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At least 19 recordsLinked to original sources

PubMed2025

Quantitative Outcomes for Shared Assessment and Management in Forensic Mental Health: A Meta-Analysis and Systematic Review.

Despite leading models of mental health care encouraging user involvement, users in forensic mental health (FMH) report poor involvement given the difficulty in reconciling shared approaches with risk-averse and legally mandated settings. While previous research has demonstrated qualitative benefits to shared approaches in FMH and has led to a proliferation of self-rated assessment tools, there remains to quantify agreement on self-rated tools and to clarify the impact of shared approaches on care. This meta-analysis examines (1) the correlation between clinician and user ratings, (2) the predictive validity of self-ratings for violence, and (3) the effects of shared risk management on violence and restriction in FMH. Five databases were searched from inception to April 2024, selecting for adult FMH inpatients, shared risk assessment, needs assessment or violence management as interventions, and quantitative outcomes (correlation, agreement, predictive validity, and effect on violence or restriction rates). Fifteen quantitative evaluations were retained. One of three planned meta-analyses could be conducted, with seven records providing paired clinician-user t-tests. Eleven more records provided clinical recommendations on operationalizing shared approaches. Random-effects meta-analysis showed a significant and large paired standard difference of .95 (95% CI = [.49,1.42]) across tools, with significant differences in DUNDRUM-3, DUNDRUM-4, and CANFOR sub-models. While acknowledging between-study heterogeneity, results substantiate quantitative differences where clinicians generally rate more needs and lesser progress than users across tools, showing that self-ratings can and should be used to broach collaborative discussions on needs and progress during FMH treatment. There remains an evidence gap for quantitative benefits in care outcomes and a need to standardize agreement measures for future comparisons and clinical sub-group analyses.

Humans↗

PubMed2026

Utility of hearing aid use on neurocognitive functions and auditory processing: A systematic review.

PURPOSE: Hearing loss not only affects the peripheral auditory system but also leads to changes in central auditory pathways and neurocognitive skills. The use of hearing aids has shown potential benefits in mitigating the adverse effects of hearing loss. Earlier literature showed various studies assessing the impact of hearing aid use on cognitive functions and auditory processing, a comprehensive review of the existing literature is warranted. Existing literature showed heterogeneous outcomes among studies investigated the effect of Hearing aid use in combating the adverse effects of hearing loss on neurocognitive functions and auditory processing. METHOD: Databases including PubMed, SciELO, Cochrane Library, PsycINFO, Web of Science, and Index Copernicus were searched (2005-2025) using English keywords on hearing aid effects on neurocognition and auditory processing in individuals with hearing loss. Studies on effect of hearing aid use on neurocognition and auditory processing were included, while those involving cochlear implant users or other neurological disorders unrelated to hearing loss were excluded. Titles, authors and publication years were examined, and duplicates were removed. RESULTS: Total of 61 research papers were found on specific area and were included in the present review. Findings of these 61 articles have been analysed and are reported in this article. The outcome of the present study showed usefulness of hearing aid use on neurocognitive functions and auditory processing. CONCLUSION: The present literature review emphasized the importance of early rehabilitation through hearing aid use to alleviate the adverse effects of hearing loss on neurocognitive function and auditory processing.

Humans↗

PubMed2026

Open Dialogue versus treatment as usual for adults presenting in crisis to mental health services in England (the ODDESSI Trial): a multisite cluster-randomised trial.

BACKGROUND: Open Dialogue is a person-centred, transdiagnostic model of mental health care that emphasises continuity, therapeutic relationships, and collaboration with the service user's social network. Open Dialogue is a service-wide approach to care involving network meetings with the service user, members of their social network, and usually two practitioners who support the network throughout the duration of care. In this cluster-randomised trial, we aimed to evaluate the clinical effectiveness of Open Dialogue versus treatment as usual for adults presenting in crisis to community mental health services in England. METHODS: This multicentre, parallel two-arm, cluster-randomised, controlled superiority trial was conducted in mental health services in five National Health Service trusts in London and the South of England. Clusters were defined at the level of primary care practices within service catchment areas. Participants were adults aged 18 years or older presenting in crisis to mental health services and registered with a practice within trial clusters. Randomisation was done at the cluster level (1:1), stratified by catchment area, and balanced on average general practice (GP) list size and Index of Multiple Deprivation (2015). The chief investigator, senior statistician, and assessors of the primary outcome were masked in the study. Participants either received Open Dialogue or treatment as usual, which refers to the functional team model currently implemented throughout English mental health services. The primary outcome was time (days) to first relapse following initial recovery from the index crisis censored at the end of the 2-year follow-up period. Participant-reported secondary outcomes were EuroQol Visual Analogue Scale, Social Provisions Scale, Lubben Social Network Scale, Questionnaire about the Process of Recovery, and the Client Satisfaction Questionnaire, measured at five timepoints over 2 years, and clinical measures were extracted from electronic health records. People with relevant lived experience were involved in the design and execution of the study. Fidelity to the model of care in Open Dialogue and treatment as usual, and adherence to the delivery of Open Dialogue, were measured prior to each site starting participant recruitment, then every 6 months thereafter until the final participant follow-up in that site. The trial was retrospectively registered (ISRCTN52653325) and is complete. FINDINGS: 185 general practices associated with six mental health Trusts across England were identified for screening. 105 practices were excluded, and 80 were included in cluster formation, forming 32 clusters that were randomly assigned (16 to treatment as usual and 16 to the Open Dialogue intervention). One mental health trust (two clusters) withdrew, resulting in five mental health trusts (30 clusters) participating in the trial. Between June 25, 2019, and Dec 9, 2021, 494 participants (266 [54%] female gender, 221 [45%] male gender, 341 [69%] White British) with a mean age of 38·1 years (SD 13·4) provided consent for study inclusion (223 in the treatment as usual group and 271 in the Open Dialogue group). Of these, 174 (78%) in the treatment as usual group and 225 (83%) in the Open Dialogue group recovered and had data enabling relapse determination; there was no significant difference between groups on the primary outcome of time to relapse following initial recovery (marginal hazard ratio 0·95 [95% CI 0·67-1·32]). For secondary outcomes, Open Dialogue was associated with significantly lower probabilities of psychiatric inpatient admission and re-referral to crisis care or secondary mental health services, and with improvements in self-rated recovery, health-related quality of life, and satisfaction with services. There were no significant differences in social network quality or size. There were 386 serious adverse events (281 in the treatment as usual group and 105 in the Open Dialogue group); 376 (97%) were deemed to be unrelated to the intervention. INTERPRETATION: Open Dialogue did not reduce time to first relapse compared with treatment as usual, the primary outcome, but it reduced acute inpatient bed use, improved service user reported outcomes and experience, and there were no significant safety concerns. Further investigation is required to determine whether Open Dialogue can enhance the effectiveness and acceptability of crisis care and continuing care in community mental health services. FUNDING: National Institute for Health Research.

Humans↗

PubMed2026

Strategies to improve recruitment to randomised trials.

BACKGROUND: Recruiting participants to randomised controlled trials (RCTs) is challenging. Identifying effective recruitment strategies would benefit health research: poor recruitment leads to underpowered trials, reducing the reliability of findings and increasing the risk of wasted resources, ethical concerns, and trial failure. Evidence to inform recruitment strategies is increasingly generated through Studies Within A Trial (SWATs), which are methodological studies embedded within host RCTs. This is an update of a review last published in 2018. OBJECTIVES: Primary: to quantify the effects of strategies to improve recruitment of participants to RCTs. Secondary: to evaluate recruitment strategies' cost-effectiveness and impact on retention, and the equity, diversity, and inclusion (EDI) characteristics of recruited participants. SEARCH METHODS: We used MEDLINE, Embase, and six other databases to identify the studies included in the review. We also sought unpublished recruitment SWATs through social media and targeted email dissemination to trial methodology networks. The latest search date was 16 February 2023. SELECTION CRITERIA: We included randomised SWATs evaluating trial recruitment strategies embedded in healthcare and non-healthcare trials. We excluded quasi-randomised, hypothetical, questionnaire-only, retention-only, or clinician incentive studies. DATA COLLECTION AND ANALYSIS: Primary outcome: proportion of eligible participants or centres recruited. SECONDARY OUTCOMES: cost-effectiveness, retention rates, and EDI characteristics of included participants. We conducted random-effects meta-analysis for strategies evaluated in at least two studies; otherwise, we synthesised results narratively. We reported effects as risk differences (RDs) with 95% confidence intervals (CIs), and assessed between-trial heterogeneity. We used GRADE to assess the certainty of evidence for the primary outcome. We expressed cost-effectiveness as the incremental cost per additional participant recruited in pounds sterling (GBP). MAIN RESULTS: We identified 91 eligible studies (53 new to this update), providing 94 comparisons and involving at least 176,747 participants. Eighty-one studies involved strategies aimed at trial participants, while 10 evaluated strategies aimed at recruiters. All were healthcare studies. We found 65 recruitment strategies; 49 were evaluated in a single study. Only five strategies were supported by high-certainty evidence according to GRADE criteria, and we focus on these strategies in the summary below. Open-label trials versus blinded, placebo trials. Open-label trials recruited more participants than blinded trials (RD 10%, 95% CI 8% to 12%; 3 studies, 9004 participants), corresponding to approximately 10 additional participants per 100 approached. The studies involved mostly women in the UK and Estonia. No cost or retention data were reported. Telephone reminder versus no telephone reminder. Telephone reminders to people who did not respond to an initial postal invitation boosted recruitment by 6% (95% CI 3% to 9%; 2 studies, 1450 participants), in trials with low underlying recruitment (we are less certain for trials with over 10% recruitment). The studies involved people with a mean age of 58 years in Canada and Norway. No cost or retention data were reported. Recruitment primer letter versus no letter. Pre-recruitment letters and leaflets designed to encourage participation made little or no difference to recruitment (absolute improvement 1%, 95% CI -1% to 2%; 2 studies, 5376 participants), and were associated with increased costs compared to not sending a primer (incremental cost: GBP 2.08). The studies involved mostly older white people in the UK and Ireland. Multimedia information via a digital link/QR code plus paper participant information leaflet (PIL) versus paper PIL alone. This made little or no difference to recruitment (absolute improvement 0%, 95% CI -1% to 1%; 7 studies, 11,612 participants) and retention (absolute improvement 0%, 95% CI -2% to 3%; 5 studies, 7403 participants), and increased costs compared to not including multimedia information (incremental cost: GBP 0.78). The studies involved people in the UK. Optimised, user-tested PIL versus standard PIL. Optimising participant information leaflets (e.g. through user-testing the leaflet with the target population to shape its content, format, and appearance) made little or no difference to recruitment: absolute improvement was 0% (95% CI 0% to 1%; 6 studies, 27,805 participants). The studies involved people in the UK. Only one study reported EDI data; participants were mostly older women. No cost or retention data were reported. We had moderate-certainty evidence for 13 other strategies; confidence was often reduced because the results came from single studies. Seven strategies involved changes to how potential participants received information; four involved changes to trial conduct; one targeted the recruiter or recruitment site; and one tested non-monetary incentives. We had much less confidence in the other 47 comparisons because the studies had design flaws, were single studies, or had very uncertain results. Costs were reported in only 17 of 91 studies. Strategy impact on retention was reported in 15 studies. All but one study (99%) were from high-income countries. The most reported demographics were age (49 studies), sex (32 studies), gender (27 studies), and education level (16 studies). AUTHORS' CONCLUSIONS: The evidence on strategies to improve trial recruitment remains broad but lacks depth. Of 65 strategies evaluated, only five were supported by high-certainty evidence. Open-label trial designs and telephone reminders to non-responders increased recruitment, while optimised participant information leaflets, recruitment primer letters, and multimedia information provided alongside a paper participant information leaflet had little or no effect. Reporting of participant characteristics was poor, limiting assessment of equity, diversity, and inclusion across most studies. Evidence is heavily skewed toward high-income countries. Future research must prioritise evaluations in low-to-middle-income settings and consistently report cost, retention, and EDI outcomes. We strongly urge the methodology research community to strengthen the evidence base by prioritising replications of existing strategies over the development and testing of new ones. FUNDING: National Institute for Health and Care Research (Advanced Fellowship, Adwoa Parker, reference:NIHR302256). Health Research Board, Republic of Ireland, Evidence Synthesis Ireland (grant ESI-2021-001) REGISTRATION: This review updates an earlier Cochrane review, which was first published in 2002 and subsequently updated in 2007, 2010, and 2018. Previous versions of the review and their protocols are available at: https://doi.org/10.1002/14651858.MR000013.pub2 https://doi.org/10.1002/14651858.MR000013.pub3 https://doi.org/10.1002/14651858.MR000013.pub4 https://doi.org/10.1002/14651858.MR000013.pub5 https://doi.org/10.1002/14651858.MR000013.pub6.

Randomized Controlled Trials as Topic↗

PubMed2026

Invasive Wickerhamomyces anomalus Infections among Injecting Drug Users, France, 2012-20241.

Wickerhamomyces anomalus is a yeast rarely involved in human invasive fungal diseases (IFD). We retrospectively analyzed 44 episodes of W. anomalus IFD in France during 2012-2024. Injecting drug use (IDU) was the main risk factor among 26/35 (74.3%) incident cases. Most infections were community acquired; overall 3-month mortality rate was 1/30 (3.3%). Short tandem repeat (STR) genotyping and whole-genome sequencing analyses revealed substantial genetic diversity among isolates. However, 1 STR genotype was shared by 2 IDU patients, suggesting common exposure. In addition, 1 isolate obtained from a cotton filter used for drug preparation was identical by STR genotyping to the bloodstream isolate from the same patient, indicating direct inoculation via contaminated material or poor injection practices. Our findings highlight the increased risk for W. anomalus IFD among IDU patients and emphasize the importance of targeted preventive measures within that population.

Humans↗

PubMed2025

Generating correlated data for omics simulation.

Simulation of realistic omics data is a key input for benchmarking studies that help users obtain optimal computational pipelines. Omics data involves large numbers of measured features on each sample and these measures are generally correlated with each other. However, simulation too often ignores these correlations, perhaps due to computational and statistical hurdles of doing so. To alleviate this, we describe three approaches for generating omics-scale data with correlated measures which mimic real datasets. These approaches are all based on a Gaussian copula approach with a covariance matrix that decomposes into a diagonal part and a low-rank part. This decomposition allows for extremely efficient simulation, overcoming a hurdle for adoption of past methods. We use these approaches to demonstrate the importance of including correlation in two benchmarking applications. First, we show that variance of results from the popular DESeq2 method increases when dependence is included. Second, we demonstrate that CYCLOPS, a method for inferring circadian time of collection from transcriptomics, improves in performance when given gene-gene dependencies in some circumstances. We provide an R package, dependentsimr, that has efficient implementations of these methods and can generate dependent data with arbitrary marginal distributions, including discrete (binary, ordered categorical, Poisson, negative binomial), continuous (normal), or with an empirical distribution.

Computer Simulation↗

PubMed2025

CCRR: a user-friendly platform for analyzing complex chromosomal rearrangements in tumors.

SUMMARY: Complex chromosomal rearrangements in tumors involve intricate genomic alterations that significantly affect gene function and contribute to cancer development. Identifying these events is crucial for cancer research but is often challenging due to the complexity and limitations of existing tools. We developed the Complex Chromosomal Rearrangements Resolver (CCRR), a comprehensive, reproducible, and user-friendly platform for analyzing complex rearrangements in tumors. CCRR integrates multiple SV and CNV detection tools within a Docker container environment, simplifying installation and configuration. It can be easily deployed, automating the execution and merging of results, providing high-confidence consensus SV and CNV calls, allowing researchers to efficiently analyze complex chromosomal rearrangements in tumors without extensive bioinformatics expertise. CCRR also includes a web server for one-click analysis and customized visualization. AVAILABILITY AND IMPLEMENTATION: The CCRR platform is freely available at https://www.ccrr.life. Source code and executables can be accessed at https://github.com/laslk/CCRR. An archived version is available at Zenodo: https://doi.org/10.5281/zenodo.15386513.

Software↗

PubMed2025

FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics.

Venous thromboembolism (VTE) is a highly prevalent medical condition with limited therapeutic options and an incomplete understanding of its acquired and inherited subtypes. The zebrafish is a model with the benefits of external development, fecundity, optical transparency, and hemostasis that demonstrates conservation with mammals. We utilized zebrafish as a phenotypic screening tool to identify novel therapeutic options for preventing VTE. A library of FDA-approved compounds was screened for suppression of acquired (elevated estrogen) and spontaneous (protein C deficiency) thrombosis. We found that thyroid hormone, receptor tyrosine kinase (RTK) inhibitors, and proton-pump inhibitors (PPIs) effectively modulated levels of thrombosis, particularly in the estrogen-induced model. These also showed a more favorable hemostatic profile than standard therapies, suggesting alternative mechanisms. Genome editing of thyroid hormone receptor proved that thyroid hormone action is on target. A retrospective electronic health record (EHR) analysis found that thyroid-hormone prescriptions in hormonal contraceptive users correlated with a higher VTE risk, potentially limiting direct repurposing but highlighting thyroid signaling as a pathway involved in estrogen-induced thrombosis. Together, these data identify several drug classes that can be tailored to specific subtypes of VTE and help elucidate distinct pathways driving thrombosis.

FDA-approved compounds↗

PubMed2025

HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures.

SUMMARY: Transcriptomic analysis is a key tool for exploring gene expression, but the complexity of biological systems often limits its insights. In particular, the lack of intermodal or multi-layered analysis hinders the ability to fully capture key cellular functions such as metabolism from transcriptomic data alone. Here, we introduce a novel approach that informs transcriptomic data analysis with metabolic network modeling to address this. Unlike traditional methods, HUman MEtabolism Specific Signature (HUMESS) uses genome-scale metabolic modeling and flux analysis to highlight reactions and involved genes based on their metabolic significance, offering a deeper understanding of transcriptomic data. Our computational pipeline, supported by a user-friendly Rshiny application, enhances gene expression analysis by uncovering metabolic phenotypic signatures. AVAILABILITY AND IMPLEMENTATION: HUMESS is open source and available under GitLab https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess with the complete documentation available at https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess/-/wikis/Home. A zenodo archive is also available at the following DOI: https://doi.org/10.5281/zenodo.15487717. An RShiny application has been developed to facilitate the exploration and analysis of HUMESS's results. The app is available online at the following address: https://shiny-bird.univ-nantes.fr/app/shinymess but can also be installed locally, available under GitLab https://gitlab.univ-nantes.fr/pare-l/shinymess.

Humans↗

PubMed2025

LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues.

Long non-coding RNAs (lncRNAs) have emerged as significant players in maintaining the morphology and function of tissues and cells. The precise regulatory effectiveness of lncRNAs is closely associated with their spatial expression patterns across tissues and cells. Here, we propose the Cellularly-Elevated LncRNA (LncCE) resource to systematically explore cellularly-elevated (CE) lncRNAs across normal and cancer tissues at single-cell resolution. LncCE encompasses 87,946 entries of CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing datasets, involving 20 fetal normal tissues, 59 adult normal tissues, 32 adult cancer types, and 5 pediatric cancer types. Two main search options are provided via a given lncRNA name or cell type. The results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, their co-expression with protein-coding genes, and their involvement in biological functions. In particular, LncCE provides quantitative visualizations of lncRNA expression changes in cancers compared to control samples, as well as clinical associations with patients' overall survival. Together, LncCE offers an extensive, quantitative, and user-friendly interface to create a CE expression atlas for lncRNAs across normal and cancer tissues at the single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.

RNA, Long Noncoding↗

PubMed2025

Establishing a national pediatric stem cell transplantation registry in Iran addressing implementation and data quality challenges.

The Iranian Pediatric Hematopoietic Stem Cell Transplantation Registry (IPED-HSCT) was established to enhance data collection, improve patient outcomes, and support clinical research in pediatric hematopoietic stem cell transplantation. This study aimed to assess the feasibility and reliability of implementing a standardized registry in pediatric settings. A community-based participatory study was conducted across three pediatric HSCT centers in Iran. The registry development involved a multi-phase approach, including pilot testing and the implementation of a web-based system. Data were collected from fifty pediatric patients who underwent HSCT for both malignant and non-malignant conditions, with a focus on data completeness and user satisfaction. Statistical analyses were performed using IBM SPSS Statistics. The registry achieved a data completeness rate exceeding 90%, with a participant demographic of 31 males (62%) and 19 females (38%). Rigorous quality control measures and real-time validation rules were implemented, enhancing data reliability. User feedback indicated high satisfaction with the platform's design and training sessions. Challenges included variations in long-term follow-up data collection across centers. The IPED-HSCT Registry demonstrates that establishing a robust pediatric HSCT registry is feasible even in resource-limited settings. Its innovative features offer a scalable model for similar initiatives in developing countries. Future research should focus on ensuring long-term sustainability and fostering international collaborations to improve pediatric HSCT outcomes globally. not applicable.

Humans↗

PubMed2026

A Smartphone-Based Ecological Momentary Intervention for Workplace Mental Health: Randomized Controlled Trial.

BACKGROUND: Work-related stress has been widely associated with an increased risk of various mental disorders and poor mental well-being. The fast-growing mobile health services industry has provided new opportunities for workplace mental health. OBJECTIVE: This randomized controlled trial examined the effectiveness of Neurum (Neurum Limited), a smartphone-based intervention tool featuring ecological momentary assessments and interventions that aims to reduce workplace stress in real-time and real-world settings. METHODS: A total of 201 working adults were recruited for a 4-week smartphone-based intervention that incorporated cognitive behavioral therapy, mindfulness exercises, and self-regulation exercises delivered on Neurum. A simple randomization procedure was used. Participants in the intervention group were encouraged to log mood journals, complete mental health exercises, and provide user feedback whenever applicable. The key outcome was measured by the Depression, Anxiety, and Stress Scale-21 items (DASS-21; Cronbach α=0.87). RESULTS: The intervention group consisted of 102 participants, while the control group consisted of 99 participants. More participants dropped out from the intervention group (n=21) than from the control group (n=2; χ21=18.259; P<.001). The final sample consisted of 178 participants (male: 85/178, 47.8%; female: 93/178, 52.2%; mean age of 34.65, SD 7.67 y). Analyses revealed that after the 4-week intervention, the DASS-21 scores decreased in the intervention group (mean difference [MD]post-pre intervention=-14.518) but increased in the control group (MDpost-pre intervention=3.319; F1,176=59.358, P<.001; η2=0.252). This effect was largely led by stress reduction (F1,176=64.679, P<.001; for the intervention group, MDpost-pre intervention=-6.692, while for the control group, MDpost-pre intervention=2.000). On average, participants completed 6.27 (SD 9.4) exercises and provided 9.74 (SD 18.2) mood journal logs, with a daily engagement of 4.95 (SD 6.89) minutes. However, the associations between the changes in DASS-21 scores and the numbers of exercises or mood journal logs did not reach statistical significance. CONCLUSIONS: This study primarily established the effectiveness of Neurum in alleviating depression, anxiety, and stress symptoms in noninstitutionalized working adults, with a satisfactory user retention rate. Despite potential health-related culture differences, Neurum contributed to evidence-based digital health in nonclinical settings for timely needs and general accessibility as an alternative to traditional, face-to-face, and high-cost mental health services. Future directions involving a personalized approach in online mental health services were discussed.

Humans↗

PubMed2026

What influenced the use of embedded genetic expertise by non-genetic clinicians: a qualitative study using the diffusion of innovations theory and theoretical domains framework.

BACKGROUND: While employing change agents is a widely used strategy to support implementation of evidence-based practices in healthcare, the perspectives of the target users of this intervention are under-explored. Within a genomic care setting in Australia, we examined non-genetic clinicians' views of and experience with embedded genetic counsellors employed as external change agents to support the adoption of genomics in clinical care. METHODS: We conducted qualitative interviews with 16 non-genetic healthcare professionals involved in different models of genomic care, all of which employed genetic counsellors as external change agents to provide embedded genetic expertise and support in non-genetic specialty clinics. The Diffusion of Innovations (DOI) theory and the Theoretical Domains Framework (TDF) were drawn upon to guide the study design and data analysis to explore the enablers/barriers to non-genetic clinicians' use of genetic expertise and the wider implementation context of the change agent approach. RESULTS: The TDF domain 'Belief about Consequences' was a positive influence on non-genetic specialists' view of the embedded change agents, when they believed that the change agents positively impacted patient outcomes and the clinicians' knowledge and practice of using genomics in routine care. Meanwhile, major barriers were related to 'Environmental Context & Resources,' e.g. time constraints and logistic hurdles of involving change agents. Perceived attributes related to 'complexity' and 'observability' of genetic expertise were critical factors influencing the decision to put the support to actual use, impacting the diffusion of the genomic innovation. CONCLUSIONS: Our study offers insights into behavioural influences and contextual conditions shaping clinicians' decisions to interact with genetic counsellor change agents and incorporate (or not) their expertise into their routine care. Such understandings can inform future design and implementation of interventions that use change agents to support the adoption of innovations, such as genomics, effectively and sustainably.

Journal Article↗

PubMed2026

Yomix: an interactive tool for the exploration of low-dimensional embeddings in omics data.

SUMMARY: In the analysis of diverse omics data, a common and important preliminary step involves computing low-dimensional embeddings using techniques such as PCA, UMAP, t-SNE, or variational autoencoders. These embeddings provide a global overview of sample distributions and their relationships, often serving as the basis for formulating biological hypotheses. To facilitate rapid and intuitive exploration of such low-dimensional embeddings, we developed Yomix, an interactive omics-agnostic visualization and data exploration tool. Yomix enables users to flexibly define subsets of interest using a lasso selection tool, instantly compute their feature signatures, and compare their distributions. Yomix is a fast and efficient tool for interactive exploration of diverse omics datasets. AVAILABILITY AND IMPLEMENTATION: Yomix and its documentation are publicly available at https://github.com/perrin-isir/yomix.

Software↗

PubMed2024

A research synthesis of humans, animals, and environmental compartments exposed to PFAS: A systematic evidence map and bibliometric analysis of secondary literature.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are a class of widely used anthropogenic chemicals. Concerns regarding their persistence and potential adverse effects have led to multiple secondary research publications. Here, we aim to assess the resulting evidence base in the systematic secondary literature by examining research gaps, evaluating the quality of reviews, and exploring interdisciplinary connections. METHODS: This study employed a systematic evidence-mapping approach to assess the secondary literature on the biological, environmental, and medical aspects of exposure to 35 fluorinated compounds. The inclusion criteria encompassed systematic reviews published in peer-reviewed journals, pre-prints, and theses. Comprehensive searches across electronic databases and grey literature identified relevant reviews. Data extraction and synthesis involved mapping literature content and narrative descriptions. We employed a modified version of the AMSTAR2 checklist to evaluate the methodological rigour of the reviews. A bibliometric data analysis uncovered patterns and trends in the academic literature. A research protocol for this study was previously pre-registered (osf.io/2tpn8) and published (Vendl et al., Environment International 158 (2022) 106973). The database is freely accessible through the interactive and user-friendly web application of this systematic evidence map at https://hi-this-is-lorenzo.shinyapps.io/PFAS_SEM_Shiny_App/. RESULTS: Our map includes a total of 175 systematic reviews. Over the years, there has been a steady increase in the annual number of publications, with a notable surge in 2021. Most reviews focused on human exposure, whereas environmental and animal-related reviews were fewer and often lacked a rigorous systematic approach to literature search and screening. Review outcomes were predominantly associated with human health, particularly with reproductive and children's developmental health. Animal reviews primarily focused on studies conducted in controlled laboratory settings, and wildlife reviews were characterised by an over-representation of birds and fish species. Recent reviews increasingly incorporated quantitative synthesis methodologies. The methodological strengths of the reviews included detailed descriptions of study selection processes and disclosure of potential conflicts of interest. However, weaknesses were observed in the critical lack of detail in reporting methods. A bibliometric analysis revealed that the most productive authors collaborate within their own country, leading to limited and clustered international collaborations. CONCLUSIONS: In this overview of the available systematic secondary literature, we map literature content, assess reviews' methodological quality, highlight data gaps, and draw research network clusters. We aim to facilitate literature reviews, guide future research initiatives, and enhance opportunities for cross-country collaboration. Furthermore, we discuss how this systematic evidence map and its publicly available database benefit scientists, regulatory agencies, and other stakeholders by providing access to current systematic secondary literature on PFAS exposure.

Bibliometrics↗

PubMed2025

qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.

SUMMARY: Clonal hematopoiesis (CH) is a molecular biomarker associated with various adverse outcomes in both healthy individuals and those with underlying conditions, including cancer. Detecting CH usually involves genomic sequencing of individual blood samples followed by robust bioinformatics data filtering. We report an R package, qcCHIP, a bioinformatics pipeline that implements permutation-based parameter optimization to guide quality control filtering and cohort-specific CH identification. We benchmark qcCHIP under various data settings, including different sequencing depths, ranges of cohort sizes, with and without normal-tumor paired samples, and across different cancer types. We show that qcCHIP allows users to customize analysis needs to generate CH calls based on cohort-specific data characteristics. AVAILABILITY AND IMPLEMENTATION: qcCHIP R package is freely accessible at GitHub https://github.com/tenglab/qcCHIP and DOI: 10.5281/zenodo.16421861.

Humans↗

PubMed2026

DeeDeeExperiment: building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor.

SUMMARY: Modern omics experiments now involve multiple conditions and complex designs, producing an increasingly large set of differential expression and functional enrichment analysis results. However, no standardized data structure exists to store and contextualize these results together with their metadata, leaving researchers with an unmanageable and potentially non-reproducible collection of results that are difficult to navigate and/or share. Here we introduce DeeDeeExperiment, a new S4 class for managing and storing omics data analysis results, implemented within the Bioconductor ecosystem, which promotes interoperability, reproducibility and good documentation. This class extends the widely used SingleCellExperiment object by introducing dedicated slots for Differential Expression (DEA) and Functional Enrichment Analysis (FEA) results, allowing users to organize, store, and retrieve information on multiple contrasts and associated metadata within a single data object, ultimately streamlining the management and interpretation of many omics datasets. AVAILABILITY AND IMPLEMENTATION: DeeDeeExperiment is available on Bioconductor under the MIT license (https://bioconductor.org/packages/DeeDeeExperiment), with its development version also available on Github (https://github.com/imbeimainz/DeeDeeExperiment).

Software↗

PubMed2026

Functional analysis of Candida albicans protein kinases identifies Crk1 as a modulator of epithelial cell damage.

UNLABELLED: The commensal and pathogenic lifestyles of the opportunistic fungal pathogen Candida albicans require complex signaling networks regulated by protein kinases. To investigate the role of C. albicans protein kinases at the intestinal epithelial interface, we screened a comprehensive protein kinase deletion library for the capacity of the mutants to damage intestinal epithelial cells (IEC). Mutants showing altered IEC cytotoxicity relative to the wild type were further analyzed for their growth and morphology, focusing on hyper-damaging strains to identify kinases that rather prevent host cell damage. Deletion of CRK1 caused increased IEC-specific damage, despite slower growth, reduced hyphal length, and reduced adhesion as compared to wild-type cells. While tissue invasion levels and the formation of transcellular tunnels of the crk1Δ/Δ mutant were increased, the translocation capacity through the IEC barrier was reduced. Transcriptional and metabolic profiling suggested a role for Crk1 in metabolic adaptation to carbon and nitrogen sources, which was validated by showing that high glucose and amino acids are required for crk1Δ/Δ to cause increased IEC damage. Deletion of CRK1 rendered C. albicans more susceptible to cell wall and membrane stressors, but caused higher resistance to a catalase-specific and histidine biosynthesis inhibitor. This phenotypic pattern of medium- and epithelial cell type-specific cytotoxicity displayed by a C. albicans protein kinase mutant suggests that Crk1 regulates processes linked to carbon and amino acid metabolism that are relevant to interactions with intestinal epithelial cells. IMPORTANCE: Microbial signal transduction pathways regulate adaptation to changing environmental conditions and facilitate the success of many microbes during interactions with their hosts. The fungal pathobiont Candida albicans exists as a harmless commensal on mucosal surfaces of most humans but can also cause superficial and invasive infections under certain circumstances. Both lifestyles require complex signaling networks, predominantly regulated by protein kinases. The C. albicans genome was predicted to encode 108 protein kinases, yet nearly 50% remain uncharacterized. We aimed to dissect the role of C. albicans protein kinases during the transition from commensal to pathogen. We showed that multiple protein kinase genes are involved in epithelial cell damage. Particularly, the protein kinase gene Crk1 was of interest because deletion of CRK1 caused increased damage to intestinal epithelial cells under distinct conditions. Our study links Crk1 with regulation of metabolic processes relevant for commensalism and pathogenicity of C. albicans.

Candida albicans↗