A comprehensive immune repertoire signature distinguishes pulmonary infiltration in SARS-CoV-2 Omicron variant infection.

Introduction: The coronavirus disease 2019 (COVID-19) global pandemic has been the most severe public health emergency since 2019. Currently, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most dominant. The most prominent symptom of SARS-CoV-2 infection is respiratory.

Cell-Free DNA in Plasma Reveals Genomic Similarity Between Biliary Tract Inflammatory Lesion and Biliary Tract Cancer.

Unlabelled: Similar clinical manifestations and imaging features between biliary tract inflammatory lesion (BTI) and biliary tract cancer (BTC) pose significant challenges for the management of BTC. To date, the molecular characteristics of the relationship between biliary tract inflammatory lesion and biliary tract cancer remain poorly elucidated. Here, we performed target deep sequencing on 45 BTC patients and 31 BTI patients based on cell-free DNA (cfDNA) in plasma.

Higher patient activation is associated with lower odds of functional limitation in older adults with chronic diseases.

Objectives: To investigate the association between patient activation and functional limitation among older adults living with multiple chronic conditions.

Methods: We performed a secondary analysis of a parent study, which examined the relationship between self-efficacy and both inflammatory biomarkers and frailty. We conducted multivariate logistic regression while controlling for the patients' sociodemographic variables and comorbidities to examine the association between self-reported functional limitation and patient activation as measured by the Patient Activation Measure (PAM-10).

Computational Identification of Migrating T cells in Spatial Transcriptomics Data.

T cells are the central players in antitumor immunity, and effective tumor killing depends on their ability to infiltrate into the tumor microenvironment (TME) while maintaining normal cytotoxicity. However, late-stage tumors develop immunosuppressive mechanisms that impede T cell movement and induce exhaustion. Investigating T cell migration in human tumors in vivo could provide novel insights into tumor immune escape, although it remains a challenging task.

Effect of novel non-coding small RNA111 of Pseudomonas aeruginosa on bacterial virulence.

Pseudomonas aeruginosa is an important gram-negative pathogen that often causes skin, respiratory, and bloodstream infections. The virulence of P. aeruginosa is regulated by sRNAs through a complex network, which is still incompletely understood.

BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data.

The field of spatially resolved transcriptomics (SRT) has greatly advanced our understanding of cellular microenvironments by integrating spatial information with molecular data collected from multiple tissue sections or individuals. However, methods for multi-sample spatial clustering are lacking, and existing methods primarily rely on molecular information alone. This paper introduces BayeSMART, a Bayesian statistical method designed to identify spatial domains across multiple samples.

Visualizing and quantifying dynamic cellular forces with photonic crystal hydrogels.

Cellular forces play a crucial role in numerous biological processes, including tissue development, morphogenesis, and disease progression. However, existing methods for detecting cellular forces, such as traction force microscopy and atomic force microscopy, often face limitations in terms of high throughput, real-time monitoring, and applicability to complex biological systems. In this study, we utilized a novel Photonic Crystal Cellular Force Microscopy (PCCFM) system to visualize and quantify dynamic cellular forces.

Mechanism of two styryl BODIPYs as fluorescent probes and protective agents in lipid bilayers against aqueous ClO.

Two styryl BODIPY derivatives, BOH and BOE, with different hydrophilic properties, were investigated for their reaction mechanisms in lipid bilayers against aqueous ClO, by both experimental and theoretical methods. Density functional theory (DFT) calculations confirmed their identical conformations in solution. Fluorescence spectra and high-resolution mass spectra corroborated the central vinyl group as a common antioxidation moiety against ClO oxidation.

Digital finance development in China: A scientometric review.

The continuous integration of digital technology and finance has spurred the rapid development of the digital finance industry, making it a critical area of interest for scholars. This study combines quantitative research methods using Citespace software for scientometric analysis and qualitative research methods involving manual selection and content analysis of key literature to summarise the research status, hot topics, and frontiers in the field of digital finance in China. The research findings highlight several influential factors in the digital finance literature, such as regional and journal distribution, institutional and author collaboration, and highly cited literature.

Small RNA GadY in enhances conjugation system of IncP-1 by targeting SdiA.

Plasmid-mediated conjugation is a common mechanism for most bacteria to transfer antibiotic resistance genes (ARGs). The conjugative transfer of ARGs is emerging as a major threat to human beings. Although several transfer-related factors are known to regulate this process, small RNAs (sRNAs)-based regulatory roles remain to be clarified.

An interpretable Bayesian clustering approach with feature selection for analyzing spatially resolved transcriptomics data.

Recent breakthroughs in spatially resolved transcriptomics (SRT) technologies have enabled comprehensive molecular characterization at the spot or cellular level while preserving spatial information. Cells are the fundamental building blocks of tissues, organized into distinct yet connected components. Although many non-spatial and spatial clustering approaches have been used to partition the entire region into mutually exclusive spatial domains based on the SRT high-dimensional molecular profile, most require an ad hoc selection of less interpretable dimensional-reduction techniques.

Bladder-resident bacteria associated with increased risk of recurrence after electrofulguration in women with antibiotic-recalcitrant urinary tract infection.

Background: Antibiotic-recalcitrant recurrent urinary tract infection (rUTI) is has become increasingly observed in postmenopausal women. Therefore, when standard antibiotic therapies have failed, some elect electrofulguration (EF) of areas of chronic cystitis when detected on office cystoscopy. EF is thought to remove tissue-resident bacteria that have been previously detected in the bladder walls of postmenopausal women with rUTI.

The mechano-chemical circuit in fibroblasts and dendritic cells drives basal cell proliferation in psoriasis.

Psoriasis is an intractable immune-mediated disorder that disrupts the skin barrier. While studies have dissected the mechanism by which immune cells directly regulate epidermal cell proliferation, the involvement of dermal fibroblasts in the progression of psoriasis remains unclear. Here, we identified that signals from dendritic cells (DCs) that migrate to the dermal-epidermal junction region enhance dermal stiffness by increasing extracellular matrix (ECM) expression, which further promotes basal epidermal cell hyperproliferation.

A Regularized Bayesian Dirichlet-multinomial Regression Model for Integrating Single-cell-level Omics and Patient-level Clinical Study Data.

The abundance of various cell types can vary significantly among patients with varying phenotypes and even those with the same phenotype. Recent scientific advancements provide mounting evidence that other clinical variables, such as age, gender, and lifestyle habits, can also influence the abundance of certain cell types. However, current methods for integrating single-cell-level omics data with clinical variables are inadequate.

iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis.

Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised accuracy and interpretability. To overcome these limitations, we have developed a multi-stage statistical method called iIMPACT. It identifies and defines histology-based spatial domains based on AI-reconstructed histology images and spatial context of gene expression measurements, and detects domain-specific differentially expressed genes.

Protective role of TRPV2 in synaptic plasticity through the ERK1/2-CREB-BDNF pathway in chronic unpredictable mild stress rats.

Purpose: Chronic stress is a significant risk factor for mood disorders such as depression, where synaptic plasticity plays a central role in pathogenesis. Transient Receptor Potential Vanilloid Type-2 (TRPV2) Ion Channels are implicated in hypothalamic-pituitary-adrenal axis disorders. Previous proteomic analysis indicated a reduction in TRPV2 levels in the chronic unpredictable mild stress (CUMS) rat model, yet its role in synaptic plasticity during depression remains to be elucidated.

Bayesian hidden mark interaction model for detecting spatially variable genes in imaging-based spatially resolved transcriptomics data.

Recent technology breakthroughs in spatially resolved transcriptomics (SRT) have enabled the comprehensive molecular characterization of cells whilst preserving their spatial and gene expression contexts. One of the fundamental questions in analyzing SRT data is the identification of spatially variable genes whose expressions display spatially correlated patterns. Existing approaches are built upon either the Gaussian process-based model, which relies on kernels, or the energy-based Ising model, which requires gene expression to be measured on a lattice grid.

Image-based profiling and deep learning reveal morphological heterogeneity of colorectal cancer organoids.

Patient-derived organoids have proven to be a highly relevant model for evaluating of disease mechanisms and drug efficacies, as they closely recapitulate in vivo physiology. Colorectal cancer organoids, specifically, exhibit a diverse range of morphologies, which have been analyzed with image-based profiling. However, the relationship between morphological subtypes and functional parameters of the organoids remains underexplored.