Integrative proteogenomic characterization of Wilms tumor.

Wilms tumor (WT), the most common pediatric renal malignancy, exhibits a relatively low mutational burden compared to adult cancers, which hinders the development of targeted therapies. To elucidate the molecular landscape of WT, we perform integrative proteomic, phosphoproteomic, transcriptomic, and whole-exome sequencing analyses of WT and normal kidney tissue adjacent to tumor. Our multi-omics approach uncovers prognostic genetic alterations, distinct molecular subgroups, immune microenvironment features, and potential biomarkers and therapeutic targets.

Leveraging diverse liquid-liquid phase separation patterns to predict the prognosis and immunotherapy of pediatric acute myeloid leukemia.

Background: Despite improvements in 5-year survival rates for pediatric acute myeloid leukemia (P-AML) over recent decades, the relapse rate remains high. This challenge is compounded by the absence of reliable prognostic biomarkers, which limits the effectiveness of predictive, preventive, and personalized approaches in P-AML management. Emerging evidence has indicated that the aberrant liquid-liquid phase separation (LLPS) can alter the spatiotemporal coordination of biomolecular condensates, thereby contributing to tumorigenesis and progression.

Advanced fractal two-scale method for 905 nm laser scattering calculation of water-covered asphalt pavement and coverage perception.

Sudden changes in pavement coverage can easily result in a vehicle's loss of control. Accurately characterizing laser scattering properties is essential for intelligent vehicle sensors like lidars to perceive pavement coverage information. In response to significant issues such as low computational efficiency, poor accuracy of existing scattering models, and the lack of methods for perceiving pavement water coverage information, this paper introduces an advanced laser scattering calculation method capable of describing water coverage conditions based on the fractal two-scale method (FTSM).

Seasonal drought shapes the relationship between stem CO efflux and belowground respiration in an even-age rubber plantation on Hainan Island, China.

Introduction: Stem CO efflux ( ) reflects the amount of photo-assimilated carbon released back into the atmosphere and plays a critical role in the carbon balance of tree and forest ecosystems. Despite previous studies indicating that a portion of stem CO originates from root respiration ( ), the seasonal dynamics of and its relationship with belowground respiration remain poorly understood, particularly in tropical regions characterized by distinct dry and wet seasons.

Methods: To address this gap, we investigated in tapping and non-tapped rubber trees, along with environmental factors and physiological traits (sap flow flux density, root respiration, and leaf area index) from 2018 to 2021.

Impact of preoperative chemotherapy cycles on tumor resectability and surgical timing in hepatoblastoma: a retrospective analysis.

Background: Hepatoblastoma (HB) is the most common malignant liver tumor in children. However, the optimal duration of preoperative chemotherapy remains unclear, particularly regarding its impact on tumor size and proximity to critical blood vessels.

Methods: This retrospective study analyzed 24 patients with HB treated at Shanghai Xinhua Hospital from 2006 to 2022.

Gradient domain model-driven algorithm unfolding network for blind image deblurring.

Blind image deblurring remains a challenging ill-posed problem due to the simultaneous estimation of clear images and blur kernels. Recently, image deblurring methods that utilize algorithm unfolding techniques have made significant advancements. However, the classical image gradient prior, despite its effectiveness, remains an unexplored avenue in deep unfolding frameworks.

Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.

MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing significant challenges for structure-based drug discovery. Here, we employ Gaussian accelerated molecular dynamics (GaMD) for enhanced sampling of MRGPRX1, successfully obtaining a stable inactive conformation of the unbound receptor for the first time.

Quantitative Characterization of Bubble Defects in Ultra-Low Expansion Quartz Glass via Ultrasonic Interaction.

The existence of bubble defects in ultra-low expansion quartz glass will affect the optical properties and mechanical strength of the material. The present paper proposes a novel defect characterization method based on ultrasonic nondestructive testing. The simulation model of bubble defect detection in ultra-low expansion quartz glass was established using numerical simulation technology, and experimental verification was carried out.

Rubber intercropping with arboreal and herbaceous species alleviated the global warming potential through the reduction of soil greenhouse gas emissions.

Agroforestry systems are known to enhance soil health and climate resilience, but their impact on greenhouse gas (GHG) emissions in rubber-based agroforestry systems across diverse configurations is not fully understood. Here, six representative rubber-based agroforestry systems (encompassing rubber trees intercropped with arboreal, shrub, and herbaceous species) were selected based on a preliminary investigation, including Hevea brasiliensis intercropping with Alpinia oxyphylla (AOM), Alpinia katsumadai (AKH), Coffea arabica (CAA), Theobroma cacao (TCA), Cinnamomum cassia (CCA), and Pandanus amaryllifolius (PAR), and a rubber monoculture as control (RM). Soil physicochemical properties, enzyme activities, and GHG emission characteristics were determined at 0-20 cm soil depth.

A novel piperine derivative HJJ_3_5 inhibits colorectal cancer progression by modulating EMT signaling pathways.

Colorectal cancer (CRC) is a fatal cancer prevalent worldwide, and epithelial-mesenchymal transition (EMT) is a key factor in tumor invasion and metastasis. Piperine, a natural alkaloid known for its antitumor properties, faces limitations in clinical use due to its moderate potency. To address this, our team synthesized and validated a new derivative, HJJ_3_5, which has shown potent antitumor activity against CRC cells.

Distinct spatiotemporal patterns between fungal alpha and beta diversity of soil-plant continuum in rubber tree.

Unlabelled: Plant-associated microbial communities strongly relate to host health and productivity. Still, our knowledge of microbial community spatiotemporal patterns in soil-plant continuum is largely limited. Here, we explored the spatiotemporal dynamics of fungal communities across multiple compartments (phyllosphere, leaf endosphere, soil, rhizosphere, rhizoplane, and root endosphere) of rubber tree in two contrasting seasons collected from Hainan Island and Xishuangbanna.

Aptamer-Gadolinium Conjugates for Targeted Magnetic Resonance Imaging of Early-Stage Bladder Cancer.

Bladder cancer (BCa) poses a significant threat to human health, with early-stage diagnosis being particularly valuable yet challenging due to the limited availability of highly efficient targeted contrast agents. In this study, we have developed a novel aptamer-gadolinium conjugate (Apt-Gd) designed as a targeted contrast agent for the magnetic resonance imaging (MRI) of early-stage BCa. The synthesis of Apt-Gd involved the direct conjugation of aptamers with chelating agents through a bioorthogonal reaction, followed by gadolinium chelation.

GraphPBSP: Protein binding site prediction based on Graph Attention Network and pre-trained model ProstT5.

Protein-protein/peptide interactions play crucial roles in various biological processes. Exploring their interactions attracts wide attention. However, accurately predicting their binding sites remains a challenging task.

Assembly and maintenance of phyllosphere microbial diversity during rubber tree leaf senescence.

Phyllosphere microorganisms execute important ecological functions including supporting host plant growth, enhancing host resistance to abiotic stresses, and promoting plant diversity. How leaf developmental stages affect plant-microbiome interactions and phyllosphere microbial community assembly and diversity is poorly understood. In this study, we utilized amplicon sequencing of 16S rRNA and ITS genes to investigate the composition and diversity of microbial communities across different leaf developmental stages of rubber trees.

Association between Higher Expression of Vav1 in Hepatocellular Carcinoma and Unfavourable Clinicopathological Features and Prognosis.

Objective: The aim was to investigate the potential relationship between Vav1 protein and prognosis in patients with hepatocellular carcinoma (HCC).

Methods: Samples were collected from 96 patients with HCC. For each patient, cancerous tissue and adjacent non-cancerous tissue were obtained.

Revealing the graded activation mechanism of neurotensin receptor 1.

Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE).

A deep attention model for wide-genome protein-peptide binding affinity prediction at a sequence level.

Peptides are pivotal in numerous biological activities by engaging in up to 40 % of protein-protein interactions in many cellular processes. Due to their exceptional specificity and effectiveness, peptides have emerged as promising candidates for drug design. However, accurately predicting protein-peptide binding affinity remains a challenging.

GDF11 OVEREXPRESSION ALLEVIATES SEPSIS-INDUCED LUNG MICROVASCULAR ENDOTHELIAL BARRIER DAMAGE BY ACTIVATING SIRT1/NOX4 SIGNALING TO INHIBIT FERROPTOSIS.

Sepsis is a lethal clinical syndrome, and acute lung injury (ALI) is the earliest and most serious complication. We aimed to explore the role of growth differentiation factor 11 (GDF11) in sepsis-induced dysfunction of lung microvascular endothelial barrier in vivo and in vitro to elucidate its potential mechanism related to sirtuin 1 (SIRT1)/NADPH oxidase 4 (NOX4) signaling. Cecal ligation and puncture (CLP)-induced sepsis mice and lipopolysaccharide (LPS)-induced pulmonary microvascular endothelial cells (PMECs) were used in this study.

ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots.

Protein-DNA interactions are pivotal to various cellular processes. Precise identification of the hotspot residues for protein-DNA interactions holds great significance for revealing the intricate mechanisms in protein-DNA recognition and for providing essential guidance for protein engineering. Aiming at protein-DNA interaction hotspots, this work introduces an effective prediction method, ESPDHot based on a stacked ensemble machine learning framework.

Identification of MYCN non-amplified neuroblastoma subgroups points towards molecular signatures for precision prognosis and therapy stratification.

Background: Despite the extensive study of MYCN-amplified neuroblastomas, there is a significant unmet clinical need in MYCN non-amplified cases. In particular, the extent of heterogeneity within the MYCN non-amplified population is unknown.

Methods: A total of 1566 samples from 16 datasets were identified in Gene Expression Omnibus (GEO) and ArrayExpress.

PMSPcnn: Predicting protein stability changes upon single point mutations with convolutional neural network.

Protein missense mutations and resulting protein stability changes are important causes for many human genetic diseases. However, the accurate prediction of stability changes due to mutations remains a challenging problem. To address this problem, we have developed an unbiased effective model: PMSPcnn that is based on a convolutional neural network.

Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src.

Osteoclasts are over-activated as we age, which results in bone loss. Src deficiency in mice leads to severe osteopetrosis due to a functional defect in osteoclasts, indicating that Src function is essential in osteoclasts. G-protein-coupled receptors (GPCRs) are the targets for ∼35% of approved drugs but it is still unclear how GPCRs regulate Src kinase activity.

Complement components regulates ferroptosis in CVB3 viral myocarditis by interatction with TFRC.

Background: Dysregulated cell death machinery and an excessive inflammatory response in Coxsackievirus B3(CVB3)-infected myocarditis are hallmarks of an abnormal host response. Complement C4 and C3 are considered the central components of the classical activation pathway and often participate in the response process in the early stages of virus infection.

Methods: In our study, we constructed a mouse model of CVB3-related viral myocarditis via intraperitoneal injection of Fer-1 and detected myocarditis and ferroptosis markers in the mouse myocardium.