Tag: nevin manimala

Genomics Proteomics Bioinformatics. 2025 Nov 24:qzaf111. doi: 10.1093/gpbjnl/qzaf111. Online ahead of print.

ABSTRACT

Depicting gene expression in a spatial context through spatial transcriptomics is beneficial for inferring cellular mechanisms. Identifying spatially variable genes is a crucial step in leveraging spatial transcriptome data to understand intricate spatial dynamics. In this study, we developed Spanve, a nonparametric statistical method for detecting spatially variable genes in large-scale spatial transcriptomics datasets by quantifying expression differences between each spot or cell and its local neighbors. This method offers a nonparametric approach for identifying spatial dependencies in gene expression without distributional assumptions. Compared with existing methods, Spanve yields fewer false positives, leading to more accurate identification of spatially variable genes. Furthermore, Spanve improves the performance of downstream spatial transcriptomics analyses including spatial domain detection and cell type deconvolution. These results show the broad application potential of Spanve in advancing our understanding of spatial gene expression patterns within complex tissue microenvironments. Spanve is publicly available at https://github.com/zjupgx/Spanve and https://ngdc.cncb.ac.cn/biocode/tool/BT7724.

PMID:41284930 | DOI:10.1093/gpbjnl/qzaf111

Int J Occup Saf Ergon. 2025 Nov 24:1-5. doi: 10.1080/10803548.2025.2586887. Online ahead of print.

ABSTRACT

Objectives. This study aimed to evaluate occupational safety perception and its influencing factors among students in the Department of Occupational Health and Safety at Sinop University, with a particular focus on the impact of socio-demographic variables and participation in occupational health and safety (OHS)-related training. Methods. A cross-sectional study was conducted with 154 OHS students in the 2022-2023 autumn term. Data from 128 students (83.1%) were collected using an informed consent form, a descriptive questionnaire and the occupational safety scale (OSS). The OSS is a 32-item Likert scale with a reliability of 0.75. Data analysis used SPSS version 25, including descriptive statistics, t tests, analysis of variance and Pearson correlation. Results. Participants had a mean age of 21.72 ± 1.33 years, 50.8% were male and 43% were second-year students. Most (73.4%) reported middle-income levels, and 66.4% had not received personal protective equipment (PPE) training. No significant correlation was found between socio-demographic factors and OHS perception scores (p > 0.05). However, students who received PPE training or participated in OHS activities had significantly higher perception scores (p = 0.018 and p = 0.002). Conclusion. OHS-related training, particularly in PPE and OHS activities, significantly improves safety perception. Expanding such training in educational settings can enhance future professionals’ safety awareness.

PMID:41284928 | DOI:10.1080/10803548.2025.2586887

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2500535122. doi: 10.1073/pnas.2500535122. Epub 2025 Nov 24.

ABSTRACT

Using data on millions of internal US migrants, we document that historical homicide rates follow migrants around the United States. Individuals born in historically safe states remain safer wherever they go, while individuals born in historically dangerous states face a greater risk, including from police violence. This pattern holds across demographic characteristics such as age, gender, and marital status, across migrant groups with different average levels of education, income, and even when comparing migrants from different states who reside in the same county. To help understand why, we conducted a large national survey that oversampled internal White US migrants. The results suggest this persistence may reflect a sociocultural adaptation to dangerous settings. Residents and migrants from historically unsafe states-mainly former frontier states and the deep South-see the world as more dangerous, react more forcefully in aggressive scenarios, value toughness, distrust law enforcement, and say they rely on self and family in violent situations. These adaptations may have kept them safe in historically dangerous states, but may increase their vulnerability to harm in safer states.

PMID:41284885 | DOI:10.1073/pnas.2500535122

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2421768122. doi: 10.1073/pnas.2421768122. Epub 2025 Nov 24.

ABSTRACT

Dogs evolved through interactions between people and gray wolves during the Late Pleistocene and have been ubiquitous in human societies ever since. Instances of wolf-to-dog introgression are rare, but adaptive introgression has been shown in association with high-altitude survival. Any widespread gene flow, however, has fallen below thresholds of detection in genome-wide statistical assessments. To reexamine evidence of dog-wolf gene flow, we analyzed 2,693 published dog and wolf genomes and combined highly sensitive local ancestry inference and phylogenomic analyses of nuclear genes, mitochondrial genomes, and Y-chromosome sequences. Although dogs and wolves segregate decisively at the nuclear level, no individual nuclear gene tree supports dog monophyly. Uniparental markers show mixed and interleaved dog and wolf clades with strong support and incongruent phylogenetic topologies. Using local ancestry inference, we find that 64.1% of modern breed dogs carry wolf ancestry from admixture that occurred nearly a thousand generations ago on average and now covers ~0.14% of their individual nuclear genomes. Among modern free-living village dogs (n = 280), 100% of analyzed genomes carry wolf ancestry. We find that wolf ancestry in dog breeds correlates with functional traits including size, breed category, and personality characteristics. In village dogs, wolf ancestry is enriched at olfactory receptor genes, suggesting adaptive introgression for sensory acuity that may have helped these free-living dogs survive in more challenging environments. In total, dog-wolf admixture has likely been an important factor in shaping the evolution of modern dogs.

PMID:41284883 | DOI:10.1073/pnas.2421768122

J Med Internet Res. 2025 Nov 24;27:e80951. doi: 10.2196/80951.

ABSTRACT

BACKGROUND: Traditional obstetric nursing training faces limitations in inadequate interactivity and nonrepeatable demonstrations, limiting students’ development of clinical thinking. Virtual reality (VR) offers a solution for complex health care education, enhancing nursing students’ clinical thinking.

OBJECTIVE: This study applied the Nonimmersive Virtual Reality System for Clinical Thinking in Obstetric Nursing (NIVRSCTON), grounded in salutogenesis theory, to examine its effects on nursing students.

METHODS: The NIVRSCTON was applied under the auspices of the Nursing Virtual Teaching Hub in the Coastal Area (NVTHCA). In September 2023, a convenience sample of 88 undergraduate nursing students from 4 partner institutions participated in the study. A single-group pre-post design and an explanatory sequential mixed methods design were used to measure changes in clinical thinking ability following the training and to assess the system’s performance. The quantitative assessment tools included the general information questionnaire, the Clinical Thinking Ability Evaluation Scale (CTAES), and the Evaluation Instrument for Virtual Reality System (EIVRS). Each student was required to submit one reflective journal developed in accordance with the Bass model. Quantitative data were analyzed using IBM SPSS (version 22.0), and qualitative data were thematically coded using NVivo (version 12; QSR International Pty Ltd).

RESULTS: After the NIVRSCTON training was completed, the students’ overall clinical thinking score increased from 49.08 (SD 11.30) to 80.50 (SD 11.01), indicating a significant improvement (t₈₇=-18.76; Cohen d=-2.82, 95% CI -34.74 to -28.08). All clinical thinking dimension scores improved, and the improvements were all statistically significant (P<.001). Critical thinking scores increased from 13.98 (SD 3.76) to 24.77 (SD 3.11; t₈₇=-20.37; Cohen d=-3.13, 95% CI -11.85 to -9.74), system thinking scores increased from 26.82 (SD 6.40) to 44.51 (SD 6.24; t₈₇=-19.18; Cohen d=-2.80, 95% CI -19.53 to -15.86), and evidence-based thinking scores improved from 18.10 (SD 4.40) to 27.31 (SD 4.61; t₈₇=-13.42; Cohen d=-2.04, 95% CI -10.57 to -7.84). The variable df is all 87. In terms of application effectiveness, the students provided the following ratings: 0.82 (SD 0.15; rated as good) for interface design, 0.82 (SD 0.15; rated as good) for technical performance, 0.83 (SD 0.14; rated as good) for learning content, and 0.85 (SD 0.15; rated as excellent) for learning function. The overall evaluation was 0.82 (SD 0.15; rated as good). Qualitative data revealed that the training not only improved the clinical thinking and decision-making skills of the nursing students but also fostered their professional attitudes, values, and emotions.

CONCLUSIONS: NIVRSCTON training enhances students’ clinical thinking and professionalism. It was well received, confirming its effectiveness. As an obstetric nursing teaching tool, it enhances clinical thinking and professional competence. It may also promote equity and access in nursing education, offering an innovative model for digital nursing education.

PMID:41284338 | DOI:10.2196/80951

Clin Spine Surg. 2025 Oct 24. doi: 10.1097/BSD.0000000000001958. Online ahead of print.

ABSTRACT

STUDY DESIGN: Prospective nonrandomized case-control study (level III).

OBJECTIVE: This study aims to evaluate the efficacy of ultrasound-guided ESPB versus LWI in postoperative analgesia and functional recovery following lumbar fusion surgeries.

SUMMARY OF BACKGROUND DATA: Major lumbar spine surgery is associated with severe postoperative pain. The ultrasound-guided Erector Spinae Plane Block (ESPB) and Local Wound Infiltration (LWI) are commonly used techniques for pain management, but their comparative effectiveness remains underexplored.

METHODS: A prospective nonrandomized case-control study was conducted at a tertiary care hospital from July 2023 to July 2024. A total of 35 patients receiving ESPB were compared with a control group receiving LWI. Postoperative pain was assessed using the numerical rating scale (NRS) at 30 minutes, 6, 12, and 24 hours. Additional parameters included opioid consumption, time to first opioid use, mobilization time, and inflammatory markers. Statistical analysis was performed, with P < 0.05 considered statistically significant.

RESULTS: ESPB provided superior postoperative pain control, with significantly lower NRS scores at 6 hours (2.93 ± 0.74 vs. 3.41 ± 0.89; P = 0.016), 12 hours (4.96 ± 1.28 vs. 5.73 ± 1.56; P = 0.027), and 24 hours with reduced opioid consumption (0.26 ± 0.086 g vs. 0.32 ± 0.14 g; P = 0.028) and delayed time to first opioid use (6.22 ± 2.68 h vs. 4.71 ± 2.88 h; P = 0.026), while inflammatory markers at 24 hours were significantly lower in the ESPB group. Patients receiving ESPB had earlier sitting (18.2 ± 7.61 h vs. 22.6 ± 9.53 h; P = 0.036) and mobilization (28.8 ± 8.46 h vs. 32.41 ± 9.36 h; P = 0.095).

CONCLUSION: Ultrasound-guided ESPB provides superior pain control, reduces opioid consumption, and effectively suppresses the inflammatory response than LWI following lumbar fusion surgeries while facilitating early mobilization, proving to be effective in multimodal pain management.

PMID:41284329 | DOI:10.1097/BSD.0000000000001958

JAMA Pediatr. 2025 Nov 24. doi: 10.1001/jamapediatrics.2025.4540. Online ahead of print.

NO ABSTRACT

PMID:41284306 | DOI:10.1001/jamapediatrics.2025.4540

JAMA Netw Open. 2025 Nov 3;8(11):e2545258. doi: 10.1001/jamanetworkopen.2025.45258.

ABSTRACT

IMPORTANCE: Assisted ventilation during delayed cord clamping (DCC) may improve the physiologic transition of extremely preterm infants immediately after birth.

OBJECTIVE: To determine whether assisted ventilation during 120 seconds of DCC was associated with reduced higher-level resuscitative interventions (intubation, chest compressions, or epinephrine administration) compared with DCC for 30 to 60 seconds followed by resuscitation.

DESIGN, SETTING, AND PARTICIPANTS: This was a secondary analysis of the VentFirst randomized clinical trial that was conducted from September 2, 2016, through February 21, 2023, at 12 centers in the US and Canada. Infants born at 23 weeks 0 days’ to 28 weeks 6 days’ gestational age (GA) were included.

INTERVENTION: Infants randomized to the intervention received either positive-pressure ventilation or continuous positive airway pressure from 30 to 120 seconds after birth, followed by umbilical cord clamping. Those randomized to control received 30 to 60 seconds of DCC followed by assisted ventilation.

MAIN OUTCOMES AND MEASURES: The main outcome was the odds of higher-level resuscitative interventions in the delivery room (DR). Intention-to-treat analyses within 2 a priori cohorts (infants breathing well and not breathing well 30 seconds after birth) used the Cochran-Mantel-Haenszel method to estimate the odds ratios (ORs) of intervention vs control.

RESULTS: All 570 infants enrolled in the trial were included. Infants had a median (IQR) GA of 26.6 (25.2-27.9) weeks and 273 (47.9%) were female. A total of 271 infants (47.5%) were assessed as not breathing well 30 seconds after birth (150 intervention and 121 control), and 299 (52.5%) were assessed as breathing well 30 seconds after birth (128 intervention and 171 control). In the not-breathing-well cohort, 146 infants (53.9%) were intubated in the DR, 4 received chest compressions (2 intervention and 2 control), and 1 received epinephrine (control). Intubation was less frequent in the intervention group (71 infants [47.3%] vs 75 infants [62.0%]; OR, 0.52; 95% CI, 0.30-0.89). When adjusted by GA strata at randomization, infants in the 26 to 28 weeks’ GA stratum who were in the intervention group were less likely to be intubated in the DR (18 of 79 infants [22.8%] vs 29 of 60 infants [48.3%]; OR, 0.32; 95% CI, 0.15-0.65). However, there was no difference in intubation rates for infants in the 23 to 25 weeks’ GA stratum (53 of 71 infants [74.7%] vs 46 of 61 infants [75.4%]; OR, 0.96; 95% CI, 0.44-2.12). Among infants breathing well at 30 seconds, 74 (24.7%) were intubated in the DR, and none received compressions or epinephrine. Intubation rates were similar between intervention and control in the breathing-well cohort.

CONCLUSIONS AND RELEVANCE: While the VentFirst trial did not find a difference in death or intraventricular hemorrhage, this secondary analysis found that assisted ventilation during DCC was associated with less intubation in the DR, primarily among infants born at 26 to 28 weeks’ gestation who were not breathing well 30 seconds after birth. Additional studies are needed before implementing assisted ventilation during DCC in clinical practice.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02742454.

PMID:41284295 | DOI:10.1001/jamanetworkopen.2025.45258

JAMA Netw Open. 2025 Nov 3;8(11):e2545294. doi: 10.1001/jamanetworkopen.2025.45294.

ABSTRACT

IMPORTANCE: Different degrees of growth delay have been reported in children with Alagille syndrome (ALGS), yet these patients are routinely evaluated using standard growth charts.

OBJECTIVE: To develop condition-specific growth charts for ALGS using modern statistical approaches.

DESIGN, SETTING, AND PARTICIPANTS: This case series used data from the international, multicenter Global Alagille Alliance (GALA) study accrued between May 14, 2018, and March 20, 2023. Children born at full term between January 1, 1997, and August 31, 2019, with a clinically and/or genetically confirmed ALGS diagnosis and their native liver were included. Data from children with a known history of prematurity were excluded for the development of the growth charts. Data were analyzed from March 25, 2023, to December 30, 2024.

EXPOSURE: Growth of children with Alagille syndrome.

MAIN OUTCOMES AND MEASURES: Generalized additive models for location scale and shape were fitted to generate percentile plots for weight and height relative to age and superimposed on US Centers for Disease Control and Prevention (CDC) growth charts to illustrate differences in growth patterns compared with children with typical development.

RESULTS: Data from 1204 children with ALGS in overlapping cohorts (median [IQR] gestational age, 38 [37-39] weeks) were analyzed (1204 in the weight cohort; 695 boys [57.7%]; 9855 weight observations; 995 with neonatal cholestasis [82.6%]; 306 receiving a liver transplant [25.4%]; 98 deaths [8.1%] and 1106 in the height cohort, 635 boys [57.4%]; 8464 height observations; 906 with neonatal cholestasis [81.9%]; 287 receiving a liver transplant [25.9%]; 86 deaths [7.8%]) were included for the modeling of the weight-for-age and height-for-age charts, respectively. The median birth weight was 2.8 kg (IQR, 2.5-3.0 kg) for boys and 2.6 kg (IQR, 2.4-2.9 kg) for girls. The median birth length was 48.0 cm (IQR, 46.0-50.0 cm) for boys and 47.0 cm (IQR, 45.0-49.0 cm) for girls. The weight-for-age and height-for-age growth charts for boys and girls with AGLS differed significantly from CDC growth charts. The estimated height at age 18 years corresponded to the 50th percentile was 171.5 cm for boys and 156.5 cm for girls on the condition-specific charts vs 176 cm and 163 cm, respectively, on the CDC growth charts.

CONCLUSIONS AND RELEVANCE: These findings suggest that condition-specific growth charts for ALGS may provide a crucial tool for clinicians to evaluate growth and aid in decision-making around listing children for liver transplant.

PMID:41284294 | DOI:10.1001/jamanetworkopen.2025.45294

J Am Soc Mass Spectrom. 2025 Nov 24. doi: 10.1021/jasms.5c00172. Online ahead of print.

ABSTRACT

The identities and outgassing rates of contaminants associated with a material determine its suitability for space applications. Thermogravimetric analysis (TGA) is one test commonly used for evaluating these material properties. During TGA, contaminants deposited on quartz crystal microbalances (QCMs) are desorbed through heating while mass spectrometer (MS) data is collected. Three factors contribute to noise and artifacts in the MS data: (a) randomness in QCM outgassing flux, (b) MS measurement noise, and (c) constant chamber background contaminants. We present a two-step noise reduction approach that addresses these sources. First, we use QCM data to determine the number of outgassing species and kinetic parameters governing their desorption. Then, we apply these parameters to fit a linear statistical model to MS data, accounting for variance across the tested discretized mass spectrum. Once the variance is known for each mass bin, we use an adapted N-sigma method to isolate signal from noise. Our approach effectively reduces all three types of noise, improving confidence and efficiency in species identification and enabling MS-based modeling for isothermal outgassing kinetics. Although our analysis relies on the relationship between QCM and MS data, it may be applicable to other test procedures taking MS data concurrently with a measured source of mass flux.

PMID:41284274 | DOI:10.1021/jasms.5c00172