Metabonomics and Transcriptomics Analyses Reveal the Underlying HPA-Axis-Related Mechanisms of Lethality in Exposed to Underwater Noise Pollution.

The problem of marine noise pollution has a long history. Strong noise (>120 dB re 1 µPa) will affects the growth, development, physiological responses, and behaviors of fish, and also can induce the stress response, posing a mortal threat. Although many studies have reported that underwater noise may affect the survival of fish by disturbing their nervous system and endocrine system, the underlying causes of death due to noise stimulation remain unknown.

stSNV: a comprehensive resource of SNVs in spatial transcriptome.

Single nucleotide variants (SNVs), as important components of genetic variation, affect gene expression, function and phenotype. Mining and summarizing the spatial distribution of SNVs in diseased and normal tissues for a better understanding of their characteristics and potential roles in cell-lineage determination, aging, or disease occurrence is significant. Herein, we have developed a comprehensive spatial mutation resource stSNV (http://bio-bigdata.

Dimension reduction, cell clustering, and cell-cell communication inference for single-cell transcriptomics with DcjComm.

Advances in single-cell transcriptomics provide an unprecedented opportunity to explore complex biological processes. However, computational methods for analyzing single-cell transcriptomics still have room for improvement especially in dimension reduction, cell clustering, and cell-cell communication inference. Herein, we propose a versatile method, named DcjComm, for comprehensive analysis of single-cell transcriptomics.

Anti-CTLA-4 m2a Antibody Exacerbates Cardiac Injury in Experimental Autoimmune Myocarditis Mice By Promoting Ccl5-Neutrophil Infiltration.

The risk for suffering immune checkpoint inhibitors (ICIs)-associated myocarditis increases in patients with pre-existing conditions and the mechanisms remain to be clarified. Spatial transcriptomics, single-cell RNA sequencing, and flow cytometry are used to decipher how anti-cytotoxic T lymphocyte antigen-4 m2a antibody (anti-CTLA-4 m2a antibody) aggravated cardiac injury in experimental autoimmune myocarditis (EAM) mice. It is found that anti-CTLA-4 m2a antibody increases cardiac fibroblast-derived C-X-C motif chemokine ligand 1 (Cxcl1), which promots neutrophil infiltration to the myocarditic zones (MZs) of EAM mice via enhanced Cxcl1-Cxcr2 chemotaxis.

A comprehensive review of the botany, phytochemistry, pharmacology, and toxicology of Murrayae Folium et Cacumen.

Murrayae Folium et Cacumen (MFC) is a plant considered to be a traditional Chinese medicine with culinary value as well. The dry leaves and twigs of and are used to treat stomach aches, rheumatism, toothaches, swelling, and insect and snake bites. They are also used to prepare spicy chicken dishes.

A comparative analysis of TCR immune repertoire in COVID-19 patients.

The coronavirus disease 2019 (COVID-19) has merged as a global health threat since its outbreak in December 2019. Despite widespread recognition, there has been a paucity of studies focusing on the T cell receptor (TCR) bias in adaptive immunity induced by SARS-CoV-2. This research conducted a comparative analysis of the TCR immune repertoire to identify notable αβ TCR bias sequences associated with the SARS-CoV-2 virus antigen.

Metabonomics and Transcriptomics Analyses Reveal the Development Process of the Auditory System in the Embryonic Development Period of the Small Yellow Croaker under Background Noise.

Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment.

Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor.

Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis.

DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data.

Motivation: Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA sequencing (scRNA-seq) technologies, it is of high importance to identify CCIs from the ever-increasing scRNA-seq data. However, limited by the algorithmic constraints, current computational methods based on statistical strategies ignore some key latent information contained in scRNA-seq data with high sparsity and heterogeneity.

Research progress of plant-derived natural alkaloids in central nervous system diseases.

Central nervous system (CNS) disease is one of the most important causes of human death. Because of their complex pathogenesis, more and more attention has been paid to them. At present, drug treatment of the CNS is the main means; however, most drugs only relieve symptoms, and some have certain toxicity and side effects.

A multifactorial analysis of FAP to regulate gastrointestinal cancers progression.

Background: Fibroblast activation protein (FAP) is a cell-surface serine protease that has both dipeptidyl peptidase as well as endopeptidase activities and could cleave substrates at post-proline bond. Previous findings showed that FAP was hard to be detected in normal tissues but significantly up-regulated in remodeling sites like fibrosis, atherosclerosis, arthritis and embryonic tissues. Though increasing evidence has demonstrated the importance of FAP in cancer progression, no multifactorial analysis has been developed to investigate its function in gastrointestinal cancers until now.

An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation.

Single-cell RNA sequencing (scRNA-seq) detects whole transcriptome signals for large amounts of individual cells and is powerful for determining cell-to-cell differences and investigating the functional characteristics of various cell types. scRNA-seq datasets are usually sparse and highly noisy. Many steps in the scRNA-seq analysis workflow, including reasonable gene selection, cell clustering and annotation, as well as discovering the underlying biological mechanisms from such datasets, are difficult.

Identification of shared characteristics in tumor-infiltrating T cells across 15 cancers.

Tumor-infiltrating T cells are essential players in tumor immunotherapy. Great progress has been achieved in the investigation of T cell heterogeneity. However, little is well known about the shared characteristics of tumor-infiltrating T cells across cancers.

Low blood carotenoid status in dementia and mild cognitive impairment: A systematic review and meta-analysis.

Background: Given their potent antioxidation properties, carotenoids play a role in delaying and preventing dementia and mild cognitive impairment (MCI). However, observational studies have found inconsistent results regarding the associations between blood carotenoid levels and the risk of dementia and MCI. We conducted this systematic review and meta-analysis to investigate the relationship between blood carotenoid levels and the risk of dementia and MCI.

Single-cell transcriptomics reveals the interaction between peripheral CD4 CTLs and mesencephalic endothelial cells mediated by IFNG in Parkinson's disease.

Parkinson's disease (PD) is characterized by dopaminergic neurons degeneration in the substantia nigra pars compacta. Increasing evidence indicates that peripheral CD4 T cells, a vital pathological component of PD, have been implicated in systemic inflammation activation, blood-brain barrier (BBB) dysfunction, central nervous system infiltration, and consequent neurons degeneration. However, there is no consensus on CD4 T cell types' exact phenotypic characteristics in systemic inflammation and the mechanism of CD4 T cells traffic into the BBB in patients with PD.

Ent-kauranes and ent-atisanes from Euphorbia wallichii and their anti-inflammatory activity.

Phytochemical investigation on the whole plant of Euphorbia wallichii led to the identification of twelve diterpenoids, including nine undescribed ones, in which wallkauranes A-E (1-5) were classified as ent-kaurane diterpenoids and wallatisanes A-D (6-9) were assigned as ent-atisane diterpenoids. The biological evaluation of these isolates against NO production was conducted in the LPS-induced RAW264.7 macrophage cells model, resulting in the identification of a series of potent NO inhibitors, with the most active wallkaurane A showing an IC value of 4.

Regional transcriptional vulnerability to basal forebrain functional dysconnectivity in mild cognitive impairment patients.

Nucleus basalis of Meynert (NbM), one of the earliest targets of Alzheimer's disease (AD), may act as a seed for pathological spreading to its connected regions. However, the underlying basis of regional vulnerability to NbM dysconnectivity remains unclear. NbM functional dysconnectivity was assessed using resting-state fMRI data of health controls and mild cognitive impairment (MCI) patients from the Alzheimer's disease Neuroimaging Initiative (ADNI2/GO phase).

Association between financial toxicity and health-related quality of life in cancer survivors: A systematic review.

Over the past decade, the number of cancer cases has continued to rise, placing a heavy burden on patients' families and healthcare systems. Although innovative treatments and drugs have improved patient outcomes, the financial toxicity (FT) of treatment is a growing concern among oncologists. Previous research have examined the impacts of FT on the HRQOL of cancer patients.

Assessment of self-reported financial toxicity among patients with nasopharyngeal carcinoma undergoing radiotherapy: A cross-sectional study in western China.

Objective : Using the Comprehensive Score for Financial Toxicity (COST) tool to measure financial toxicity (FT) among nasopharyngeal cancer (NPC) patients in western China and investigate the association between FT and psychological distress.

Methods: We conducted a cross-sectional study of survivors with NPC in a tertiary oncology hospital in China. FT was assessed using the COST (Chinese version), a validated instrument widely used both at home and abroad.

iASPP suppression mediates terminal UPR and improves BRAF-inhibitor sensitivity of colon cancers.

Unfolded protein response (UPR) signaling is activated under endoplasmic reticulum (ER) stress, an emerging cancer hallmark, leading to either adaptive survival or cell death, while the mechanisms underlying adaptation-death switch remain poorly understood. Here, we examined whether oncogene iASPP regulates the switch and how the mechanisms can be used in colon cancer treatment. iASPP is downregulated when cells undergo transition from adaptation to death during therapy-induced ER stress.

Prevalence and risk factors of self-reported financial toxicity in cancer survivors: A systematic review and meta-analyses.

Background: Similar to the side effects of cancer treatment, financial toxicity (FT) can affect the quality of life of patients, which has attracted increasing attention in the field of oncology. Despite the fact that the estimated prevalence and risk factors of FT are widely reported, these results have not been synthesized.

Objectives: This review is aimed to systematically assess the prevalence and risk factors of self-reported FT.