Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.

Alzheimer's disease (AD) is a complex disease, and numerous cellular events may be involved in etiology. RNAseq-based transcriptome data hold multilayer information content, which could be crucial in unraveling molecular mysteries of AD. It enables quantification of gene expression levels, identification of genomic variants, and elucidation of splicing anomalies such as exon skipping and intron retention.

Integration of genomic and transcriptomic layers in RNA-Seq data leads to protein interaction modules with improved Alzheimer's disease associations.

Alzheimer's disease (AD) is the most common neurodegenerative disease, and it is currently untreatable. RNA sequencing (RNA-Seq) is commonly used in the literature to identify AD-associated molecular mechanisms by analysing changes in gene expression. RNA-Seq data can also be used to detect genomic variants, enabling the identification of the genes with a higher load of deleterious variants in patients compared with controls.

Is It Necessary to Endoscopically Evaluate the Anastomosis in Robotic or Laparoscopic Surgical Procedures for Colorectal Cancer?

In the surgical treatment of colorectal cancers, disease-free survival and life expectancy are inversely proportional to the increase in complications. We evaluated the superiority of colonoscopy and air and water tests in detecting anastomotic leaks in sigmoid and rectosigmoid junction colon cancers. Data of patients who underwent robotic/laparoscopic surgical procedures for sigmoid and rectosigmoid junctional colon cancers at a single center between January 2018 and February 24 were retrospectively evaluated.

Comparative Proteomics Highlights that GenX Exposure Leads to Metabolic Defects and Inflammation in Astrocytes.

Exposure to PFAS such as GenX (HFPO dimer acid) has become increasingly common due to the replacement of older generation PFAS in manufacturing processes. While neurodegenerative and developmental effects of legacy PFAS exposure have been studied in depth, there is a limited understanding specific to the effects of GenX exposure. To investigate the effects of GenX exposure, we exposed to GenX and assessed the motor behavior and performed quantitative proteomics of fly brains to identify molecular changes in the brain.

A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.

Genome-scale metabolic models (GEMs) cover the entire list of metabolic genes in an organism and associated reactions, in a tissue/condition non-specific manner. RNA-seq provides crucial information to make the GEMs condition-specific. Integrative Metabolic Analysis Tool (iMAT) and Integrative Network Inference for Tissues (INIT) are the two most popular algorithms to create condition-specific GEMs from human transcriptome data.

Deciphering Antibiotic-Targeted Metabolic Pathways in : Insights from Transcriptomics and Genome-Scale Metabolic Modeling.

In the ongoing battle against antibiotic-resistant infections, has emerged as a critical pathogen in healthcare settings. To understand its response to antibiotic-induced stress, we integrated transcriptomic data from various antibiotics (amikacin sulfate, ciprofloxacin, polymyxin-B, and meropenem) with metabolic modeling techniques. Key metabolic pathways, including arginine and proline metabolism, glycine-serine and threonine metabolism, glyoxylate and dicarboxylate metabolism, and propanoate metabolism, were significantly impacted by all four antibiotics across multiple strains.

Electrophysiological evaluation of alterations in penile sensation due to penile prosthesis implantation in patients with erectile dysfunction.

Objective: The present study was aimed to determine the effect of penile prosthesis implantation (PPI) surgery on penile sensation by evaluating the penile electromyography (EMG) variables.

Methods: The research was designed as a prospective study. Thirty patients who were diagnosed with organic erectile dysfunction and had underwent PPI surgery between January 2017 and January 2018 in the Urology Clinic of Antalya Training and Research Hospital were included in this study.

Multi-omics analyses highlight molecular differences between clinical and neuropathological diagnoses in Alzheimer's disease.

Both clinical diagnosis and neuropathological diagnosis are commonly used in literature to categorize individuals as Alzheimer's disease (AD) or non-AD in omics analyses. Whether these diagnostic strategies result in distinct profiles of molecular abnormalities is poorly understood. Here, we analysed one of the most commonly used AD omics datasets in the literature from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort and compared the two diagnosis strategies using brain transcriptome and metabolome by grouping individuals as non-AD and AD according to clinical or neuropathological diagnosis separately.

Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma.

Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer.

Effect of Robotic Inferior Mesenteric Artery Ligation Level on Low Anterior Resection Syndrome in Rectum Cancer.

Life expectancy of patients with rectal cancer is increasing day by day with innovative treatments. Low anterior resection syndrome (LARS), which disrupts the comfort of life in these patients, has become a serious problem. We aimed to evaluate the effect of high ligation (HL) and low ligation (LL) techniques on LARS in rectal cancer surgery performed with the robotic method.

A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer.

Background: Prioritizing candidate drugs based on genome-wide expression data is an emerging approach in systems pharmacology due to its holistic perspective for preclinical drug evaluation. In the current study, a network-based approach was proposed and applied to prioritize plant polyphenols and identify potential drug combinations in breast cancer. We focused on MEK5/ERK5 signalling pathway genes, a recently identified potential drug target in cancer with roles spanning major carcinogenesis processes.

Effect of RNA-Seq data normalization on protein interactome mapping for Alzheimer's disease.

High throughput RNA sequencing brings new perspective to the elucidation of molecular mechanisms of diseases. Normalization is the first and most important step for RNA-Seq data, and it can differ based on the purpose of the analysis. Within-sample normalization methods (eg.

Prognostic implications of response to neoadjuvant chemotherapy in breast cancer subtypes.

The current study was designed to assess the response to treatment, as well as clinical and survival outcomes, across different breast cancer subtypes in patients who underwent neoadjuvant chemotherapy (NAC). From 2014 to 2019, a total of 139 patients who were histologically confirmed to have breast cancer, underwent NAC, and subsequently received breast and axillary surgery, were retrospectively included in this study. The rates of pathological complete response (pCR) to NAC were significantly higher for HER2-positive and triple-negative subtypes than for luminal A and HER2-negative subtypes ( = 0.

Transcriptome-based biomarker prediction for Parkinson's disease using genome-scale metabolic modeling.

Parkinson's disease (PD) is the second most common neurodegenerative disease in the world. Identification of PD biomarkers is crucial for early diagnosis and to develop target-based therapeutic agents. Integrative analysis of genome-scale metabolic models (GEMs) and omics data provides a computational approach for the prediction of metabolite biomarkers.

Integrated FDG-PET/CT contribution over cross-sectional imaging in recurrence or progression of pancreaticobiliary neoplasms.

Purpose: We aim to compare FDG-PET/CT and cross-sectional imaging (contrastenhanced CT/MRI) diagnostic abilities in detecting recurrence/progression of pancreaticobiliary system tumors and to reveal the clinical impact of integrated FDGPET/CT to CT/MRI on patient management.

Materials And Methods: FDG-PET/CT and CT/MRI scans of 70 patients from initiation of treatment until proven recurrence/progression were retrospectively evaluated. FDGPET/CT and contrast-enhanced CT/MRI accuracy, sensitivity, specificity, PPV and NPV are compared in terms of overall recurrence/progression diagnosis and sitespecific concern; local disease, local lymph node, and distant organ metastasis.

The effect of alpha-lipoic acid on oxidative parameters, SCUBE-1 and SCUBE-2 in hepatic ischemia-reperfusion injury in cholestatic rats.

Objective: The aim of the study was to evaluate the protective effects of alpha-lipoic acid (ALA) on the liver, oxidative parameters, and signal peptide-CUB-epidermal growth factor-like domain-containing proteins 1 and 2 (SCUBE-1 and -2) in an experimental cholestatic hepatic ischemia-reperfusion (IR) model.

Materials And Methods: Twenty-four female rats were included in the study and divided into four groups of six rats each. Group 1 was the control group, in which only laparotomy was performed; Group 2 underwent laparotomy and received alpha-lipoic acid (ALA) on a daily basis; bile duct ligation was performed in Group 3; bile duct ligation was performed, and ALA was administered to Group 4.

Vaccination status of COVID-19 patients followed up in the ICU in a country with heterologous vaccination policy: A multicenter national study in Turkey.

Objective: Vaccination against severe acute respiratory syndrome coronavirus-2 (SARS-2) prevents the development of serious diseases has been shown in many studies. However, the effect of vaccination on outcomes in COVID-19 patients requiring intensive care is not clear.

Methods: This is a retrospective multicenter study conducted in 17 intensive care unit (ICU) in Turkey between January 1, 2021, and December 31, 2021.

A new metabolic model of and the integrative analysis of Parkinson's disease.

High conservation of the disease-associated genes between flies and humans facilitates the common use of to study metabolic disorders under controlled laboratory conditions. However, metabolic modeling studies are highly limited for this organism. We here report a comprehensively curated genome-scale metabolic network model of using an orthology-based approach.

Rectus abdominis and rectus femoris muscle thickness in determining nutritional risk in critically ill patients: a prospective cohort study in Turkey.

Objectives: Malnutrition is a clinical condition that is frequently seen in critically ill patients in the intensive care unit (ICU). Although there are many scoring systems and tools used to determine nutritional risk, those that can be used in critically ill patients in the ICU are very few. The scoring systems used are insufficient to identify ICU patients with malnutrition or at risk.

Brain-wide transcriptome-based metabolic alterations in Parkinson's disease: human inter-region and human-experimental model correlations.

Alterations in brain metabolism are closely associated with the molecular hallmarks of Parkinson's disease (PD). A clear understanding of the main metabolic perturbations in PD is therefore important. Here, we retrospectively analysed the expression of metabolic genes from 34 PD-control post-mortem human brain transcriptome data comparisons from literature, spanning multiple brain regions.

A transcriptome based approach to predict candidate drug targets and drugs for Parkinson's disease using an 6-OHDA model.

The most common treatment strategies for Parkinson's disease (PD) aim to slow down the neurodegeneration process or control the symptoms. In this study, using an PD model we carried out a transcriptome-based drug target prediction strategy. We identified novel drug target candidates by mapping genes upregulated in 6-OHDA-treated cells on a human protein-protein interaction network.