Harnessing Machine Learning to Enhance Transition State Search with Interatomic Potentials and Generative Models.

Transition state (TS) search is crucial for illuminating chemical reaction mechanisms but remains the major bottleneck in automated discovery because of the high computational cost. Recently, machine learning interatomic potentials (MLIPs) and generative models have shown promise in accelerating TS search, but their comparative strengths and limitations remain unclear. In this study, the first systematic and rigorous benchmarking framework is established to evaluate the effectiveness of ML methods in TS search, enabling a standardized and application-relevant assessment of their performance.

Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge and Reasoning Capability of Large Language Models.

Large language models (LLMs) have shown promise in science, such as structure-property prediction and acting as AI agents, yet their intrinsic knowledge and reasoning capability for scientific discovery remains underexplored. We introduce LLM-EO, an integration of LLMs into evolutionary optimization, and demonstrate its success in optimizing transition metal complexes (TMCs). LLM-EO demonstrates advantages in few-sample learning due to the intrinsic chemical knowledge embedded within LLMs and their ability to leverage entire historical data collected during optimizations.

Host Lifeform Shapes Phyllospheric Microbiome Assembly in Mountain Lake: Deterministic Selection and Stochastic Colonization Dynamics.

The phyllosphere microbiome of aquatic macrophytes constitutes an integral component of freshwater ecosystems, serving crucial functions in global biogeochemical cycling and anthropogenic pollutant remediation. In this study, we examined the assembly mechanisms of epiphytic bacterial communities across four phylogenetically diverse macrophyte species (, , , and ) inhabiting Ningwu Mayinghai Lake (38.87° N, 112.

Glucose deprivation-restoration induces labile iron overload and ferroptosis in renal tubules through V-ATPase-mTOR axis-mediated ferritinophagy and iron release by TPC2.

Renal ischemia-reperfusion injury (IRI), a common complication following kidney transplantation and partial nephrectomy, is the leading cause of renal dysfunction with limited treatment. Excessive cellular iron accumulation drives lipid peroxidation and activates pathways associated with ferroptosis, which has been implicated in renal IRI. However, the regulatory mechanisms of cellular iron metabolism and its relationship with ferroptosis during ischemia-reperfusion (IR) remain unclear.

Identification of c-Jun phosphorylation as a crucial mediator of complement activation in renal ischemia-reperfusion injury revealed by phosphoproteomics and functional validation.

Background: Ischemia reperfusion injury (IRI) is an unavoidable condition that primarily affects graft function in renal transplantation. Blockage of complement activation by complement receptor immunoglobulin/ factor H (CRIg/FH), a novel complement inhibitor, shows great potency to ameliorate renal IRI. Sublytic membrane attack complex (MAC) disrupts cellular functions via the activation of different protein kinases and phosphorylation of critical signal transduction factors.

Thrombin generation indices and Wells score predict pulmonary embolism in patients with acute exacerbation of chronic obstructive pulmonary disease.

Objective: This study investigated the predictive value of thrombin generation indices and Wells score in the development of Pulmonary Embolism (PE) in patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD).

Methods: 160 patients who were admitted for AECOPD and underwent CT Pulmonary Arteriography (CTPA) were collected. Among them, a total of 62 cases were diagnosed with PE as the AECOPD with PE group, and the other 98 cases were not diagnosed with PE as the AECOPD group.

Codelivery of ERCC2 small interfering RNA and cisplatin with macrophage-derived mimetic nanovesicles for enhanced bladder cancer treatment.

Cisplatin-based chemotherapy plays a vital role in the management of muscle-invasive bladder cancer (MIBC); however, off-tumor toxicity and resistance often lead to cancer recurrence and eventual treatment failure. The loss of function of the nucleotide excision repair gene excision repair cross-complementing rodent repair deficiency gene 2 ( ERCC2 ) in cancer cells correlates with sensitivity to cisplatin, while its overexpression causes cisplatin resistance. Small interfering RNA (siRNA) knockdown of ERCC2 combined with cisplatin treatment may improve therapeutic outcomes in patients with bladder cancer.

Periosteum-derived mesenchymal stem cell alleviates renal fibrosis through mTOR-mediated Treg differentiation.

Background: Mesenchymal stem cells (MSCs) are the hotspots of cellular therapy due to their low immunogenicity, potent immunoregulation, and unique renoprotection. The present study aimed to investigate the effects of periosteum-derived MSCs (PMSCs) in ischemia-reperfusion (IR)-mediated renal fibrosis.

Methods: Using cell proliferation assay, flow cytometry, immunofluorescence, and histologic analysis, the differences in cell characteristics, immunoregulation, and renoprotection of PMSCs were compared to the bone marrow-derived MSCs (BMSCs), the most frequently studied stem cells in cellular therapy.

Monomethyl fumarate prevents alloimmune rejection in mouse heart transplantation by inducing tolerogenic dendritic cells.

Dendritic cells (DCs) are important targets for eliciting allograft rejection after transplantation. Previous studies have demonstrated that metabolic reprogramming of DCs can transform their immune functions and induce their differentiation into tolerogenic DCs. In this study, we aim to investigate the protective effects and mechanisms of monomethyl fumarate (MMF), a bioactive metabolite of fumaric acid esters, in a mouse model of allogeneic heart transplantation.

Inhibition of ALKBH5 attenuates I/R-induced renal injury in male mice by promoting Ccl28 m6A modification and increasing Treg recruitment.

Ischemia reperfusion injury (IRI) is a common cause of acute kidney injury (AKI). The role of Nmethyladenosine (m6A) modification in AKI remains unclear. Here, we characterize the role of AlkB homolog 5 (ALKBH5) and m6A modification in an I/R-induced renal injury model in male mice.

Does the built environment of settlements affect our sentiments? A multi-level and non-linear analysis of Xiamen, China, using social media data.

Introduction: Humans spend most of their time in settlements, and the built environment of settlements may affect the residents' sentiments. Research in this field is interdisciplinary, integrating urban planning and public health. However, it has been limited by the difficulty of quantifying subjective sentiments and the small sample size.

Formyl peptide receptor 2 activation by mitochondrial formyl peptides stimulates the neutrophil proinflammatory response via the ERK pathway and exacerbates ischemia-reperfusion injury.

Background: Ischemia-reperfusion injury (IRI) is an inevitable process in renal transplantation that significantly increases the risk of delayed graft function, acute rejection, and even graft loss. Formyl peptide receptor 2 (FPR2) is an important receptor in multiple septic and aseptic injuries, but its functions in kidney IRI are still unclear. This study was designed to reveal the pathological role of FPR2 in kidney IRI and its functional mechanisms.

Bone marrow mesenchymal stem cell-derived exosomal miR-21a-5p alleviates renal fibrosis by attenuating glycolysis by targeting PFKM.

Renal fibrosis is a common pathological feature and outcome of almost all chronic kidney diseases, and it is characterized by metabolic reprogramming toward aerobic glycolysis. Mesenchymal stem cell-derived exosomes (MSC-Exos) have been proposed as a promising therapeutic approach for renal fibrosis. In this study, we investigated the effect of MSC-Exos on glycolysis and the underlying mechanisms.

Exosome-Derived From Sepsis Patients' Blood Promoted Pyroptosis of Cardiomyocytes by Regulating miR-885-5p/HMBOX1.

Background: Septic myocardial depression has been associated with increased morbidity and mortality. miR-885-5p has been shown to regulate cell growth, senescence, and/or apoptosis. Published studies demonstrated that Homeobox-containing protein 1 (HMBOX1) inhibits inflammatory response, regulates cell autophagy, and apoptosis.

Corrigendum: Myeloid-Derived Suppressor Cells Alleviate Renal Fibrosis Progression Regulation of CCL5-CCR5 Axis.

[This corrects the article DOI: 10.3389/fimmu.2021.

Myeloid-Derived Suppressor Cells Alleviate Renal Fibrosis Progression Regulation of CCL5-CCR5 Axis.

Background: Renal fibrosis is inevitable in all progressive chronic kidney diseases (CKDs) and represents a serious public health problem. Immune factors contribute to the progression of renal fibrosis. Thus, it is very possible that immunosuppression cells, such as myeloid-derived suppressor cells (MDSCs), could bring benefits to renal fibrosis.

Single-cell RNA Sequencing in Immunology.

The complex immune system is involved in multiple pathological processes. Single-cell RNA sequencing (scRNA-seq) is able to analyze complex cell mixtures correct to a single cell and single molecule, thus is qualified to analyze immune reactions in several diseases. In recent years, scRNA-seq has been applied in many researching fields and has presented many innovative results.

Electron-Deficient Polycyclic π-System Fused with Multiple B←N Coordinate Bonds.

An extensive polycyclic π-system with 23 fused rings is synthesized via a highly efficient borylation reaction, in which four B-N covalent bonds and four B←N coordinate bonds are formed in one pot. B←N coordinate bonds not only lock the backbone into a near-coplanar conformation but also decrease the LUMO energy level to around -3.82 eV, demonstrating the dual utility of this strategy for the synthesis of extensive rigid polycyclic molecules and the development of -type conjugated materials for organic electronics and organic photovoltaics.