Tag: nevin manimala

Bioinformatics. 2024 Dec 26;5(1):vbaf230. doi: 10.1093/bioadv/vbaf230.

ABSTRACT

SUMMARY: Several approaches have been proposed to reconstruct interactions between groups of cells or individual cells from single-cell transcriptomics data, leveraging prior information about known ligand-receptor interactions. To enhance downstream analyses, we present an end-to-end dimensionality reduction workflow, specifically tailored for single-cell cell-cell interaction data. In particular, we demonstrate that sparse dimensionality reduction can pinpoint specific ligand-receptor interactions in relation to clusters of cell pairs. For sparse dimensionality reduction, we focus on the Boosting Autoencoder approach. Overall, we provide a comprehensive workflow, including result visualization, that simplifies the analysis of interaction patterns in cell pairs. This is supported by a Jupyter notebook that can readily be adapted to different datasets.

AVAILABILITY AND IMPLEMENTATION: https://github.com/NiklasBrunn/Sparse-dimension-reduction.

PMID:41092369 | DOI:10.1093/bioadv/vbaf230

Adv Sci (Weinh). 2025 Oct 15:e10189. doi: 10.1002/advs.202510189. Online ahead of print.

ABSTRACT

Metabolite concentrations vary by age and sex, yet age- and sex-specific metabolomic risk scores and biological ageing clocks for mortality prediction remain undeveloped. Nuclear magnetic resonance (NMR)-based metabolomic profiling is conducted in 209144 UK Biobank participants (12347 deaths) and 6820 from the German ESTHER study (804 deaths). Mortality risk scores are derived using least absolute shrinkage and selection operator (LASSO)-regularized Cox regression, and metabolomics-based mortality risk clocks (MetaboMR clocks) are constructed using elastic net regression in sex- and age-stratified subgroups (50-59 and 60-69 years). Models are trained in 70% of UK Biobank and validated internally (30%) and externally in ESTHER. 68 metabolites are significantly associated with 10-year all-cause mortality in both cohorts. 20, 18, 12, and 13 metabolites improved 10-year mortality prediction in younger and older men, younger and older women. Metabolite-augmented models improved c-statistics by 0.036-0.084 across subgroups. In the external validation set, each year of age acceleration is associated with an 8% and 9% higher 10-year mortality risk for MetaboMR clock1 and clock2. Sex- and age-specific metabolomic risk scores significantly enhance 10-year mortality prediction beyond traditional models. The MetaboMR clocks may serve as measures of biological ageing and support personalized risk stratification in clinical settings.

PMID:41092367 | DOI:10.1002/advs.202510189

Int J Surg. 2025 Oct 14. doi: 10.1097/JS9.0000000000003670. Online ahead of print.

NO ABSTRACT

PMID:41092365 | DOI:10.1097/JS9.0000000000003670

J Pharm Pharmacol. 2025 Oct 15:rgaf097. doi: 10.1093/jpp/rgaf097. Online ahead of print.

ABSTRACT

INTRODUCTION: Renal ischemia-reperfusion (RIR) induces inflammation, oxidative stress, and impaired renal function, partly through reduced nitric oxide (NO) availability. Rosuvastatin enhances NO production and has reported organ-protective effects. This study examined whether rosuvastatin confers renoprotection in RIR through NO-dependent mechanisms.

MATERIALS AND METHODS: Five groups of rats (n = 6) were used: control, RIR, RIR + rosuvastatin, RIR + rosuvastatin + L-NAME (NG-Nitro-L-arginine methyl ester), and RIR + rosuvastatin + L-arginine. Drugs were administered once daily from 3 days before ischemia until 24 h after reperfusion. Twenty-four-hour urine, blood, and kidney tissues were collected for analysis. Statistical tests were performed with Prism software.

RESULTS: Rosuvastatin significantly reduced serum urea and creatinine levels versus RIR alone. Glomerular filtration rate increased, though proteinuria remained unchanged. Inflammatory cytokines and oxidative stress decreased markedly, while tissue NO levels rose in the rosuvastatin group. L-NAME co-treatment diminished these effects, whereas L-arginine enhanced them, indicating NO involvement.

CONCLUSION: Rosuvastatin ameliorated renal injury in RIR, likely through activation of NO signaling. These findings suggest a potential therapeutic role for rosuvastatin in ischemic renal injury.

PMID:41092343 | DOI:10.1093/jpp/rgaf097

Microbiology (Reading). 2025 Oct;171(10). doi: 10.1099/mic.0.001616.

ABSTRACT

Consumers’ healthy lifestyle practices have heightened the appeal of minimally processed foods, especially the fermented kind. Kefir and nabeez with numerous benefits are world-famous beverages. This study aimed to explore the enterococcal and lactococcal probiotic strains associated with these beverages. Artisanal recipes were used to make kefir and nabeez, and bacteria were isolated using classical culturing techniques. The isolates were screened based on antimicrobial potential, safety and probiotic attributes. The bacterial isolates obtained from three fermented beverages, milk kefir, water kefir and nabeez, were assessed for safety concerns, and those deemed safe were tested for antagonistic potential. Strains of Enterococcus durans (NPL1395_MK, NPL1396_MK and NPL1480_MK), Enterococcus faecium (NPL1390_MK, NPL1420_WK and NPL1427_Nb) and Lactococcus lactis (NPL1426_Nb, NPL1428_Nb and NPL1436_Nb) demonstrated interesting antimicrobial characteristics against food-borne pathogens. Strains from milk kefir and nabeez could tolerate strong acidic and bile stress. All strains were susceptible to lysozyme and phenol at the concentrations tested but demonstrated significant antioxidant potentials, exopolysaccharide production and bile salt hydrolase activities. Cholesterol assimilation was most significant in milk kefir and nabeez strains, which also had good adherence and biofilm formation. Statistical analysis of performance data using the principal component analysis identified L. lactis strain NPL1428_Nb as the best. It exhibited good potential to persist in the human gut based on its ability to tolerate in vitro mixtures simulating the gastrointestinal tract digestive fluids, using the static digestion model. Therefore, strain NPL1428_Nb of traditional fermented beverage provenance has good prospects for use in probiotic product development.

PMID:41091549 | DOI:10.1099/mic.0.001616

J Med Internet Res. 2025 Oct 15;27:e79161. doi: 10.2196/79161.

ABSTRACT

BACKGROUND: Breast cancer is the most common cancer diagnosis among women, with approximately 2.3 million new cases annually. When faced with a cancer diagnosis, individuals often turn to the internet for information or reassurance, despite the risk of encountering low-quality or incorrect information. While this observation is well documented in English, limited work has been done to understand the quality of breast cancer information in Spanish, the second most commonly spoken language in the United States.

OBJECTIVE: This study uses natural language processing methods and quantitative modeling to analyze English and Spanish breast cancer posts from Facebook, a vital source of health-related information for 40% of English-speaking and 60% of Spanish-speaking adults in the United States.

METHODS: Using the CrowdTangle application programming interface, we collected and processed 243,029 English-language and 96,334 Spanish-language Facebook posts. We applied BERTopic with the all-MiniLM-L6 model and k-means clustering to infer thematic structures and used coherence scores to determine the optimal number of topics for each language. Descriptive statistics compared metadata differences across languages. We calculated descriptive statistics and ran inferential tests for likes, comments, and shares. Finally, we examined the top 1% (n=2430 English and n=963 Spanish) of the most engaged content to analyze differences in poster characteristics across languages.

RESULTS: Coherence scores indicated an optimal topic solution of k=40 (coherence=0.58) for English and k=30 (coherence=0.52) for Spanish. Thematically, we observed similar content in both languages, with topics spanning mammography, breast cancer events, pink ribbon month, and personal narratives. However, Spanish posts included local and municipal breast cancer events not present in English. Additionally, Spanish posts were more likely to mention at-home breast exams, which are no longer recommended in the United States. Engagement behavior showed statistically significant differences by language across likes, comments, and shares. English posts exhibited more consistent liking and sharing behavior, while Spanish posts showed more consistency in commenting. The top 1% (n=2430) of engaged content in English came from leading breast cancer nonprofits, whereas in Spanish (n=963, 1%), it originated from local governments or food and beverage companies.

CONCLUSIONS: Facebook breast cancer content is generally consistent across languages. However, differences in engagement behavior suggest that English- and Spanish-speaking populations engage with content differently, highlighting cultural variability that warrants further exploration. Notably, leading cancer authorities may not have a strong presence in Spanish, indicating that the most accurate and up-to-date information may not be reaching a population particularly prone to worse breast cancer prognoses.

PMID:41091542 | DOI:10.2196/79161

Microb Genom. 2025 Sep;11(9). doi: 10.1099/mgen.0.001495.

ABSTRACT

Background. Shigella species are pathogenic bacteria that cause gastrointestinal symptoms ranging from mild watery diarrhoea to bacillary dysentery. Transmission is faecal-oral and historically associated with international travel. Recently, sexual transmission has been documented among gay, bisexual and other men who have sex with men (GBMSM). Through routine surveillance, we observed an increase in notifications of S. flexneri serotype 1b. We investigated the emergence of this serotype and examined possible drivers of transmission.Methods. We used historical data and whole-genome sequencing data from S. flexneri 1b isolates submitted to the United Kingdom Health Security Agency (UKHSA) to determine the relatedness of isolates and describe the population structure using phylogenetics. We tested for associations with possible epidemiological, biological and genetic drivers.Results. Between 1 January 2004 and 30 June 2024, 1,672 isolates of S. flexneri 1b were identified. Prior to 2019, there was a median of 12.5 [interquartile range (IQR) 10-17] notifications per quarter, rising to a median of 39.5 (IQR 23-58) notifications from 2019 to 2024. The rise was predominantly among adult males, consistent with patterns seen in prior sexually transmitted shigellosis epidemics among GBMSM. Unlike previous outbreaks of shigellosis among GBMSM, the emergence of S. flexneri 1b showed no evidence of an association with the acquisition of antimicrobial resistance determinants.Conclusions. Shigellosis can have severe clinical outcomes, and the repeated emergence of Shigella variants among GBMSM highlights the significance of the sexual transmission pathway. Continued surveillance of Shigella subtypes is necessary to inform public health interventions aimed at preventing sexual transmission of enteric pathogens in the GBMSM community.

PMID:41091541 | DOI:10.1099/mgen.0.001495

J Integr Complement Med. 2025 Oct 15. doi: 10.1177/27683605251387011. Online ahead of print.

ABSTRACT

Background: India bears a heavy burden of iron deficiency anemia (IDA), affecting nearly 50% of the population and contributing to adverse pregnancy outcomes, accounting for 20% of maternal deaths. While IDA continues to be a major health issue in India, there is a lack of comparative data on the efficacy of Ayurvedic treatments. This review aims to fill this evidence gap by systematically evaluating and ranking the efficacy of different Ayurvedic treatments for IDA using network meta-analysis (NMA). Methods: A systematic search was undertaken on May 1, 2024 using MEDLINE (via PubMed), Scopus, ScienceDirect, AYUSH Research Portal, and Google Scholar to locate randomized controlled trial (RCTs) evaluating interventions and their impact on hemoglobin (Hb) and serum ferritin. We conducted a random-effects NMA using a frequentist framework to estimate the mean difference (MD) and 95% confidence intervals (CIs) for the effects of interventions on outcomes, accounting for heterogeneity (I²). Results: Nineteen RCTs, comprising 2,121 individuals, assessed 26 different treatments for IDA and met the eligibility criteria. Results from the reference-based forest plots of the sensitivity analysis and corresponding P-scores revealed that both Sarva-Jvara-Hara-Lauha (SJHL) and Pippalyadi Yoga demonstrated statistically significant improvements in Hb levels, with MDs of 1.82 g/dL (95% CI: 0.66-2.98) and 1.45 g/dL (95% CI: 1.21-1.69), respectively. Among the interventions, Bibhitakadi Vatak demonstrated strong effectiveness in raising serum ferritin levels (MD: 3.87 ng/mL; 95% CI: -13.32-21.06). Conclusion: SJHL and Bibhitakadi Vatak were found to be the most effective strategies for treating IDA. Additional research is needed to substantiate these findings and assess their wider impact on public health. Trial Registration: PROSPERO registration number CRD42024541803.

PMID:41091535 | DOI:10.1177/27683605251387011

J Ethn Subst Abuse. 2025 Oct 15:1-21. doi: 10.1080/15332640.2025.2572334. Online ahead of print.

ABSTRACT

Substance misuse frequently serves as a primary coping mechanism in response to trauma. Because Black Adults disproportionately experience greater rates of trauma exposure than White adults, it is essential to determine buffers against racial trauma and subsequent substance use consequences. Previous literature has linked discrimination, a core contributing factor to racial trauma to substance misuse. The study aimed to determine the relationship between racial trauma and substance misuse among Black Americans and other potential moderating factors. Black Americans from across the U.S. (n = 327, M_age = 39.20, SD_age = 12.01) were recruited via Prolific to answer an online survey through Qualtrics. Linear regression analyses showed that racial trauma was positively associated with Alcohol Use Disorder. Denial coping was found to be a statistically significant moderator of this relationship. However, analyses did not find a significant relationship between racial trauma and drug use disorders. The absence of an association underscores the need for future research to examine factors that may reveal or clarify this potential relationship.

PMID:41091524 | DOI:10.1080/15332640.2025.2572334

JAMA Psychiatry. 2025 Oct 15. doi: 10.1001/jamapsychiatry.2025.2962. Online ahead of print.

ABSTRACT

IMPORTANCE: There have only been 3 efficacy trials reporting head-to-head comparisons of pharmacotherapy and trauma-focused psychotherapy for posttraumatic stress disorder (PTSD), and none were conducted in primary care. In addition, few trials have examined treatment sequences for patients not responding to an initial treatment.

OBJECTIVE: To test the hypothesis that (1) brief trauma-focused psychotherapy (written exposure therapy [WET]) is more effective than a choice of 3 selective serotonin reuptake inhibitors (SSRIs; ie, sertraline, fluoxetine, or paroxetine) and (2) WET augmentation is more effective than switching to the serotonin-norepinephrine reuptake inhibitor (SNRI) venlafaxine for those not responding to an SSRI.

DESIGN, SETTING, AND PARTICIPANTS: This was a pragmatic comparative effectiveness trial conducted from April 2021 to June 2024 that randomized primary care patients to 1 of 3 treatment sequences: (1) SSRI followed by WET augmentation, (2) SSRI followed by switch to SNRI, or (3) WET followed by SSRI. Effectiveness in this pragmatic trial depends on treatment engagement and treatment fidelity. The study included patients meeting clinical criteria for PTSD from primary care clinics of 7 federally qualified health centers and 8 Department of Veterans Affairs medical centers.

INTERVENTIONS: SSRI followed by WET augmentation, SSRI followed by switch to SNRI, or WET followed by SSRI.

MAIN OUTCOMES AND MEASURES: PTSD symptom severity, as measured by the DSM-5 PTSD Checklist (PCL-5).

RESULTS: A total of 700 patients (mean [SD] age, 45.1 [15.4] years; 368 men [62.1%]). The mean (SD) baseline PCL-5 score was 52.8 (11.1), indicating considerable symptom severity. At 4 months, 144 of 278 patients (51.8%) randomized to an SSRI were adherent and reported a 14.0-point PCL-5 decrease, whereas 11 of 352 patients (31.5%) randomized to WET completed all sessions and reported a 12.1-point decrease. There was no significant between-group difference (adjusted mean difference [MD], 1.79; 95% CI, -0.76 to 4.34; P = .17). For the 122 of 295 patients (41.4%) randomized to an SSRI who did not respond to treatment, those randomized to switch to the SNRI reported a 9.2-point PCL-5 decrease compared with a 2.3-point decrease for those randomized to WET augmentation, which was a statistically significant between-group difference (adjusted MD, 10.19; 95% CI, 4.97-15.41; P < .001).

CONCLUSIONS AND RELEVANCE: Study results showed that treatment of PTSD in primary care with either SSRIs or WET was feasible and effective. For patients not responding to an SSRI, switching to an SNRI may be more effective than WET augmentation.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04597190.

PMID:41091477 | DOI:10.1001/jamapsychiatry.2025.2962