TAA) literature is unclear. We hypothesize that compared with non-OA status, OA status is associated with increased social media dissemination, and readership, but not with citation count. This study aimed to analyze social media attention, citations, readership, and cost of TAA OA and non-OA publications. Methods: Using a PubMed query search, there were 368 publications from 81 journals, with 25% (91/368) being OA articles and 75% (277/368) non-OA articles from 2016 to 2023. We analyzed the Altmetric Attention Score (AAS), Mendeley readership score, and citations between OA vs non-OA articles. Citations and cost of OA articles were determined using an altered timeline and publisher's website, respectively. Subgroup analysis was performed among articles published in the top 5 TAA journals (Tables 2 and 3). Negative binomial regression was used while adjusting for days since publication. Significance was considered at P <.05. Results: OA publication was associated with a larger mean AAS score (8.7 ± 37.0 vs 4.8 ± 26.3), Mendeley readership (42.4 ± 41.6 vs 34.9 ± 25.7), and Twitter mentions (4.6 ± 7.4 vs 3.3 ± 8.1), but not citations (19.7 ± 24.8 vs 20.3 ± 23.5) (Table 1). Conclusion: TAA OA publications and top 5 journals were associated with significantly increased social media attention but not Mendeley readership or citation counts.

K-Means clustering of dermatology journals: comparing the distribution of "free-to-publish" and "pay-to-publish" models.

This study investigates the impact of Free-to-Publish (F2P) versus Pay-to-Publish (P2P) models in dermatology journals, focusing on their differences in terms of journal metrics, Article Processing Charges (APCs), and Open Access (OA) status. Utilizing k-means clustering, the research evaluates dermatology journals based on SCImago Journal Rankings (SJR), H-Index, and Impact Factor (IF), and examines the correlation between these metrics, APCs, and OA status (Full or Hybrid). Data from the SCImago Journal Rank and Journal Citation Report databases were used, and metrics from 106 journals were normalized and grouped into three tiers.The study reveals a higher proportion of F2P journals, especially in higher-tier journals, indicating a preference for quality-driven research acceptance. Conversely, a rising proportion of P2P journals in lower tiers suggests potential bias towards the ability to pay. This disparity poses challenges for researchers from less-funded institutions or those early in their careers. The study also finds significant differences in APCs between F2P and P2P journals, with hybrid OA being more common in F2P.Conclusively, the study highlights the disparities in dermatology journals between F2P and P2P models and underscores the need for further research into authorship demographics and institutional affiliations in these journals. It also establishes the effectiveness of k-means clustering as a standardized method for assessing journal quality, which can reduce reliance on potentially biased individual metrics.

Digital Health Education for the Future: The SaNuRN (Santé Numérique Rouen-Nice) Consortium's Journey.

SaNuRN is a five-year project by the University of Rouen Normandy (URN) and the Côte d'Azur University (CAU) consortium to optimize digital health education for medical and paramedical students, professionals, and administrators. The project includes a skills framework, training modules, and teaching resources. In 2027, SaNuRN is expected to train a significant portion of the 400,000 health and paramedical professions students at the French national level. Our purpose is to give a synopsis of the SaNuRN initiative, emphasizing its novel educational methods and how they will enhance the delivery of digital health education. Our goals include showcasing SaNuRN as a comprehensive program consisting of a proficiency framework, instructional modules, and educational materials and explaining how SaNuRN is implemented in the participating academic institutions. SaNuRN is a project aimed at educating and training health-related and paramedics students in digital health. The project results from a cooperative effort between URN and CAU, covering four French departments. The project is based on the French National Referential on Digital Health (FNRDH), which defines the skills and competencies to be acquired and validated by every student in the health, paramedical, and social professions curricula. The SaNuRN team is currently adapting the existing URN and CAU syllabi to FNRDH and developing short-duration video capsules of 20 to 30 minutes to teach all the relevant material. The project aims to ensure that the largest student population earns the necessary skills, and it has developed a two-tier system involving facilitators who will enable the efficient expansion of the project's educational outreach and support the students in learning the needed material efficiently. With a focus on real-world scenarios and innovative teaching activities integrating telemedicine devices and virtual professionals, SaNuRN is committed to enabling continuous learning for healthcare professionals in clinical practice. The SaNuRN team introduced new ways of evaluating healthcare professionals by shifting from a knowledge-based to a competencies-based evaluation, aligning with the Miller teaching pyramid and using the Objective Structured Clinical Examination and Script Concordance Test in digital health education. Drawing on the expertise of URN, CAU, and their public health and digital research laboratories and partners, the SaNuRN project represents a platform for continuous innovation, including telemedicine training and living labs with virtual and interactive professional activities. The SaNuRN project provides a comprehensive, personalized 30-hour training package for health and paramedical students, addressing all 70 FNRDH competencies. The program is enhanced using AI and NLP to create virtual patients and professionals for digital healthcare simulation. SaNuRN teaching materials are open-access. The project collaborates with academic institutions worldwide to develop educational material in digital health in English and multilingual formats. SaNuRN offers a practical and persuasive training approach to meet the current digital health education requirements.

Generative AI, UK Copyright and Open Licences: considerations for UK HEI copyright advice services.

With the enormous growth in interest and use of generative artificial intelligence (AI) systems seen since the launch of ChatGPT in autumn 2022 have come questions both about the legal status of AI outputs, and of using protected works as training inputs. It is inevitable that UK higher education institution (HEI) library copyright advice services will see an increase in questions around use of works with AI as a result. Staff working in such library services are not lawyers or able to offer legal advice to their academic researchers. Nonetheless, they must look at the issues raised, consider how to advise in analogous situations of using copyright material, and offer opinion to researchers accordingly. While the legal questions remain to be answered definitively, copyright librarians can still offer advice on both open licences and use of copyright material under permitted exceptions. We look here at how library services can address questions on copyright and open licences for generative AI for researchers in UK HEIs.

Brief Educational Workshops in Secondary Schools Trial (BESST trial), a school-based cluster randomised controlled trial of the DISCOVER workshop for 16-18-year-olds: recruitment and baseline characteristics.

BACKGROUND: The Brief Educational Workshops in Secondary Schools Trial (BESST) is an England-wide school-based cluster randomised controlled trial assessing the clinical and cost-effectiveness of an open-access psychological workshop programme (DISCOVER) for 16-18-year-olds. This baseline paper describes the self-referral and other recruitment processes used in this study and the baseline characteristics of the enrolled schools and participants. METHOD: We enrolled 900 participants from 57 Secondary schools across England from 4th October 2021 to 10th November 2022. Schools were randomised to receive either the DISCOVER day-long Stress workshop or treatment as usual which included signposting information. Participants will be followed up for 6 months with outcome data collection at baseline, 3-month, and 6-month post randomisation. RESULTS: Schools were recruited from a geographically and ethnically diverse sample across England. To reduce stigma, students were invited to self-refer into the study if they wanted help for stress. Their mean age was 17.2 (SD = 0.6), 641 (71%) were female and 411 (45.6%) were from ethnic minority groups. The general wellbeing of our sample measured using the Mood and Feelings Questionnaire (MFQ) found 314 (35%) of students exhibited symptoms of depression at baseline. Eighty percent of students reported low wellbeing on the Warwick Edinburgh Mental Wellbeing Scale (WEMWBS) suggesting that although the overall sample mean is below the cut-off for depression, the self-referral approach used in this study supports distressed students in coming forward. CONCLUSION: The BESST study will continue to follow up participants to collect outcome data and results will be analysed once all the data have been collected. TRIAL REGISTRATION: ISRCTN registry ISRCTN90912799. Registered on 28 May 2020.

The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This Portal has been coupled with other resources like Viral AI and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this Portal, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

Dissemination of scientific information through open access by research scientists in a developing country.

This study investigated the perceptions and factors that researchers had about Open Access (OA) publishing, specifically how it affected their decision to publish or not. The Diffusion of Innovation Theory by Rogers served as the study's main guide, and 15 research scientists from Ghana's Council of Scientific and Industrial Research's Crop Research Institute provided qualitative data for the study through semi-structured interviews and the interpretivist research paradigm. Convenience sampling was used to choose the participants, and thematic analysis was used to analyse and present the research results in themes. The study's conclusions showed that all of the participants benefited from OA and that they were all aware of its application for disseminating scientific information. High Article Processing Charges (APC) and credibility issues were also mentioned in the study as significant obstacles to using OA for the dissemination of scientific information. The study suggests that in order for scientists to use Open Access (OA) for the sharing of scientific information, they must be given the means to distinguish trustworthy journals from predatory ones.

A pathway to strengthening open science: comments on the draft South African Ethics in Health Research Guidelines.

The recently released draft South African Ethics in Health Research Guidelines: Principles, Processes and Structures (Draft Guidelines) by the National Health Research Ethics Council recognize open data and provide guiding principles for this in the context of health research in South Africa. While its inclusion is a positive development, there is room for improvement. Although the Draft Guidelines leverage the Draft National Policy on Data and Cloud, it lacks incorporation of other relevant government policies, notably the Draft National Open Science Policy, and fails to sufficiently detail the principles of open science and open access. This limited scope and lack of comprehensive definition and detailed guidance present challenges for researchers in conducting ethical and responsible health research in South Africa. It constrains the Draft Guidelines from fully aligning with national imperatives and from fostering African-centric approaches. To address these issues, it is recommended that the Draft Guidelines integrate broader policies and principles, enhance clarity through comprehensive definitions, provide detailed guidance on open access, and promote African-centric approaches. Implementing these solutions will strengthen the Draft Guidelines, aligning them with national visions of open science, and thereby harnessing the full potential of South Africa's diverse scientific community in advancing health research.

State of open science in cancer research.

PURPOSE: This study has been focused on assessing the Open Science scenario of cancer research during the period 2011-2021, in terms of the derived scientific publications and raw data dissemination. METHODS: A cancer search equation was executed in the Science Citation Index-Expanded, collecting the papers signed by at least one Spanish institution. The same search strategy was performed in the Data Citation Index to describe dataset diffusion. RESULTS: 50,822 papers were recovered, 71% of which belong to first and second quartile journals. 59% of the articles were published in Open Access (OA) journals. The Open Access model and international collaboration positively conditioned the number of citations received. Among the most productive journals stood out Plos One, Cancers, and Clinical and Translational Oncology. 2693 genomics, proteomics and metabolomics datasets were retrieved, being Gene Expression Omnibus the favoured repository. CONCLUSIONS: There has been an increase in oncology publications in Open Access. Most were published in first quartile journals and received higher citations than non-Open Access articles, as well as when oncological investigation was performed between international research teams, being relevant in the context of Open Science. Genetic repositories have been the preferred for sharing oncology datasets. Further investigation of research and data sharing in oncology is needed, supported by stronger Open Science policies, to achieve better data sharing practices among three scientific main pillars: researchers, publishers, and scientific organizations.

The impact of open access on citations, Pageviews, and downloads: a scientometric analysis in Postgraduate Medical Journal.

PURPOSE: The influence of Open Access (OA) on the citation impact of scholarly articles remains a topic of considerable debate. This study aims to elucidate the relationship between OA publication and citation metrics, as well as article visibility, within the context of the Postgraduate Medical Journal (PMJ). METHODS: We conducted a retrospective analysis of 373 articles published in PMJ between 2020 and 2021. Data on OA status, citations, page views, PDF downloads, and other relevant variables were extracted from Journal Citation Reports and PMJ's official website. Multivariable linear regression and other statistical analyses were used to assess the impact of OA on these metrics. RESULTS: OA articles (n = 78) demonstrated significantly higher citation counts, page views, and PDF downloads compared with subscription-based articles (n = 295). Specifically, OA articles showed a significant increase in citation frequency with a ß coefficient of 25.08 and a 95% CI of 17.168-32.992 (P < .001). Similarly, OA status was independently associated with increases in page views [ß = 288.636, 95%CI: 177.749-399.524, P < .001] and PDF downloads [ß = 118.966, 95%CI: 86.357-151.575, P < .001]. Strong correlations among total citations, page views, and PDF downloads were observed in both OA and subscription articles. CONCLUSION: The study highlights a significant and independent association of OA publishing with increased citation counts, page views, and PDF downloads in PMJ, suggesting that OA articles have broader reach and greater visibility. Further research, including randomized controlled studies across various journals, is needed to confirm these findings and explore the full impact of OA publishing.

The World's consumption of free web-based Otolaryngology-Head and Neck Surgery educational resources: A global assessment of video usage trends.

Objectives: Online educational platforms with open access have seen a growing adoption in the field of medical education. However, the extent of their global usage is still unclear. To fill this knowledge gap, our objective is to examine the usage patterns of two renowned open-access resources in Otolaryngology. This includes identifying the most sought-after topics and understanding the demographics of their users. Methods: Retrospective study of web analytics data between 2016 and 2021 extracted from the Headmirror.com and Mayo Clinic Otolaryngology YouTube channel platforms analyzing demographic and education topic trends via descriptive, geospatial, time-series, t-tests, and ANOVA analyses. Results: Viewership spanned 124 countries in 7 different geographic regions, with 72 countries comprising low- to middle-income countries, mostly represented ages of 25-34 years old, came from high-income countries rather than low-income (p < .001), and used mobile phones followed by computers for device access. Video-educational material comprised of subspecialty topics on Rhinology and Sinus Surgery (25%) at the highest end and Facial Trauma (1%) at the lowest. Controlling for the age of the video content, the most-accessed videos comprised of subspecialty topics on Head and Neck Surgery at the highest end and Laryngology at the lowest with significant differentiation across topics of interest (p < .044). Conclusions: This assessment of web-analytics platforms from two widely used otolaryngology free, online-access materials showed increasing global usage trends with significant differentiating factors along viewership demographics, as well as sought-after subspecialty topics of interest. In turn, our results not only lay the groundwork for characterizing the global otolaryngology audience but also for future development of targeted educational materials and accessibility initiatives aimed at ameliorating global educational disparities in the field.