Association of Computed Tomography Scan-Assessed Body Composition with Immune and PI3K/AKT Pathway Proteins in Distinct Breast Cancer Tumor Components.

This hypothesis-generating study aims to examine the extent to which computed tomography-assessed body composition phenotypes are associated with immune and phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathways in breast tumors. A total of 52 patients with newly diagnosed breast cancer were classified into four body composition types: adequate (lowest two tertiles of total adipose tissue [TAT]) and highest two tertiles of total skeletal muscle [TSM] areas); high adiposity (highest tertile of TAT and highest two tertiles of TSM); low muscle (lowest tertile of TSM and lowest two tertiles of TAT); and high adiposity with low muscle (highest tertile of TAT and lowest tertile of TSM). Immune and PI3K/AKT pathway proteins were profiled in tumor epithelium and the leukocyte-enriched stromal microenvironment using GeoMx (NanoString).

Multiomic molecular patterns of lipid dysregulation in a subphenotype of sepsis with higher shock incidence and mortality.

Background: Lipids play a critical role in defense against sepsis. We sought to investigate gene expression and lipidomic patterns of lipid dysregulation in sepsis.

Methods: Data from four adult sepsis studies were analyzed and findings were investigated in two external datasets.

asmbPLS: biomarker identification and patient survival prediction with multi-omics data.

Introduction: With the advancement of high-throughput studies, an increasing wealth of high-dimensional multi-omics data is being collected from the same patient cohort. However, leveraging this multi-omics data to predict survival outcomes poses a significant challenge due to its complex structure.

Methods: In this article, we present a novel approach, the Adaptive Sparse Multi-Block Partial Least Squares (asmbPLS) Regression model, which introduces a dynamic assignment of penalty factors to distinct blocks within various PLS components, facilitating effective feature selection and prediction.

Carvacrol, a monoterpenoid, binds quorum sensing proteins (LasI and LasR) and swarming motility protein BswR of resulting in loss of pathogenicity: an in silico approach.

The pathogenic utilizes a quorum-sensing pathway for biofilm formation. The quorum-sensing proteins LasI and LasR of the Las system, alongside the swarming motility protein BswR, play a crucial role in the biofilm-mediated antibiotic resistance phenomenon. In this in silico study, LasI, LasR, and BswR were the prime targets for binding studies by promising drug candidates like linalool, ferutinin, citronellal, and carvacrol.

A dispensable SepIVA orthologue in Streptomyces venezuelae is associated with polar growth and not cell division.

Background: SepIVA has been reported to be an essential septation factor in Mycolicibacterium smegmatis and Mycobacterium tuberculosis. It is a coiled-coil protein with similarity to DivIVA, a protein necessary for polar growth in members of the phylum Actinomycetota. Orthologues of SepIVA are broadly distributed among actinomycetes, including in Streptomyces spp.

TWCOM: an R package for inference of cell-cell communication on spatially resolved transcriptomics data.

Summary: The inference of cell-cell communication is important, as it unveils the intricate cellular behaviors at the molecular level, providing crucial insights essential for understanding complex biological processes and informing targeted interventions in various pathological contexts. Here, we present TWCOM, an R package that implements a Tweedie distribution-based model for accurate cell-cell communication inference. Operating under a generalized additive model framework, TWCOM adeptly handles both single-cell resolution and spot-based spatially resolved transcriptomics data, providing a versatile tool for robust biological sample analysis.

Association of computed tomography scan-assessed body composition with immune and PI3K/AKT pathway proteins in distinct breast cancer tumor components.

This hypothesis-generating study aims to examine the extent to which computed tomography-assessed body composition phenotypes are associated with immune and PI3K/AKT signaling pathways in breast tumors. A total of 52 patients with newly diagnosed breast cancer were classified into four body composition types: adequate (lowest two tertiles of total adipose tissue [TAT]) and highest two tertiles of total skeletal muscle [TSM] areas); high adiposity (highest tertile of TAT and highest two tertiles of TSM); low muscle (lowest tertile of TSM and lowest two tertiles of TAT); and high adiposity with low muscle (highest tertile of TAT and lowest tertile of TSM). Immune and PI3K/AKT pathway proteins were profiled in tumor epithelium and the leukocyte-enriched stromal microenvironment using GeoMx (NanoString).

Marine-Derived Cytosine Arabinoside (Ara-C) Inhibits Biofilm Formation by Inhibiting PEL Operon Proteins (Pel A and Pel B) of Pseudomonas aeruginosa: An In Silico Approach.

Pseudomonas aeruginosa (P. aeruginosa) is a gram-negative biofilm-forming opportunistic human pathogen whose vital mechanism is biofilm formation for better survival. PelA and PelB proteins of the PEL operon are essential for bacterial-synthesized pellicle polysaccharide (PEL), which is a vital structural component of the biofilm.

Biofilm-producing antibiotic-resistant bacteria in Indian patients: a comprehensive review.

For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable impact in the field of infectious diseases, in particular healthcare-associated infections related to indwelling devices such as catheters, implants, artificial heart valves, and prosthetic joints. Bacterial biofilm potentially adheres to any biotic or abiotic surfaces that give specific shelter to the microbial community, making them less susceptible to many antimicrobial agents and even resistant to the immune cells of animal hosts.

Inferring Cell-Cell Communications from Spatially Resolved Transcriptomics Data Using a Bayesian Tweedie Model.

Cellular communication through biochemical signaling is fundamental to every biological activity. Investigating cell signaling diffusions across cell types can further help understand biological mechanisms. In recent years, this has become an important research topic as single-cell sequencing technologies have matured.

Association of air pollution with postmenopausal breast cancer risk in UK Biobank.

Background: We investigated the association of several air pollution measures with postmenopausal breast cancer (BCa) risk.

Methods: This study included 155,235 postmenopausal women (of which 6146 with BCa) from UK Biobank. Cancer diagnoses were ascertained through the linkage to the UK National Health Service Central Registers.

Clustering single-cell multimodal omics data with jrSiCKLSNMF.

The development of multimodal single-cell omics methods has enabled the collection of data across different omics modalities from the same set of single cells. Each omics modality provides unique information about cell type and function, so the ability to integrate data from different modalities can provide deeper insights into cellular functions. Often, single-cell omics data can prove challenging to model because of high dimensionality, sparsity, and technical noise.

Expression Predicts Poor Outcomes and Mortality From Sepsis.

Unlabelled: This is a study of lipid metabolic gene expression patterns to discover precision medicine for sepsis.

Objectives: Sepsis patients experience poor outcomes including chronic critical illness (CCI) or early death (within 14 d). We investigated lipid metabolic gene expression differences by outcome to discover therapeutic targets.

mTOR pathway candidate genes and energy intake interaction on breast cancer risk in Black women from the Women's Circle of Health Study.

Background: Excessive energy intake has been shown to affect the mammalian target of the rapamycin (mTOR) signaling pathway and breast cancer risk. It is not well understood whether there are gene-environment interactions between mTOR pathway genes and energy intake in relation to breast cancer risk.

Methods: The study included 1642 Black women (809 incident breast cancer cases and 833 controls) from the Women's Circle of Health Study (WCHS).

asmbPLS: Adaptive Sparse Multi-block Partial Least Square for Survival Prediction using Multi-Omics Data.

Background: As high-throughput studies advance, more and more high-dimensional multi-omics data are available and collected from the same patient cohort. Using multi-omics data as predictors to predict survival outcomes is challenging due to the complex structure of such data.

Results: In this article, we introduce an adaptive sparse multi-block partial least square (asmbPLS) regression method by assigning different penalty factors to different blocks in different PLS components for feature selection and prediction.

Association Between Recreational Physical Activity and mTOR Signaling Pathway Protein Expression in Breast Tumor Tissue.

Unlabelled: Physical activity (PA) is associated with decreased signaling in the mTOR pathway in animal models of mammary cancer, which may indicate favorable outcomes. We examined the association between PA and protein expression in the mTOR signaling pathway in breast tumor tissue. Data on 739 patients with breast cancer, among which 125 patients had adjacent-normal tissue, with tumor expression for mTOR, phosphorylated (p)-mTOR, p-AKT, and p-P70S6K were analyzed.

mTOR pathway candidate genes and physical activity interaction on breast cancer risk in black women from the women's circle of health study.

Background: Physical activity has been shown to affect the mammalian target of rapamycin (mTOR) signaling pathway and consequently breast carcinogenesis. Given that Black women in the USA are less physically active, it is not well understood whether there are gene-environment interactions between mTOR pathway genes and physical activity in relation to breast cancer risk in Black women.

Methods: The study included 1398 Black women (567 incident breast cancer cases and 831 controls) from the Women's Circle of Health Study (WCHS).

mTOR pathway candidate genes and obesity interaction on breast cancer risk in black women from the Women's Circle of Health Study.

Background: Obesity is known to stimulate the mammalian target of rapamycin (mTOR) signaling pathway and both obesity and the mTOR signaling pathway are implicated in breast carcinogenesis. We investigated potential gene-environment interactions between mTOR pathway genes and obesity in relation to breast cancer risk among Black women.

Methods: The study included 1,655 Black women (821 incident breast cancer cases and 834 controls) from the Women's Circle of Health Study (WCHS).

DHCR7 Expression Predicts Poor Outcomes and Mortality from Sepsis.

Sepsis patients experience poor outcomes including chronic critical illness (CCI) or early death (within 14 days). We investigated lipid metabolic gene expression differences by outcome to discover therapeutic targets. Secondary analysis of samples from prospectively enrolled sepsis patients and a zebrafish sepsis model for drug discovery.

Intraindividual Reliability of Opportunistic Computed Tomography-Assessed Adiposity and Skeletal Muscle Among Breast Cancer Patients.

Background: Adiposity and skeletal muscle levels assessed on computed tomography (CT) scans are prognostic indicators for patients with breast cancer. However, the intraindividual reliability of temporal changes in body composition assessed on opportunistic CT scans is unclear.

Methods: This retrospective study included 50 patients newly diagnosed with breast cancer who had archived CT scans pre- and postsurgery for breast cancer.

Impact of Skin Biopsy and Clinical-Pathologic Correlation in Dermatology Inpatient Consults.

Background While studies of hospital dermatology have demonstrated diagnostic discordance between primary teams and dermatology consultants, little is known about the impact of biopsy and clinical-pathologic correlation (CPC) in consultation. This study compares biopsy performance based on diagnostic discordance and evaluates the impact of CPC on the diagnosis. Methods This was a retrospective review of 376 dermatologic consultations at a single academic medical center between July 1, 2017, and June 27, 2018.

SAREV: A review on statistical analytics of single-cell RNA sequencing data.

Due to the development of next-generation RNA sequencing (NGS) technologies, there has been tremendous progress in research involving determining the role of genomics, transcriptomics and epigenomics in complex biological systems. However, scientists have realized that information obtained using earlier technology, frequently called 'bulk RNA-seq' data, provides information averaged across all the cells present in a tissue. Relatively newly developed single cell (scRNA-seq) technology allows us to provide transcriptomic information at a single-cell resolution.

MarZIC: A Marginal Mediation Model for Zero-Inflated Compositional Mediators with Applications to Microbiome Data.

Background: The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data and that the relative abundances have to sum to one. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are not zero (i.