Nevin Manimala

Bioinformatics. 2025 Nov 9:btaf605. doi: 10.1093/bioinformatics/btaf605. Online ahead of print.

ABSTRACT

SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

AVAILABILITY AND IMPLEMENTATION: HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.

PMID:41206936 | DOI:10.1093/bioinformatics/btaf605

Bioinformatics. 2025 Nov 9:btaf616. doi: 10.1093/bioinformatics/btaf616. Online ahead of print.

ABSTRACT

MOTIVATION: The most informative genome-wide association studies (GWAS) are meta-analyses that have combined multiple studies to increase the GWAS sample size. Statistical fine-mapping is a key downstream analysis of GWAS to jointly evaluate the probability of causality of all variants in a genomic region of interest. Current fine-mapping methods are miscalibrated in the meta-analysis setting due to variation in sample size across the variants.

RESULTS: We introduce FINEMAP-miss, a new fine-mapping method that extends the FINEMAP model to account for variant-specific missingness. We show that FINEMAP-miss is well-calibrated in meta-analysis simulations where the standard fine-mapping fails. Compared to the summary statistics imputation approach, FINEMAP-miss provides clear improvement when the causal variants have low imputation information or when the sample size or complexity of the meta-analysis setting increase. We successfully apply FINEMAP-miss on a breast cancer GWAS meta-analysis where neither the standard fine-mapping nor the summary statistics imputation are applicable.

AVAILABILITY: An open source implementation of FINEMAP-miss as an R package (“finemapmiss”) is available at https://github.com/JoonasKartau/finemapmiss. The archived version of FINEMAP-miss used for this publication can be found on Zenodo at https://doi.org/10.5281/zenodo.17492622.

SUPPLEMENTARY INFORMATION: Supplementary Data is available at the journal’s web site.

PMID:41206934 | DOI:10.1093/bioinformatics/btaf616

J Natl Cancer Inst. 2025 Nov 9:djaf326. doi: 10.1093/jnci/djaf326. Online ahead of print.

ABSTRACT

INTRODUCTION: Although myeloma represents a key success story in oncology, some drugs have failed to meet primary endpoints in randomized controlled trials (RCTs), despite promising early-phase activity. This analysis aimed to understand factors that increase the likelihood of meeting primary endpoints in myeloma RCTs.

METHODS: Myeloma RCTs published through October 2023 were identified using MEDLINE, PubMed, Embase, and the Cochrane Registry. Studies were classified as head-to-head (substituting one regimen for another) or add-on (adding one drug to existing regimen). Trials were considered successful if they achieved statistical significance for primary outcomes. Logistic regression identified predictors of meeting trial endpoints.

RESULTS: A total of 145 comparisons from 123 RCTs were included. Only two factors were independently associated with meeting primary endpoints in multivariate analysis. Higher median participant age was associated with lower odds of meeting the primary endpoint (OR per one-year increase, 0.90, 95% CI: 0.83-0.98). Overall survival (OS) was the primary endpoint in 20/145 comparisons, of which 3/20 met their endpoint. Selecting OS as primary endpoint was associated with reduced likelihood of success compared with progression-free survival by 94% (OR: 0.06, 95% CI: 0.01-0.23). Head-to-head design was not associated with lower success rates than add-on design (OR: 0.59; 95% CI: 0.22-1.62).

CONCLUSION: Two key factors predicted higher likelihood of meeting endpoints: younger patient age and primary endpoints other than overall survival. Although head-to-head design is considered riskier, it was not associated with decreased success. This analysis aims to better inform clinicians, industry, and regulators in myeloma drug development.

PMID:41206930 | DOI:10.1093/jnci/djaf326

Oncologist. 2025 Nov 9:oyaf375. doi: 10.1093/oncolo/oyaf375. Online ahead of print.

ABSTRACT

BACKGROUND: Blinded independent central review (BICR) mitigates assessment bias in oncology trials but imposes significant operational burdens. Its value in hematologic malignancies-where multimodal response criteria reduce reliance on subjective imaging assessments compared to solid tumors-remains unestablished. This meta-analysis evaluates BICR-investigator concordance specifically in hematology trials.

METHODS: We systematically identified Phase II/III hematology trials (2014-2024) reporting progression-free survival (PFS) and/or objective response rate (ORR) assessments by both investigators and BICR from PubMed. Agreement was quantified using Pearson/Spearman correlation, pooled hazard ratio ratio (HRR, HRINV/HRBICR) for PFS, and odds ratio ratio for ORR (OddsRR, ORINV/ORBICR). We also analyzed the odds ratio for ORR for single arms (OddsINV/OddsBICR). Subgroup analyses assessed the impact of masking, cancer type based on imaging dependence, and sample size.

RESULTS: Data from 70 studies (37 PFS comparisons; 23 ORR comparisons; 29 single-arm ORR) were analyzed. For PFS, the pooled HRR was 0.96 (95% CI: 0.89,1.03), with perfect agreement in statistical significance (Cohen’s kappa = 1). For ORR, the pooled OddsRR was 0.99 (95% CI: 0.85, 1.14). Single-arm trials showed minimal odds difference between assessors (OR = 1.02, 95% CI: 0.90, 1.17). Subgroup analyses (masking, cancer type, sample size) consistently showed high agreement.

CONCLUSIONS: Investigator and BICR assessments demonstrated substantial concordance in hematology trials. The common applications of BICR in registration trials provide minimal added value for primary endpoint validation in this setting. We recommend prioritizing investigator training and standardized criteria to optimize resource allocation.

PMID:41206920 | DOI:10.1093/oncolo/oyaf375

J Am Med Inform Assoc. 2025 Nov 9:ocaf193. doi: 10.1093/jamia/ocaf193. Online ahead of print.

ABSTRACT

OBJECTIVE: Stigmatizing language (SL) in Electronic Health Records (EHRs) can perpetuate biases and negatively impact patient care. This study introduces a novel method for automatically detecting such language to improve healthcare documentation practices.

MATERIALS AND METHODS: We developed a multi-stage transfer learning framework integrating semantic, syntactic, and task adaptation using three datasets: hate speech, clinical phenotypes, and stigmatizing language. Experiments were conducted on stigmatizing language dataset which consists of 4,129 de-identified EHR notes (72.7% stigmatizing, 27.3% non-stigmatizing), split 80/20 for training and testing. Longformer, BERT, and ClinicalBERT models were evaluated, and model performance was assessed on 35 randomized subsets of the test set (each comprising 70% of test data). The Wilcoxon-Mann-Whitney test was used to evaluate statistical significance, with Bonferroni correction applied to control for multiple hypothesis testing. Baseline models included zero-shot and few-shot GPT-4o, Support Vector Machine, Random Forest, Logistic Regression, and Multinomial Naive Bayes.

RESULTS: The proposed framework achieved the highest accuracy, with fully adapted Longformer reaching 89.83%. Performance improvements remained statistically significant after Bonferroni correction compared to all baselines (p < .05). The framework demonstrated robust gains across different stigmatizing language types.

DISCUSSION: This study underscores the value of domain-adaptive NLP for detecting stigmatizing language in EHRs. The multi-stage transfer learning framework effectively captures subtle biases often missed by conventional models, enabling more objective and respectful clinical documentation.

CONCLUSION: This framework offers a statistically validated, high-performing framework for detecting stigmatizing language in EHRs, supporting responsible AI and promoting equity in clinical care.

PMID:41206907 | DOI:10.1093/jamia/ocaf193

JAMA. 2025 Nov 9. doi: 10.1001/jama.2025.21077. Online ahead of print.

ABSTRACT

IMPORTANCE: Risk stratification strategies in primary prevention of coronary events lack precision.

OBJECTIVE: To determine whether prediction of first coronary events is improved by adding information on coronary atherosclerosis from coronary computed tomography angiography (CCTA) to a model using the pooled cohort equation (PCE) risk score tool and the coronary artery calcification score (CACS).

DESIGN, SETTING, AND PARTICIPANTS: Observational cohort study including individuals aged 50 to 64 years randomly recruited from the general population and examined at 6 university hospitals in Sweden from 2013 to 2018, with a median follow-up of 7.8 years. A sample of 30 154 individuals underwent cardiopulmonary imaging, physical examinations, routine laboratory tests, questionnaires, and/or functional tests. This study included 24 791 individuals without previous cardiovascular disease for whom high-quality CCTA images were available. Events were followed up via registers until September 2024.

EXPOSURES: The information used from the CCTA images was the extent of coronary atherosclerosis (segment involvement score), presence of noncalcified atherosclerosis, and presence of coronary obstructive disease (stenosis ≥50%).

MAIN OUTCOMES AND MEASURES: The outcome was a composite of first occurrence of nonfatal myocardial infarction or death from coronary heart disease.

RESULTS: During follow-up, 304 coronary events occurred. Segment involvement scores of 3 to 4 and greater than 4 and presence of noncalcified atherosclerosis were associated with hazard ratios of 2.71 (95% CI, 1.34-5.44), 5.27 (95% CI, 2.50-11.07), and 1.66 (95% CI, 1.23-2.22), respectively. In a model based on the PCE and CACS, CCTA-derived data improved risk discrimination (C statistic improved from 0.764 to 0.779; P = .004) and risk reclassification (net reclassification improvement of 0.133 [95% CI, 0.031-0.165]), conferred a net correct upward reclassification of 14.2% in those with events and incorrectly classified 1.6% of participants not experiencing an event into a higher-risk category. Because of the low event rate in the cohort, reclassification mainly occurred in the group classified as at low risk (<5%) according to the PCE.

CONCLUSIONS AND RELEVANCE: Information on coronary atherosclerosis from CCTA modestly improved risk prediction beyond traditional risk factors and CACS in identifying individuals at risk of coronary events and in need of primary prevention.

PMID:41206900 | DOI:10.1001/jama.2025.21077

Int J Speech Lang Pathol. 2025 Nov 9:1-20. doi: 10.1080/17549507.2025.2582522. Online ahead of print.

ABSTRACT

PURPOSE: This systematic review examined the effectiveness and instructional characteristics of morphological awareness interventions for children aged 3 to 12 diagnosed with Developmental Language Disorder, in English- or Spanish-speaking contexts. It aimed to determine the outcomes of MA interventions and identify the instructional components most supported by evidence.

METHOD: Following PRISMA guidelines, a systematic search was conducted across five major databases (PsycINFO, PubMed, SCOPUS, Web of Science, and ERIC) between September and November 2024. Ten studies published between 1980 and 2024 met the inclusion criteria. The review synthesised results concerning both intervention outcomes and instructional features, using Frizelle and McKean’s (2022) Dose Form Framework.

RESULT: Only four studies reported statistically significant improvements in morphological awareness, with large effect sizes, indicating potential benefits of morphological awareness interventions for children with Developmental Language Disorder. However, many studies lacked rigorous methodology or failed to disaggregate outcomes for children with Developmental Language Disorder, limiting generalizability. Interventions with the strongest evidence base were those using explicit, clinician-directed instruction targeting affix identification and word construction.

CONCLUSION: The findings suggest promising but limited evidence supporting the effectiveness of morphological awareness interventions for children with Developmental Language Disorder. Further high-quality, controlled studies with detailed statistical reporting and consistent diagnostic labelling are needed. Structured, explicit instruction appears to be a critical feature of effective programs and should be prioritised in clinical and educational practice.

PMID:41206861 | DOI:10.1080/17549507.2025.2582522

Environ Geochem Health. 2025 Nov 9;47(12):557. doi: 10.1007/s10653-025-02855-5.

ABSTRACT

This study investigates how seasonal variability influences soil metal contamination, spatial distribution, sources, and associated health and ecological risks in a Pb-Zn mining district of southeastern Nigeria. Using ICP-MS analysis, multivariate statistics, and geospatial mapping, we examined Cu, Zn, Ni, Mn, Co, Fe, Cd, Cr, and Pb across dry and wet seasons. Mean metal levels across both seasons followed the order: Fe˃Pb˃Mn˃Zn˃Cr˃Cu˃Ni˃Co˃Cd. Multivariate evaluations predicted anthropogenic sources for Pb, Cu, Cd, and Zn, and geogenic sources for Fe, Co, and Ni. While the mean concentrations of Ni and Co aligned with regulatory and background thresholds, those of Cu, Fe, Cd, Cr, and Pb exceeded them. Non-carcinogenic and carcinogenic health risks were recorded for Cr and Pb across both seasons and exposure groups. Geospatial mappings recorded minimal seasonal variations for Zn hotspots, but high variability for Fe. This study highlights how seasonal variations affect metal pollution patterns in areas affected by artisanal mining. The findings help improve risk assessments, support efforts to protect public health, and guide policies that promote safer and more sustainable mining practices globally.

PMID:41206838 | DOI:10.1007/s10653-025-02855-5

Eur J Pediatr. 2025 Nov 9;184(12):741. doi: 10.1007/s00431-025-06594-8.

ABSTRACT

Deferred cord clamping (DCC) enhances placental transfusion, yet its feasibility in extremely preterm infants requiring resuscitation remains uncertain. Intact cord resuscitation (ICR) may allow simultaneous placental transfusion and stabilization. This study evaluated the feasibility and short-term outcomes of ICR in infants born at 23^0/7 to 25^6/7 weeks of gestation. This single-center case-series study compared two consecutive two-year periods before and after the introduction of ICR (September 2023) in extremely preterm infants requiring delivery room resuscitation. Infants born during the earlier period underwent early cord clamping (ECC). Specialized trolleys were not available; instead, stabilization was performed in a sterile polyethylene bag placed on the mother’s abdomen. The primary outcome was survival at day 7. Secondary outcomes included admission vital signs, laboratory parameters, early morbidities, and transfusion requirements. Twenty-two infants were analyzed (12 ECC, 10 ICR). Baseline characteristics were similar. Apgar scores at 5 and 10 min were higher in ICR (p = 0.02 and p < 0.001). On neonatal intensive care unit admission, mean arterial pressure and hemoglobin levels were significantly higher in ICR (respectively, p < 0.001 and 0.04). Red blood cell transfusion and inotrope use were more frequent in ECC, though not statistically significant. The incidence of any grade intraventricular hemorrhage (IVH) and grade ≥ 2 IVH did not differ. Early mortality occurred in 6 ECC infants (50%), but in none of the ICR infants (p = 0.04).

CONCLUSION: In this case-series, ICR was feasible without specialized equipment in extremely preterm infants and was not associated with adverse outcomes. The procedure appeared to support early hemodynamic stabilization and short-term survival, providing preliminary observations that warrant confirmation in larger prospective studies.

WHAT IS KNOWN: • ICR was shown to be feasible and safe in extremely preterm infants born at 23-25 weeks of gestation, even without specialized resuscitation trolleys. • Compared with early cord clamping, ICR was associated with higher Apgar scores, improved hemodynamic stability, higher hemoglobin levels, and enhanced early survival.

WHAT IS NEW: • Deferred cord clamping (DCC) increases blood volume, hemoglobin, reduces transfusion needs, and lowers intraventricular hemorrhage (IVH) risk in neonates. • Intact cord resuscitation (ICR) has been proposed to combine placental transfusion with timely stabilization, though its feasibility in this high-risk group is still debated.

PMID:41206833 | DOI:10.1007/s00431-025-06594-8

AIDS Behav. 2025 Nov 9. doi: 10.1007/s10461-025-04916-3. Online ahead of print.

ABSTRACT

The 2022 mpox outbreak significantly impacted gay, bisexual, and other men who have sex with men (MSM) in the U.S., with Los Angeles representing nearly 40% of California cases. Limited data exist on how MSM living with and without HIV navigated the outbreak and their decision-making regarding vaccination. Between November 2023 and March 2024, we conducted a mixed-methods study with 21 cisgender MSM in Los Angeles who completed a semi-structured interview and quantitative survey. Recruitment prioritized diversity in mpox vaccination history, HIV status, race, and ethnicity. Interviews were recorded, transcribed, and analyzed using thematic content analysis; surveys were analyzed using descriptive statistics. Participants had a mean age of 40 years; 33% were living with HIV; 48% identified as Black/African American or mixed-race, 38% White; nearly half identified as Hispanic/Latinx (48%); 57% reported receiving at least one mpox vaccine dose, and 38% reported two doses for maximum protection. Knowledge about mpox transmission, prevention, treatment, and outcomes varied. Participants self-reported hearing that mpox could be transmitted by skin-skin contact (76%), kissing (67%), engaging in oral sex (67%), and contact with semen (33%); 62% had heard there was a treatment for mpox, 14% thought that mpox was not curable, and 48% believed that mpox was likely to cause death. Psychosocial impacts were prominent at both individual and community levels, including fear and distress. Mpox vaccination was motivated by fear and a desire for protection, facilitated by accessible venues and peer influence. Barriers included initially poor availability of vaccine and the specific eligibility criteria requirements for vaccination early on in the epidemic. Logistical challenges, such as long wait times (> 2 h), work hours, lack of transportation, mistrust in research, and confusing initial rollout also presented unique barriers. LGBTQ+ community-based organizations and peer networks were the primary trusted source of mpox-related information. Most initially adopted risk reduction behaviors but generally viewed the mpox response more favorably than COVID-19 due to time differences in vaccine availability. Post-vaccination, many resumed pre-outbreak activities, feeling more prepared for future outbreaks despite some lingering concerns. Findings underscore varied mpox knowledge and significant psychosocial impacts, reminiscent of the early HIV epidemic. Key facilitators and barriers to vaccination highlight the critical reliance on LGBTQ+ community-based organizations and peer networks for sources of trustworthy information. Providing referrals to mental health counseling and other forms of support during vaccination is recommended.

PMID:41206825 | DOI:10.1007/s10461-025-04916-3