Open Science Research Articles

The Role of Energy Balance-Related Behaviors (EBRBs) and their Determinants on the Prevalence of Overweight and Obesity in Children in Need, in Greece: A Scoping Review.

There is scarce literature concerning 'children in need' at a European level (including Greece), particularly regarding energy balance-related behaviors (EBRBs) associated with overweight and obesity. This scoping review aimed to synthesize evidence on the EBRBs associated with overweight and obesity among 'children in need' in Greece and their key determinants. Inclusion criteria included children (0-18years) who were 'in need', living with overweight or obesity, residing in Greece, and which included data on EBRBs and their potential determinants. APA PsychInfo, CINAHL, Cochrane CENTRAL, EMBASE, MEDLINE, as well as grey literature (in Greek/English), were searched (without publication date limitations). Data was extracted using an adapted Joanna Briggs Institute tool. Seven studies were identified (n = 141-7,283 participants), highlighting prevalent EBRBs, categorized into groups; nutrition (lower diet quality, poor dietary habits, higher intake of carbohydrates, sugar sweetened beverage consumption, low adherence to the Mediterranean diet pattern, lack of daily breakfast consumption), sleep (low sleep duration), and sedentary behaviors / physical activity (television in children's bedrooms, high screen time, low physical activity, high sedentary time). Key determinants included low parental education, food culture, food preparation by grandmothers, the home environment, parental dietary choices, and lower socioeconomic status, etc. CONCLUSION: This review identified specific EBRBs associated with overweight and obesity affecting children in need in Greece and their determining factors. These findings should guide future research, tailored intervention programs, and public health policies (i.e. the European Child Guarantee Strategy) targeted at this understudied priority population of children in need, in Greece. Review registration number: Open Science Framework: https://osf.io/w7qdu.

A service evaluation of the uptake and effectiveness of a digital delivery of the NHS health check service

ObjectivesTo compare the uptake, effectiveness and costs of a digital version of the National Health Service (NHS) Health Check (DHC) to the standard face-to-face NHS Health Check (F2F).Participants and settingA...

Working with people living with motor neurone disease and the impact on professionals' emotional and psychological well-being: A scoping review.

Integrated multidisciplinary care is required to manage the progressive and debilitating symptoms associated with motor neurone disease. Professionals can find providing the level of care required by this population clinically and emotionally challenging. To support those working with these patients it is important to understand the experience of the entire multidisciplinary team involved and the impact of working with motor neurone disease on their emotional and psychological well-being. To identify what is known about (1) healthcare professionals' experience of working with motor neurone disease and (2) the impact of this work on their emotional and psychological well-being. Scoping review. Review protocol registered on Open Science Framework. Five electronic databases were searched in January 2023 and 2024. Grey literature and hand searches were completed. Fifty-one sources published between 1990 and 2023 were included. A total of 1692 healthcare professionals are represented. Three main categories were identified: (1) The demands of providing motor neurone disease care. (2) Factors influencing professionals' ability to provide desired levels of care. (3) The emotional impact of working with motor neurone disease. Subcategories are depicted within these. Positive experiences included job satisfaction, enhanced perspective and receiving gratitude, while negative implications such as stress, emotional exhaustion and burnout also featured. The demands of motor neurone disease patient care, the organisation of services and resources required to meet patient and family needs and the emotional burden for professionals involved, warrant greater recognition in clinical practice, guidelines and future research.

The optimal approach for retrieving systematic reviews was achieved when searching MEDLINE and Epistemonikos in addition to reference checking: a methodological validation study

BackgroundSystematic reviews (SRs) are used to inform clinical practice guidelines and healthcare decision making by synthesising the results of primary studies. Efficiently retrieving as many relevant SRs as possible is challenging with a minimum number of databases, as there is currently no guidance on how to do this optimally. In a previous study, we determined which individual databases contain the most SRs, and which combination of databases retrieved the most SRs. In this study, we aimed to validate those previous results by using a different, larger, and more recent set of SRs.MethodsWe obtained a set of 100 Overviews of Reviews that included a total of 2276 SRs. SR inclusion was assessed in MEDLINE, Embase, and Epistemonikos. The mean inclusion rates (% of included SRs) and corresponding 95% confidence intervals were calculated for each database individually, as well as for combinations of MEDLINE with each other database and reference checking. Features of SRs not identified by the best database combination were reviewed qualitatively.ResultsInclusion rates of SRs were similar in all three databases (mean inclusion rates in % with 95% confidence intervals: 94.3 [93.9–94.8] for MEDLINE, 94.4 [94.0-94.9] for Embase, and 94.4 [93.9–94.9] for Epistemonikos). Adding reference checking to MEDLINE increased the inclusion rate to 95.5 [95.1–96.0]. The best combination of two databases plus reference checking consisted of MEDLINE and Epistemonikos (98.1 [97.7–98.5]). Among the 44/2276 SRs not identified by this combination, 34 were published in journals from China, four were other journal publications, three were health agency reports, two were dissertations, and one was a preprint. When discounting the journal publications from China, the SR inclusion rate in the recommended combination (MEDLINE, Epistemonikos and reference checking) was even higher than in the previous study (99.6 vs. 99.2%).ConclusionsA combination of databases and reference checking was the best approach to searching for biomedical SRs. MEDLINE and Epistemonikos, complemented by checking the references of the included studies, was the most efficient and produced the highest recall. However, our results point to the presence of geographical bias, because some publications in journals from China were not identified.Study registrationhttps://doi.org/10.17605/OSF.IO/R5EAS (Open Science Framework).

Systematic review and meta-analysis of combined cognitive-behavioral therapy and physical activity and exercise interventions for pediatric chronic disease.

Cognitive-behavioral (CBT) interventions combined with either a physical activity (CBT+PA) or exercise intervention (CBT+Ex) are becoming more common in pediatric populations. Considering the independent effects of PA and exercise on health and psychological outcomes, it is unclear whether CBT alone differs from CBT+PA or CBT+Ex in efficacy. The main objective of this systematic review and meta-analysis of randomized clinical trials (RCTs) was to assess the efficacy of CBT+PA and CBT+Ex interventions in pediatric chronic disease. This review included RCTs in children (≤18 years) with a chronic condition, a CBT+Ex or CBT+PA intervention, and an objective measure of PA&Ex. Seven databases were searched using MeSH terms and key terms and included studies published before July 1, 2023. Abstracts were reviewed for inclusion by two independent reviewers, data was extracted by three independent reviewers. Risk of bias (RoB 2) and study quality were coded. Random effect meta-analyses of differences in between-group change in PA&Ex were conducted. Eligible studies (k = 5) reported outcomes for a combined 446 children. A small, nonsignificant overall effect was found (d = 0.10, 95% CI -0.16, 0.35) indicating intervention groups (CBT+PA or CBT+Ex) increased engagement in PA&Ex more than comparator groups (CBT). Additional analyses were inconclusive due to the small number of eligible studies. Additional RCTs are needed with integrated PA&Ex interventions targeting pediatric chronic disease. Future trials should report more detailed PA&Ex data. The full protocol for this analysis was prospectively registered in Open Science Framework (project ID: osf.io/m4wtc).

The influence of maternal long term health conditions including multimorbidity on child oral health: A scoping review and evidence gap map protocol

Objective This scoping review will map the extent and type of evidence in relation to the association between maternal long term health conditions (LTCs), including multimorbidity, and child oral health. Introduction Newer theories are emerging that detail the many factors that can influence child oral health at child, family and community levels. More recently, the association between maternal general health and child oral health has been explored, with preliminary evidence suggesting a link between shared environmental factors and diet/substance use during pregnancy causing childhood caries. Inclusion criteria All published studies that describe the relationship between maternal LTCs (including multimorbidity) and child oral health. There will be no limitation on the date of publication due to the limited number of studies available from the initial search of PubMed. The review will exclude case studies, abstracts, and grey literature. Literature must be in English language. Methods The following databases will be searched; CINAHL, Cochrane Library, Maternity and Infant Care, Medline via PubMed, Scopus, Web of Science. The search will include sources in English only and will be undertaken between April and July 2024. Studies to be included will be of any type of study design that describe a relationship between maternal long term health conditions, including maternal long term oral health conditions, and child oral health. Data extraction will be undertaken using tabulation of results by at least two independent reviewers. Narrative analysis of the evidence will be undertaken, and results will be presented in a narrative and tabular manner due to the heterogenous and limited evidence base found in the test search. This review has been registered prospectively on Open Science Framework, (https://doi.org/10.17605/OSF.IO/ECSWJ). The review will also inform an Evidence Gap Map (EGM) to illustrate the current evidence base regarding maternal health factors that influence child oral health.

Validity of data extraction in acupuncture meta-analysis: a reproducibility study protocol

IntroductionSystematic review and meta-analysis occupy the apex of the evidence pyramid, serving as the most comprehensive and reliable form of evidence-based assessment. Data extraction is a crucial juncture in meta-analysis,...

Physiological signal analysis and open science using the Julia language and associated software

In this mini review, we propose the use of the Julia programming language and its software as a strong candidate for reproducible, efficient, and sustainable physiological signal analysis. First, we highlight available software and Julia communities that provide top-of-the-class algorithms for all aspects of physiological signal processing despite the language’s relatively young age. Julia can significantly accelerate both research and software development due to its high-level interactive language and high-performance code generation. It is also particularly suited for open and reproducible science. Openness is supported and welcomed because the overwhelming majority of Julia software programs are open source and developed openly on public platforms, primarily through individual contributions. Such an environment increases the likelihood that an individual not (originally) associated with a software program would still be willing to contribute their code, further promoting code sharing and reuse. On the other hand, Julia’s exceptionally strong package manager and surrounding ecosystem make it easy to create self-contained, reproducible projects that can be instantly installed and run, irrespective of processor architecture or operating system.

From Policy to Practice: Data Sharing Challenges and Opportunities for Mixed Methods Research in the Era of U.S. Open Science Initiatives

The “Year of Open Science” initiative, spearheaded by the White House in 2023, catalyzed the adoption of national open science policies across U.S. Federal Government agencies, but open science is an international movement. This paper elucidates the evolving landscape of open science policies, particularly focusing on the Data Management and Sharing Plans by agencies like NIH, NSF, and CDC. While quantitative research (and qualitative research to some degree) has received considerable attention in data sharing, this paper highlights the underexplored terrain of mixed methods research. Through detailed analysis and examples, it advocates for tailored guidelines and collaborative efforts to bridge the gap in data sharing practices, emphasizing the unique challenges and opportunities inherent in mixed methods research.

Gerontologic Biostatistics and Data Science: Aging Research in the Era of Big Data.

Introduced in 2010, the sub-discipline of gerontologic biostatistics was conceptualized to address the specific challenges of analyzing data from clinical research studies involving older adults. Since then, the evolving technological landscape has led to a proliferation of advancements in biostatistics and other data sciences that have significantly influenced the practice of gerontologic research, including studies beyond the clinic. Data science is the field at the intersection of statistics and computer science, and although the term "data science" was not widely used in 2010, the field has quickly made palpable impacts on gerontologic research. In this Review in Depth, we describe multiple advancements of biostatistics and data science that have been particularly impactful. Moreover, we propose the sub-discipline of "gerontologic biostatistics and data science", or GBDS, which subsumes gerontologic biostatistics into a more encompassing practice. Prominent GBDS advancements that we discuss herein include cutting-edge methods in experimental design and causal inference, adaptations of machine learning, the rigorous quantification of deep phenotypic measurement, and analysis of high-dimensional -omics data. We additionally describe the need for integration of information from multiple studies and propose strategies to foster reproducibility, replicability, and open science. Lastly, we provide information on software resources for GBDS practitioners to apply these approaches to their own work and propose areas where further advancement is needed. The methodological topics reviewed here aim to enhance data-rich research on aging and foster the next generation of gerontologic researchers.

Enhancing the accessibility of science at The Lancet with native language abstracts

Today, 98% of peer-reviewed scientific publishing is in English, which is also the official language of most scientific events and international academic journals. UNESCO, through its Recommendation on Open Science, has called on scientific institutions to foster multilingualism in the practice of science, in scientific publications, and in academic communications. At The Lancet, we recognize the need to provide more equitable and inclusive access to scientific knowledge by providing abstracts translated into relevant languages. Following a pilot, a workflow for abstract translation was devised. I present here details of our abstract translation procedure and rollout.

Deep Configuration Performance Learning: A Systematic Survey and Taxonomy

Performance is arguably the most crucial attribute that reflects the quality of a configurable software system. However, given the increasing scale and complexity of modern software, modeling and predicting how various configurations can impact performance becomes one of the major challenges in software maintenance. As such, performance is often modeled without having a thorough knowledge of the software system, but relying mainly on data, which fits precisely with the purpose of deep learning. In this paper, we conduct a comprehensive review exclusively on the topic of deep learning for performance learning of configurable software, covering 1,206 searched papers spanning six indexing services, based on which 99 primary papers were extracted and analyzed. Our results outline key statistics, taxonomy, strengths, weaknesses, and optimal usage scenarios for techniques related to the preparation of configuration data, the construction of deep learning performance models, the evaluation of these models, and their utilization in various software configuration-related tasks. We also identify the good practices and potentially problematic phenomena from the studies surveyed, together with a comprehensive summary of actionable suggestions and insights into future opportunities within the field. To promote open science, all the raw results of this survey can be accessed at our repository: https://github.com/ideas-labo/DCPL-SLR .

Open Science at the Generative AI Turn: An Exploratory Analysis of Challenges and Opportunities

Abstract Technology influences Open Science (OS) practices, because conducting science in transparent, accessible, and participatory ways requires tools/platforms for collaboration and sharing results. Due to this relationship, characteristics of employed technologies directly impact OS objectives. Generative Artificial Intelligence (GenAI) is increasingly used by researchers for tasks such as text refining, code generation/editing, reviewing literature, data curation/analysis. Nevertheless, concerns about openness, transparency and bias suggest that GenAI may benefit from greater engagement with OS. GenAI promises substantial efficiency gains but is currently fraught with limitations that could negatively impact core OS values such as fairness, transparency and integrity, and harm various social actors. In this paper, we explore possible positive and negative impacts of GenAI on OS. We use the taxonomy within the “UNESCO Recommendation on Open Science” to systematically explore the intersection of GenAI and OS. We conclude that using GenAI could advance key OS objectives by broadening meaningful access to knowledge, enabling efficient use of infrastructure, improving engagement of societal actors, and enhancing dialogue among knowledge systems. However, due to GenAI limitations, it could also compromise the integrity, equity, reproducibility, and reliability of research. Hence, sufficient checks, validation and critical assessments are essential when incorporating GenAI into research workflows. Peer Review https://www.webofscience.com/api/gateway/wos/peer-review/10.1162/qss_a_00337

From the Lab to Librarianship: Advancing Open Science

Three library professionals share their perspectives on transitioning from STEM research to librarianship. A STEM PhD or postdoctoral researcher can bring technical expertise and a deep understanding of researcher culture to library services and at the same time put their skill sets to use in unexpected and interesting ways. A postdoctoral position focused on an emerging area such as open science can provide the perfect opportunity for libraries to leverage the unique skill sets of doctoral students who are increasingly exploring careers beyond research track faculty.

Expanding Horizons: From Information to Inspiration at the AAAS Annual Meeting

The authors attended the 2024 annual meeting of the American Association for the Advancement of Science (AAAS) as part of a cohort of Science, Technology, Engineering, and Mathematics (STEM) librarians sponsored by the partnership between the Association of College and Research Libraries (ACRL) and AAAS. We describe two sessions, one on combating misinformation and one on open science. For these topics especially, hearing the perspectives of scientists was particularly valuable and interesting to us as librarians. We share our reasoning for attending a science disciplinary conference rather than a library conference in these days when one must carefully weigh a national or international conference against all the other demands on a librarian’s professional development budget.

Accuracy Standards of Wearable Technologies for Assessment of Soccer Kicking: Protocol for a Systematic Literature Review.

Wearable technology is widely applied in performance monitoring, an integral part of sports and exercise sciences. The kick movement in soccer exemplifies a sports technique that could benefit from appropriate biomechanics assessment methodologies. However, the accuracy of wearables in quantifying soccer kick mechanics, particularly under field conditions, remains unclear. This study aims to present a protocol for a systematic review to discuss the measurement properties (validity, reliability, and/or accuracy aspects) of wearable technology systems explicitly used to measure ball-kicking features in soccer. This review protocol was preregistered in the Open Science Framework. A total of 2 authors will perform searches in major electronic databases using specific keyword combinations in PubMed, Physical Therapy and Sports Medicine, Web of Science, ProQuest, IEEE Xplore, EBSCOHost, and Scopus. Following a specific population, intervention, comparison, outcome framework (population: soccer players and/or collected human data in a football-related environment; intervention: at least 1 wearable used; comparator: criterion measures, repeated testing sessions and/or actual values; outcome: ball kicking data), studies will be screened based on predetermined inclusion and exclusion criteria. The methodological quality of the included studies will be assessed using the "consensus-based standards for the selection of health measurement instruments" checklist (in studies concerning validity or reliability) or the "quality assessment of diagnostic accuracy studies" tool (in studies concerning accuracy). Data extraction will be conducted to determine the level of evidence according to the "best evidence synthesis method," and an evidence gap map will be constructed. The Cohen κ coefficient will be used to estimate the interevaluator agreement. This ongoing systematic review has completed database searches and is currently in the screening phase. Depending on the number and consistency of studies, results may be presented by meta-analysis or qualitative synthesis, with subgroup analyses considering factors such as gender, age, and playing level. The final results are expected by July 2024, with manuscript submission anticipated by November 2024. Our study will provide a comprehensive summary of the highest level of evidence available on the use of wearables for the assessment of soccer kick mechanics, providing practical guidance for athletes and sports sciences professionals regarding the validity and reliability aspects of using wearable technology to measure ball-kicking features in soccer. OSF registries https://osf.io/zm3j6. DERR1-10.2196/57433.

Experiences of Nurses Speaking Up in Healthcare Settings: A Qualitative Metasynthesis.

To systematically review and synthesise qualitative research on nurses' experiences of speaking up in various contexts and to identify factors facilitating or impeding such a behaviour. This review was conducted as a qualitative metasynthesis, utilising the qualitative meta-ethnography approach. A total of 6250 articles were screened. Two reviewers screened titles, abstracts and full texts. A total of 15 studies were included in this review. Researchers conducted a quality appraisal using the JBI critical appraisal checklist for qualitative research. An a priori protocol was created and registered on the Open Science Framework. Literature searches were conducted in five international bibliographic databases (MEDLINE, Embase, PsycINFO, CINAHL and ProQuest Dissertations and Theses Global) and five Korean databases (RISS, KISS, DBpia, KCI and NDSL). Three main themes were identified from the 15 studies used in the metasynthesis: (1) decisional complexity of speaking up, (2) motivators for speaking up and (3) barriers to speaking up. Nurses experienced challenges in speaking up. They were, and continue to be, concerned about negative responses. Hierarchy structure and poor work environment were identified as barriers to speaking up; professional responsibility and a supportive atmosphere were identified as facilitators for speaking up. This review synthesised nurses' experiences of speaking up and influencing factors. Speaking up is crucial for nurses to improve patient safety, as frontline nurses are ideally positioned to observe early indicators of unsafe conditions in healthcare delivery. Identified motivators and barriers of nurses' speaking-up behaviour offer considerations and opportunities for healthcare leaders and managers. This could lead to improvement in patient safety through the establishment of a safety culture that facilitates nurses' speaking-up behaviour. The review adhered to the ENTREQ guideline. No patient or public contribution has been made in this review.

An international, cross-sectional survey of preprint attitudes among biomedical researchers

Background Preprints are scientific manuscripts that are made available on open-access servers but are not yet peer-reviewed. Although preprints are becoming more prevalent, uptake is not optimal. Understanding researchers’ opinions and attitudes toward preprints is valuable to optimize their use. Understanding knowledge gaps and researchers’ attitudes toward preprinting can assist stakeholders, such as journals, funding agencies, and universities, to use preprints more effectively. Here, we aimed to collect perceptions and behaviours regarding preprints across an international sample of biomedical researchers. Methods Corresponding authors of articles published in biomedical research journals were identified from a random sample of journals from the MEDLINE database. Their names and email addresses were extracted to invite them to our anonymous, cross-sectional survey, which asked participants questions about their knowledge, attitudes, and opinions regarding preprinting. Results The survey was completed by 730 respondents providing a response rate of 3.20% and demonstrated a wide range of attitudes and opinions about preprints with authors from various disciplines and career stages worldwide. Most respondents were familiar with the concept of preprints but most had not previously posted one. The lead author of the project and journal policy had the greatest impact on decisions to post a preprint, whereas employers/research institutes had the least impact. Supporting open science practices was the highest ranked incentive, while increasing authors’ visibility was the highest ranked motivation for publishing preprints. Conclusions Although many biomedical researchers recognize the benefits of preprints, there is still hesitation among others to engage in this practice. This may be due to the general lack of peer review of preprints and little enthusiasm from external organizations such as journals, funding agencies, and universities. Future work is needed to determine optimal ways to improve researchers’ attitudes through modifications to current preprint systems and policies.

Automated Detection of Oral Malignant Lesions Using Deep Learning: Scoping Review and Meta-Analysis.

Oral diseases, specifically malignant lesions, are serious global health concerns requiring early diagnosis for effective treatment. In recent years, deep learning (DL) has emerged as a powerful tool for the automated detection and classification of oral lesions. This research, by conducting a scoping review and meta-analysis, aims to provide an overview of the progress and achievements in the field of automated detection of oral lesions using DL. A scoping review was conducted to identify relevant studies published in the last 5 years (2018-2023). A comprehensive search was conducted using several electronic databases, including PubMed, Web of Science, and Scopus. Two reviewers independently assessed the studies for eligibility and extracted data using a standardized form, and a meta-analysis was conducted to synthesize the findings. Fourteen studies utilizing various DL algorithms were identified and included for the detection and classification of oral lesions from clinical images. Among these, three were included in the meta-analysis. The estimated pooled sensitivity and specificity were 0.86 (95% confidence interval [CI] = 0.80-0.91) and 0.67 (95% CI = 0.58-0.75), respectively. The results of meta-analysis indicate that DL algorithms improve the diagnosis of oral lesions. Future research should develop validated algorithms for automated diagnosis. Open Science Framework (https://osf.io/4n8sm).

Intestinal transport of organic food compounds and drugs: A scoping review on the alterations observed in chronic kidney disease

Background and aimsAround 850 million people worldwide are affected by chronic kidney disease (CKD). Patients with CKD often develop malnutrition and sarcopenia and changes in the pharmacokinetics of drugs. A reduced kidney function partially explains the prolonged half-life of certain drugs due to decreased renal clearance, which leads to an increased risk of adverse effects. While the intestine plays a fundamental role in this context, a systematic review of the effects of CKD on intestinal transport is lacking. We aimed to systematically summarize all the available evidence on intestinal transport of organic food components (carbohydrates/sugar, proteins/amino acids, fats, vitamins) and drugs (including drug transporters) in chronic kidney disease. MethodsWe conducted a systematic search of all the articles published until the 1st of April 2024, on five databases i.e. Embase, PubMed, Web of Science Core Collection, Cochrane Library, and Scopus. This systematic review was registered on the Open Science Framework (OSF) (osf.io/5e6wb) and was carried out according to the PRISMA 2020 guidelines. ResultsFrom 9205 articles identified, 68 met the inclusion criteria. Absorption of organic food compounds seems to be altered, in general, and reduced for vitamins. The expression of intestinal efflux drug transporters may be altered in CKD. ConclusionsDespite alterations in intestinal transport is suggested to be altered in CKD, the lack of recent studies, the paucity of human data and the heterogeneity of the methodologies used underscore the need for more research on the effect of CKD and uremia on intestinal transport.