LoreX: A Low-Energy Region Explorer Boosts Efficient Crystal Structure Prediction.

Machine learning has boosted the remarkable development of crystal structure prediction (CSP), greatly accelerating modern materials design. However, slow location of the low-energy regions on the potential energy surface (PES) is still a key bottleneck for the overall search efficiency. Here, we develop a low-energy region explorer (LoreX) to rapidly locate low-energy regions on the PES.

Association between high-sensitivity C-reactive protein and bleeding in dual antiplatelet therapy age: a retrospective observational study.

Objectives: The aim of the present study was to investigate the association of high-sensitivity C-reactive protein (hs-CRP) with bleeding events among patients with acute coronary syndrome (ACS) received dual antiplatelet therapy (DAPT) after percutaneous coronary intervention.

Design: An observational and multicentre study was conducted among non-ST-segment elevation ACS (NSTE-ACS).

Setting: The study was conducted at five medical centres in China.

Soft X-ray tomography analysis of mitochondria dynamics in Saccharomyces cerevisiae.

Background: Mitochondria are highly dynamic organelles that constantly undergo processes of fission and fusion. The changes in mitochondrial dynamics shape the organellar morphology and influence cellular activity regulation. Soft X-ray tomography (SXT) allows for three-dimensional imaging of cellular structures while they remain in their natural, hydrated state, which omits the need for cell fixation and sectioning.

Corrigendum to "Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography" [J. Struct. Biol.: X 10(2024) 100113].

[This corrects the article DOI: 10.1016/j.yjsbx.

Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography.

Cryo-soft X-ray tomography (cryo-SXT) is a newly developed technique for imaging 3D whole cells in nearly native states. Cryo-SXT users require the preparation of numerous cryo-sample grids to use the allocated beamtime to study cellular phenomena under various conditions. Therefore, it is important to promptly prepare cryo-sample grids as efficiently and carefully as possible to minimize ice contamination on the frozen sample grid.

Edge sites regulation, strain and electric field effect on MoS2/CoS2 heterojunction catalysts for hydrogen evolution reaction.

Heterojunction catalysts in the field of hydrogen evolution reaction (HER) from electrocatalytic water splitting have recently become a hot research topic. In this paper, we systematically calculated the HER catalytic performance of a MoS2/CoS2 heterojunction for the first time, considering the effect of edge sites regulation, strain and electric field. The results indicate that the MoS2/CoS2 heterojunction exhibits synergistic catalytic performance compared to MoS2 and CoS2, the HER catalytic activity of which can be improved by exposing more edge sites or regulating the S content on the edges, with an optimized ratio of 25%.

Enhancing protein-ligand binding affinity prediction through sequential fusion of graph and convolutional neural networks.

Predicting protein-ligand binding affinity is a crucial and challenging task in structure-based drug discovery. With the accumulation of complex structures and binding affinity data, various machine-learning scoring functions, particularly those based on deep learning, have been developed for this task, exhibiting superiority over their traditional counterparts. A fusion model sequentially connecting a graph neural network (GNN) and a convolutional neural network (CNN) to predict protein-ligand binding affinity is proposed in this work.

Quantum Mechanics-Based Fast and Reliable Prediction of Binding Pose Structures.

Predicting the binding poses of docking with an accurate estimation of binding energies is highly important but very challenging in computational drug design. A quantum mechanics (QM) calculation-based docking approach considering multiple conformations and orientations of the ligand is introduced here to tackle the problem. This QM docking consists of three steps: generating an ensemble of binding poses with a conventional docking simulation, computing the binding energies with self-consistent charge density functional theory tightly binding with dispersion correction (DFTB-D) to selecting the 10 top binding modes, and optimizing the selected binding mode structures using the ONIOM(DFTB:PM7) technique to determine the binding poses.

Downsizing and soft X-ray tomography for cellular uptake of interpenetrated metal-organic frameworks.

Metal-organic frameworks (MOFs) are porous materials with potential in biomedical applications such as sensing, drug delivery, and radiosensitization. However, how to tune the properties of the MOFs for such applications remains challenging. Herein, we synthesized two MOFs, Zr-PEB and Hf-PEB.

Multiparametric MRI-based radiomics nomogram for identifying cervix-corpus junction cervical adenocarcinoma from endometrioid adenocarcinoma.

Objective: To developed a magnetic resonance imaging (MRI) radiomics nomogram to identify adenocarcinoma at the cervix-corpus junction originating from the endometrium or cervix in order to better guide clinical treatment.

Methods: Between February 2011 and September 2021, the clinicopathological data and MRI in 143 patients with histopathologically confirmed cervical adenocarcinoma (CAC, n = 86) and endometrioid adenocarcinoma (EAC, n = 57) were retrospectively analyzed at the cervix-corpus junction. Radiomics features were extracted from fat-suppressed T2-weighted imaging (FS-T2WI), diffusion-weighted imaging (DWI), apparent diffusion coefficient (ADC) maps, and delayed phase contrast-enhanced T1-weighted imaging (CE-T1WI) sequences.

Semaglutide alleviates gut microbiota dysbiosis induced by a high-fat diet.

This study investigated the effects of semaglutide (Sema) on the gut microbiota of obese mice induced with high-fat diet (HFD). Male C57BL/6 J mice aged 6 weeks were enrolled and randomly distributed to four groups, which were provided with a normal control diet (NCD,NCD + Sema) and a 60% proportion of a high-fat diet (HFD,HFD + Sema), respectively. HFD was given for 10 weeks to develop an obesity model and the intervention was lasted for 18 days.

Guiding the postoperative radioactive iodine-131 therapy for patients with papillary thyroid carcinoma according to the prognostic risk groups: a SEER-based study.

Purpose: The effectiveness of iodine-131(I) therapy in patients with papillary thyroid cancer (PTC) of various stage is controversial. This study aimed to use prognostic risk groups to guide I therapy in patients with PTC after radical thyroidectomy.

Methods: Data of 53,484 patients with PTC after radical thyroidectomy were collected from the Epidemiology and End Results (SEER) database.

Association between admission-blood-glucose-to-albumin ratio and clinical outcomes in patients with ST-elevation myocardial infarction undergoing percutaneous coronary intervention.

Introduction: It is unclear whether admission-blood-glucose-to-albumin ratio (AAR) predicts adverse clinical outcomes in patients with ST-segment elevation myocardial infarction (STEMI) who are treated with percutaneous coronary intervention (PCI). Here, we performed a observational study to explore the predictive value of AAR on clinical outcomes.

Methods: Patients diagnosed with STEMI who underwent PCI between January 2010 and February 2020 were enrolled in the study.

Correlation between connexin 43 expression in circulating tumor cells and biological characteristics of breast cancer.

Background: Connexin 43 (Cx43) has been closely linked to the occurrence and progression of breast cancer. Distant metastasis of breast cancer is aided by the epithelial-mesenchymal transition of circulating tumor cells (CTCs). However, the impact of Cx43 expression on CTCs and the extent of its role in the disease remain unclear.

A global database for modeling tumor-immune cell communication.

Communications between tumor cells and surrounding immune cells help shape the tumor immunity continuum. Recent breakthroughs in high-throughput technologies as well as computational algorithms had reported many important tumor-immune cell (TIC) communications, which were scattered in thousands of published studies and impeded systematical characterization of the TIC communications across cancer. Here, a comprehensive database, TICCom, was developed to model TIC communications, containing 739 experimentally-validated or manually-curated interactions collected from more than 3,000 literatures as well as 4,537,709 predicted interactions inferred via six computational algorithms by reanalyzing 32 scRNA-seq datasets and bulk RNA-seq data across 25 cancer types.

Development and validation of MRI-based radiomics model to predict recurrence risk in patients with endometrial cancer: a multicenter study.

Objectives: To develop a fusion model based on clinicopathological factors and MRI radiomics features for the prediction of recurrence risk in patients with endometrial cancer (EC).

Methods: A total of 421 patients with histopathologically proved EC (101 recurrence vs. 320 non-recurrence EC) from four medical centers were included in this retrospective study, and were divided into the training (n = 235), internal validation (n = 102), and external validation (n = 84) cohorts.

Blockade of Indoleamine 2,3-Dioxygenase attenuates lipopolysaccharide-induced kidney injury by inhibiting TLR4/NF-κB signaling.

Blockade of indoleamine 2,3-dioxygenase (IDO) has been shown to alleviate lipopolysaccharide (LPS)-induced endotoxic shock and reduce sepsis mortality, but its effect on LPS-induced kidney damage has not been reported. Herein, we established a mouse kidney injury model by intraperitoneal injection of 10 mg/kg LPS and established an in vitro renal tubular epithelial cell injury model by stimulating TCMK-1 cells with 10 mg/L LPS. We found that pretreatment with 1-methyl tryptophan (1-MT), an IDO inhibitor, significantly improved LPS-induced mouse survival, and IDO knockout (KO) mice also had higher survival rates after LPS exposure than wild-type mice.

Uncovering the Enhancement Mechanism of the Oxygen Reduction Reaction on Perovskite/Ruddlesden-Popper Oxide Heterostructures (Nd,Sr)CoO/(Nd,Sr)CoO and (Nd,Sr)CoO/(Nd,Sr)CoO.

Although the perovskite (Nd,Sr)CoO (NSC)/Ruddlesden-Popper (R-P) oxide (Nd,Sr)CoO (NSC) heterostructure is reported to improve the oxygen reduction reaction (ORR) activity by 2-3 orders of magnitude, the enhancement mechanism remains unclear. For the first time, we conclude that there are two main factors that can enhance the ORR activity: (1) Oxygen adsorbed on such heterostructures would gain more electrons, promoting the oxygen adsorption. (2) The more distant rock-salt layers on the heterointerfaces can facilitate the insertion of interstitial oxygen and form a high-speed transport channel of interstitial oxygen.

Safety and immunogenicity of the third (booster) dose of inactivated and recombinant protein SARS-CoV-2 vaccine for patients with endocrine-related cancer.

Background: Our study aimed to evaluate the safety and immunogenicity of the third (booster) dose of the COVID-19 vaccine for patients with endocrine-related cancers.

Methods: This observational study involved 94 breast cancer patients, 92 thyroid cancer patients, and 123 healthy individuals who had received the third (booster) dose of the COVID-19 vaccine. Data on the adverse effects, serum anti-receptor binding domain (RBD)-immunoglobulin (Ig) G, and neutralizing antibodies (NAbs) were collected prospectively.

Preoperative prediction of miliary changes in the small bowel mesentery in advanced high-grade serous ovarian cancer using MRI radiomics nomogram.

Purpose: To develop and validate an MRI-based radiomics nomogram for the preoperative prediction of miliary changes in the small bowel mesentery (MCSBM) in advanced high-grade serous ovarian cancer (HGSOC).

Materials And Methods: One hundred and twenty-eight patients with pathologically proved  advanced HGSOC (training cohort: n = 91; validation cohort: n = 37) were retrospectively included. All patients were initially evaluated as MCSBM-negative by preoperative imaging modalities but were finally confirmed by surgery and histopathology (MCSBM-positive: n = 53; MCSBM-negative: n = 75).

Magnetic resonance-based radiomics nomogram for predicting microsatellite instability status in endometrial cancer.

Background: Microsatellite instability (MSI) status is an important indicator for screening patients with endometrial cancer (EC) who have potential Lynch syndrome (LS) and may benefit from immunotherapy. This study aimed to develop a magnetic resonance imaging (MRI)-based radiomics nomogram for the prediction of MSI status in EC.

Methods: A total of 296 patients with histopathologically diagnosed EC were enrolled, and their MSI status was determined using immunohistochemical (IHC) analysis.

Clinical Features and Prognosis Analysis of Hormone Receptor-Positive, HER2-Negative Breast Cancer with Differential Expression Levels of Estrogen and Progesterone Receptors: A 10-Year Retrospective Study.

Background: Estrogen and progesterone receptor status can predict breast cancer patient prognosis and treatment sensitivity, but research on low ER and PR levels and expression balance remains limited.

Methods: From January 2010 to October 2016, 283 ER+/PR+/HER2-breast cancer patients who met the inclusion criteria were enrolled and divided into the H group (ER > 10%,  = 261) and the group (1% ≤ ER ≤ 10%,  = 22). Groups were further divided into the HH group (ER > 10%/PR > 20%,  = 201), the HL group (ER > 10%/ER 1% ≤ PR ≤ 20% PR,  = 60), the LH group (1% ≤ ER ≤ 10%/PR > 20%,  = 5), and the LL group (1% ≤ ER ≤ 10%/1% ≤ PR ≤ 20%,  = 17).

[Corrigendum] miR‑382 inhibits breast cancer progression and metastasis by affecting the M2 polarization of tumor‑associated macrophages by targeting PGC‑1α.

Subsequently to the publication of the above article, the authors have contacted the Editorial Office to explain that Fig. 7 was published containing an erroneously placed data panel. Specifically, the center panel of the images selected for the invasion assay experiments portrayed in Fig.