Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors.

Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded-targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements.

Prodromal depression and subsequent risk of developing Parkinson's disease: a systematic review with meta-analysis.

Parkinson's disease (PD) is a progressive neurological disorder that predominately affects dopaminergic neurons. We believe that this pooling of data will help to better understand the prodromal nature of depression in PD. We conducted this study in accordance with PRISMA guidelines 2020.

Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression.

To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not rely strictly on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion.

Anesthesia Management for Pediatric Patient With Multiple Endocrine Neoplasia Type 2B: A Case Report.

Administering anesthesia to patients with pheochromocytoma may cause an exacerbation of catecholamine secretion from the pheochromocytoma secondary to drug administration, stress, or manipulation of the tumor. We present a pediatric patient with undiagnosed multiple endocrine neoplasia type 2B (pheochromocytoma, thyroid carcinoma, and mucosal neuromas), initially diagnosed and treated for postviral myocarditis and cardiomyopathy, who presented for abdominal magnetic resonance imaging (MRI) under general anesthesia. Untreated cardiomyopathy poses an extra anesthesia mortality risk for patients with pheochromocytoma usually due to myocardial failure, myocardial infarction, or hypertensive hemorrhage into the myocardium or brain.

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.

We present the experimental protocol and data analysis toolbox for multi-contact 4C (MC-4C), a new proximity ligation method tailored to study the higher-order chromatin contact patterns of selected genomic sites. Conventional chromatin conformation capture (3C) methods fragment proximity ligation products for efficient analysis of pairwise DNA contacts. By contrast, MC-4C is designed to preserve and collect large concatemers of proximity ligated fragments for long-molecule sequencing on an Oxford Nanopore or Pacific Biosciences platform.

Physicians' Response to Patients' Quality-of-Life Goals.

Purpose: Patients are able to participate in quality-of-life (QOL) discussions, but clinicians struggle to incorporate this information into encounters and shared decision making. We designed a study to determine if a clinician-initiated prompt could make patient visits more goal directed.

Methods: Patients were given a previsit questionnaire that included QOL questions.

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.

Robustly predicting outcome for cancer patients from gene expression is an important challenge on the road to better personalized treatment. Network-based outcome predictors (NOPs), which considers the cellular wiring diagram in the classification, hold much promise to improve performance, stability and interpretability of identified marker genes. Problematically, reports on the efficacy of NOPs are conflicting and for instance suggest that utilizing random networks performs on par to networks that describe biologically relevant interactions.

Enhancer hubs and loop collisions identified from single-allele topologies.

Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles.

Effect of creatine monohydrate supplementation on learning, memory and neuromuscular coordination in female albino mice.

Background: Research findings made over the last few years have highlighted the important role of creatine (Cr) in health and disease. However, limited information is available regarding the effect of Cr supplementation on cognation. Present study was designed to determine the effect of variable doses of Cr (1% and 3%) on selected parameters of female albino mice behaviour.

Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics.

Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types.

FERAL: network-based classifier with application to breast cancer outcome prediction.

Motivation: Breast cancer outcome prediction based on gene expression profiles is an important strategy for personalize patient care. To improve performance and consistency of discovered markers of the initial molecular classifiers, network-based outcome prediction methods (NOPs) have been proposed. In spite of the initial claims, recent studies revealed that neither performance nor consistency can be improved using these methods.

Phenotypic and Genetic Characterization of Carbapenemase and ESBLs Producing Gram-negative Bacteria (GNB) Isolated from Patients with Cystic Fibrosis (CF) in Tehran Hospitals.

Background: Cystic Fibrosis (CF) is an autosomal recessive genetic disorder in white populations caused by mutation in a gene that encodes Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. Since frequent respiratory tract infections are the major problem in patients with CF, obligation to identify the causative bacteria and determining their antibiotic resistance pattern is crucial. The purpose of this project was to detect Gram-negative bacteria (GNB) isolated from sputa of CF patients and to determine their antibiotic resistance pattern.

Microbial modulation of energy availability in the colon regulates intestinal transit.

Gut microbiota contribute to host metabolic efficiency by increasing energy availability through the fermentation of dietary fiber and production of short-chain fatty acids (SCFAs) in the colon. SCFAs are proposed to stimulate secretion of the proglucagon (Gcg)-derived incretin hormone GLP-1, which stimulates insulin secretion (incretin response) and inhibits gastric emptying. We find that germ-free (GF) and antibiotic-treated mice, which have severely reduced SCFA levels, have increased basal GLP-1 levels in the plasma and increased Gcg expression in the colon.

A comparison of two different techniques for the detection of blood parasite, Theileria annulata, in cattle from two districts in Khyber Pukhtoon Khwa Province (Pakistan).

The present study was carried out to determine the prevalence of Theileria annulata in large ruminants from two districts, Peshawar and Kohat, in Khyber Pukhtoon Khwa (Pakistan). Blood samples were collected from 95 cattle. Data on the characteristics of animals and herds were collected through questionnaires.