MEGA-GO: Functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network.

Motivation: The increasing accessibility of large-scale protein sequences through advanced sequencing technologies has necessitated the development of efficient and accurate methods for predicting protein function. Computational prediction models have emerged as a promising solution to expedite the annotation process. However, despite making significant progress in protein research, graph neural networks face challenges in capturing long-range structural correlations and identifying critical residues in protein graphs.

Global Burden of Cardiovascular Diseases and its Risk Factors, 1990-2021: A Systematic Analysis for the Global Burden of Disease Study 2021.

Background: Cardiovascular diseases (CVD) represent a major global health challenge, necessitating up-to-date data on its burden for effective care planning and resource allocation. This study comprehensively analyzes the global, regional, and national CVD burden and associated risks from 1990 to 2021.

Methods And Results: We performed a secondary analysis of CVD burden and risk factors using the Global Burden of Disease (GBD) 2021 study.

Practical application of CS-CG Stabilised soil in subgrade construction.

To enhance the water stability and bearing capacity of the Shandong Ming Dong Expressway's soaked subgrade, carbide slag (CS) and coal gangue powder (CG) were used as stabilisers. Stabiliser dosages of 5%, 10%, and 15%, with the CS:CG ratios of 0:100, 30:70, 50:50, 70:30, and 100:0, were tested. The study evaluated the performance of CS-CG stabilised soil through unconfined compressive strength (UCS) tests at 7 and 28 days, six dry-wet cycles, a 30-day water immersion test, pH test, swell rate test, XRD, SEM, and MIP analyses.

Freshwater Salinization Mitigated NO Emissions in Submerged Plant-Covered Systems: Insights from Attached Biofilms.

Submerged plants (SMPs) play a critical role in improving water quality and reducing NO greenhouse gas emissions. However, freshwater salinization represents a major environmental challenge in aquatic systems. To investigate the impact of salinization on NO emissions, this study conducted indoor mesocosm experiments simulating SMP and nonsubmerged plant (Non_SMP) areas in freshwater lakes.

Simultaneous Induction of Immunogenic Pyroptosis and PD-L1 Downregulation by One Single Photosensitizer for Synergistic Cancer Photoimmunotherapy.

Pyroptosis, an excellent form of immunogenic cell death that can effectively activate antitumor immune responses, is attracting considerable interest as a promising approach for cancer immunotherapy. Immunogenic pyroptosis can recruit and stimulate dendritic cells to provoke further activation and tumor infiltration of T cells by releasing danger-associated molecular patterns, thus improving the tumor response to PD-1/PD-L1 checkpoint blockade immunotherapy. Here, we report the discovery of a bifunctional photosensitizer Nile Violet that can simultaneously trigger caspase-3/GSDME-mediated immunogenic pyroptosis and PD-L1 downregulation for cancer photoimmunotherapy.

Cell-type-specific networks during hippocampal seizures at the micro- and macroscale.

Epilepsy is a network disorder, involving neural circuits at both the micro- and macroscale. While local excitatory-inhibitory imbalances are recognized as a hallmark at the microscale, the dynamic role of distinct neuron types during seizures remain poorly understood. At the macroscale, interactions between key nodes within the epileptic network, such as the central median thalamic nucleus (CMT), are critical to the, hippocampal epileptic process.

ZW sex chromosome differentiation in paleognathous birds is associated with mitochondrial effective population size but not mitochondrial genome size or mutation rate.

Eukaryotic genome size varies considerably, even among closely related species. The causes of this variation are unclear, but weak selection against supposedly costly "extra" genomic sequences has been central to the debate for over 50 years. The mutational hazard hypothesis, which focuses on the increased mutation rate to null alleles in superfluous sequences, is particularly influential, though challenging to test.

Asymmetric PtO-O Dual Active Sites Induced by NbO Clusters Promotes CO Synergistical Oxidation.

Pt/CeO single-atom catalysts are attractive materials for CO oxidation but normally show poor activity below 150 °C mainly due to the unicity of the originally symmetric PtO structure. In this work, a highly active and stable Pt/CeO single-site catalyst with only 0.1 wt % Pt loading, achieving a satisfied complete conversion of CO at 150 °C, can be obtained through fabricating asymmetric PtO-oxygen vacancies (O) dual-active sites induced by well-dispersed NbO clusters.

Calothrixin B by docking JAK2 is a potential therapeutic inhibitor for pancreatic ductal adenocarcinoma.

Objectives: Pancreatic cancer, a highly invasive and prognostically unfavorable malignant tumor, consistently exhibits resistance to conventional chemotherapy, leading to substantial side effects and diminished patient quality of life. This highlights the critical need for the discovery of novel, effective, and safe chemotherapy drugs. This study aimed to explore bioactive compounds, particularly natural products, as an alternative for JAK2 protein inhibitor in cancer treatment.

Long-term smoking contributes to aging frailty and inflammatory response.

In recent years, the health challenges linked to frailty in the elderly, particularly those worsened by cigarette smoke, have become more pronounced. However, quantitative studies examining the impact of smoking dosage on frailty in this population remain limited. To address this gap, we developed a model using smoke-exposed elderly mice.

Discovery of Novel Hydrazide-Based HDAC3 Inhibitors as Epigenetic Immunomodulators for Cancer Immunotherapy.

Based on our previous work, a series of imidazole-based small molecules were designed and synthesized as HDAC3 inhibitors. Among them, compound showed selective HDAC3 inhibition activity with an IC of 53 nM (SI = 75 for HDAC3 over HDAC1). Further studies revealed that could dose-dependently induce the expression of PD-L1 in MC38 cells by activating the PD-L1 transcription.

Atomic Imaging of the Surface Termination and Reconstruction of Low and High Index Iridium Oxide Surfaces and Insights into Their Facet-Dependent Oxygen Evolution Activities.

Resolving the atomic surface structure, particularly surface termination or reconstruction, is essential for understanding the catalytic properties of metal oxides. Although rutile phase iridium dioxide (IrO) is the state-of-the-art electrocatalyst for the oxygen evolution reaction (OER) in water splitting, the atomic-level surface structures of IrO remain largely unexplored, limiting our understanding of its facet-dependent OER activities. Herein, we perform aberration-corrected integrated differential phase contrast scanning transmission electron microscopy of the low- and high-index surface structures of spindle-shaped IrO nanorods and reveal distinct surface terminations and/or reconstructions on different surfaces.

Genome-Wide Analysis of the CsAP2/ERF Gene Family of Sweet Orange (Citrus sinensis) and Joint Analysis of Transcriptional Metabolism under Salt Stress.

Background: Sweet orange is an important economic crop, and salt stress can inhibit its growth and development.

Methods: In this study, we identified AP2/ERF genes in sweet orange via bioinformatics and performed a combined transcription‒metabolism analysis, which revealed for the first time the integrated molecular mechanism of salt stress regulation in sweet orange.

Key Results: A total of 131 sweet orange AP2/ERF genes were identified and categorized into five groups.

Protocol for estimating the contrast transfer function and absolute tilt angle offset for cryo-electron tomography using CTFMeasure.

Contrast transfer function (CTF) estimation is essential to the data processing workflow of cryo-electron tomography (cryoET). Here, we present a protocol for CTF estimation of the cryoET tilt series with CTFMeasure. CTFMeasure can estimate the CTF parameters together with the absolute tilt angle offset of the sample.

Protocol for recombinant rabies virus titration by quantitative PCR.

Preparing high-titer virus and performing accurate titer determination are critical to subsequent experiments. However, not all applied recombinant rabies viruses, such as the L-deleted virus, are equipped with fluorescent proteins for titration by fluorescence-activated cell sorting (FACS). Here, we present a quantitative reverse-transcription PCR (RT-qPCR) approach for titrating recombinant rabies virus.

Protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms.

Gut-microbiome-combined metabolomics studies in cerebrovascular disease highlight the microbiota-gut-brain axis in neurological disorders. Here, we present a protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms. We describe steps for sample collection, fecal genomic DNA extraction, rRNA PCR amplification, sequencing library construction, and rRNA sequencing.

Superhydrophobic and Self-Healing Porous Organic Macrocycle Crystals for Methane Purification under Humid Conditions.

Purifying methane from natural gas using adsorbents not only requires the adsorbents to possess excellent separation performance but also to overcome additional daunting challenges such as humidity interference and durability requirements for sustainable use. Herein, porous organic crystals of a new macrocycle () with superhydrophobic and self-healing features are prepared and employed for the purification of methane (>99.99% purity) from ternary methane/ethane/propane mixtures under 97% relative humidity.

Bioinformatic identification of important roles of COL1A1 and TNFRSF12A in cartilage injury and osteoporosis.

Objective: The aim of this study was to identify the key regulatory mechanisms of cartilage injury and osteoporosis through bioinformatics methods, and to provide a new theoretical basis and molecular targets for the diagnosis and treatment of the disease.

Methods: Microarray data for cartilage injury (GSE129147) and osteoporosis (GSE230665) were first downloaded from the GEO database. Differential expression analysis was applied to identify genes that were significantly up-or down-regulated in the cartilage injury and osteoporosis samples.

Fructose-Modified Chitosan/Gelatin 3D Composite Sponge for Enhanced Rapid Hemostasis.

Managing uncontrolled and noncompressible bleeding presents a major challenge in emergency trauma care. Methods to halt bleeding quickly and efficiently, without applying direct pressure on the wound, have become a key focus of research. Herein, a novel fructose-modified chitosan/gelatin composite sponge has been developed, exhibiting high elasticity, low rebound pressure, and excellent cell compatibility.

Changes in Axial Length in Patients of Acute Retinal Necrosis Undergoing Vitrectomy.

Purpose: To observe the changes in the axial length (AL) in patients of acute retinal necrosis (ARN) undergoing vitrectomy and investigate the correlated factors.

Methods: Retrospective case series. Patients diagnosed as ARN undergoing vitrectomy with silicone oil (SO) tamponade, and with attached retina more than one year after silicone oil removal (SOR) were included.

N-acetyl-tryptophan in Acute Kidney Injury after Cardiac Surgery.

Background: Cardiac surgery-associated acute kidney injury is a common serious complication after cardiac surgery. Currently, there are no specific pharmacological therapies. Our understanding of its pathophysiology remains preliminary.

Predicting transcriptional changes induced by molecules with MiTCP.

Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.

A whole-body imaging technique for tumor-specific diagnostics and screening of B7-H3-targeted therapies.

Background: B7-H3 or CD276 is notably overexpressed in various malignant tumor cells in humans, with extremely high expression rates. The development of a radiotracer that targets B7-H3 may provide a universal tumor-specific imaging agent and allow the noninvasive assessment of the whole-body distribution of B7-H3-expressing lesions.

Methods: We enhanced and optimized the structure of an affibody (ABY) that targets B7-H3 to create the radiolabeled radiotracer [68Ga]Ga-B7H3-BCH, and then, we conducted both foundational experiments and clinical translational studies.

Integrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis.

Objective: This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.

Methods: Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes.