Improving the Reliability of Language Model-Predicted Structures as Docking Targets through Geometric Graph Learning.

Applying artificial intelligence techniques to flexibly model the binding between the ligand and protein has attracted extensive interest in recent years, but their applicability remains improved. In this study, we have developed CarsiDock-Flex, a novel two-step flexible docking paradigm that generates binding poses directly from predicted structures. CarsiDock-Flex consists of an equivariant deep learning-based model termed CarsiInduce to refine ESMFold-predicted protein pockets with the induction of specific ligands and our existing CarsiDock algorithm to redock the ligand into the induced binding pockets.

Triptolide Causes Spermatogenic Disorders by Inducing Apoptosis in the Mitochondrial Pathway of Mouse Testicular Spermatocytes.

Triptolide (TP) is a diterpenoid compound extracted from the traditional Chinese medicinal herb Tripterygium wilfordii. It has antitumor and anti-inflammatory effects and stimulates immunity. However, its serious side effects, especially reproductive toxicity, limit its clinical application.

Effect of porcine collagen matrix versus rotated pedicle palatal connective tissue flap on the soft-tissue closure after the immediate posterior implantation: study protocol for a randomised controlled trial.

Introduction: Soft-tissue defect is commonly seen in immediate maxillary posterior implantation because of tooth extraction wound and tension from bone graft. Bone graft materials exposure has a significant detrimental influence on bone augmentation. However, previous studies lack sufficient evidence to guide wound closure after immediate posterior implantation.

Effect of the stability of the poly(gamma-glutamic acid)-ACP dispersion system on biomimetic mineralization of type I collagen.

: To explore the relationship between the stability of poly(gamma-glutamic acid) (γ-PGA) dispersion systems with γ-PGA of different molecular weights (MWs) and concentrations and type I collagen mineralization. : γ-PGA was used as a noncollagenous protein (NCP) analogue to regulate the stability of supersaturated γ-PGA-stabilized amorphous calcium phosphate (PGA-ACP) solutions by changing the γ-PGA MW (2, 10, 100, 200 and 500 kDa) and concentration (400, 500 and 600 μg mL). Then, the optical density (OD) at 72 h was measured to determine the PGA-ACP solution stability.

Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health.

The Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals.

Comparison of differences in transcriptional and genetic profiles between intra-central nervous system and extra-central nervous system large B-cell lymphoma.

Primary central nervous system diffused large B-cell lymphoma (PCNS-DLBCL) is a rare type of non-Hodgkin lymphoma restricted to the central nervous system (CNS). To explore its specific pathogenesis and therapeutic targets, we performed multi-omics sequencing on tumor samples from patients diagnosed with PCNS-DLBCL, secondary CNS-DLBCL or extracranial (ec) DLBCL.By single-cell RNA sequencing, highly proliferated and dark zone (DZ)-related B cell subclusters, MKI67_B1, PTTG1_B2 and BTG1_B3, were predominant significantly in PCNS-DLBCL.

Synergetic degradation of PFOS by HALT conditions enhanced by Fe-based amorphous alloys.

Global concern over per- and polyfluoroalkyl substances (PFASs), especially perfluorooctane sulfonate (PFOS), disposal prompts the search for effective degradation methods. Subcritical water hydrothermal treatment shows promise but suffers from unclear degradation pathways, hindering engineering application design due to unknown intermediate products. This study introduces Fe-based amorphous alloy to enhance the subcritical water hydrothermal degradation of PFOS, achieving a degradation rate of approximately 85 % under optimized conditions of 325 °C and 1 M sodium bicarbonate (NaHCO₃), compared to 56 % without the alloy.

Determining the Optimal Age for Extracranial-Intracranial Bypass Surgery: A Post Hoc Analysis of the CMOSS Randomized Trial.

Background: Previous trials have failed to demonstrate the benefits of extracranial-intracranial (EC-IC) bypass surgery for patients with carotid or middle cerebral artery occlusion. However, little evidence has focused on the effect of age on prognosis. This study aimed to explore whether EC-IC bypass surgery can provide greater benefits than medical therapy alone in specific age groups.

Butyric acid alleviates LPS-induced intestinal mucosal barrier damage by inhibiting the RhoA/ROCK2/MLCK signaling pathway in Caco2 cells.

Butyric acid (BA) can potentially enhance the function of the intestinal barrier. However, the mechanisms by which BA protects the intestinal mucosal barrier remain to be elucidated. Given that the Ras homolog gene family, member A (RhoA)/Rho-associated kinase 2 (ROCK2)/Myosin light chain kinase (MLCK) signaling pathway is crucial for maintaining the permeability of the intestinal epithelium, we further investigated whether BA exerts a protective effect on epithelial barrier function by inhibiting this pathway in LPS-induced Caco2 cells.

Revisiting Endoplasmic Reticulum Homeostasis, an Expanding Frontier Between Host Plants and Pathogens.

The endoplasmic reticulum (ER) serves as the primary site for protein biosynthesis and processing, with ER homeostasis being essential for the survival of plant cells. Numerous studies have underscored the pivotal role of the ER as a battleground for host-pathogen interactions. Pathogens secrete effectors to subvert the host ER and manipulate ER-mediated defense responses, fostering an infection-permissive environment for their proliferation.

The association of RBP4 with chronic kidney diseases in southern Chinese population.

Background: Retinol binding protein 4 (RBP4), as a novel adipokine, has been proven to be highly related to insulin resistance, obesity, diabetes, hypertension, hyperuricemia and other metabolic diseases, which are all risk factors for chronic kidney disease (CKD). However, there is a lack of sufficient studies to explore the relationship between RBP4 and CKD, and no reports have described the predictive value of RBP4 for CKD. This study was designed to clarify the relationship between RBP4 and CKD and its potential predictive value.

Integration of ATAC-Seq and RNA-Seq Reveals VDR-SELENBP1 Axis Promotes Adipogenesis of Porcine Intramuscular Preadipocytes.

Intramuscular fat (IMF) content plays a crucial role in determining pork quality. Recent studies have highlighted transcriptional mechanisms controlling adipogenesis in porcine IMF. However, the changes in chromatin accessibility during adipogenic differentiation are still not well understood.

OPA1 Mediated Fatty Acid β-Oxidation in Hepatocyte: The Novel Insight for Melatonin Attenuated Apoptosis in Concanavalin A Induced Acute Liver Injury.

Melatonin (MLT) has been reported to attenuate Concanavalin A (Con A)-induced acute liver injury via the inhibition of immune cells. Whereas the response of hepatocyte to Con A-caused inflammatory storm and the mechanism of MLT on hepatocyte remain not fully understood. Our RNA-seq and bioinformatic analyses suggested that OPA1 and fatty acid β-oxidation might be critical.

Study of the Brain Functional Connectivity Processes During Multi-Movement States of the Lower Limbs.

Studies using source localization results have shown that cortical involvement increased in treadmill walking with brain-computer interface (BCI) control. However, the reorganization of cortical functional connectivity in treadmill walking with BCI control is largely unknown. To investigate this, a public dataset, a mobile brain-body imaging dataset recorded during treadmill walking with a brain-computer interface, was used.

A Multimodal Deep Learning Nomogram for the Identification of Clinically Significant Prostate Cancer in Patients with Gray-Zone PSA Levels: Comparison with Clinical and Radiomics Models.

Rationale And Objectives: To establish a multimodal deep learning nomogram for predicting clinically significant prostate cancer in patients with gray-zone PSA levels.

Methods: This retrospective study enrolled 303 patients with pathological results between January 2018 and December 2022. Clinical variables and the PI-RADS v2.

Fecal microbiota transplantation and short-chain fatty acids improve learning and memory in fluorosis mice by BDNF-PI3K/AKT pathway.

Fluoride, an environmental toxicant, not only arouses intestinal microbiota dysbiosis, but also causes neuronal apoptosis and a decline in learning and memory ability. The purpose of this study was to explore whether fecal microbiota transplantation (FMT) from healthy mice and bacteria-derived metabolites short-chain fatty acids (SCFAs) supplement protect against fluoride-induced learning and memory impairment. Results showed that FMT reversed the elevated percentage of working memory errors (WME) and reference memory errors (RME) in fluorosis mice during the eight-arm maze test.

GABAergic neurons in the central amygdala promote emergence from isoflurane anesthesia in mice.

Background: Recent evidence indicates that general anesthesia and sleep-wake behavior share some overlapping neural substrates. GABAergic neurons in the central amygdala (CeA) have a high firing rate during wakefulness and play a role in regulating arousal-related behaviors. The objective of this study is to investigate whether CeA GABAergic neurons participate in the regulation of isoflurane general anesthesia and uncover the underlying neural circuitry.

A Multi-Omics Prognostic Model Capturing Tumor Stemness and the Immune Microenvironment in Clear Cell Renal Cell Carcinoma.

Cancer stem-like cells (CSCs), a distinct subset recognized for their stem cell-like abilities, are intimately linked to the resistance to radiotherapy, metastatic behaviors, and self-renewal capacities in tumors. Despite their relevance, the definitive traits and importance of CSCs in the realm of oncology are still not fully comprehended, particularly in the context of clear cell renal cell carcinoma (ccRCC). A comprehensive understanding of these CSCs' properties in relation to stemness, and their impact on the efficacy of treatment and resistance to medication, is of paramount importance.

DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.

Background: Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples.

ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research.

ImageGP is an extensively utilized, open-access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, ImageGP 2 (available at https://www.

Profile of cross-reactivity to common pollen allergens in Northwest China based on component resolved diagnosis.

The prevalence of allergic diseases such as Allergic Rhinitis and Asthma is steadily increasing globally, with pollen allergy being one of the most significant sensitizing factors. However, the cross-reactivity of different pollen allergies remains unclear, posing challenges in the diagnosis and treatment of individuals with multiple sensitivities. In this study, the Component Resolved Diagnosis technique was performed to simultaneously measure the specific IgE concentrations of 52 patients against Art v and its components (Art v 1), Phl p and its components (Phl p 1, Phl p 4, Phl p 5, Phl p 6, Phl p 7, Phl p 12), Bet v and its components (Bet v 1, Bet v 2), Amb a and its component (Amb a 1), and Amb p.