DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations.

Accurate computational identification of B-cell epitopes is crucial for the development of vaccines, therapies, and diagnostic tools. However, current structure-based prediction methods face limitations due to the dependency on experimentally solved structures. Here, we introduce DiscoTope-3.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in >3,000 published studies.

DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Motivation: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information.

Results: In this article, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localization of RNA molecules via fine-tuning.

Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing.

The microbiome plays a significant role in shaping the health and functioning of the systems it inhabits. The seminal microbiome of stallions has implications for the health of the reproductive tract, sperm quality during preservation and antibiotic use in semen extenders. Diverse bacteria are present on the external genital tract and a mix of commensal microorganisms populates various parts of the reproductive tract, influencing the seminal bacterial content.

A Comparison of Items and Constructs of Standardized Health-Related Quality of Life and Mental Well-Being Measures.

Objectives: This study aimed to explore the internal constructs of the concepts being measured by EQ-5D-5L (a health-related quality of life measure that can produce preference-based utility values) and the 12-item General Health Questionnaire (GHQ-12, a mental well-being measure) and to understand to what extent the items of EQ-5D-5L and GHQ-12 associate with each other.

Methods: We used data from 12 701 respondents participating in a Belgian survey in 2022. Correlation coefficients between GHQ-12 and EQ-5D-5L were calculated at both the aggregate and item levels.

Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae.

Klebsiella pneumonia is a serious pathogen involved in a range of infections. The increasing frequency of infection associated with K. pneumoniae and accelerated development of antimicrobial resistance has limited the available options of antibiotics for the treatment of infection.

A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients.

Psoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut microbiome in gut and skin health having already been demonstrated in many research studies, the potential effect of probiotics on GI comorbidities in psoriasis patients is unclear.

Accurate identification of structural variations from cancer samples.

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs.

Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India.

A crowded vegetable market serves as a mass gathering, posing a potential risk for infection transmission. In this study, we isolated a multidrug-resistant Acinetobacter baumannii strain, VRL-M19, from the air of such a market and conducted comparative genomics and phenotypic characterization. Antimicrobial susceptibility testing, genome sequencing using Illumina HiSeq X10, and pan-genome analysis with 788 clinical isolates identified core, accessory, and unique drug-resistant determinants.

Comprehending conformational changes in EmrE, multidrug transporter at different pH: insights from molecular dynamics simulations.

EmrE is a small multidrug resistance (SMR) pump of antiparallel topology that confers resistance to a broad range of polyaromatic cations in . Atomic-level understanding of conformational changes for the selectivity of substrate and transport of a diverse array of drugs through the smallest known efflux pumps is crucial to multi-drug resistance. Therefore, the present study aims to provide insights into conformational changes during the transport through EmrE transporter at different pH.

Novel Multi-Strain E3 Probiotic Formulation Improved Mental Health Symptoms and Sleep Quality in Hong Kong Chinese.

Mental health issues have emerged as a significant concern in public health, given their association with physical and psychological comorbidities and the resultant socioeconomic burdens. Recent studies have highlighted the interplay between gut microbes and brain functions through the gut-brain axis. To investigate this further, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among Southern Chinese individuals to explore the role of the gut microbiome in depression, anxiety, and sleep disturbance.

Structural insights into the activation mechanism of phosphoinositide 3-kinase alpha.

Phosphoinositide 3-kinases (PI3Ks) are lipid kinases known to regulate important cellular functions by phosphorylating the inositol ring of inositol-phospholipids (PtdIns) at 3' position. The PI3Kα is a heterodimer and the activation of the catalytic subunit (p110α) is regulated by its regulatory subunit (p85α). The current work deals with studying the activation mechanism of the PI3Kα using multi micro-second molecular dynamic simulations.

Tetrahydropalmatine from medicinal plants activates human glucokinase to regulate glucose homeostasis.

Many synthetic glucokinase activators (GKAs), modulating glucokinase (GK), an important therapeutic target in diabetes have failed to clear clinical trials. In this study, an in silico structural similarity search with differing scaffolds of reference GKAs have been used to identify derivatives from natural product databases. Ten molecules with good binding score and similar interactions to that in the co-crystallized GK as well good activation against recombinant human GK experimentally were identified.

Key risk factors associated with fractal dimension based geographical clustering of COVID-19 data in the Flemish and Brussels region, Belgium.

Introduction: COVID-19 remains a major concern globally. Therefore, it is important to evaluate COVID-19's rapidly changing trends. The fractal dimension has been proposed as a viable method to characterize COVID-19 curves since epidemic data is often subject to considerable heterogeneity.

Hesperidin Methyl Chalcone reduces extracellular Aβ peptide aggregation and fibrillation and also protects Neuro 2a cells from Aβ induced neuronal dysfunction.

In the present study, we evaluated the neuroprotective potential of Hesperidin Methyl Chalcone (HMC) against the neurotoxicity induced by Aβ peptide HMC demonstrated higher free-radical scavenging activity than Hesperidin in initial cell-free studies. Investigations using the fluorescent dye thioflavin T with Aβ peptide showed that HMC has the ability to combat extracellular amyloid aggregation by possessing anti-aggregation property against oligomers and by disaggregating mature fibrils. Also, the results of the molecular simulation studies show that HMC ameliorated oligomer formation.

Neutralizing Antibody Response to Genotypically Diverse Measles Viruses in Clinically Suspected Measles Cases.

The neutralizing antibody (Nt-Ab) response to vaccine and wild-type measles viruses (MeV) was studied in suspected measles cases reported during the years 2012-2016. The neutralization activity against MeV A, D4 and D8 genotypes was studied on sera (Panel A; n = 68 (measles-immunized) and Panel B; n = 50 (unvaccinated)) that were either laboratory confirmed or not confirmed by the presence of IgM antibodies. Additionally, the Nt-Ab response in Panel A was measured against the MeV vaccine and four wild-type viruses.

Association of and GLUR4 Ion Transporters with Neoadjuvant Chemoresistance in Luminal Locally Advanced Breast Cancer.

Chemoresistance to standard neoadjuvant treatment commonly occurs in locally advanced breast cancer, particularly in the luminal subtype, which is hormone receptor-positive and represents the most common subtype of breast cancer associated with the worst outcomes. Identifying the genes associated with chemoresistance is crucial for understanding the underlying mechanisms and discovering effective treatments. In this study, we aimed to identify genes linked to neoadjuvant chemotherapy resistance in 62 retrospectively included patients with luminal breast cancer.

Lactate receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4.

Background: The lactate receptor GPR81 contributes to cancer development through unclear mechanisms. Here, we investigate the roles of GPR81 in three-dimensional (3D) and in vivo growth of breast cancer cells and study the molecular mechanisms involved.

Methods: GPR81 was stably knocked down (KD) in MCF-7 human breast cancer cells which were subjected to RNA-seq analysis, 3D growth, in situ- and immunofluorescence analyses, and cell viability- and motility assays, combined with KD of key GPR81-regulated genes.

Impacts of zoning and landscape structure on the relative abundance of wild boar assessed through a Bayesian N-mixture model.

Increasing human-wild boar interactions have led to damage to agricultural crops, traffic collisions and disease transmissions. Dividing natural areas in zones with differential hunting pressure is one of the currently adopted management strategies. However, the effectiveness of this approach is under debate.

The effect of anterior quadratus lumborum block on morphine consumption in minimally invasive colorectal surgery: a multicentre, double-blind, prospective randomised placebo-controlled trial.

We investigated the efficacy and safety of a bilateral anterior quadratus lumborum block in patients undergoing minimally invasive colorectal surgery. This was a two-centre, double-blind, prospective, randomised, placebo-controlled trial including 150 patients undergoing laparoscopic colorectal surgery (left- or right hemicolectomy, sigmoidectomy) who were enrolled in the institutional abdominal enhanced recovery programme. Before induction of anaesthesia, patients received a bilateral anterior quadratus lumborum block in the left and right lateral decubitus position under ultrasound guidance and were allocated randomly to receive 30 ml of ropivacaine 0.