Systematic analysis of the molecular mechanisms of methotrexate therapy for rheumatoid arthritis using text mining.

Objectives: The purpose of this study was to determine the expression of related genes in patients with rheumatoid arthritis (RA) treated with methotrexate (MTX), to identify hub genes, and to systematically analyse the functions, pathways, and networks of these genes.

Methods: The PubMed identifiers (PMIDs) of relevant publications were obtained from the PubMed database, and gene data were extracted from these documents using the text mining software PubTator. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to obtain enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway information.

Understanding the Activity of Single-Atom Catalysis from Frontier Orbitals.

The d-band center and charge states are often used to analyze the catalytic activity of noble or transition metal surfaces and clusters, but their applicability for single-atom catalysts (SACs) is unsure. This work suggests that the spatial structure and orientation of frontier orbitals which are closest to the Fermi level of SACs play a vital role. Taking adsorption of several molecules and CO oxidization on C_{3}N-supported single-atom Au as examples, we demonstrate that adsorption and catalytic activities are well correlated with the characteristics of frontier orbitals.

AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses.

CRISPR-Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR-Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR-Cas systems.

Identification of CTLA-4 associated with tumor microenvironment and competing interactions in triple negative breast cancer by co-expression network analysis.

The study of CTLA-4 inhibitors has been one of the hot spots in the field of tumor immunotherapy. As the most immunogenic subtype of breast cancer, Triple negative breast cancer (TNBC) has a great potential in the treatment strategy. The aim of this study was to explore the relevant genes and pathways of CTLA-4 in TNBC and to explore the prognostic value, so as to provide a theoretical basis for clinical studies.

Molecular characterization, expression and immune functions of two C-type lectin from Venerupis philippinarum.

In the present study, two C-type lectins (designated as VpClec-3 and VpClec-4) were identified and characterized from the manila clam Venerupis philippinarum. Multiple alignment and phylogenetic relationship analysis strongly suggested that VpClec-3 and VpClec-4 belong to the C-type lectin family. In nonstimulated clams, the VpClec-3 transcript was dominantly expressed in the hepatopancreas, while the VpClec-4 transcript was mainly expressed in gill tissues.

Chemistry of Advanced Nanomedicines in Cancer Cell Metabolism Regulation.

Tumors reprogram their metabolic pathways to meet the bioenergetic and biosynthetic demands of cancer cells. These reprogrammed activities are now recognized as the hallmarks of cancer, which not only provide cancer cells with unrestricted proliferative and metastatic potentials, but also strengthen their resistance against stress conditions and therapeutic challenges. Although recent progress in nanomedicine has largely promoted the developments of various therapeutic modalities, such as photodynamic therapy, photothermal therapy, nanocatalytic therapy, tumor-starving/suffocating therapy, etc.

Tunable layered-magnetism-assisted magneto-Raman effect in a two-dimensional magnet CrI.

We used a combination of polarized Raman spectroscopy experiment and model magnetism-phonon coupling calculations to study the rich magneto-Raman effect in the two-dimensional (2D) magnet CrI We reveal a layered-magnetism-assisted phonon scattering mechanism below the magnetic onset temperature, whose Raman excitation breaks time-reversal symmetry, has an antisymmetric Raman tensor, and follows the magnetic phase transitions across critical magnetic fields, on top of the presence of the conventional phonon scattering with symmetric Raman tensors in -layer CrI We resolve in data and by calculations that the first-order phonon of the monolayer splits into an -fold multiplet in -layer CrI due to the interlayer coupling [Formula: see text] and that the phonons within the multiplet show distinct magnetic field dependence because of their different layered-magnetism-phonon coupling. We further find that such a layered-magnetism-phonon coupled Raman scattering mechanism extends beyond first-order to higher-order multiphonon scattering processes. Our results on the magneto-Raman effect of the first-order phonons in the multiplet and the higher-order multiphonons in -layer CrI demonstrate the rich and strong behavior of emergent magneto-optical effects in 2D magnets and underline the unique opportunities of spin-phonon physics in van der Waals layered magnets.

Observation of the polaronic character of excitons in a two-dimensional semiconducting magnet CrI.

Exciton dynamics can be strongly affected by lattice vibrations through electron-phonon coupling. This is rarely explored in two-dimensional magnetic semiconductors. Focusing on bilayer CrI, we first show the presence of strong electron-phonon coupling through temperature-dependent photoluminescence and absorption spectroscopy.

Photocurrent Imaging of Multi-Memristive Charge Density Wave Switching in Two-Dimensional 1T-TaS.

Transport studies of atomically thin 1T-TaS have demonstrated the presence of intermediate resistance states across the nearly commensurate (NC) to commensurate (C) charge density wave (CDW) transition, which can be further switched electrically. While this presents exciting opportunities for memristor applications, the switching mechanism could be potentially attributed to the formation of inhomogeneous C and NC domains. Here, we present combined electrical driving and photocurrent imaging of ultrathin 1T-TaS in a heterostructure geometry.

Azopolymer-Based Nanoimprint Lithography: Recent Developments in Methodology and Applications.

Nanofabrication on soft polymeric surfaces is an essential process in many fields, for example, chip manufacturing, microfluidics, high efficiency solar cells, and anticounterfeiting. In order to achieve these applications, various nanofabrication methods have been explored. Among them, nanoimprint lithography (NIL) has drawn worldwide attention because of its cheap and fast processability.

dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates.

PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active EnZymes) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.

Baohuoside i suppresses breast cancer metastasis by downregulating the tumor-associated macrophages/C-X-C motif chemokine ligand 1 pathway.

Background: Breast cancer is the most common malignancy in women and metastasis is the leading cause of breast cancer-related deaths. Our previous studies have shown that XIAOPI formula, a newly approved drug by the State Food and Drug Administration of China (SFDA), can dramatically inhibit breast cancer metastasis by modulating the tumor-associated macrophages/C-X-C motif chemokine ligand 1 (TAMs/CXCL1) pathway. However, the bioactive compound accounting for the anti-metastatic effect of XIAOPI formula remains unclear.

Biases of Happy Faces in Face Classification Processing of Depression in Chinese Patients.

We explored the face classification processing mechanism in depressed patients, especially the biases of happy faces in face classification processing of depression. Thirty patients with the first episode of depression at the First Affiliated Hospital of Harbin Medical University were selected as the depression group, while healthy people matched for age, gender, and educational level were assigned to the control group. The Hamilton Depression Scale and Hamilton Anxiety Scale were used to select the subjects; then, we used the forced face classification paradigm to collect behavioral (response time and accuracy) and event-related potential (ERP) data of the subjects.

Prognostic value of depression and anxiety on breast cancer recurrence and mortality: a systematic review and meta-analysis of 282,203 patients.

Depression and anxiety are common comorbidities in breast cancer patients. Whether depression and anxiety are associated with breast cancer progression or mortality is unclear. Herein, based on a systematic literature search, 17 eligible studies involving 282,203 breast cancer patients were included.

Identification of a Novel Prognostic Classification Model in Epithelial Ovarian Cancer by Cluster Analysis.

Background: Heterogeneity plays an essential role in ovarian cancer. Patients with different clinical features may manifest diverse patterns in diagnosis, treatment, and prognosis. The aim of the present study was to identify a novel ovarian cancer-classification model through cluster analysis and assess its significance in prognosis.

Intrinsic brain activity changes in temporal lobe epilepsy patients revealed by regional homogeneity analysis.

Purpose: Temporal lobe epilepsy is increasingly being recognized as a disorder associated with brain networks extending outside the seizure onset zone. In the current study, we aim to clarify regional functional changes using a regional homogeneity method.

Methods: We retrospectively included resting-state fMRI data from 14 left and 18 right temporal lobe epilepsy patients.

Dextran sulfate-modified pH-sensitive layered double hydroxide nanocomposites for treatment of rheumatoid arthritis.

To reduce the side effects of methotrexate and increase its anti-inflammatory effect, we developed a drug delivery system, dextran sulfate-modified methotrexate-loaded layered double hydroxide nanocomposites (LDH-MTX-DS), with both targeting and pH-sensitivity for the treatment of rheumatoid arthritis. The nanocomposites had a mean particle size of 303.1 ± 8.

A New Concept for the Treatment and Rehabilitation of Patients with Pathologic Comorbidities Using Cutting-Edge Digital Technologies in Dental Orthopaedics.

Objectives:  This article investigates the specific aspects of overactive or exaggerated vomiting reflexes affecting the procedure of dental examination and impression in patients with complete secondary adentia, who need orthopaedic dental treatment.

Materials And Methods:  The prevailing manifestation degree of exaggerated vomiting reflex was diagnosed among patients with complete secondary adentia and exaggerated vomiting reflex.

Statistical Analysis:  Exaggerated vomiting reflexes occur when a patient suffers from dentophobia, the term, which is otherwise known as the fear of dentists.

Formation of phytosterol photooxidation products: A chemical reaction mechanism for light-induced oxidation.

Phytosterols (PS) are a group of sterols distributed in foods and plants, where it is prone to oxidation. In this work, we studied the reaction mechanism of phytosterols, using density functional theory (DFT) calculation and experimental methods to study the photooxidation of phytosterols. Under LED light illumination, experimental photooxidation of these phytosterols gives rise to the prior three kind oxides of phytosterol: 6α-OH, 7α-OH, and 7β-OH.

Systematic profiling of alternative splicing in -negative gastric cancer and their clinical significance.

Background: Alternative splicing (AS) may cause structural and functional variations in the protein to promote the proliferation of tumor cells. However, there is no comprehensive analysis of the clinical significance of AS in -negative gastric cancer (HP GC).

Methods: The clinical, gene expression profile data and AS events of 138 HP GC patients were obtained from the database named the cancer genome atlas.

Caveolin-1 inhibits breast cancer stem cells via c-Myc-mediated metabolic reprogramming.

Breast cancer stem cells (BCSCs) are considered to be the root of breast cancer occurrence and progression. However, the characteristics and regulatory mechanisms of BCSCs metabolism have been poorly revealed, which hinders the development of metabolism-targeted treatment strategies for BCSCs elimination. Herein, we demonstrated that the downregulation of Caveolin-1 (Cav-1) usually occurred in BCSCs and was associated with a metabolic switch from mitochondrial respiration to aerobic glycolysis.

AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses.

Anti-CRISPR (Acr) proteins encoded by (pro)phages/(pro)viruses have a great potential to enable a more controllable genome editing. However, genome mining new Acr proteins is challenging due to the lack of a conserved functional domain and the low sequence similarity among experimentally characterized Acr proteins. We introduce here AcrFinder, a web server (http://bcb.