Microbial agents suppress jujube black spot disease and enhance jujube quality by regulating soil physicochemical and microbial properties.

Background: Jujube black spot disease, caused by the soil-borne pathogenic fungus Alternaria alternata, threatens the sustainability of the jujube industry by adversely affecting yield. However, it is unclear whether microbial agents can increase yield by improving soil, inhibiting jujube black spots, and regulating microbial communities.

Results: Bacillus velezensis strain SDTB038 had significant inhibitory effects on A.

Fatty acid metabolism after short-term fasting: POMC response and EPA signal maintain homeostasis in tilapia.

Detecting and responding to fluctuations in fatty acid levels is crucial for maintaining the homeostasis of fatty acid metabolism. This study examined changes in neuropeptide levels and fatty acid sensing systems in tilapia following 24-hour fasting. Subsequently, an EPA compensation experiment was conducted to examine the regulatory effects of hypothalamic neuropeptides on feeding activity, fatty acid sensing systems activation, and alterations in AMPK and AKT signaling pathways in tilapia.

The burden of refraction disorders in 204 countries and territories from 1990 to 2021: A systematic analysis from the global burden of disease 2021.

Background: Refraction disorders are common eye conditions that cause blurred vision and, if left uncorrected, remain a leading cause of moderate to severe visual impairment worldwide. Despite this, a comprehensive assessment of the associated burden is lacking. This study aims to describe and predict the burden and regional distribution of refraction disorders using data from the 2021 Global Burden of Disease (GBD) study.

Incidence, mortality, and global burden of retinoblastoma in 204 countries worldwide from 1990 to 2021: Data and systematic analysis from the Global Burden of Disease Study 2021.

Background: Retinoblastoma (Rb), the primary intraocular malignancy in children, poses significant risks, yet its overall burden remains inadequately assessed. This study aims to analyze global Rb trends using Global Burden of Disease, Injuries, and Risk Factors study (GBD) 2021 data.

Methods: GBD 2021 data was analyzed to assess Rb incidence, mortality, and disability-adjusted life years (DALYs) from 1990 to 2021.

AI-driven eyelid tumor classification in ocular oncology using proteomic data.

Eyelid tumors pose diagnostic challenges due to their diverse pathological types and limited biopsy materials. This study aimed to develop an artificial intelligence (AI) diagnostic system for accurate classification of eyelid tumors. Utilizing mass spectrometry-based proteomics, we analyzed proteomic data from eight tissue types and identified eighteen novel biomarkers based on 233 formalin-fixed, paraffin-embedded (FFPE) samples from 150 patients.

Causal associations between severe COVID-19 and diseases of seven organs: a proteome-wide mendelian randomization study.

The coronavirus disease 2019 (COVID-19) pandemic poses an enormous threat to public health worldwide. Many retrospective studies and case reports to date have shown associations between severe COVID-19 and diseases of multi-organs. However, the research on the causal mechanisms behind this phenomenon is neither extensive nor comprehensive.

Improved Precision and Safety of Supra-Tentorial Intracranial Hematoma Puncture Using C-Arm CT Four-Dimensional Navigation.

BACKGROUND Spontaneous intracerebral hemorrhage has a high fatality rate within the initial month after onset. This study determined the safety and therapeutic efficacy of minimally invasive puncture for supra-tentorial intracranial hematoma under C-arm computed tomography (CT) 4-dimensional navigation. MATERIAL AND METHODS We retrospectively analyzed 64 patients with supra-tentorial cerebral hemorrhage from June 2020 to May 2023; 31 patients were assigned to the study group (C-arm CT navigation puncture) and 33 patients were in the control group (conventional CT-guided puncture).

The regulation of prolactin secretion and its targeting function of teleost.

Prolactin is involved in regulating various physiological activities of vertebrates and is one of the most momentous pituitary hormones. However, not enough attention is currently paid to prolactin, especially in teleost. This paper aims to gather, organize, and analyze recent studies on the regulation and functions of prolactin.

DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins.

Draft Genome Sequence Resource of Sweet Cherry Virescence Phytoplasma Strain SCV-TA2020 Associated with Sweet Cherry Virescence Disease in China.

Sweet cherry virescence phytoplasma strain SCV-TA2020, a related strain of ' Phytoplasma ziziphi', is a pathogen associated with sweet cherry virescence disease in China. Here, we provide the first-draft genome sequence of SCV-TA2020, which consists of 775,344 bases, with a GC content of 23.21%.

Artificial intelligence defines protein-based classification of thyroid nodules.

Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here we report the feasibility and clinical utility of developing an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules: based initially on formalin-fixed paraffin-embedded (FFPE), and further refined for fine-needle aspiration (FNA) tissue specimens of minute amounts which pose technical challenges for other methods. We first developed a neural network model of 19 protein biomarkers based on the proteomes of 1724 FFPE thyroid tissue samples from a retrospective cohort.

ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets.

Summary: The rapid progresses of high-throughput sequencing technology-based omics and mass spectrometry-based proteomics, such as data-independent acquisition and its penetration to clinical studies have generated increasing number of proteomic datasets containing hundreds to thousands of samples. To analyze these quantitative proteomic datasets and other omics (e.g.

BatchServer: A Web Server for Batch Effect Evaluation, Visualization, and Correction.

Batch effects are unwanted data variations that may obscure biological signals, leading to bias or errors in subsequent data analyses. Effective evaluation and elimination of batch effects are necessary for omics data analysis. In order to facilitate the evaluation and correction of batch effects, here we present BatchSever, an open-source R/Shiny based user-friendly interactive graphical web platform for batch effects analysis.

PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation.

The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS.

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery.

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples.

A circulating extracellular vesicles-based novel screening tool for colorectal cancer revealed by shotgun and data-independent acquisition mass spectrometry.

: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liquid biopsies are increasingly being considered for diagnosing cancer due to low invasiveness and high reproducibility. In addition, circulating extracellular vesicles (crEVs, extracellular vesicles isolated from plasma) expressing tumour-specific proteins are potential biomarkers for various cancers.

Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS.

We reported and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in preclassified clinical specimens. The method uses a 15 min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration, and OpenSWATH software for data analysis. We applied the method to a cohort containing 204 FFPE tissue samples from 58 prostate cancer patients and 10 benign prostatic hyperplasia patients.

High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification.

Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh-frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort.

In-depth serum proteomics reveals biomarkers of psoriasis severity and response to traditional Chinese medicine.

Serum and plasma contain abundant biological information that reflect the body's physiological and pathological conditions and are therefore a valuable sample type for disease biomarkers. However, comprehensive profiling of the serological proteome is challenging due to the wide range of protein concentrations in serum. : To address this challenge, we developed a novel in-depth serum proteomics platform capable of analyzing the serum proteome across ~10 orders or magnitude by combining data obtained from Data Independent Acquisition Mass Spectrometry (DIA-MS) and customizable antibody microarrays.

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues Using PCT-SWATH.

Purpose: To rapidly identify protein abundance changes in biopsy-level fresh-frozen hepatocellular carcinoma (HCC).

Experimental Design: The pressure-cycling technology (PCT) is applied and sequential window acquisition of all theoretical mass spectra (SWATH-MS) workflow is optimized to analyze 38 biopsy-level tissue samples from 19 HCC patients. Each proteome is analyzed with 45 min LC gradient.

The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.

Background: Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis.

Results: To understand the genetic structure of TuMV from radish in China, the 3'-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates.

Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants.

Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking.