Diagnostic accuracy of metagenomic next-generation sequencing in pulmonary tuberculosis: a systematic review and meta-analysis.

Background: Metagenomic next-generation sequencing (mNGS) has emerged as a promising tool in clinical practice due to its unbiased approach to pathogen detection. Its diagnostic performance in pulmonary tuberculosis (PTB), however, remains to be fully evaluated.

Objective: This study aims to systematically review and Meta-analyze the diagnostic accuracy of mNGS in patients with PTB.

Mouse Tail-Skin Dissociation and Preparation of Live Single-Cell Suspension for Downstream Analysis of Melanocytes.

Isolating high-quality viable single cells from mouse tail skin, a well-established model for studying skin cells and melanoma pathogenesis, is challenging due to the presence of dense connective tissue and hair follicles. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying skin cell heterogeneity. However, the lack of a robust protocol for the efficient generation of highly viable single-cell suspension from mouse tail skin has limited its application for studying melanocyte-interacting cells and characterizing the melanocyte niche.

Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites.

Background: Breast cancer, the most common cancer type among women, was recently found to contain a specific tumor microbiome, but its impact on host biology remains unclear. CD8 tumor-infiltrating lymphocytes (TILs) are pivotal effectors of anti-tumor immunity that influence cancer prognosis and response to therapy. This study aims to elucidate interactions between CD8 TILs and the breast tumor microbiome and metabolites, as well as how the breast tumor microbiome may affect the tumor metabolome.

Real-world efficacy and safety of open-source automated insulin delivery for people with type 1 diabetes mellitus: Experience from mainland China.

Background: Open-source automated insulin delivery systems are increasingly adopted yet predominantly discussed outside of Asia. This study aimed to describe efficacy and safety of android artificial pancreas (AAPS) in people with type 1 diabetes mellitus (T1DM) from mainland China.

Methods: This real-world study recruited people who initiated AAPS for ≥ 3 months between 2019 and 2024.

The efficacy and safety of anlotinib combined with chemotherapy in treatment of advanced soft tissue sarcoma.

Background: To evaluate the efficacy and safety of anlotinib combined with chemotherapy in the treatment of advanced soft tissue sarcoma (STS).

Methods: A total of 14 patients with advanced STS consisting of 4 liposarcoma, 3 undifferentiated polymorphous sarcoma, 2 synovial sarcoma, 1 Extraosseous ewing sarcoma, 1 spindle cell sarcoma, 1 Sarcomatoid malignant mesothelioma, 1 hemangiosarcoma, and 1 fibrosarcoma, were treated with anlotinib plus chemotherapy. The anlotinib was combined with chemotherapy as the first-line treatment in 13 patients, and as second-line treatment in 1 patient.

Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.

Circulating cell-free DNA (cfDNA) fragment end motif profiles are a promising biomarker in precision oncology. Here, we present a protocol for analyzing plasma cfDNA fragment end motifs from ultra-low-pass whole-genome sequencing (WGS) data. We detail a pipeline composed of sequential bash scripts for processing post-alignment BAM files.

Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.

DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads.

Correlation between triglyceride-glucose index and diabetic kidney disease risk in adults with type 1 diabetes mellitus.

Background: The triglyceride-glucose (TyG) index is identified as an alternative indicator of insulin resistance (IR) and is associated with macro- and micro-vascular diseases among patients with type 2 diabetes mellitus. The relationship between the TyG index and IR and its impact on diabetic kidney disease (DKD) remains unclear among adults with type 1 diabetes mellitus(T1DM).

Methods: This study comprised a cross-sectional analysis using data from the Guangdong T1DM Translational Medicine Study (GTT) and a longitudinal analysis using data from the type 1 diabetes (T1D) Exchange registry study.

Geniposide ameliorates diabetic nephropathy in type 2 diabetic mice by targeting AGEs-RAGE-dependent inflammatory pathway.

Background: Diabetic nephropathy (DN) is a prevalent complication of diabetes mellitus and the primary cause of morbidity and mortality in end-stage renal disease. The receptor for advanced glycation end products (RAGE) plays a crucial role in mediating AGE-triggered inflammation, which has been implicated in DN pathogenesis. While geniposide, a natural compound, has demonstrated anti-inflammatory and hypoglycemic properties, its potential to mitigate AGE-induced renal inflammation and consequently impede DN progression remains unexplored.

Giraffe: A tool for comprehensive processing and visualization of multiple long-read sequencing data.

Third-generation sequencing techniques have become increasingly popular due to their capacity to produce long, high-quality reads. Effective comparative analysis across various samples and sequencing platforms is essential for understanding biological mechanisms and establishing benchmark baselines. However, existing tools for long-read sequencing predominantly focus on quality control (QC) and processing for individual samples, complicating the comparison of multiple datasets.

(+)-Catechins Play a Protective Role in Diabetic Kidney Disease by Alleviating EMT through Multiple Pathways.

Scope: Diabetic nephropathy (DN), a complication of diabetes mellitus, is becoming a significant global health concern, with no complete cure currently available. Tea is regarded as an essential component of a balanced diet and contains (+)-Catechin (CE), which exert a range of pharmacological effects. Consequently, CE may be a potential treatment for DN.

Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing.

Nanopore sequencing technologies have enabled the direct detection of base modifications in DNA or RNA molecules. Despite these advancements, the tools for visualizing electrical current, essential for analyzing base modifications, are often lacking in clarity and compatibility with diverse nanopore pipelines. Here, we present Nanopore Current Events Magnifier (nanoCEM, https://github.

Lag effect of ambient temperature on respiratory emergency department visits in Beijing: a time series and pooled analysis.

Background: Although the association between ambient temperature and mortality of respiratory diseases was numerously documented, the association between various ambient temperature levels and respiratory emergency department (ED) visits has not been well studied. A recent investigation of the association between respiratory ED visits and various levels of ambient temperature was conducted in Beijing, China.

Methods: Daily meteorological data, air pollution data, and respiratory ED visits data from 2017 to 2018 were collected in Beijing.

Genome‑wide analysis of the MYB gene family in pumpkin.

The gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the genes of were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition.

Aquaporin ZmTIP2;3 Promotes Drought Resistance of Maize through Symbiosis with Arbuscular Mycorrhizal Fungi.

Arbuscular mycorrhizal fungi symbiosis plays important roles in enhancing plant tolerance to biotic and abiotic stresses. Aquaporins have also been linked to improved drought tolerance in plants and the regulation of water transport. However, the mechanisms that underlie this association remain to be further explored.

A SCYL2 gene from Oryza sativa is involved in phytosterol accumulation and regulates plant growth and salt stress.

Rice is a crucial food for humans due to its high nutritional value. Phytosterols, essential components of the plant membrane lipid bilayer, play a vital role in plant growth and contribute significantly to lipid-lowering, antitumor, and immunomodulation processes. In this study, SCY1-like protein kinases 2 (SCYL2) was found to be closely related to the accumulation of phytosterols.

Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing.

The escalating prevalence of multidrug-resistant (MDR) bacteria pose a significant public health threat. Understanding the genomic features and deciphering the antibiotic resistance profiles of these pathogens is crucial for development of effective surveillance and treatment strategies. In this study, we employed the R10.

Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.

This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes.

Impact of ambient temperature, diurnal temperature range on hyperventilation syndrome emergency admission: a time-series analysis in Beijing, China.

Objectives: To assess the association between ambient temperature and diurnal temperature range (DTR) on emergency admissions for hyperventilation syndrome (HVS).

Design: Distributed lag non-linear model design was used with a lag time to 5 days.

Setting: Emergency admission data used were from the Beijing Red Cross Emergency Centre (2017-2018).

Screening immune-related blood biomarkers for DKD-related HCC using machine learning.

Background: Diabetes mellitus is a significant health problem worldwide, often leading to diabetic kidney disease (DKD), which may also influence the occurrence of hepatocellular carcinoma (HCC). However, the relationship and diagnostic biomarkers between DKD and HCC are unclear.

Methods: Using public database data, we screened DKD secretory RNAs and HCC essential genes by limma and WGCNA.

Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome.

Individuals with PTEN hamartoma tumor syndrome (PHTS) harbor pathogenic germline PTEN variants that confer a significantly increased lifetime risk of various organ-specific cancers including second primary malignant neoplasms (SMNs). Currently, there are no reliable biomarkers that can predict individual-level cancer risk. Despite the highly promising value of cell-free DNA (cfDNA) as a biomarker for underlying sporadic cancers, the utility of cfDNA in individuals with known cancer-associated germline variants and subclinical cancers remains poorly understood.