DASES: a database of alternative splicing for esophageal squamous cell carcinoma.

Esophageal carcinoma ranks as the sixth leading cause of cancer-related mortality globally, with esophageal squamous cell carcinoma (ESCC) being particularly prevalent among Asian populations. Alternative splicing (AS) plays a pivotal role in ESCC development and progression by generating diverse transcript isoforms. However, the current landscape lacks a specialized database focusing on alternative splicing events (ASEs) derived from a large number of ESCC cases. Additionally, most existing AS databases overlook the contribution of long non-coding RNAs (lncRNAs) in ESCC molecular mechanisms, predominantly focusing on mRNA-based ASE identification. To address these limitations, we deployed DASES (http://www.hxdsjzx.cn/DASES). Employing a combination of publicly available and in-house ESCC RNA-seq datasets, our extensive analysis of 346 samples, with 93% being paired tumor and adjacent non-tumor tissues, led to the identification of 257 novel lncRNAs in esophageal squamous cell carcinoma. Leveraging a paired comparison of tumor and adjacent normal tissues, DASES identified 59,094 ASEs that may be associated with ESCC. DASES fills a critical gap by providing comprehensive insights into ASEs in ESCC, encompassing lncRNAs and mRNA, thus facilitating a deeper understanding of ESCC molecular mechanisms and serving as a valuable resource for ESCC research communities.

Adverse health consequences of undiagnosed hearing loss at middle age: A prospective cohort study with the UK Biobank.

OBJECTIVES: Hearing impairment is common in the middle-aged population but remains largely undiagnosed and untreated. The knowledge about to what extent and how hearing impairment matters for health is currently lacking. Thus, we aimed to comprehensively examine the adverse health consequences as well as the comorbidity patterns of undiagnosed hearing loss. STUDY DESIGN: Based on the prospective cohort of the UK Biobank, we included 14,620 individuals (median age 61 years) with audiometry-determined (i.e., speech-in-noise test) objective hearing loss and 38,479 individuals with subjective hearing loss (i.e., tested negative but with self-reported hearing problems; median age 58 years) at recruitment (2006-2010), together with 29,240 and 38,479 matched unexposed individuals respectively. MAIN OUTCOME MEASURES: Cox regression was used to determine the associations of both hearing-loss exposures with the risk of 499 medical conditions and 14 cause-specific deaths, adjusting for ethnicity, annual household income, smoking and alcohol intake, exposure to working noise, and BMI. Comorbidity patterns following both exposures were visualized by comorbidity modules (i.e., sets of connected diseases) identified in the comorbidity network analyses. RESULTS: During a median follow-up of 9 years, 28 medical conditions and mortality related to nervous system disease showed significant associations with prior objective hearing loss. Subsequently, the comorbidity network identified four comorbidity modules (i.e., neurodegenerative, respiratory, psychiatric, and cardiometabolic diseases), with the most pronounced association noted for the module related to neurodegenerative diseases (meta-hazard ratio [HR] = 2.00, 95%confidence interval [CI] 1.67-2.39). For subjective hearing loss, we found 57 associated medical conditions, which were partitioned into four modules (i.e., diseases related to the digestive, psychiatric, inflammatory, and cardiometabolic systems), with meta-HRs varying from 1.17 to 1.25. CONCLUSIONS: Undiagnosed hearing loss captured by screening could identify individuals with at greater risk of multiple adverse health consequences, highlighting the importance of screening for speech-in-noise hearing impairment in the middle-aged population, for potential early diagnosis and intervention.

SurgSmart: an artificial intelligent system for quality control in laparoscopic cholecystectomy: an observational study.

BACKGROUND: The rate of bile duct injury in laparoscopic cholecystectomy (LC) continues to be high due to low critical view of safety (CVS) achievement and the absence of an effective quality control system. The development of an intelligent system enables the automatic quality control of LC surgery and, eventually, the mitigation of bile duct injury. This study aims to develop an intelligent surgical quality control system for LC and using the system to evaluate LC videos and investigate factors associated with CVS achievement. MATERIALS AND METHODS: SurgSmart, an intelligent system capable of recognizing surgical phases, disease severity, critical division action, and CVS automatically, was developed using training datasets. SurgSmart was also applied in another multicenter dataset to validate its application and investigate factors associated with CVS achievement. RESULTS: SurgSmart performed well in all models, with the critical division action model achieving the highest overall accuracy (98.49%), followed by the disease severity model (95.45%) and surgical phases model (88.61%). CVSI, CVSII, and CVSIII had an accuracy of 80.64, 97.62, and 78.87%, respectively. CVS was achieved in 4.33% in the system application dataset. In addition, the analysis indicated that surgeons at a higher hospital level had a higher CVS achievement rate. However, there was still considerable variation in CVS achievement among surgeons in the same hospital. CONCLUSIONS: SurgSmart, the surgical quality control system, performed admirably in our study. In addition, the system's initial application demonstrated its broad potential for use in surgical quality control.

Proliferative exhausted CD8+ T cells exacerbate long-lasting anti-tumor effects in human papillomavirus-positive head and neck squamous cell carcinoma.

The survival prognosis of human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) is largely different, and little is known about the anti-tumor mechanism of tumor-infiltrated exhausted CD8+ T cells (Tex) in HNSCC. We performed cell-level multi-omics sequencing on human HNSCC samples to decipher the multi-dimensional characteristics of Tex cells. A proliferative exhausted CD8+ T cell cluster (P-Tex) which was beneficial to survival outcomes of patients with HPV-positive HNSCC was identified. Interestingly, P-Tex cells expressed CDK4 genes as high as cancer cells, which could be simultaneously inhibited by CDK4 inhibitors and might be a potential reason for the ineffectiveness of CDK4 inhibitors in treating HPV-positive HNSCC. P-Tex cells could aggregate in the antigen-presenting cell niches and activate certain signaling pathways. Together, our findings suggest a promising role for P-Tex cells in the prognosis of patients with HPV-positive HNSCC by providing modest but persistent anti-tumor effects.

Association of sleep behaviour and pattern with the risk of glaucoma: a prospective cohort study in the UK Biobank.

OBJECTIVES: Given the role of intraocular pressure in glaucoma, the patient's sleeping pattern might contribute to the development and progression of glaucoma. We performed a study to understand the association between sleep behaviours and glaucoma. DESIGN: Our study was a prospective cohort study. SETTING: This was a prospective cohort study in the UK Biobank. Self-reported data on five sleep behaviours were collected using a questionnaire at baseline. We identified four sleep patterns based on a cluster analysis of the sleep behaviours. PARTICIPANTS: In the UK Biobank, 409 053 participants were recruited between 2006 and 2010 and followed for a diagnosis of glaucoma. We identified glaucoma as any hospital admission with a diagnosis of glaucoma, based on UK Biobank inpatient hospital data. Individuals who withdrew from the UK Biobank, or were diagnosed with glaucoma before recruitment, or had self-reported surgery or laser treatment for glaucoma, or had no information on sleep behaviors were excluded. PRIMARY AND SECONDARY OUTCOME MEASURES: We estimated hazard ratios (HRs) with 95% confidence intervals (CI) using Cox proportional hazards models to estimate the associations of different sleep behaviors, as well as identified sleep patterns, with the risk of glaucoma, adjusting for multiple confounders. RESULTS: Compared with individuals who had a healthy sleep pattern, an excess risk of any glaucoma was observed among individuals with snoring and daytime sleepiness (HR 1.11, 95% CI 1.03 to 1.19) or insomnia and short/long sleep duration (HR 1.13, 95% CI 1.06 to 1.20), but not late chronotype sleep pattern (HR 0.98, 95% CI 0.93 to 1.03). CONCLUSION: Snoring, daytime sleepiness, insomnia, and short/long duration, individually or jointly, were all associated with the risk of glaucoma. These findings underscore the need for sleep intervention for individuals at high risk of glaucoma as well as potential ophthalmologic screening among individuals with chronic sleep problems for glaucoma prevention.

The role of genetic predisposition in cardiovascular risk after cancer diagnosis: a matched cohort study of the UK Biobank.

BACKGROUND: Evidence is scarce regarding the potential modifying role of disease susceptibility on the association between a prior cancer diagnosis and cardiovascular disease (CVD). METHODS: We conducted a matched cohort study of UK Biobank including 78,860 individuals with a cancer diagnosis between January 1997 and January 2020, and 394,300 birth year and sex individually matched unexposed individuals. We used Cox model to assess the subsequent relative risk of CVD, which was further stratified by individual genetic predisposition. RESULTS: During nearly 23 years of follow-up, an elevated risk of CVD was constantly observed among cancer patients, compared to their matched unexposed individuals. Such excess risk was most pronounced (hazard ratio [HR] = 5.28, 95% confidence interval [CI] 4.90-5.69) within 3 months after a cancer diagnosis, which then decreased rapidly and stabilised for >6 months (HR = 1.22, 95% CI 1.19-1.24). For all the studied time periods, stratification analyses by both levels of polygenic risk score for CVD and by family history of CVD revealed higher estimates among individuals with lower genetic risk predisposition. CONCLUSIONS: Our findings suggest that patients with a recent cancer diagnosis were at an increased risk of multiple types of CVD and the excess CVD risk was higher among individuals with lower genetic susceptibility to CVD, highlighting a general need for enhanced psychological assistance and clinical surveillance of CVD among newly diagnosed cancer patients.

Medical conditions associated with coffee consumption: Disease-trajectory and comorbidity network analyses of a prospective cohort study in UK Biobank.

BACKGROUND: Habitual coffee consumption has been associated with multiple health benefits. A comprehensive analysis of disease trajectory and comorbidity networks in relation to coffee consumption is, however, currently lacking. OBJECTIVES: We aimed to comprehensively examine the health outcomes associated with habitual coffee consumption, through clarifying its disease trajectory and comorbidity networks. METHODS: Based on the UK Biobank cohort, we included 395,539 individuals with available information on coffee intake collected at recruitment between 2006 and 2010. These individuals were categorized as having low (<1 cup per day), moderate (1-3 cups), and high (≥4 cups) levels of coffee intake, and were followed through 2020 to ascertain 496 medical conditions. Cox regression was used to assess the associations between high-level coffee intake and the risk of medical conditions with a prevalence ≥0.5% in the study population, after adjusting for multiple confounders, using low-level coffee intake as the reference. Disease-trajectory and comorbidity network analyses were then applied to visualize the temporal and nontemporal relationships between the medical conditions that had an inverse association with high-level coffee intake. RESULTS: During a median follow-up of 11.8 years, 31 medical conditions were found to be associated with high-level coffee intake, among which 30 showed an inverse association (HRs ranged from 0.61 to 0.94). The inverse associations were more pronounced for women, compared with men. Disease-trajectory and comorbidity network analyses of these 30 conditions identified 4 major clusters of medical conditions, mainly in the cardiometabolic and gastrointestinal systems, among both men and women; 1 cluster of medical conditions following alcohol-related disorders, primarily among men; as well as a cluster of estrogen-related conditions among women. CONCLUSIONS: Habitual coffee consumption was associated with lower risks of many medical conditions, especially those in the cardiometabolic and gastrointestinal systems and those related to alcohol use and estrogen regulation.

Disease trajectories and mortality among individuals diagnosed with depression: a community-based cohort study in UK Biobank.

Patients with depression are at increased risk for a range of comorbid diseases, with, however, unclear explanations. In this large community-based cohort study of the UK Biobank, 24,130 patients diagnosed with depression were compared to 120,366 matched individuals without such a diagnosis. Follow-up was conducted from 6 months after the index date until death or the end of 2019, for the occurrence of 470 medical conditions and 16 specific causes of death. The median age at the time of the depression diagnosis was 62.0 years, and most of the patients were female (63.63%). During a median follow-up of 4.94 years, 129 medical conditions were found to be significantly associated with a prior diagnosis of depression, based on adjusted Cox regression models. Using disease trajectory network analysis to visualize the magnitude of disease-disease associations and the temporal order of the associated medical conditions, we identified three main affected disease clusters after depression (i.e., cardiometabolic diseases, chronic inflammatory diseases, and diseases related to tobacco abuse), which were further linked to a wider range of other conditions. In addition, we also identified three depression-mortality trajectories leading to death due to cardiovascular disease, respiratory system disease and malignant neoplasm. In conclusion, an inpatient diagnosis of depression in later life is associated with three distinct network-based clusters of medical conditions, indicating alterations in the cardiometabolic system, chronic status of inflammation, and tobacco abuse as key pathways to a wide range of other conditions downstream. If replicated, these pathways may constitute promising targets for the health promotion among depression patients.

Association between Serum Uric Acid and Nonalcoholic Fatty Liver Disease in Nonobese Postmenopausal Women: A Cross-sectional Study.

This study aimed to determine the association between serum uric acid (sUA) and nonalcoholic fatty liver disease (NAFLD) in nonobese postmenopausal women. A total of 4323 female individuals over 18 years of age participated in this cross-sectional study. The subjects were divided into four groups according to menopause status and body mass index. sUA quartiles in this female population were categorized as follows: Q1 ≤ 230 mmol/L, Q2: 231-270 mmol/L, Q3: 271-310 mmol/L and Q4: ≥ 311 mmol/L. The presence or absence of NAFLD was assessed by abdominal ultrasonography. The prevalence of NAFLD was 38.8% in the general population, and the average age was 46.5 ± 11.3 years. Among nonobese and obese subjects, the prevalence of NAFLD was lower in nonmenopausal subjects than in postmenopausal subjects (nonobese: 20.74% vs 45.26%, respectively, P < 0.0001; obese: 70.51% vs 84.35%, respectively, P < 0.0001). After adjusting for age, current smoking status, current alcohol drinking status, diabetes, hypertension disease and triglyceride, the ORs (95% CIs) for NAFLD among individuals in Q2-Q4 were 1.518 (1.062-2.169), 1.431 (1.010-2.027) and 2.054 (1.442-2.927), respectively, P value for trend <0.0001. Higher sUA levels can be used as a predictive biomarker for NAFLD in nonobese postmenopausal women.