dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research.

Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.

A Study of Disease Prognosis in Lung Adenocarcinoma Using Single-Cell Decomposition and Immune Signature Analysis.

The development of tumors is a highly complex process that entails numerous interactions and intricate relationships between the host immune system and cancer cells. It has been demonstrated in studies that the treatment response of patients can be correlated with the tumor microenvironment (TME). Consequently, the examination of diverse immune profiles within the TME can facilitate the elucidation of tumor development and the development of advantageous models for diagnoses and prognoses.

Comparative analysis of readmission rates and outcomes: Sleeve gastrectomy with versus without Nissen fundoplication using a National Database.

Laparoscopic sleeve gastrectomy (LSG) is the most frequently performed bariatric procedure. To study the safety of LSG done with Nissen Fundoplication (NF) in patients affected by obesity and GERD and assess the complication rate. A retrospective cohort study using the Nationwide Readmissions Database from 2016 to 2019.

An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria.

The rise of antibiotic resistance necessitates effective alternative therapies. Antimicrobial peptides (AMPs) are promising due to their broad inhibitory effects. This study focuses on predicting the minimum inhibitory concentration (MIC) of AMPs against whom-priority pathogens: ATCC 25923, ATCC 25922, and ATCC 27853.

Bariatric surgery: trends in utilization, complications, conversions and revisions.

Background: Sleeve gastrectomy (SG) increased in popularity after 2010 but recent data suggest it has concerning rates of gastroesophageal reflux and need for conversions. This study aims to evaluate recent trends in the utilization of bariatric procedures, associated complications, and conversions using an administrative claims database in the United States.

Methods: We included adults who had bariatric procedures from 2000 to 2020 with continuous enrollment for at least 6 months in the MarketScan Commercial Claims and Encounters database.

Evaluation of 30-day outcomes for open ventral hernia repair using self-gripping versus nonself-gripping mesh.

Background: The use of mesh is standard of care for large ventral hernias repaired on an elective basis. The most used type of mesh includes synthetic polypropylene mesh; however, there has been an increase in the usage of a new polyester self-gripping mesh, and there are limited data regarding its efficacy for ventral hernia. The purpose of the study is to determine whether there is a difference in surgical site occurrence (SSO), surgical site infection (SSI), surgical site occurrence requiring procedural intervention (SSOPI), and recurrence at 30 days after ventral hernia repair (VHR) using self-gripping (SGM) versus non-self-gripping mesh (NSGM).

Assessing Non-Specific Neck Pain through Pose Estimation from Images Based on Ensemble Learning.

Background: Mobile phones, laptops, and computers have become an indispensable part of our lives in recent years. Workers may have an incorrect posture when using a computer for a prolonged period of time. Using these products with an incorrect posture can lead to neck pain.

Updates in Bariatric Surgery.

Bariatric surgery is currently the most effective long-term treatment for morbid obesity as well as type-2 diabetes mellitus. The field of metabolic and bariatric surgery has seen tremendous growth over the past decade with dramatically reduced risks. This article aims to provide an update on bariatric surgery, highlighting the latest outcomes, improvements, and challenges in the field.

Application of machine learning to predict postoperative gastrointestinal bleed in bariatric surgery.

Background: Postoperative gastrointestinal bleeding (GIB) is a rare but serious complication of bariatric surgery. The recent rise in extended venous thromboembolism regimens as well as outpatient bariatric surgery may increase the risk of postoperative GIB or lead to delay in diagnosis. This study seeks to use machine learning (ML) to create a model that predicts postoperative GIB to aid surgeon decision-making and improve patient counseling for postoperative bleeds.

Hypertension as a Novel Link for Shared Heritability in Age at Menarche and Cardiometabolic Traits.

Context: Extremely early age at menarche, also called precocious puberty, has been associated with various cardiometabolic traits, but their shared heritability remains unclear.

Objectives: This work aimed to identify new shared genetic variants and their pathways for age at menarche and cardiometabolic traits and to investigate the influence of central precocious puberty on childhood cardiometabolic traits.

Methods: Using the conjunction false discovery rate method, this study analyzed genome-wide association study data from the menarche-cardiometabolic traits among 59 655 females of Taiwanese ancestry and systemically investigated pleiotropy between age at menarche and cardiometabolic traits.

Targeted next-generation sequencing for genetic variants of left ventricular mass status among community-based adults in Taiwan.

Left ventricular mass is a highly heritable disease. Previous studies have suggested common genetic variants to be associated with left ventricular mass; however, the roles of rare variants are still unknown. We performed targeted next-generation sequencing using the TruSight Cardio panel, which provides comprehensive coverage of 175 genes with known associations to 17 inherited cardiac conditions.

Systolic blood pressure as the mediator of the effect of early menarche on the risk of coronary artery disease: A Mendelian randomization study.

Background: Menarche timing may not be directly associated with the risk of coronary artery disease (CAD). Therefore, we investigated the roles of metabolic factors in explaining the effect of age at menarche on CAD risk.

Methods: We identified women with age at menarche and CAD by using three analytical methods: Mendelian randomization (MR), logistic regression analysis, and Cox proportional hazard regression.

Comparison of Robotic, Laparoscopic, and Open Unilateral Repair of Non-recurrent Inguinal Hernia.

Background: There is a paucity of data comparing open, robotic, and laparoscopic approaches on unilateral, non-recurrent inguinal hernias. Our study presents a large, retrospective triple-arm outcome analysis between robotic, laparoscopic, and open unilateral, non-recurrent inguinal hernia repairs at a single institution.

Methods: 706 patients who underwent elective, non-recurrent inguinal hernia repair performed by 8 general surgeons at a single institution from 2016 to 2019 were reviewed retrospectively.

Anti-Angiogenetic and Anti-Lymphangiogenic Effects of a Novel 2-Aminobenzimidazole Derivative, MFB.

Background And Purpose: Benzimidazoles have attracted much attention over the last few decades due to their broad-spectrum pharmacological properties. Increasing evidence is showing the potential use of benzimidazoles as anti-angiogenic agents, although the mechanisms that impact angiogenesis remain to be fully defined. In this study, we aim to investigate the anti-angiogenic mechanisms of MFB, a novel 2-aminobenzimidazole derivative, to develop a novel angiogenesis inhibitor.

Identification of Differentially Expressed Genes in Different Glioblastoma Regions and Their Association with Cancer Stem Cell Development and Temozolomide Response.

The molecular heterogeneity of gene expression profiles of glioblastoma multiforme (GBM) are the most important prognostic factors for tumor recurrence and drug resistance. Thus, the aim of this study was to identify potential target genes related to temozolomide (TMZ) resistance and GBM recurrence. The genomic data of patients with GBM from The Cancer Genome Atlas (TCGA; 154 primary and 13 recurrent tumors) and a local cohort (29 primary and 4 recurrent tumors), samples from different tumor regions from a local cohort (29 tumor and 25 peritumoral regions), and Gene Expression Omnibus data (GSE84465, single-cell RNA sequencing; 3589 cells) were included in this study.

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version.

A retrospective quantitative implementation evaluation of Safer Opioid Prescribing, a Canadian continuing education program.

Background: Continuing health professions education (CHPE) is an important policy intervention for the opioid epidemic. Besides effectiveness or impact, health policy implementation should be studied to understand how an intervention was delivered within complex environments. Implementation outcomes can be used to help interpret CHPE effects and impacts, help answer questions of "how" and "why" programs work, and inform transferability.

Radiomic Immunophenotyping of GSEA-Assessed Immunophenotypes of Glioblastoma and Its Implications for Prognosis: A Feasibility Study.

Characterization of immunophenotypes in glioblastoma (GBM) is important for therapeutic stratification and helps predict treatment response and prognosis. Radiomics can be used to predict molecular subtypes and gene expression levels. However, whether radiomics aids immunophenotyping prediction is still unknown.

Computational analysis for identification of the extracellular matrix molecules involved in endometrial cancer progression.

Recurrence and poorly differentiated (grade 3 and above) and atypical cell type endometrial cancer (EC) have poor prognosis outcome. The mechanisms and characteristics of recurrence and distal metastasis of EC remain unclear. The extracellular matrix (ECM) of the reproductive tract in women undergoes extensive structural remodelling changes every month.

Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method.

Succinylation is a type of protein post-translational modification (PTM), which can play important roles in a variety of cellular processes. Due to an increasing number of site-specific succinylated peptides obtained from high-throughput mass spectrometry (MS), various tools have been developed for computationally identifying succinylated sites on proteins. However, most of these tools predict succinylation sites based on traditional machine learning methods.

Identification of potential biomarkers related to glioma survival by gene expression profile analysis.

Background: Recent studies have proposed several gene signatures as biomarkers for different grades of gliomas from various perspectives. However, most of these genes can only be used appropriately for patients with specific grades of gliomas.

Methods: In this study, we aimed to identify survival-relevant genes shared between glioblastoma multiforme (GBM) and lower-grade glioma (LGG), which could be used as potential biomarkers to classify patients into different risk groups.