TPepRet: a deep learning model for characterizing T cell receptors-antigen binding patterns.

Motivation: T-cell receptors (TCRs) elicit and mediate the adaptive immune response by recognizing antigenic peptides, a process pivotal for cancer immunotherapy, vaccine design, and autoimmune disease management. Understanding the intricate binding patterns between TCRs and peptides is critical for advancing these clinical applications. While several computational tools have been developed, they neglect the directional semantics inherent in sequence data, which are essential for accurately characterizing TCR-peptide interactions.

Human-in-the-loop machine learning-based quantitative assessment of hemifacial spasm based on volumetric interpolated breath-hold examination MR.

Objective: The purpose of this study was to assess the severity of hemifacial spasm (HFS) through quantitative measures that associated it with neurovascular contact (NVC).

Methods: We enrolled 108 HFS patients (63 severe and 45 mild cases) and implemented a human-in-the-loop approach to develop a quantitative NVC feature package. This process involved using interactive segmentation on three-dimensional volumetric interpolated breath-hold examination (VIBE) MR images to delineate vascular and nerve structures.

Chemoprevention Strategies for Precancerous Gastric Lesions Beyond Helicobacter pylori Eradication.

Gastric cancer (GC) is a significant global health challenge, particularly in high-incidence regions like East Asia. Despite improvements in screening and treatment, the progressive nature of precancerous lesions-such as atrophic gastritis, intestinal metaplasia, and dysplasia-necessitates effective prevention strategies. This review evaluates the role of chemoprevention in GC, focusing on agents designed to target these precancerous lesions.

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data.

Motivation: Numerous microbiome studies have revealed significant associations between the microbiome and human health and disease. These findings have motivated researchers to explore the causal role of the microbiome in human complex traits and diseases. However, the complexities of microbiome data pose challenges for statistical analysis and interpretation of causal effects.

FSH exacerbates bone loss by promoting osteoclast energy metabolism through the CREB-MDH2-NAD axis.

Aims: Osteoclast energy metabolism is a promising target for treating diseases characterized by high osteoclast activity, such as osteoporosis. However, the regulatory factors involved in osteoclast bioenergetic processes are still in the early stages of being fully understood. This study reveals the effects of follicle-stimulating hormone (FSH) on osteoclast energy metabolism.

White lies for coral reefs: Dynamics of two-patch coral reefs model with asymmetric dispersal.

Coral reef ecosystem is a crucial component of marine ecosystems and is undergoing severe degradation due to the combined dural impact of environmental changes and human activities. Soundscape technology is an innovative coral reef restoration approach that attracts fish to degraded reefs. Inspired by such technique, a five-dimensional mathematical dynamical model incorporating the asymmetric dispersal of parrotfish is formulated to characterize the dynamic interaction among macroalgae, coral, algal turf, and parrotfish in coral reef ecosystem.

The influence of microplastics on hypertension-associated cardiovascular injury via the modulation of gut microbiota.

Microplastics (MPs) have been found to interfere with the gut microbiota and compromise the integrity of the gut barrier. Excessive exposure to MPs markedly elevates the risk of cardiovascular disease, yet their influence on hypertension remains elusive, calling for investigation into their potential impacts on blood pressure (BP) regulation. In the present study, an increase in the concentration of MPs was observed in the fecal samples of individuals suffering from hypertension, as compared to the controls.

Chronic Cr(VI) exposure-induced biotoxicity involved in liver microbiota-gut axis disruption in Phoxinus lagowskii Dybowski based on multi-omics technologies.

Cr(VI) is widely used in industry and has high toxicity, making it one of the most common environmental pollutants. Long-term exposure to Cr(VI) can cause metabolic disorders and tissue damage. However, the effects of Cr(VI) on liver and gut microbes in fish have rarely been reported.

A Comprehensive OBD Data Analysis Framework: Identification and Factor Analysis of High-Emission Heavy-Duty Vehicles.

On-Board Diagnostic (OBD) systems enable real-time monitoring of NOx emissions from heavy-duty diesel vehicles (HDDVs). However, few studies have focused on the root cause analysis of these emissions using OBD data. To address this gap, this study proposes an integrated analysis framework for HDDV NOx emissions that combines data processing, high-emission vehicle identification, and emission cause analysis.

Preexisting multimorbidity predicts greater mortality risks related to long-term PM exposure.

Long-term health risk assessments related to ambient fine particulate matter (PM) exposure have been more limited to general population but not towards individuals suffering from multimorbidity. While both multimorbidity and PM are independently linked to elevated mortality risk, their combined effects and interactions remain practically unexplored. A cross-cohort analysis was undertaken on data from 3 prospective cohorts, initially enrolling 869038 adults aged ≥18 years followed up during 2005-2022.

Speciation, Distribution and Environmental Risk of Dominant Silver-Containing Nanoparticles in the Taihu Lake, China.

Silver-containing nanoparticles (AgCNPs) have attracted increasing concerns because of their potential adverse effects on aquatic ecosystems. However, minimal information is available regarding their concentration, distribution, and speciation in the actual environment. In this work, different species of AgCNPs, including silver nanoparticles (AgNPs), silver chloride (AgCl NPs) and silver sulfide (AgS NPs) in water and sediment samples from Taihu Lake were analyzed by a multistep selective dissolution method combined with single-particle inductively coupled plasma mass spectrometry.

The risk assessment and burden of cancer attributable to dietary cadmium exposure in China, 2019.

Dietary Cadmium (Cd) intake is essential for Cd exposure. However, the burden of cancer attributable to dietary Cd intake remains to be determined in China. To estimate the level of dietary Cd exposure, we merged the Cd concentrations in food from literature and the foods consumption from national dietary surveys.

Geographic heterogeneity of polycyclic aromatic hydrocarbons in Yangtze River sediments: Evidence from the longest river in Asia.

This work is the first comprehensive survey of the Yangtze River, covering its origin to the estuary mouth. It focuses on the geographical and industrial factors influencing the distribution of polycyclic aromatic hydrocarbons (PAHs) in sediments, along with their contamination levels, sources, and ecological risks. The total concentrations of PAHs ranged from 2.

Proteomics analysis reveals the antagonistic interaction between high CO and warming in the adaptation of the marine diatom Thalassiosira weissflogii in future oceans.

While it is known that warming and rising CO level might interactively affect the long-term adaptation of marine diatoms, the molecular and physiological mechanisms underlying these interactions in the marine diatom Thalassiosira weissflogii on an evolutionary scale remain largely unexplored. In this study, we investigated the changes in metabolic pathways and physiological responses of T. weissflogii under long-term ocean acidification and/or warming conditions (∼3.

Progress in the genetics and epigenetics of pelvic floor disorder.

Pelvic floor disorder (PFD) is a common gynecological disorder, and with the ageing of the population, PFD has a serious impact on the physical and mental health of patients and their quality of life. The most prominent of these are pelvic organ prolapse (POP) and urinary incontinence (UI), about which the etiology is still unclear, and it is urgent to explore their pathogenesis. Advances in genetics and epigenetics have provided new insights into the pathophysiology of PFD.

Developmental endothelial locus-1 as a potential biomarker for the formation and progression of intracranial aneurysm.

Background: Intracranial aneurysms (IAs) are pathological dilations occurring at major branch points of cerebral arteries, which can lead to aneurysmal subarachnoid hemorrhage (aSAH) upon rupture. Recent studies have identified developmental endothelial locus-1 (DEL1) as closely associated with IA, though its role remains not fully understood. This study aimed to investigate serum DEL1 level differences in IA patients and explore its function in vascular endothelial cells.

Identification of novel hub gene and biological pathways associated with ferroptosis in In-Stent restenosis.

Background: In-stent restenosis (ISR) is one of the most significant complications following percutaneous coronary intervention (PCI) in patients with coronary artery disease (CAD). Ferroptosis is a novel cell death mode characterized by iron overload and lipid peroxidation. However, the role of ferroptosis in vascular smooth muscle cells (VSMCs) regulating neointimal formation during restenosis remains unclear.

Circulating miR-574-5p shows diagnostic and prognostic significance and regulates oxygen-glucose deprivation (OGD)-induced inflammatory activation of microglia by targeting ATP2B2.

Background: Early screening is critical for the prevention of ischemic stroke. miR-574-5p was considered a promising biomarker for ischemic stroke but lacks direct confirmation. This study evaluated miR-574-5p in discriminating ischemic stroke and predicting the severity and prognosis of patients, aiming to provide novel insights into the clinical prevention of ischemic stroke.

Performance of four thermophilic bacteria for primary sludge hydrolysis: Sludge disintegration and hydrolase activities.

Thermophilic bacteria (TB) pretreatment is an efficient and environmentally friendly way for accelerating sludge hydrolysis. In this study, a complete comparison of the hydrolysis performance of Bacillus sp. AT07-1 (X1), Parageobacillus toebii X2 (X2), Geobacillus kaustophilus X3 (X3) and Parageobacillus toebii R-35642 (X4) was performed.

Promoting caproate production using anaerobically digested sludge-derived biochar: Performances, mechanisms, and environmental impacts.

Carbon chain elongation offers a promising pathway for converting waste resources into caproate. However, challenges in yield and selectivity have limited its broader application. To address these limitations, anaerobically digested sludge-derived biochar (ADS-B) was incorporated into the carbon chain elongation process.

Effects of stratified microbial extracellular polymeric substances on microalgae dominant biofilm formation and nutrients turnover under batch and semi-continuous operation.

Extracellular polymeric substances (EPS) are well-acknowledged to accelerate microalgal biofilm formation, yet specific role of stratified EPS is unknown. Bacterial biofilm stratified EPS could enrich phosphorus, whether microalgal biofilm stratified EPS could also realize phosphorus or nitrogen enrichment remains unclarified. This study investigated microalgae dominant biofilm growth characteristics and nutrients removal via inoculating microalgae and stratified bacterial EPS at various microalgae:bacteria ratios.

Thyroxine alleviates interstitial lung disease induced by combined radiotherapy and immunotherapy.

Immune checkpoint blockade (ICB) combined with radiotherapy (RT) has improved patients survival, but also increased the risk of pulmonary adverse effects (AEs). Therefore, to explore potential drug targets for interstitial lung disease (ILD), we investigated the interaction of ICB and RT in pulmonary AEs using the disproportionality analysis and COX regression. Genome-wide association studies, transcriptome analysis, and vivo models highlighted the role of programmed death-ligand-1 (PD-L1) in ILD.