Association between Solid Cooking Fuel Use and Frailty Trajectories: Findings from a Nationwide Cohort in China.

Objective: Burning solid cooking fuel contributes to household air pollution and is associated with frailty. However, how solid cooking fuel use contributes to the development of frailty has not been well illustrated.

Methods: This study recruited 8,947 participants aged ≥ 45 years from the China Health and Retirement Longitudinal Study, 2011-2018.

Procyanidin B2 Attenuates Pathologic Cardiac Fibrosis and Inflammation: Role of PPARγ.

Procyanidin B2 (PB2) is a prominent procyanidin isomer. Its effects and mechanisms in cardiac remodeling are not fully understood. Peroxisome proliferator-activated receptor gamma (PPAR-γ) plays a crucial role in regulating cardiac hypertrophy, fibrosis, and inflammation.

Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.

Latest advancements in the high-throughput single-cell genome (scDNA) and transcriptome (scRNA) sequencing technologies enabled cell-resolved investigation of tissue clones. However, it remains challenging to cluster and couple single cells for heterogeneous scRNA and scDNA data generated from the same specimen. In this study, we present a computational framework called CCNMF, which employs a novel Coupled-Clone Non-negative Matrix Factorization technique to jointly infer clonal structure for matched scDNA and scRNA data.

A comparative study of structural variant calling in WGS from Alzheimer's disease families.

Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins.

Molecular mechanism of NAD and NMN binding to the Nudix homology domains of DBC1.

Deleted in breast cancer 1 (DBC1) is a human nuclear protein that modulates the activities of various proteins involved in cell survival and cancer progression. Oxidized form of nicotinamide adenine dinucleotide (NAD) is suggested to bind to the Nudix homology domains (NHDs) of DBC1, thereby regulating DBC1-Poly (ADP-ribose) polymerase 1 (PARP1) interactions, resulting in the restoration of DNA repair. Using Nuclear Magnetic Resonance (NMR) and Isothermal Titration Calorimetry (ITC), we confirmed NAD and its precursor nicotinamide mononucleotide (NMN) both bind the NHD domain of DBC1 (DBC1).

Mechanism through which the hsa-circ_0000992- hsa- miR- 936-AKT3 regulatory network promotes the PM-induced inflammatory response in human bronchial epithelial cells.

Background: Studies have shown that fine particulate matter (PM) remains a significant problem in developing countries and plays a critical role in the onset and progression of respiratory illnesses. Circular RNAs (circRNAs) are involved in many pathophysiological processes,but their relationship to PM pollution is largely unexplored.

Objectives: To elucidate the functional role of hsa_circ_0000992 in PM-induced inflammation in a human bronchial epithelial cell line (16HBE) and to clarify whether the competing endogenous RNA (ceRNA) mechanism is involved in the interrelationships between hsa_circ_0000992 and hsa-miR-936 and the inflammatory signaling pathways.

Crystal Structure of Fungal Nonspecific Phospholipase C Unveils a Distinct Catalytic Mechanism.

Nonspecific phospholipase C (NPC) plays a pivotal role in hydrolyzing phospholipids, releasing diacylglycerol─an essential second messenger. Extensive research has elucidated the structure and function of bacterial and plant NPCs, but our understanding of their fungal counterparts remains limited. Here, we present the first crystal structure of a fungal NPC derived from (RePLC), unraveling its distinguishable features divergent from other known phospholipase C.

: A high-throughput tool for alignment-free phylogenetics.

Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present , a novel high-throughput tool for alignment-free phylogenetic analysis. computes the pairwise distance matrix between molecular sequences, using seven widely accepted -mer based distance measures.

Tumor tissue microorganisms are closely associated with tumor immune subtypes.

Studies have found that different immune subtypes are present in the same tumor. Different tumor subtypes have different tumor microenvironments (TME). This means that the efficacy of immunotherapy in actual applications will, therefore, have different results.

Regularized survival learning and cross-database analysis enabled identification of colorectal cancer prognosis-related immune genes.

Colon adenocarcinoma is the most common type of colorectal cancer. The prognosis of advanced colorectal cancer patients who received treatment is still very poor. Therefore, identifying new biomarkers for prognosis prediction has important significance for improving treatment strategies.

Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites.

High-grade (grade 3) neuroendocrine neoplasms (G3 NENs) have poor survival outcomes. From a clinical standpoint, G3 NENs are usually grouped regardless of primary site and treated similarly. Little is known regarding the underlying genomics of these rare tumors, especially when compared across different primary sites.

Joint Analysis of Microbial and Immune Cell Abundance in Liver Cancer Tissue Using a Gene Expression Profile Deconvolution Algorithm Combined With Foreign Read Remapping.

Recent transcriptomics and metagenomics studies showed that tissue-infiltrating immune cells and bacteria interact with cancer cells to shape oncogenesis. This interaction and its effects remain to be elucidated. However, it is technically difficult to co-quantify immune cells and bacteria in their respective microenvironments.

Prediction of breast cancer risk based on flow variant analysis of circulating peripheral blood mononuclear cells.

Identifying women at high risk for developing breast cancer is potentially lifesaving. Patients with pathogenic genetic variants can embark on a program of surveillance for early detection, chemoprevention, and/or prophylactic surgery. Newly diagnosed cancer patients can also use the results of gene panel sequencing to make decisions about surgery; therefore, rapid turnaround time for results is critical.

Differential effects of phenolic extracts from red-fleshed apple peels and flesh induced G1 cell cycle arrest and apoptosis in human breast cancer MDA-MB-231 cells.

Red-fleshedapples are preferredbecause of their high content of phenolics and antioxidants in peel and pulp. Herein, we evaluated the mechanisms of apple peel polyphenolic extracts (APP) and apple flesh polyphenolic extracts (AFP) from the new red-fleshed apple in inhibiting cell proliferation and inducing apoptosis on human breast cancer MDA-MB-231 cells. The antiproliferative activities were determined by the CCK8 assay.

Transcriptional Changes in CD16+ Monocytes May Contribute to the Pathogenesis of COVID-19.

The COVID-19 pandemic has caused more than three million deaths globally. The severity of the disease is characterized, in part, by a dysregulated immune response. CD16+ monocytes are innate immune cells involved in inflammatory responses to viral infections, and tissue repair, among other functions.

Phytochemical profiles, antioxidant, and antiproliferative activities of red-fleshed apple as affected by in vitro digestion.

The aim of this study was to characterize the phenolic profiles in the extracts and digesta (after in vitro digestion) of different red-fleshed apple fruit parts and to assess the effects of digestion on the in vitro antioxidant capacity and antiproliferative activity. The main polyphenols were identified by UPLC-MS/MS and HPLC. Our results indicate that the digesta had less total phenolics, flavonoids, and anthocyanins, but more free phenolic acids, than the extracts.

[A genetic sub-structure study of the Tibetan population in Southwest China].

Tibetan is a typical ethnic minority population in Southwest China, which can be divided into U-Tsang, Kham, Amdo, Jiarong and other sub-populations. However, the genetic structure of these sub-populations has not been comprehensively analyzed, especially from the perspective of paternal and maternal lineages. Based on genetic markers of autosomes, the Y chromosome and mitochondria, we studied four Tibetan populations (the U-Tsang population in Tibet Autonomous Region; the Kham population in Garze, Sichuan province; the Amdo population in Qinghai province and the Jiarong population in Aba, Sichuan province) to interpret their genetic structure.

[Human facial shape related SNP analysis in Han Chinese populations].

Human facial morphology is one of the important visible biological characteristics. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. This study extracted 136 Euclidean distance phenotypes from 17 facial features of high-resolution 3D facial images in 1177 Chinese Han adult males.

The ancestry inference of Chinese populations using 74-plex SNPs system.

A panel of ancestry informative SNPs (AISNPs) can be used to analyze the genetic components of a population and infer the ancestral origin of a DNA sample. Previously, we have selected a 74-AISNPs panel and used it to infer the ancestry of unknown individuals in the following ten geographical regions: Sub-Saharan Africa, North Africa, Europe, Pacific, Americas, Southwest Asia, South Asia, North Asia, East Asia and Southeast Asia. We have also established a 74-plex SNPs assay based on SEQUENOM system.

Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.

DNA copy number aberrations (CNA) are frequently observed in colorectal cancers (CRC). There is an urgent need for CNA-based biomarkers in clinics,. n For Stage III CRC, if combined with imaging or pathologic evidence, these markers promise more precise care.

Phytochemical profiles, antioxidant, and antiproliferative activities of four red-fleshed apple varieties in China.

Red-fleshed apples are preferred because of their high content of phenolics and antioxidants. In this study, the phenolic characteristics, antioxidant properties, and antihuman cancer cell properties of the four hybrids of Malus sieversii f. niedzwetzkyana (Ledeb.

The statistical power of -mer based aggregative statistics for alignment-free detection of horizontal gene transfer.

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer (HGT). However, with the rapid increase of sequencing depth, hundreds of thousands of contigs are routinely assembled from metagenomics studies, which challenges alignment-based HGT analysis by overwhelming the known reference sequences. Detecting HGT by -mer statistics thus becomes an attractive alternative.

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls.

The human gut microbiota plays a major role in maintaining human health and was recently recognized as a promising target for disease prevention and treatment. Many diseases are traceable to microbiota dysbiosis, implicating altered gut microbial ecosystems, or, in many cases, disrupted microbial enzymes carrying out essential physio-biochemical reactions. Thus, the changes of essential microbial enzyme levels may predict human disorders.

Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.

The human genome is composed of two haplotypes, otherwise called diplotypes, which denote phased polymorphisms and structural variations (SVs) that are derived from both parents. Diplotypes place genetic variants in the context of cis-related variants from a diploid genome. As a result, they provide valuable information about hereditary transmission, context of SV, regulation of gene expression and other features which are informative for understanding human genetics.