Metabolomic biomarkers and altered phenylalanine metabolic pathway in preschool children with atopic dermatitis - A pilot study.

Background Atopic dermatitis (AD) has high prevalence in children. Current AD diagnosis and management focuses only on clinical phenotypes, but do not explore the endophenotypes, which are more important because they are a series of biomarkers linking clinical phenotype and genotype Aims Metabolomics can qualitatively and quantitatively capture real-time dynamic changes in a wide range of small molecule metabolites. This pilot study evaluated metabolomics biomarkers and altered metabolic pathways in preschool children with AD, aiming to explore the underlying molecular mechanisms and signalling pathways of the disease.

Impact of Microparticle Transarterial Chemoembolization (mTACE) on myeloid-derived suppressor cell subtypes in hepatocellular carcinoma: Clinical correlations and therapeutic implications.

Background: Myeloid-derived suppressor cells (MDSCs) play a pivotal role in immunosuppression and tumor progression in hepatocellular carcinoma (HCC). While various treatments like surgical resection, ablation, and radiotherapy have been studied for their effects on circulating MDSC frequencies in HCC patients, the findings remain inconclusive. Transarterial Chemoembolization (TACE) stands as the standard care for unresectable HCC, with Microparticle TACE (mTACE) gaining prominence for its capacity to induce significant tumor necrosis.

Global optimization radiometric calibration method for an infrared system with a wide dynamic range.

Considering the conventional calibration restriction of the complicated calibration procedures, narrow dynamic range, and less correlation in the calibration data, a global optimization radiometric calibration method is proposed in this paper. First, a unified database is generated by integrating different gray-level images, neutral density attenuators, integration times, and target radiations under the deduced infrared physical model. Then, the calibration coefficients are automatically learned through the relative error backward propagation network.

Accurate de novo peptide sequencing using fully convolutional neural networks.

De novo peptide sequencing, which does not rely on a comprehensive target sequence database, provides us with a way to identify novel peptides from tandem mass spectra. However, current de novo sequencing algorithms suffer from low accuracy and coverage, which hinders their application in proteomics. In this paper, we present PepNet, a fully convolutional neural network for high accuracy de novo peptide sequencing.

Longitudinal Serum Proteomics Characterization of CD19-CAR-T Cell Therapy for B-Cell Malignancies.

Chimeric antigen receptor (CAR)-modified T cells have demonstrated remarkable efficacy in treating B-cell leukemia. However, treated patients may potentially develop side effects, such as cytokine release syndrome (CRS), the mechanisms of which remain unclear. Here, we collected 43 serum samples from eight patients with B-cell acute lymphoblastic leukemia (B-ALL) before and five time points after CD19-specific CAR-T cell treatment.

3DMolMS: prediction of tandem mass spectra from 3D molecular conformations.

Motivation: Tandem mass spectrometry is an essential technology for characterizing chemical compounds at high sensitivity and throughput, and is commonly adopted in many fields. However, computational methods for automated compound identification from their MS/MS spectra are still limited, especially for novel compounds that have not been previously characterized. In recent years, in silico methods were proposed to predict the MS/MS spectra of compounds, which can then be used to expand the reference spectral libraries for compound identification.

Apigenin attenuates atherosclerosis and non-alcoholic fatty liver disease through inhibition of NLRP3 inflammasome in mice.

Apigenin (APN), a flavone found in several plant foods with various biological properties such as anti-obesity, anti-inflammation and other abilities, alleviates atherosclerosis and non-alcoholic fatty liver disease (NAFLD) induced by a high fat diet (HFD) in mice. However, the underlying mechanisms have not been fully understood. In this study, we investigated the role of NLRP3 in anti-atherosclerosis and anti-NAFLD effect of APN in mouse models with NLRP3 deficiency.

Non-Specific Signal Peptidase Processing of Extracellular Proteins in N315.

is one of the major community-acquired human pathogens, with growing multidrug-resistance, leading to a major threat of more prevalent infections to humans. A variety of virulence factors and toxic proteins are secreted during infection via the general secretory (Sec) pathway, which requires an N-terminal signal peptide to be cleaved from the N-terminus of the protein. This N-terminal signal peptide is recognized and processed by a type I signal peptidase (SPase).

GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching.

Liquid chromatography coupled with tandem mass spectrometry is commonly adopted in large-scale glycoproteomic studies involving hundreds of disease and control samples. The software for glycopeptide identification in such data (e.g.

Relationship between body mass index and physical fitness index in Chinese college students: Results from a cross-sectional survey.

Background: To explore the cross-sectional relationship between the body mass index (BMI) and physical fitness index (PFI) of Chinese college students.

Methods: In total, 30 497 (male 16 197, 55.5%) Chinese college students aged 19-22 were tested for height, weight and five physical fitness indicators (50-m sprint, sit and reach, standing long jump, 1000/800-m run, pull-up/bent-leg sit-up).

Association between Mutation in SMARCAD1 and Basan Syndrome with Cutaneous Squamous Cell Carcinoma.

Background: Basan syndrome is a rare autosomal-dominant ectodermal dysplasia with certain clinic-pathological features caused by mutations in the SMARCAD1 gene. Currently, no skin malignancy related to Basan syndrome has been reported. This study was aimed at identifying related gene mutations in a new Chinese pedigree with Basan syndrome and discovering the possible association between Basan syndrome and cutaneous squamous cell carcinoma (cSCC).

Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.

Background: A few recent large efforts significantly expanded the collection of human-associated bacterial genomes, which now contains thousands of entities including reference complete/draft genomes and metagenome assembled genomes (MAGs). These genomes provide useful resource for studying the functionality of the human-associated microbiome and their relationship with human health and diseases. One application of these genomes is to provide a universal reference for database search in metaproteomic studies, when matched metagenomic/metatranscriptomic data are unavailable.

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.

Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals.

A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing.

With the accumulation of MS/MS spectra collected in spectral libraries, the spectral library searching approach emerges as an important approach for peptide identification in proteomics, complementary to the commonly used protein database searching approach, in particular for the proteomic analyses of well-studied model organisms, such as human. Existing spectral library searching algorithms compare a query MS/MS spectrum with each spectrum in the library with matched precursor mass and charge state, which may become computationally intensive with the rapidly growing library size. Here, the software msSLASH, which implements a fast spectral library searching algorithm based on the Locality-Sensitive Hashing (LSH) technique, is presented.

Nr2e3 is a genetic modifier that rescues retinal degeneration and promotes homeostasis in multiple models of retinitis pigmentosa.

Recent advances in viral vector engineering, as well as an increased understanding of the cellular and molecular mechanism of retinal diseases, have led to the development of novel gene therapy approaches. Furthermore, ease of accessibility and ocular immune privilege makes the retina an ideal target for gene therapies. In this study, the nuclear hormone receptor gene Nr2e3 was evaluated for efficacy as broad-spectrum therapy to attenuate early to intermediate stages of retinal degeneration in five unique mouse models of retinitis pigmentosa (RP).

Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network.

The ability to predict tandem mass (MS/MS) spectra from peptide sequences can significantly enhance our understanding of the peptide fragmentation process and could improve peptide identification in proteomics. However, current approaches for predicting high-energy collisional dissociation (HCD) spectra are limited to predict the intensities of expected ion types, that is, the a/b/c/x/y/z ions and their neutral loss derivatives (referred to as ). In practice, backbone ions only account for <70% of total ion intensities in HCD spectra, indicating many intense ions are ignored by current predictors.

Decitabine enhances cytotoxic effect of T cells with an anti-CD19 chimeric antigen receptor in treatment of lymphoma.

CD19-directed chimeric antigen receptor (CAR) T cells have substantial benefit in the treatment of patients with B-cell malignancies. However, despite encouraging therapeutic efficiency, there is limited overall response rate when anti-CD19 CAR-T cells are used to treat patients with relapsed and refractory (R/R) B cell lymphomas. Therefore, it further investigation is urgently needed to improve treatment efficacy.

Interleukin-37 sensitize the elderly type 2 diabetic patients to insulin therapy through suppressing the gut microbiota dysbiosis.

Objective: The morbidity and prevalence of type 2 diabetes mellitus (DM) are increasing in the elderly population. Interleukin 37 (IL-37) play important roles in anti-inflammatory and anti-bacteria immune responses, but its role in the development of type 2 DM in the elderly is unclear. Therefore, we investigated whether IL-37 is associated with type 2 DM in the elderly and the underlying mechanism.

A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.

Matching metagenomic and/or metatranscriptomic data, currently often under-used, can be useful reference for metaproteomic tandem mass spectra (MS/MS) data analysis. Here we developed a software pipeline for identification of peptides and proteins from metaproteomic MS/MS data using proteins derived from matching metagenomic (and metatranscriptomic) data as the search database, based on two novel approaches Graph2Pro (published) and Var2Pep (new). Graph2Pro retains and uses uncertainties of metagenome assembly for reference-based MS/MS data analysis.