A Multipole-Based Reactive Force Field for Hydrocarbons.

The computational complexity of quantum chemistry methods has prompted the development of reactive force fields, facilitating practical applications of molecular dynamics simulations for large-scale reactive systems. Current reactive force fields typically employ intricate corrections based on prior chemical knowledge, which severely impedes their further advancement. This study presents a new atomic multipole-based reactive model with bond free (OPERATOR).

GQ262 Attenuates Pathological Cardiac Remodeling by Downregulating the Akt/mTOR Signaling Pathway.

Cardiac remodeling, a critical process that can lead to heart failure, is primarily characterized by cardiac hypertrophy. Studies have shown that transgenic mice with Gαq receptor blockade exhibit reduced hypertrophy under induced pressure overload. GQ262, a novel Gαq/11 inhibitor, has demonstrated good biocompatibility and specific inhibitory effects on Gαq/11 compared to other inhibitors.

Prebiotics improve frailty status in community-dwelling older individuals in a double-blind, randomized, controlled trial.

BACKGROUNDFrailty significantly affects morbidity and mortality rates in the older population (age >65 years). Age-related degenerative diseases are influenced by the intestinal microbiota. However, limited research exists on alterations in the intestinal microbiota in frail older individuals, and the effectiveness of prebiotic intervention for treating frailty remains uncertain.

Insight of the molecular mechanism of inhibitors located at different allosteric sites regulating the activity of wild type and mutant KRAS (G12).

As the important hub of many cellular signaling networks, KRAS (Kirsten rat sarcoma viral oncogene homologue) has been identified as a tumor biomarker. It is the frequently mutated oncogene in human cancers, and KRAS protein activation caused by mutations, such as G12D, has been found in many human tumors tissues. Although, there are two specific allosteric sites (AS1 and AS2) on the KRAS protein that can be used as the targets for inhibitor development, the difference of regulatory mechanisms between two individual allosteric sites still not be reported.

Si-Ni-San alleviates intestinal and liver damage in ulcerative colitis mice by regulating cholesterol metabolism.

Ethnopharmacological Relevance: Si-Ni-San (SNS), a traditional Chinese medicinal formula derived from Treatise on Febrile Diseases, is considered effective in the treatment of inflammatory bowel diseases based upon thousands of years of clinical practice. However, the bioactive ingredients and underlying mechanisms are still unclear and need further investigation.

Aim Of The Study: This study aimed to evaluate the effect, explore the bioactive ingredients and the underlying mechanisms of SNS in ameliorating ulcerative colitis (UC) and associated liver injury in dextran sodium sulphate (DSS)-induced mouse colitis models.

Chemoproteomic Profiling of Signaling Metabolite Fructose-1,6-Bisphosphate Interacting Proteins in Living Cells.

Fructose-1,6-bisphosphate (FBP), a cellular endogenous sugar metabolite in the glycolytic pathway, has recently been reported to act as a signaling molecule to regulate various cellular events through the engagement of important proteins. Though tremendous progress has been made in identifying specific FBP-protein interactions, the comprehensive identification of FBP-interacting proteins and their regulatory mechanisms remains largely unexplored. Here, we describe a concise synthetic approach for the scalable preparation of a photoaffinity FBP probe that enables the quantitative chemoproteomic profiling of FBP-protein interactions based on photoaffinity labeling (PAL) directly in living cells.

LC-MS/MS profiling of colon oxysterols and cholesterol precursors in mouse model of ulcerative colitis.

Oxysterols and cholesterol precursors are being increasingly investigated in humans and laboratory animals as markers for various diseases in addition to their important functions. However, the quantitative analysis of these bioactive molecules is obstructed by high structural similarity, poor ionization efficiency and low abundance. The current assay methods are still cumbersome to be of practical use, and their applicability in different bio-samples needs to be evaluated and optimized as necessary.

Asparagine Synthetase Marks a Distinct Dependency Threshold for Cardiomyocyte Dedifferentiation.

Background: Adult mammalian cardiomyocytes have limited proliferative capacity, but in specifically induced contexts they traverse through cell-cycle reentry, offering the potential for heart regeneration. Endogenous cardiomyocyte proliferation is preceded by cardiomyocyte dedifferentiation (CMDD), wherein adult cardiomyocytes revert to a less matured state that is distinct from the classical myocardial fetal stress gene response associated with heart failure. However, very little is known about CMDD as a defined cardiomyocyte cell state in transition.

Late Positivity Correlates with Subjective Reports: Evidence from the Low-frequency and High-frequency Reporting Tasks.

Identifying the neural correlates of consciousness (NCCs) is an important way to understand the fundamental nature of consciousness. By recording event-related potentials (ERPs) using EEG, researchers have found three potential electrophysiological NCCs: early positive correlate of consciousness (enhanced P1), visual awareness negativity (VAN), and late positivity (LP). However, LP may reflect post-perceptual processing associated with subjective reports rather than consciousness per se.

Oleanolic acid derivative alleviates cardiac fibrosis through inhibiting PTP1B activity and regulating AMPK/TGF-β/Smads pathway.

Cardiac fibrosis (CF) in response to persistent exogenous stimuli or myocardial injury results in cardiovascular diseases (CVDs). Protein tyrosine phosphatase 1B (PTP1B) can promote collagen deposition through regulating AMPK/TGF-β/Smads signaling pathway, and PTP1B knockout improves cardiac dysfunction against overload-induced heart failure. Oleanolic acid (OA) has been proven to be an inhibitor of PTP1B, and its anti-cardiac remodeling effects have been validated in different mouse models.

Structural insights into the mechanism of GTP initiation of microtubule assembly.

In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT.

Chemical index components and quality control of Traditional Chinese Medicine: "Never change a winning team"? -A case study of volatile oil from Bupleuri radix.

Chemical index components, especially those defined as quality control (QC) markers through spectrum-effect relationship approach, are commonly suggested and adopted as indicator for quality control of Traditional Chinese Medicines (TCMs). However, are chemical index components and quality control of TCMs "never change a winning team"? In this study, under the ponderation of the applicability of QC markers strategy, spectrum-effect relationship and OPLS-DA between GC×GC-MS fingerprint and inhibitory effect on the expression of extracellular secretory TNF-α of volatile oil from Bupleuri radix (BVO) was studied with the purpose of discovery of QC markers and establish a bioactive compounds-based QC method. 290 compounds of BVO were identified by GC×GC-MS.

The PIWI-specific insertion module helps load longer piRNAs for translational activation essential for male fertility.

PIWI-clade proteins harness piRNAs of 24-33 nt in length. Of great puzzles are how PIWI-clade proteins incorporate piRNAs of different sizes and whether the size matters to PIWI/piRNA function. Here we report that a PIWI-Ins module unique in PIWI-clade proteins helps define the length of piRNAs.

A Reactive Force Field for Molecular Dynamics Simulations of Glucose in Aqueous Solution.

To expand the capabilities of reactive force field (ReaxFF) in simulations of biological processes involving glucose, in this work, using Metropolis Monte Carlo algorithm, new ReaxFF parameters for glucose have been developed to better describe the properties of glucose in water during molecular dynamics (MD) simulations. With the newly trained ReaxFF, the mutarotation of glucose in water can be better described, as suggested by our metadynamics simulations. In addition, the newly trained ReaxFF can better describe the distributions of the three stable conformers along the key dihedral angle of α-anomer and β-anomer.

RNA Folding Based on 5 Beads Model and Multiscale Simulation.

RNA folding prediction is very meaningful and challenging. The molecular dynamics simulation (MDS) of all atoms (AA) is limited to the folding of small RNA molecules. At present, most of the practical models are coarse grained (CG) model, and the coarse-grained force field (CGFF) parameters usually depend on known RNA structures.

Study on Long Term Property of Soft Soil Solidified with Industrial Waste Residue and Regenerated Fine Aggregate.

The long-term properties of solidified soft soil, including an immersion test, the dry-wet cycle and the freeze-thaw cycle, were systematically studied. Firstly, the immersion stability of solidified soft soil was confirmed. The appearance of soft soil solidified by a solidified agent and raw fine aggregate did not change significantly, and it was still intact without damage when the soaking time increased up to 28 d.

Protective Efficacy on Adult Ischemic Myocardium under Bypass: Del Nido vs. St. Thomas Blood Cardioplegia.

Purpose: To compare the myocardial protective efficacy of del Nido cardioplegia (DNC) with St. Thomas blood cardioplegia (SBC) in adult cardiac surgery.

Methods: From January to December 2021, all the patients who underwent elective cardiac operation were randomly divided into two cohorts based on the type of cardioplegia: DNC group and SBC group.

Influence of Recycled Fine Aggregate Content on Properties of Soft Soil Solidified by Industrial Waste Residue.

The influence of recycled fine aggregate content on the properties of soft soil solidified by industrial waste residue was systematically studied. First, the addition of recycled fine aggregate may provide skeleton support, which was conducive to improving the solidification properties. Comparing the addition of recycled fine aggregate content and a composite solidification agent separately, the compressive strength increased 48.

Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation.

RNA folding prediction is a challenge. Currently, many RNA folding models are coarse-grained (CG) with the potential derived from the known RNA structures. However, this potential is not suitable for modified and entirely new RNA.

Study on the Association Between Dietary Habits, Patterns and Frailty of the Elderly: A Cross-Sectional Survey from Communities in China.

Objective: The purpose of this study was to explore the effects of Chinese dietary habits and patterns on frailty among elderly people in Xi'an the community. We also sought to provide dietary suggestions for prevention of frailty.

Methods: A cross-sectional survey was conducted and participants were divided into three groups: non-frail group, pre-frail group, and frail group.

Galectin-9 expression predicts poor prognosis in hepatitis B virus-associated hepatocellular carcinoma.

Objectives: The aim of this study was to explore the expression of Galectin-9 in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC), evaluate its clinicopathological significance, and investigate whether Galecin-9 expression has prognostic value in HBV-associated HCC.

Methods: Immunohistochemistry staining was performed to examine the expression of Galectin-9 in paraffin-embedded tissues from 140 cases of HBV-associated HCC specimens. The association between Gal-9 expression, clinicopathological features and prognosis was analyzed by Kaplan-Meier method, log-rank test and Cox regression analysis.

A double bilayer to study the nonequilibrium environmental response of GIRK2 in complex states.

G protein-gated inwardly rectifying potassium (GIRK) channels play essential roles in electrical signaling in neurons and muscle cells. Nonequilibrium environments provide crucial driving forces behind many cellular events. Here, we apply the antiparallel alignment double bilayer model to study GIRK2 in response to the time-dependent membrane potential.