Tag: nevin manimala

Genome Biol. 2025 Sep 27;26(1):314. doi: 10.1186/s13059-025-03790-5.

ABSTRACT

We introduce hybrid BAG-seq: a high-throughput, multi-omic method that simultaneously captures DNA and RNA from single nuclei. We apply this protocol to 65,499 single nuclei from samples of five uterine cancer patients and validate the clustering using RNA-only and DNA-only protocols from the same tissues. Multiple tumor genome or expression clusters are often present within a patient, with different tumor clones projecting into distinct or shared expression states, demonstrating nearly all possible genome-transcriptome correlations. We also identify mutant stroma with significant X chromosome loss in various cell types and patient-specific stromal subtypes exhibiting aberrant expression patterns.

PMID:41015771 | DOI:10.1186/s13059-025-03790-5

Genome Biol. 2025 Sep 27;26(1):313. doi: 10.1186/s13059-025-03775-4.

ABSTRACT

The availability of large genome datasets has changed the microbiology research landscape. Analyzing such data requires computationally demanding analyses, and new approaches have come from different data analysis philosophies. Machine learning and statistical inference have overlapping knowledge discovery aims and approaches. However, machine learning focuses on optimizing prediction, whereas statistical inference focuses on understanding the processes relating variables. In this review, we outline the different aspirations, precepts, and resulting methodologies, with examples from microbial genomics. Emphasizing complementarity, we argue that the combination and synthesis of machine learning and statistics has potential for pathogen research in the big data era.

PMID:41015769 | DOI:10.1186/s13059-025-03775-4

Eur J Med Res. 2025 Sep 27;30(1):885. doi: 10.1186/s40001-025-03122-0.

ABSTRACT

OBJECTIVE: Thyroid hormones significantly influence multiple physiological systems, particularly the respiratory system. Despite limited research on asthma-thyroid associations, emerging studies have begun exploring this link. This cross-sectional study investigates relationships between asthma, thyroid function, and thyroid hormone sensitivity in U.S. adults using NHANES data.

METHODS: A total of 8160 participants were included in this study. Weighted analyses of data from the 2007-2012 National Health and Nutrition Examination Survey (NHANES) were performed to examine the associations between asthma, thyroid function, and thyroid hormone sensitivity indices. Subgroup analyses and ROC curve investigations were also conducted. Additionally, a retrospective cohort of 30 asthma patients and 30 non-asthmatic controls seen at Zhongshan Hospital, Xiamen University between July 2023 and July 2025 was extracted; FT3 levels were compared and asthma control was evaluated across FT3 tertiles. Thyroid function parameters assessed were as follows: free triiodothyronine (FT3), free thyroxine (FT4), total triiodothyronine (TT3), total thyroxine (TT4), thyroid-stimulating hormone (TSH), thyroid peroxidase antibody (TPOAb), thyroglobulin antibody (TgAb), and thyroglobulin (Tg). Thyroid hormone sensitivity indices-namely, the FT3/FT4 ratio, thyrotroph T4 resistance index (TT4RI), thyroid-stimulating hormone index (TSHI), and thyroid feedback quantile index (TFQI)-were calculated from serum FT3, FT4, and TSH values.

RESULTS: Asthmatics exhibited higher FT3 and FT3/FT4 levels but lower TPOAb than non-asthmatics. However, adjusted models (2 and 3) revealed an inverse association between asthma risk and FT3/FT4 (β: – 0.05, 95% CI – 0.09 to – 0.01). Quartile stratification maintained this inverse trend, with significant dose-response relationships in unadjusted Model 1 (P < 0.05). Subgroup analyses showed Mexican American asthmatics had lower FT3 and FT3/FT4 levels. ROC curves indicated superior predictive accuracy for TPOAb (AUC = 0.60) compared to FT3/FT4. Our institutional validation revealed that asthma patients had significantly lower FT3 levels than controls, and higher FT3 was associated with a lower proportion of acute exacerbations; however, the trend did not reach statistical significance.

CONCLUSION: FT3 and FT3/FT4 levels may inversely correlate with asthma risk, though causality remains unclear due to study design limitations. Further research is warranted.

PMID:41015767 | DOI:10.1186/s40001-025-03122-0

Int J Gynecol Cancer. 2025 Sep 4:102135. doi: 10.1016/j.ijgc.2025.102135. Online ahead of print.

ABSTRACT

OBJECTIVE: Risk-reducing salpingo-oophorectomy has been adopted in China as an effective preventive measure against ovarian cancer, particularly for individuals with breast cancer gene (BRCA) mutations. While the procedure’s efficacy in reducing ovarian cancer risk is well established, the associated psychophysical and social impacts have received limited attention. Understanding these impacts is critical for enhancing patient care and improving quality of life.

METHODS: This retrospective study included 154 BRCA mutation carriers who underwent risk-reducing salpingo-oophorectomy at Fudan University Shanghai Cancer Center between October 2016 and March 2024. A total of 136 patients were successfully followed up for quality-of-life assessment. Data were collected using the Self-Rating Anxiety Scale, Menopause Rating Scale, Decision Regret Scale, Decision Conflict Scale, and self-reported evaluations. Descriptive statistics were employed to summarize the data, and subgroup analyses were conducted to identify potential influencing factors.

RESULTS: The median age of participants was 46 years. Personal histories of breast cancer were reported in 63.97% (87/136) of the patients, and 8.82% (12/136) were diagnosed with occult ovarian cancer or precancerous lesions post-surgery. Among the cohort, 71.32% (97/136) were postmenopausal. Of the premenopausal patients, only 6 attempted hormone replacement therapy. Anxiety levels and menopausal symptoms were not significantly associated with clinical or demographic variables. Most patients reported low decision regret, with 89.71% (122/136) expressing complete satisfaction with the surgery and only 5.88% (8/136) reporting persistent stress. However, sexual dysfunction was reported by 46.32% (63/136).

CONCLUSION: Risk-reducing salpingo-oophorectomy is associated with significant challenges, particularly concerning sexual dysfunction. These findings underscore the need for comprehensive preoperative counseling that distinctly addresses biomedical, physiological, and psychosocial considerations, alongside postoperative support to manage the quality-of-life impacts of risk-reducing salpingo-oophorectomy.

PMID:41015764 | DOI:10.1016/j.ijgc.2025.102135

Curr Probl Diagn Radiol. 2025 Sep 19:S0363-0188(25)00164-1. doi: 10.1067/j.cpradiol.2025.09.004. Online ahead of print.

ABSTRACT

PURPOSE: To correlate placental ultrasound shear wave elastography (SWE) values with perinatal outcomes in Gestational Diabetes Mellitus (GDM).

METHODS: The study included 160 pregnant women, comprising 80 GDM and 80 healthy controls. Ultrasound SWE was performed on the placenta, and mean SWE and velocity values were derived from six measurements. Both the cases and controls were followed to record Apgar scores and NICU admission. Statistical analysis was done, and the SWE values were compared to correlate these values with perinatal outcomes.

RESULTS: A positive correlation was observed between SWE values and maternal fasting blood glucose (FBS) levels (rho = 0.32, p = 0.001), indicating that higher glucose levels are associated with increased placental stiffness. In the control group, the mean SWE was 2.48 kPa, while in the GDM group, it increased to 7.74 kPa, reflecting the impact of a diabetic environment on placental stiffness. The mean velocity was also higher in the GDM group (1.47 m/s) as compared to the control group (mean = 0.87 m/s). A moderate negative correlation between APGAR (1-min) and mean SWE was found at <32 weeks of gestation (rho = -0.48, p = 0.017). No significant correlation was found with NICU admissions.

CONCLUSION: Placental stiffness differs significantly between GDM and controls, with higher values in GDM. Ultrasound SWE can substantially contribute to the management of GDM and improve the outcomes. A negative correlation between SWE and 1-minute APGAR score at <32 weeks of gestation is associated with a lower score, indicating the effect of increased placental stiffness on perinatal outcomes.

PMID:41015728 | DOI:10.1067/j.cpradiol.2025.09.004

Acad Radiol. 2025 Sep 26:S1076-6332(25)00865-7. doi: 10.1016/j.acra.2025.09.012. Online ahead of print.

ABSTRACT

BACKGROUND: With increasing imaging demands, radiologists face growing workload pressures, often resulting in delays and reduced diagnostic efficiency. Recent advances in artificial intelligence (AI) have introduced tools for automated report generation, particularly in simpler imaging modalities, such as X-rays. However, limited research has assessed AI performance in complex studies such as MRI and CT scans, where report accuracy and clinical interpretation are critical.

OBJECTIVE: To evaluate the performance of a semi-automated AI-based reporting platform in generating radiology reports for complex imaging studies, and to compare its accuracy, efficiency, and user confidence with the traditional dictation method.

METHODOLOGY: This study involved 100 imaging cases, including MRI knee (n=21), MRI lumbar spine (n=30), CT head (n=23), and CT Abdomen and Pelvis (n=26). Consultant musculoskeletal radiologists reported each case using both traditional dictation and the AI platform. The radiologist first identified and entered the key positive findings, based on which the AI system generated a full draft report. Reporting time was recorded, and both methods were evaluated on accuracy, user confidence, and overall reporting experience (rated on a scale of 1-5). Statistical analysis was conducted using two-tailed t-tests and 95% confidence intervals.

RESULTS: AI-generated reports demonstrated significantly improved performance across all parameters. The mean reporting time reduced from 6.1 to 3.43 min (p<0.0001) with AI-assisted report generation. Accuracy improved from 3.81 to 4.65 (p<0.0001), confidence ratings increased from 3.91 to 4.67 (p<0.0001), and overall reporting experience favored using the AI platform for generating radiology reports (mean 4.7 vs. 3.69, p<0.0001). Minor formatting errors and occasional anatomical misinterpretations were observed in AI-generated reports, but could be easily corrected by the radiologist during review.

CONCLUSION: The AI-assisted reporting platform significantly improved efficiency and radiologist confidence without compromising accuracy. Although the tool performs well when provided with key clinical findings, it still requires expert oversight, especially in anatomically complex reporting. These findings support the use of AI as a supportive tool in radiology practice, with a focus on data integrity, consistency, and human validation.

PMID:41015710 | DOI:10.1016/j.acra.2025.09.012

ISA Trans. 2025 Sep 16:S0019-0578(25)00517-8. doi: 10.1016/j.isatra.2025.09.012. Online ahead of print.

ABSTRACT

The present study explores the stability problem of nonlinear time-delay systems subject to delayed impulses. Specifically, this paper addresses the dual aspects of both delayed impulsive control and perturbation issues on nonlinear systems with time-varying delays. In particular, by employing Halanay-type inequality techniques, we establish some sufficient criteria to ensure the exponential stability of the aforementioned time-delay systems. Moreover, we remove previous restrictions on the relative sizes of time delays in both continuous dynamics and impulses. It is shown that, under certain conditions, the delays in impulses may be arbitrarily finite and even exceed the duration of the impulsive intervals, but such delayed impulses solely affect the convergence rate of the addressed system without undermining its stability. Furthermore, this study’s theoretical results are applied to the stabilization of sewage treatment systems and the impulsive synchronization of Chua’s circuits. Two illustrative examples are given to demonstrate the effectiveness and validity of the derived results.

PMID:41015707 | DOI:10.1016/j.isatra.2025.09.012

Vet Anaesth Analg. 2025 Sep 8:S1467-2987(25)00218-1. doi: 10.1016/j.vaa.2025.09.002. Online ahead of print.

ABSTRACT

OBJECTIVE: To determine the anesthetic and analgesic protocols and techniques used in cats undergoing elective neutering in Ontario, Canada and to obtain veterinarians’ opinions regarding their choices.

STUDY DESIGN: Cross-sectional survey.

ANIMALS: Client-owned cats undergoing elective neutering in Ontario, Canada.

METHODS: A confidential mixed-mode survey about anesthetic and analgesic management practices used in client-owned cats undergoing elective neutering was distributed to veterinarians (n = 2921) working in companion animal practice in Ontario. Descriptive statistics were generated. Logistic regression was used to identify associations between demographic factors and protocols. Chi-square analysis was used to compare protocols used in cats undergoing ovariohysterectomy (OVH) versus castration.

RESULTS: Four hundred and thirty-one individuals (14.8%) completed the survey. Most respondents used a sedative before induction of anesthesia (OVH: 368/387; 95.1% and castration 360/381; 94.5%) and gave an opioid and/or a non-steroidal anti-inflammatory drug perioperatively (OVH: 379/381; 99.7% and castration: 379/382; 99.2%). Respondents placed an intravenous catheter and performed orotracheal intubation more frequently in cats undergoing OVH (catheter: 366/387; 94.6% and intubation: 379/386; 98.2%) compared with castration (catheter: 219/380; 57.6% and intubation: 166/375; 44.3%) (p < 0.001). Respondents more closely followed current anesthesia guidelines relative to their peers if they: graduated during or after 2000, were women, performed 1-10 OVHs per week, worked in an urban setting, in a companion animal practice, with three or more veterinarians or three to five registered veterinary technicians. Most respondents were very satisfied or satisfied with their current anesthetic drug protocol for cats undergoing elective OVH (396/412; 96.1%) and castration (386/413; 93.4%).

CONCLUSIONS AND CLINICAL RELEVANCE: Most veterinarians in Ontario who participated in the survey follow many of the current guidelines regarding anesthetic and analgesia management practices for cats undergoing elective neutering. Anesthetic protocols varied with respondent demographics; however, most respondents were satisfied with their choices.

PMID:41015686 | DOI:10.1016/j.vaa.2025.09.002

J Racial Ethn Health Disparities. 2025 Sep 27. doi: 10.1007/s40615-025-02660-x. Online ahead of print.

ABSTRACT

BACKGROUND: The sexual partner’s HIV status trajectory of young men who have sex with men (YMSM) has a significant impact on HIV prevention. There are some potential associations between adverse experiences and HIV status trajectories of sexual partners among YMSM. This study aimed to examine the trajectory of HIV status in sexual partners and to investigate effects of adversity experiences on the sexual partner’s HIV status trajectories.

METHOD: Study data (N = 411) were derived from a 5-year YMSM cohort conducted in Central China from 2017 to 2021. The adversity experiences, including adverse childhood experiences (ACEs), sexual minority discrimination, everyday discrimination, and internalized discrimination, were measured at baseline. Other psychosocial variables including resilience and social support were measured at baseline. The HIV status of YMSM partners was examined at baseline and each follow-up survey. The group-based trajectory modeling (GBTM) was used to derive trajectories of partners’ HIV status, and the multinomial logistic regression was used to examine the association between adversity experiences and the trajectories.

RESULTS: The GBTM categorized the HIV status of YMSM sexual partners into four groups, including Group I (low risk), Group II (risk reduction), Group III (increased risk) and Group IV (high risk). The ACEs among YMSM were associated with a higher risk of their sexual partners being categorized into Group III (OR [95% CI] = 1.353 [1.012, 1.808], p = 0.041) and Group IV (OR [95% CI] = 1.268 [1.023, 1.571], p = 0.030). Among YMSM, older age (OR [95% CI] = 1.245 [1.041, 1.489], p = 0.016) and lower education level (OR [95% CI] = 4.053 [1.710, 9.606], p < 0.001) were associated with a higher risk of their sexual partners being categorized into Group IV. Other adversity experiences and psychosocial variables did not show significant impacts on the trajectories.

CONCLUSIONS: ACEs among YMSM exerted a significant impact on the HIV status trajectories of their sexual partners. Our findings underscore that YMSM with a history of ACEs were more likely to have sexual partners in higher-risk HIV status groups, which implies a greater potential for HIV transmission within their sexual networks.

PMID:41015657 | DOI:10.1007/s40615-025-02660-x

Pediatr Res. 2025 Sep 27. doi: 10.1038/s41390-025-04411-4. Online ahead of print.

ABSTRACT

BACKGROUND/AIMS: Limited post-menstrual age (PMA) stratified data are available for the morbidities and length of stay (LOS) for the largest group of preterm infants. We investigated the incidence, types and interactions of morbidities that prolong the LOS at 33-36 weeks PMA.

METHODS: Electronic and bedside charts of 1209 infants were visually reviewed. Major outcomes included respiratory support, achievement of gavage-free feeding and maternal/infant variables associated with shorter/longer than Median LOS. Fisher’s exact tests/ANOVA/logistic regression were used for statistical analyses.

RESULTS: The Median (IQR, Range) of the LOS were distinct at each and even within PMA between 33 and 36 weeks (P < 0.001). 63% of infants born at 33-weeks received respiratory support vs. 46, 39 and 7% born at 34-, 35- and 36-weeks, respectively (P < 0.001). Multiple births, BW within a given PMA, SGA status, respiratory support, RDS, delayed gavage-free feeds and birthplace were associated with longer than Median LOS at each PMA (P ≤ 0.04). Achievement of gavage-free feeding was consistently the main determinant of early discharge home across all PMAs (P < 0.001).

CONCLUSIONS: Our newer approach in identifying relationship among morbidities in infant born at 33-36 weeks PMA fills important knowledge gaps. These data will facilitate evidence-based clinical care, educational-needs, health care resource planning and parental counseling.

IMPACT: Either grouped and/or fragmented data are available for morbidities in infants born between 33 and 36 weeks post-menstrual age (PMA), which represents >80% of all preterm infants. We demonstrate that respiratory insufficiency, type of respiratory support, delayed gavage-free feedings and length of stay (LOS) are inter-dependent and PMA-specific. Using a novel approach, we provide new significant data that identify clinical variables, associated with shorter and longer than Median LOS at each and even within a given PMA. Comprehensive analysis of morbidities suggests that preterm infants should neither be grouped, nor PMA alone be used for discharge planning and parental counseling.

PMID:41015648 | DOI:10.1038/s41390-025-04411-4