proteins train

The coronavirus disease 2019 (COVID-19) has raised concerns about the potential complications it may cause in pregnant women. Therefore, biomarkers that can predict the course of COVID-19 in pregnant women may be of great benefit as they would provide valuable insights into the prognosis and, thus, the management of the disease. In this context, the objective of this study is to identify the biomarkers that can predict COVID-19 progression in pregnant women, focusing on composite hemogram parameters and systemic inflammatory and spike markers...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 disease, which represents a new life-threatening disaster. Regarding viral infection, many therapeutics have been investigated to alleviate the epidemiology such as vaccines and receptor decoys. However, the continuous mutating coronavirus, especially the variants of Delta and Omicron, are tended to invalidate the therapeutic biological product. Thus, it is necessary to develop molecular entities as broad-spectrum antiviral drugs...

BACKGROUND: Accurately predicting kidney outcomes in IgA nephropathy is crucial for clinical decision making. Insufficient use of longitudinal data in previous studies has limited the accuracy and interpretability of prediction models for failing to reflect the chronic nature of IgA nephropathy. This study aimed at establishing a multivariable dynamic deep learning model using comprehensive longitudinal data for the prediction of kidney outcomes in IgA nephropathy. METHODS: In this retrospective cohort study of 2,056 IgA nephropathy patients at 18 kidney centers, a total of 28,317 data points were collected by the sliding window method...

INTRODUCTION: Many COVID-19 patients display adverse symptoms, such as reduced physical ability, poor quality of life, and impaired pulmonary function. Therefore, this systematic review is aimed at evaluating the effectiveness of physical exercise on various psychophysiological indicators among COVID-19 patients who may be at any stage of their illness (i.e., critically ill, hospitalized, postdischarge, and recovering). METHODS: A systematic search was conducted in PubMed, Scopus, ScienceDirect, Web of Science, and Google Scholar from 2019 to 2021...

Background and aims: Serum polyclonal free light chains (FLCs) levels are associated with overall survival in the general population, reflecting their utility as a biomarker of underlying immune activation and inflammation. Regular exercise is known to ameliorate low-grade inflammation in chronic diseases such as type 2 diabetes; however, the effects of different exercise training modalities on FLCs in adults with type 2 diabetes is unknown. This study investigated the effects of 9-month of aerobic, resistance or combined supervised exercise on serum FLCs in 164 patients with type 2 diabetes (age 58 ± 8 years; 63% female)...

Renal involvement of systemic lupus erythematosus needs aggressive treatment. Despite the development of multiple international guidelines, differences in practices exist. This study aimed to explore the current practices of pediatric rheumatologists and nephrologists for the diagnosis, management, and monitoring of lupus nephritis (LN) in Saudi Arabia through a survey. Among the 61 respondents, 54.1% were pediatric nephrologists and 49.9% were pediatric rheumatologists. Predominantly, the participating physicians received training either nationally (57%) or in North America (45%)...

Protein acetylation is one of the extensively studied post-translational modifications (PTMs) due to its significant roles across a myriad of biological processes. Although many computational tools for acetylation site identification have been developed, there is a lack of benchmark dataset and bespoke predictors for non-histone acetylation site prediction. To address these problems, we have contributed to both dataset creation and predictor benchmark in this study. First, we construct a non-histone acetylation site benchmark dataset, namely NHAC, which includes 11 subsets according to the sequence length ranging from 11 to 61 amino acids...

BACKGROUND: In recent years, there has been a growing interest in utilizing computational approaches to predict drug-target binding affinity, aiming to expedite the early drug discovery process. To address the limitations of experimental methods, such as cost and time, several machine learning-based techniques have been developed. However, these methods encounter certain challenges, including the limited availability of training data, reliance on human intervention for feature selection and engineering, and a lack of validation approaches for robust evaluation in real-life applications...

This study aimed to investigate the effects of exercise on excessive mitochondrial fission, insulin resistance, and inflammation in the muscles of diabetic rats. The role of the irisin/AMPK pathway in regulating exercise effects was also determined. Thirty-two 8-week-old male Wistar rats were randomly divided into four groups (n = 8 per group): one control group (Con) and three experimental groups. Type 2 diabetes mellitus (T2DM) was induced in the experimental groups via a high-fat diet followed by a single intraperitoneal injection of streptozotocin (STZ) at a dosage of 30 mg/kg body weight...

This cluster randomised clinical trial carried out in 20 primary care centres in Barcelona was aimed at assessing the effect of a continuous intervention focused on C-reactive protein (CRP) rapid testing and training in enhanced communication skills (ECS) on antibiotic consumption for adults with acute cough due to lower respiratory tract infection (LRTI). The interventions consisted of general practitioners and nurses' use of CRP point-of-care and training in ECS separately and combined, and usual care. The primary outcomes were antibiotic consumption and variation of the quality-adjusted life years during a 6-week follow-up...

The identification of an effective inhibitor is an important starting step in drug development. Unfortunately, many issues such as the characterization of protein binding sites, the screening library, materials for assays, etc., make drug screening a difficult proposition. As the size of screening libraries increases, more resources will be inefficiently consumed. Thus, new strategies are needed to preprocess and focus a screening library towards a targeted protein. Herein, we report an ensemble machine learning (ML) model to generate a CDK8-focused screening library...

Determining binding affinities in protein-protein and protein-peptide complexes is a challenging task that directly impacts the development of peptide and protein pharmaceuticals. Although several models have been proposed to predict the value of the dissociation constant and the Gibbs free energy, they are currently not capable of making stable predictions with high accuracy, in particular for complexes consisting of more than two molecules. In this work, we present ProBAN, a new method for predicting binding affinity in protein-protein complexes based on a deep convolutional neural network...

Liver fibrosis is a coordinated response to tissue injury that is mediated by immune cell interactions. A mitochondria-regulated information-processing (MIP) nanosystem that promotes immune cell communication and interactions to inhibit liver fibrosis is designed. The MIP nanosystem mimics the alkaline amino acid domain of mitochondrial precursor proteins, providing precise targeting of the mitochondria. The MIP nanosystem is driven by light to modulate the mitochondria of hepatic stellate cells, resulting in the release of mitochondrial DNA into the fibrotic microenvironment, as detected by macrophages...

BACKGROUND: Previous studies suggested that zinc finger protein 536 (ZNF536) was abundant in the central brain and regulated neuronal differentiation. However, the role of ZNF536 in cancer has remained unclear. METHODS: ZNF536 mutation, copy number alteration, DNA methylation, and RNA expression were explored using public portals. Data from The Cancer Genome Atlas (TCGA) were utilized to analyze pathways and tumor microenvironment (TME), with a focus on prognosis in both TCGA and immunotherapy pan-cancer cohorts...

Extracellular matrix diseases like fibrosis are elusive to diagnose early on, to avoid complete loss of organ function or even cancer progression, making early diagnosis crucial. Imaging the matrix densities of proteins like collagen in fixed tissue sections with suitable stains and labels is a standard for diagnosis and staging. However, fine changes in matrix density are difficult to realize by conventional histological staining and microscopy as the matrix fibrils are finer than the resolving capacity of these microscopes...

Translation initiation is the primary determinant of the rate of protein production. The variation in the rate with which this step occurs can cause up to three orders of magnitude differences in cellular protein levels. Several mRNA features, including mRNA stability in proximity to the start codon, coding sequence length, and presence of specific motifs in the mRNA molecule, have been shown to influence the translation initiation rate. These molecular factors acting at different strengths allow precise control of in vivo translation initiation rate and thus the rate of protein synthesis...

BACKGROUND: C-reactive protein (CRP) represents an early clinical biomarker that indicates the presence of inflammatory or infectious conditions in the human body. Today's procedures approved by the Food and Drug Administration (FDA) imply expensive equipment and highly trained personnel to perform the test. Therefore, a new diagnostic method with high detection efficiency and less cost is urgently needed for delivering rapid and timely results in point-of-care (POC) service. RESULTS: Herein, we propose a new, equipment-free, and portable sensing method for the future POC detection of CRP based on the Tyndall effect (TE)...

The discovery that contracting skeletal muscle generates reactive oxygen species (ROS) was first reported over 40 years ago. The prevailing view in the 1980s was that exercise-induced ROS production promotes oxidation of proteins and lipids resulting in muscle damage. However, a paradigm shift occurred in the 1990s as growing research revealed that ROS are signaling molecules, capable of activating transcriptional activators/coactivators and promoting exercise-induced muscle adaptation. Growing evidence supports the notion that reduction-oxidation (redox) signaling pathways play an important role in the muscle remodeling that occurs in response to endurance exercise training...

Bladder cancer (BC) is ranked as the ninth most common malignancy worldwide, with approximately 570,000 new cases reported annually and over 200,000 deaths. Cystoscopy remains the gold standard for the diagnosis of BC, however, its invasiveness, cost, and discomfort have driven the demand for the development of non-invasive, cost-effective alternatives. Nuclear matrix protein 22 (NMP22) is a promising non-invasive diagnostic tool, having received FDA approval. Traditional methods for detecting NMP22 require a laboratory environment equipped with specialized equipment and trained personnel, thus, the development of NMP22 detection devices holds substantial potential for application...

MOTIVATION: Protein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structural data, making the partitioning of these structures into domains essential for inferring evolutionary relationships and functional classification. RESULTS: This paper presents Chainsaw, a supervised learning approach to domain parsing that achieves accuracy that surpasses current state-of-the-art methods...