Tag: pubmed

Genome Biol. 2025 Sep 9;26(1):272. doi: 10.1186/s13059-025-03709-0.

ABSTRACT

BACKGROUND: Most RNA-seq datasets harbor genes with extreme expression levels in some samples. Such extreme outliers are usually treated as technical errors and are removed from the data before further statistical analysis. Here we focus on the patterns of such outlier gene expression to investigate whether they provide insights into the underlying biology.

RESULTS: Our study is based on multiple datasets, including data from outbred and inbred mice, GTEx data from humans, data from different Drosophila species, and single-nuclei sequencing data from human brain tissues. All show comparable general patterns of outlier gene expression, indicating this as a generalizable biological effect. Different individuals can harbor very different numbers of outlier genes, with some individuals showing extreme numbers in only one out of several organs. Outlier gene expression occurs as part of co-regulatory modules, some of which correspond to known pathways. In a three-generation family analysis in mice, we find that most extreme over-expression is not inherited, but appears to be sporadically generated. Genes encoding prolactin and growth hormone are also among the co-regulated genes with extreme outlier expression, both in mice and humans, for which we include also a longitudinal expression analysis for protein data.

CONCLUSIONS: We show that outlier patterns of gene expression are a biological reality occurring universally across tissues and species. Most of the outlier expression is spontaneous and not inherited. We suggest that the outlier patterns reflect edge of chaos effects that are expected for systems of non-linear interactions and feedback loops, such as gene regulatory networks.

PMID:40926263 | DOI:10.1186/s13059-025-03709-0

Subst Abuse Treat Prev Policy. 2025 Sep 8;20(1):36. doi: 10.1186/s13011-025-00670-w.

ABSTRACT

BACKGROUND: Alcohol use disorder (AUD) is conceptualized as a dimensional phenomenon in the DSM-5, but electronic health records (EHRs) rely on binary AUD definitions according to the ICD-10. The present study classifies AUD severity levels using EHR data and tests whether increasing AUD severity levels are linked with increased comorbidity.

METHODS: Billing data from two German statutory health insurance companies in Hamburg included n = 21,954 adults diagnosed with alcohol-specific conditions between 2017 and 2021. Based on ICD-10 alcohol-specific diagnoses, patients were classified into five AUD severity levels: 1 (F10.0, T51.0 or T51.9); 2 (F10.1); 3 (F10.2); 4 (F10.3/4); 5 (K70 + or one of the following diagnoses: K70.0-4, K70.9, K85.2, K85.20, K86.0, 10.5-9, E24.4, G31.2, G62.1, G72.1, I42.6, K29.2). Generalized estimating equation regression models for count data (Poisson distribution) were used to assess associations with the Elixhauser Comorbidity Score (ECS).

RESULTS: Across the study period, the annual prevalence of any AUD diagnosis varied between 2.7% and 2.9%. A dose-response relationship was observed between AUD severity and ECS, indicating that individuals with higher AUD severity experience more comorbid conditions, particularly cardiovascular and liver diseases.

CONCLUSIONS: The proposal to define AUD severity levels based on ICD-10 diagnoses allows for a more nuanced analysis of AUD in EHR data.

PMID:40926261 | DOI:10.1186/s13011-025-00670-w

BMC Oral Health. 2025 Sep 8;25(1):1404. doi: 10.1186/s12903-025-06796-4.

ABSTRACT

AIM: The purpose of this study was to assess the accuracy of a customized deep learning model based on CNN and U-Net for detecting and segmenting the second mesiobuccal canal (MB2) of maxillary first molar teeth on cone beam computed tomography (CBCT) scans.

METHODOLOGY: CBCT scans of 37 patients were imported into 3D slicer software to crop and segment the canals of the mesiobuccal (MB) root of the maxillary first molar. The annotated data were divided into two groups: 80% for training and validation and 20% for testing. The data were used to train the AI model in 2 separate steps: a classification model based on a customized CNN and a segmentation model based on U-Net. A confusion matrix and receiver-operating characteristic (ROC) analysis were used in the statistical evaluation of the results of the classification model, whereas the Dice-coefficient (DCE) was used to express the segmentation accuracy.

RESULTS: F1 score, testing accuracy, recall and precision values were 0.93, 0.87, 1.0 and 0.87 respectively, for the cropped images of MB root of maxillary 1st molar teeth in the testing group. The testing loss was 0.4, and the area under the curve (AUC) value was 0.57. The segmentation accuracy results were satisfactory, where the DCE of training was 0.85 and DCE of testing was 0.79.

CONCLUSION: MB2 in the maxillary first molar can be precisely detected and segmented via the developed AI algorithm in CBCT images.

TRIAL REGISTRATION: Current Controlled Trial Number NCT05340140. April 22, 2022.

PMID:40926256 | DOI:10.1186/s12903-025-06796-4

Crit Care. 2025 Sep 8;29(1):395. doi: 10.1186/s13054-025-05649-4.

ABSTRACT

BACKGROUND: Gender disparities persist in medical research. This study assessed gender representation trends in first and senior authorships in the five highest-ranked critical care journals (by impact factor) over a 20-year period.

METHODS: We analyzed author gender distribution from 2005 to 2024. Author gender was determined using NamSor for web-based gender prediction. We assessed trends in female first, senior, and combined first and senior authorships by calculating percentages, and annual changes by linear regression for multiple and single author publications.

RESULTS: Among 42,970 articles, 34,743 had multiple authors and 8,227 had a single author. Despite progress over the past two decades, women remain underrepresented in critical care research leadership with 7.8% of publications having both female first and senior authors, compared to 56.7% with both positions held by men. Single authors were female in 23.6%. Linear regression showed increasing female authorships between – 0.1 and + 0.6% points per year depending on the journal, author position, and time period. Sensitivity analyses including only publications with more than 80% probability of correct gender classification yielded congruent results.

CONCLUSIONS: Despite small but constant growth rates of female representation as first or senior authors in high impact critical care journals over the past 20 years, women remain clearly underrepresented. Given the current rate of change, it will take decades to achieve gender parity. The observed gender disparity in authorships likely reflects underlying gender inequities in critical care career trajectories, highlighting the need for institutional changes.

PMID:40926253 | DOI:10.1186/s13054-025-05649-4

J Occup Med Toxicol. 2025 Sep 8;20(1):29. doi: 10.1186/s12995-025-00468-3.

ABSTRACT

BACKGROUND: This study examines trends in delta-9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH) positivity rates in pre-employment urine drug screenings at a single university-based hospital occupational medicine clinic from 2017 to 2022, following California’s recreational cannabis legalization in 2016, with sales beginning officially on January 1, 2018.

METHODS: Retrospective analysis of 21,546 de-identified urine drug screenings from 2017 to 2022 was conducted. Initial screening used instant urine drug immunoassays (50 ng/mL cutoff for THC-COOH), followed by confirmatory gas chromatography-mass spectrometry (15 ng/mL cutoff). Positivity rates were calculated annually, and descriptive statistics summarized age and gender distributions among positive cases. The Cochran-Armitage trend test assessed temporal trends.

RESULTS: Of 21,546 screenings, 92 (0.44%) were THC-COOH-positive. The positivity rate increased from 0.12% (4/3,215) in 2017 to 0.94% (45/4,784) in 2022 (Cochran-Armitage, Z = 5.19, p < 0.001), a 683.33% relative increase (absolute change: 0.82%). Among positive cases, 76% were aged 20-39 (mean: 29.00 years, SD = 9.5), and the female proportion rose from 25.00 to 62.22%. Median THC-COOH levels ranged from 60.00 to 176.50 ng/mL (overall: 145.0, IQR: 309.5).

CONCLUSION: THC-COOH positivity rates increased significantly post-legalization, potentially influenced by increased cannabis use. Urine tests detect past use, not impairment, highlighting the need for impairment-focused testing per Assembly Bill 2188 (2024). Missing total sample demographic data limit age/gender subgroup analyses.

PMID:40926239 | DOI:10.1186/s12995-025-00468-3

Microb Cell Fact. 2025 Sep 9;24(1):201. doi: 10.1186/s12934-025-02832-8.

ABSTRACT

BACKGROUND AND AIM: Synthetic dyes in the textile industry pose risks to human health and environmental safety. The current study aims to examine the efficacy of a novel esterase derived from an endophyte fungus in decolorizing diverse dyes, focusing on its production, purification, optimization, and characterization.

RESULTS: Trichoderma afroharzianum AUMC16433, a novel fungal endophyte with esterase-producing ability, was first detected from the cladodes of Opuntia ficus indica by ITS-rRNA sequencing. Furthermore, several fermentation variables that augment esterase production were improved by utilising the Plackett-Burman design and RSM. Ammonium sulphate precipitation at 60% and Sephacryl S300 HR gel filtration were employed to purify the isolated esterase to a specific activity of 1372.1 U/mg with a 2.29-fold increase and a recovery of 42.87%. The enzyme’s molecular weight was ascertained to be 43 kDa via SDS-PAGE. The isolated esterase revealed peak activity at 40 °C and pH 8. The kinetic characteristics of esterase were Vmax = 2.717 U/mL and Km = 3.33 mM. The half-life time was 54.4% at 50 °C after 4 h, and the enzyme still retained 14.7% of its activity after 24 h at 50 °C. Esterase decolorized several synthetic dyes used industrially, with the highest decolorization rate in malachite green after 24 h with 66%, and successfully degraded both bromothymol blue and tartrazine with 65.5% and 65.3%, respectively, in the same time frame. Crystal violet and methyl red showed moderate decolorization, with decolorization rates of 57.1% and 43.1%, respectively.

CONCLUSIONS: The esterase enzyme isolated for the first time from the new endophytic Trichoderma afroharzianum has a high dyes decolorization potential, which offers it a sustainable strategy for addressing environmental contamination issues.

PMID:40926235 | DOI:10.1186/s12934-025-02832-8

BMC Public Health. 2025 Sep 9;25(1):3046. doi: 10.1186/s12889-025-24015-1.

ABSTRACT

BACKGROUND: Mental health problems are common in the working-age population. More knowledge is needed on how to support work participation and reduce sickness absence. The objective of the study was to estimate the distribution of mental well-being and work capacity in women and men in a working population and assess the association between mental well-being and work capacity, while adjusting for sociodemographic characteristics, health status, and working positions.

METHODS: Cross-sectional data were collected through an online survey distributed to individuals who were currently working. The study population consisted of 8462 employees (58% women). The WHO-5 Mental Well-being Index (scale ranging from 0 to 100 with higher scores representing a better mental well-being) and the Capacity to Work Instrument (C2WI) (scale ranging from 14 to 56 with higher scores representing a more strained work capacity) were used. Univariable and multivariable linear regressions were used to assess the associations between self-perceived mental well-being and capacity to work, adjusting for sociodemographic characteristics, health status, and working positions.

RESULTS: Low self-perceived mental well-being and strained work capacity were more common among women, particularly younger aged (18-34 years). Poor health status was associated with strained work capacity in both men and women. Regression analyses showed that lower self-perceived mental well-being was significantly associated with strained work capacity. Among women, the fully adjusted model showed a regression coefficient (B) of – 0.253 (95% CI: -0.264 to – 0.242); among men, it was – 0.225 (95% CI: -0.237 to – 0.213).

CONCLUSIONS: This study, focusing on a currently working population, identified disparities in self-perceived mental well-being and work capacity across gender and age groups. These findings underscore the importance of early workplace interventions to support mental well-being and work capacity in these sub-groups. Notably, the association between the WHO-5 and C2WI may be partly attributable to item-level overlap, as certain C2WI items may capture symptoms related to mental health. This potential overlap should be considered when interpreting the findings.

PMID:40926225 | DOI:10.1186/s12889-025-24015-1

BMC Ophthalmol. 2025 Sep 9;25(1):500. doi: 10.1186/s12886-025-04247-w.

ABSTRACT

BACKGROUND: To evaluate the ganglion cell complex thickness in patients taking oral hydroxychloroquine.

METHODS: In this hospital-based, cross-sectional, non-interventional, comparative study, 87 eyes of 87 patients taking hydroxychloroquine were recruited. All the patients underwent complete ophthalmological evaluation along with dilated fundus examination. Patients were divided into two groups based on the duration of hydroxychloroquine intake: Group 1 (62 patients having duration of hydroxychloroquine intake < 5 years) and Group 2 (25 patients having duration of hydroxychloroquine intake ≥ 5 years). Age and gender-matched healthy volunteers with normal ocular findings were taken as controls. Average, superior, inferior GCC thickness, focal loss volume, and global loss volume were measured by RTvue XR Avanti SD-OCT.

RESULTS: The average, superior, and inferior GCC thicknesses were significantly reduced in both Group 1 (< 5 years) and Group 2 (≥ 5 years) as compared to controls (p < 0.001). In Group 1, mean GCC values were 94.70 ± 6.34 μm (average), 94.43 ± 6.28 μm (superior), and 94.74 ± 6.81 μm (inferior), while the corresponding values in controls were 99.79 ± 4.61 μm, 99.38 ± 4.63 μm, and 99.97 ± 4.61 μm. Likewise, FLV and GLV in Group 1 were 1.76 ± 2.5% and 4.07 ± 3.27%, significantly higher than in controls (0.72 ± 0.45% and 1.39 ± 1.1%, respectively; p = 0.002 for FLV, p = 0.001 for GLV). Similarly, in Group 2, mean GCC thicknesses were 92.70 ± 6.39 μm (average), 92.44 ± 5.92 μm (superior), and 93.32 ± 7.25 μm (inferior), all significantly lower than in controls (p < 0.001). While GLV was significantly elevated in Group 2 (4.46 ± 4.42%; p-0.003), the difference in FLV (1.23 ± 1.12%) was not statistically significant compared to controls (p-0.077).

CONCLUSION: The Ganglion Cell Complex thickness was significantly thinner in patients taking hydroxychloroquine along with elevated Focal Loss Volume % and Global Loss Volume %. However, no statistically significant correlation was observed between GCC thickness and duration of hydroxychloroquine use.

PMID:40926218 | DOI:10.1186/s12886-025-04247-w

BMC Psychiatry. 2025 Sep 9;25(1):854. doi: 10.1186/s12888-025-07296-z.

ABSTRACT

Obsessive-compulsive disorder (OCD) is a chronic and disabling condition affecting approximately 3.5% of the global population, with diagnosis on average delayed by 7.1 years or often confounded with other psychiatric disorders. Advances in electroencephalography (EEG) analysis using machine learning hold promise for the development of OCD-specific biological markers. This systematic review aims to evaluate studies that classify individuals with OCD from other groups based on EEG data. Following PRISMA guidelines, we searched the Web of Science, Scopus, PubMed, and IEEE databases through February 2025; of 42 screened studies, 11 met inclusion criteria for final analysis. Data were extracted across four domains: general information, population characteristics, EEG features, and machine learning features. Results revealed extensive heterogeneity in study populations, associated symptoms, EEG preprocessing methods, validation strategies, and reporting of model accuracy, underscoring the need for harmonized standards. Notably, only a few studies provided statistical interpretation of their models. None of reviewed studies employed modern interpretability techniques such as SHAP or LIME methods that, beyond reducing “black-box” opacity, can inform optimal electrode placement for neurofeedback or transcranial electrical stimulation. Many studies were constrained by cultural limitations, small sample sizes and lack of demographic information e.g., age, gender, medication. This work represents the first systematic review of EEG-ML classification studies in OCD and emphasizes the urgent need for methodological standardization in this emerging field.

PMID:40926215 | DOI:10.1186/s12888-025-07296-z

BMC Public Health. 2025 Sep 9;25(1):3039. doi: 10.1186/s12889-025-24447-9.

ABSTRACT

BACKGROUND: People living in prison face exceptionally high prevalence rates of tooth decay, periodontal disease, and poor oral health-related quality of life. Despite its importance, various aspects of oral healthcare in prison settings remain understudied. The present study investigates the barriers and facilitators associated with providing and utilizing oral health services in prison settings, drawing on insights from prison health experts, managerial and custodial staff, healthcare providers, and individuals with lived experience of imprisonment.

METHODS: From March to June 2023, a total of fifteen participants participated in semi-structured in-depth interviews. Interviews were conducted until data saturation to identify barriers and facilitators of oral health services in prisons. Potential areas for improvement were also explored. Thematic analysis was used to analyze the data. Themes and sub-themes were derived from the dataset and converted into preliminary codes which aligned with research objectives.

RESULTS: The first topic, barriers, included two themes: organizational barriers related to the provision of services, and individual barriers related to the utilization of services. The second topic, facilitating factors, included six themes: funding, community partnership, substance use treatment, communicating with policy makers, transportation, and education.

CONCLUSION: Ensuring the oral health of incarcerated individuals is a fundamental aspect of their right to health and a crucial factor in their successful reintegration into society. Formerly incarcerated people are often hard to reach in the community, making the period of confinement a unique opportunity to deliver quality oral healthcare. Given that most incarcerated individuals will eventually return to their communities, providing comprehensive healthcare, including oral health interventions, represents a valuable public health investment.

PMID:40926212 | DOI:10.1186/s12889-025-24447-9