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Cancer Research and Treatment Jun 2024In 2024, medical researchers in the Republic of Korea were invited to amend the health and medical data utilization guidelines (Government Publications Registration...
PURPOSE
In 2024, medical researchers in the Republic of Korea were invited to amend the health and medical data utilization guidelines (Government Publications Registration Number: 11-1352000-0052828-14). This study aimed to show the overall impact of the guideline revision, with a focus on clinical genomic data.
MATERIALS AND METHODS
This study amended the pseudonymization of genomic data defined in the previous version through a joint study led by the Ministry of Health and Welfare, the Korea Health Information Service, and the Korea Genome Organization. To develop the previous version, we held three conferences with four main medical research institutes and seven academic societies. We conducted two surveys targeting special genome experts in academia, industry, and institutes.
RESULTS
We found that cases of pseudonymization in the application of genome data were rare and that there was ambiguity in the terminology used in the previous version of the guidelines. Most experts (> ~90%) agreed that the 'reserved' condition should be eliminated to make genomic data available after pseudonymization. In this study, the scope of genomic data was defined as clinical next generation sequencing data, including FASTQ, BAM/SAM, VCF, and medical records. Pseudonymization targets genomic sequences and metadata, embedding specific elements, such as germline mutations, short tandem repeats, single-nucleotide polymorphisms, and identifiable data (for example, ID or environmental values). Expression data generated from multi-omics can be used without pseudonymization.
CONCLUSION
This amendment will not only enhance the safe use of healthcare data but also promote advancements in disease prevention, diagnosis, and treatment.
PubMed: 38853539
DOI: 10.4143/crt.2024.146 -
European Heart Journal. Cardiovascular... Jun 2024Direct oral anticoagulants (DOACs) are increasingly used off-label to treat patients with left ventricular thrombus (LVT). We analyzed available meta-data comparing...
AIMS
Direct oral anticoagulants (DOACs) are increasingly used off-label to treat patients with left ventricular thrombus (LVT). We analyzed available meta-data comparing DOACs and vitamin K antagonists (VKAs) for efficacy and safety.
METHODS
We conducted a systematic search and meta-analysis of observational and randomized data comparing DOACs versus VKAs in patients with LVT. Endpoints of interest were stroke or systemic embolism, thrombus resolution, all-cause death, and a composite bleeding endpoint. Estimates were pooled using a random-effect model meta-analysis, and their robustness was investigated using sensitivity and influential analyses.
RESULTS
We identified 22 articles (18 observational studies, 4 small randomized clinical trials) reporting on a total of 3,587 patients (2,489 VKA vs. 1,098 DOAC therapy). The pooled estimates for stroke or systemic embolism (OR 0.81; 95% CI [0.57, 1.15]) and thrombus resolution (OR 1.12; 95% CI [0.86; 1.46]) were comparable, and there was low heterogeneity overall across the included studies. DOAC use was associated with lower odds of all-cause death (OR 0.65; 95%CI [0.46; 0.92]) and a composite bleeding endpoint (OR 0.67; 95%CI [0.47; 0.97]). A risk of bias was evident particularly for observational reports, with some publication bias suggested in funnel plots.
CONCLUSION
In this comprehensive analysis of mainly observational data, the use of DOACs was not associated with a significant difference in stroke or systemic embolism, or thrombus resolution compared to VKA therapy. The use of DOACs was associated with a lower rate of all-cause death and fewer bleeding events. Adequately sized randomized clinical trials are needed to confirm these findings, which could allow a wider adoption of DOACs in patients with LVT.
PubMed: 38845369
DOI: 10.1093/ehjcvp/pvae042 -
BMJ Paediatrics Open Jun 2024As a topic of inquiry in its own right, data management for interdisciplinary research projects is in its infancy. Key issues include the inability of researchers to...
INTRODUCTION
As a topic of inquiry in its own right, data management for interdisciplinary research projects is in its infancy. Key issues include the inability of researchers to effectively query diverse data outputs and to identify potentially important synergies between discipline-specific data. Equally problematic, few semantic ontologies exist to better support data organisation and discovery. Finally, while interdisciplinary research is widely regarded as beneficial to unpacking complex problems, non-researchers such as policy-makers and planners often struggle to use and interrogate the related datasets. To address these issues, the following article details the design and development of the UKRI GCRF Action Against Stunting Hub (AASH)'s All-Hub Data Repository (AHDR).
METHODS AND ANALYSIS
The AHDR is a single application, single authentication web-based platform comprising a data warehouse to store data from across the AASH's three study countries and to support data querying. Four novel components of the AHDR are described in the following article: (1) a unique data discovery tool; (2) a metadata catalogue that provides researchers with an interface to explore the AASH's data outputs and engage with a new semantic ontology related to child stunting; (3) an interdisciplinary aid to support a directed approach to identifying synergies and interactions between AASH data and (4) a decision support tool that will support non-researchers in engaging with the wider evidence-based outputs of the AASH.
ETHICS AND DISSEMINATION
Ethical approval for this study was granted by institutional ethics committees in the UK, India, Indonesia and Senegal. Results will be disseminated via publications in peer-reviewed journals; presentations at international conferences and community-level public engagement events; key stakeholder meetings; and in public repositories with appropriate Creative Commons licences allowing for the widest possible use.
Topics: Humans; Growth Disorders; Interdisciplinary Research; Child; United Kingdom; Databases, Factual; Child, Preschool
PubMed: 38843904
DOI: 10.1136/bmjpo-2023-002443 -
Cureus Jun 2024Background and objective While musculoskeletal (MSK) disorders account for a significant number of primary care and emergency department (ED) visits, there are widely...
Background and objective While musculoskeletal (MSK) disorders account for a significant number of primary care and emergency department (ED) visits, there are widely recognized shortcomings and gaps in MSK education throughout medical training. Undergraduate medical education (UME) frequently fails to impart clinically relevant MSK knowledge, while many emergency medicine (EM) residency graduates report feeling unprepared to manage MSK complaints. Existing MSK assessments are not tailored to EM and may inaccurately assess specialty-specific MSK knowledge. The novel validated Musculoskeletal Emergency Medicine Assessment Tool (MEAT) holds great promise in standardizing EM MSK knowledge assessment. This trial of feasibility was conducted to assess the viability and practicality of using MEAT to evaluate MSK knowledge among incoming resident physicians in EM programs. Methods This feasibility study involved 21 incoming EM resident physicians from two programs at a single institution. MEAT was administered online during orientation, and demographic data and survey metadata were collected. UME MSK education details were obtained, and MEAT scores were analyzed. Results Participants reported no difficulties in accessing or understanding the 50-question online MEAT, resulting in a 100% response rate. The average pretest score for all interns was 29.9, with a median of 30. Most participants had documented UME MSK education, but curricular content varied widely. The participants took an average of 32 minutes to complete the assessment. Conclusions MEAT demonstrated successful implementation and high response rates, suggesting a high level of feasibility. The tool can be used to assess baseline MSK knowledge and ultimately track progression during residency with the potential for evaluating educational interventions once further validation studies have been performed. Further adoption of MEAT across multiple EM residency programs will help to enhance the tool's generalizability.
PubMed: 38841295
DOI: 10.7759/cureus.61740 -
Ecology and Evolution Jun 2024Body size is a fundamental biological trait shaping ecological interactions, evolutionary processes, and our understanding of the structure and dynamics of marine...
Body size is a fundamental biological trait shaping ecological interactions, evolutionary processes, and our understanding of the structure and dynamics of marine communities on a global scale. Accurately defining a species' body size, despite the ease of measurement, poses significant challenges due to varied methodologies, tool usage, and subjectivity among researchers, resulting in multiple, often discrepant size estimates. These discrepancies, stemming from diverse measurement approaches and inherent variability, could substantially impact the reliability and precision of ecological and evolutionary studies reliant on body size data across extensive species datasets. This study examines the variation in reported maximum body sizes across 69,570 individual measurements of maximum size, ranging from <0.2 μm to >45 m, for 27,271 species of marine metazoans. The research aims to investigate how reported maximum size variations within species relate to organism size, taxonomy, habitat, and the presence of skeletal structures. The investigation particularly focuses on understanding why discrepancies in maximum size estimates arise and their potential implications for broader ecological and evolutionary studies relying on body size data. Variation in reported maximum sizes is zero for 38% of species, and low for most species, although it exceeds two orders of magnitude for some species. The likelihood of zero variation in maximum size decreased with more measurements and increased in larger species, though this varied across phyla and habitats. Pelagic organisms consistently had low maximum size range values, while small species with unspecified habitats had the highest variation. Variations in maximum size within a species were notably smaller than interspecific variation at higher taxonomic levels. Significant variation in maximum size estimates exists within marine species, and partially explained by organism size, taxonomic group, and habitat. Variation in maximum size could be reduced by standardized measurement protocols and improved meta-data. Despite the variation, egregious errors in published maximum size measurements are rare, and their impact on comparative macroecological and macroevolutionary research is likely minimal.
PubMed: 38840585
DOI: 10.1002/ece3.11506 -
BMC Public Health Jun 2024The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of...
The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC's NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.
Topics: Humans; Disease Outbreaks; Africa, Eastern; Genomics; High-Throughput Nucleotide Sequencing; Drug Resistance, Bacterial; Bacteria; Genome, Bacterial; East African People
PubMed: 38840103
DOI: 10.1186/s12889-024-18990-0 -
Scientific Data Jun 2024The Individual Brain Charting (IBC) is a multi-task functional Magnetic Resonance Imaging dataset acquired at high spatial-resolution and dedicated to the cognitive...
The Individual Brain Charting (IBC) is a multi-task functional Magnetic Resonance Imaging dataset acquired at high spatial-resolution and dedicated to the cognitive mapping of the human brain. It consists in the deep phenotyping of twelve individuals, covering a broad range of psychological domains suitable for functional-atlasing applications. Here, we present the inclusion of task data from both naturalistic stimuli and trial-based designs, to uncover structures of brain activation. We rely on the Fast Shared Response Model (FastSRM) to provide a data-driven solution for modelling naturalistic stimuli, typically containing many features. We show that data from left-out runs can be reconstructed using FastSRM, enabling the extraction of networks from the visual, auditory and language systems. We also present the topographic organization of the visual system through retinotopy. In total, six new tasks were added to IBC, wherein four trial-based retinotopic tasks contributed with a mapping of the visual field to the cortex. IBC is open access: source plus derivatives imaging data and meta-data are available in public repositories.
Topics: Humans; Brain; Brain Mapping; Magnetic Resonance Imaging; Motion Pictures; Visual Cortex
PubMed: 38839770
DOI: 10.1038/s41597-024-03390-1 -
Folia Microbiologica Jun 2024Recurrent acute otitis media (rAOM) poses a significant challenge in children aged 1 to 6 years, characterized by frequent and treatment-resistant ear infections. While...
Recurrent acute otitis media (rAOM) poses a significant challenge in children aged 1 to 6 years, characterized by frequent and treatment-resistant ear infections. While existing studies predominantly focus on alterations in the nasopharyngeal microbiome associated with rAOM, our research explores the understudied association with the gut microbiome. In this cross-sectional observational prospective study, we enrolled 35 children aged 1 to 6 years during the 2021/2022 cold season. The test group comprised children with rAOM (n = 16), and the control group consisted of generally healthy children (n = 19). Samples (stool and nasopharyngeal swabs) were collected in late spring to ensure an antibiotic-free period. Detailed metadata was gathered through a questionnaire examining factors potentially influencing microbiota. Microbiota composition was assessed through amplicon sequencing of the V3-V4 region of the 16S rRNA gene. Our findings revealed limited alterations in gut microbiota composition among children with rAOM compared to healthy controls. Six bacterial taxa (Veillonella, Lachnospiraceae, Ruminococcaceae, Lachnospiraceae, Bacteroides and Blautia) were differentially represented with weak statistical significance. However, several bacterial taxa displayed correlations with multiple consecutive infections, with Turicibacter showing the most significant association. Additionally, day care centre attendance emerged as a potent gut microbiota modifier, independent of rAOM. Although our study identified limited differences in gut microbiota composition between children with rAOM and healthy controls, the observed correlations between the number of infections and specific bacterial taxa suggest a potential link between rAOM and the gut microbiota, warranting further investigation.
PubMed: 38837014
DOI: 10.1007/s12223-024-01174-z -
Microbial Genomics Jun 2024is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic...
is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of clinical isolates. To better understand the metabolic repertoire of in infection, we deeply profiled a representative set from a library of 971 clinical isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multilocus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective pangenome metabolic repertoire. Characterizing this rich set of clinical isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.
Topics: Pseudomonas aeruginosa; Humans; Phenotype; Pseudomonas Infections; Genotype; Metabolic Networks and Pathways; Whole Genome Sequencing; Multilocus Sequence Typing; Genome, Bacterial; Genetic Variation
PubMed: 38836744
DOI: 10.1099/mgen.0.001259 -
Scientific Data Jun 2024Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant...
Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage.
Topics: Humans; Metadata; Cells
PubMed: 38834597
DOI: 10.1038/s41597-024-03416-8