PbsNRs: predict the potential binders and scaffolds for nuclear receptors.

Nuclear receptors (NRs) are a class of essential proteins that regulate the expression of specific genes and are associated with multiple diseases. In silico methods for prescreening potential NR binders with predictive binding ability are highly desired for NR-related drug development but are rarely reported. Here, we present the PbsNRs (Predicting binders and scaffolds for Nuclear Receptors), a user-friendly web server designed to predict the potential NR binders and scaffolds through proteochemometric modeling.

Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.

Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable therapeutic phages that are capable of infecting pathogens from massive phage databases has been a principal step in phage therapy design. Experimental methods to identify phage-host interaction (PHI) are time-consuming and expensive; high-throughput computational method to predict PHI is therefore a potential substitute.

Neo-intline: integrated pipeline enables neoantigen design through the in-silico presentation of T-cell epitope.

Neoantigen vaccines are one of the most effective immunotherapies for personalized tumour treatment. The current immunogen design of neoantigen vaccines is usually based on whole-genome sequencing (WGS) and bioinformatics prediction that focuses on the prediction of binding affinity between peptide and MHC molecules, ignoring other peptide-presenting related steps. This may result in a gap between high prediction accuracy and relatively low clinical effectiveness.

The volatile anesthetic isoflurane differentially inhibits voltage-gated sodium channel currents between pyramidal and parvalbumin neurons in the prefrontal cortex.

Background: How volatile anesthetics work remains poorly understood. Modulations of synaptic neurotransmission are the direct cellular mechanisms of volatile anesthetics in the central nervous system. Volatile anesthetics such as isoflurane may reduce neuronal interaction by differentially inhibiting neurotransmission between GABAergic and glutamatergic synapses.

Comparison of Performances among Four Bleeding-Prediction Scores in Elderly Cancer Patients with Venous Thromboembolism.

The performances of RIETE, VTE-BLEED, SWITCO65 + , and Hokusai-VTE scores for predicting major bleeding events in hospitalized elderly cancer patients with venous thromboembolism (VTE) have not been evaluated. This study validated the performances of these scoring systems in a cohort of elderly cancer patients with VTE. Between June 2015 and March 2021, a total of 408 cancer patients (aged ≥ 65 years) with acute VTE were consecutively enrolled.

Loss of sodium leak channel (NALCN) in the ventral dentate gyrus impairs neuronal activity of the glutamatergic neurons for inflammation-induced depression in male mice.

Background: The dentate gyrus (DG) has been implicated in the pathophysiology of depression. Many studies have revealed the cellular types, neural circuits, and morphological changes of the DG involved in the development of depression. However, the molecular regulating its intrinsic activity in depression is unknown.

Association between radiotherapy and risk of death from cardiovascular diseases in lung and bronchus cancer.

Background: Radiotherapy plays an important role in the treatment of lung cancer. However, radiation-related deaths from cardiovascular disease (CVD) are a concern in these patients, and few studies have examined CVD-related death associated with lung cancer. We aimed to evaluate the risk of CVD-related death after radiotherapy in patients with lung and bronchus cancer.

High-fidelity standard model reconstruction and verification of an airliner based on point clouds.

Computational fluid dynamics (CFD) numerical simulation as the primary research tool is particularly essential for its credibility during the aerodynamic design of aircraft. To further promote CFD verification and validation on the airliner, a high-fidelity model reconstruction of the airliner is fundamental. Based on this, we put forward a novel framework, to our best knowledge, to reconstruct a high-fidelity standard model for an airliner efficiently, and the feasibility and accuracy of these reconstructed models are accessed by the CFD simulation-based validation method.

Univ-flu: A structure-based model of influenza A virus hemagglutinin for universal antigenic prediction.

The rapid mutations on hemagglutinin (HA) of influenza A virus (IAV) can lead to significant antigenic variance and consequent immune mismatch of vaccine strains. Thus, rapid antigenicity evaluation is highly desired. The subtype-specific antigenicity models have been widely used for common subtypes such as H1 and H3.

Exploring the Dynamic of Bacterial Communities in Manila Clam () During Refrigerated Storage.

Microorganism contamination is one of the most important factors affecting the spoilage and food safety of Manila clams. This study aimed to gain insights into bacterial composition and the dynamic change of bacterial communities on retailed Manila clam during refrigerated storage within the edible period. High-throughput sequencing was conducted to monitor the bacterial population with the prolongation of storage time of Day 0, Day 1, and Day 3.

Insights into Adaptive Mechanisms of Extreme Acidophiles Based on Quorum Sensing/Quenching-Related Proteins.

Quorum sensing (QS) is a unique mechanism for microorganisms to coordinate their activities through intercellular communication, including four main types of autoinducer-1 (AI-1, namely, -acyl homoserine lactone [AHL]), AI-2, AI-3, and diffusible signaling factor [DSF]) based on signaling molecules. Quorum quenching (QQ) enzymes can disrupt the QS phenomenon by inactivating signaling molecules. QS is proposed to regulate biofilm formation in extremely acidic environments, but the QS/QQ-related genomic features in most acidophilic bacteria are still largely unknown.

Mesoporous NiO@ZnO nanofiber membranes single-nozzle electrospinning for urine metabolism analysis of smokers.

An effective matrix is very important for impact laser desorption/ionization mass spectrometry (LDI-MS), and the physicochemical properties of the matrix nanostructures can impact the LDI-MS performance. In this study, a simple and efficient single-nozzle electrospinning strategy using polystyrene (PS) spheres and polyvinyl pyrrolidone (PVP) to construct a mesoporous NiO@ZnO nanofiber membrane was developed. Compared with the NiO and ZnO nanomaterials alone, the obtained NiO@ZnO nanofiber membrane was proven to be an efficient material as the matrix to increase the intensity of the mass spectrum speaks of small molecules.

Mesoporous ZnO nanosheet as gas sensor for sensitive triethylamine detection.

In this paper, mesoporous ZnO nanosheets were synthesized by the hydrothermal method using polystyrene-polyacrylic acid (PS-PAA) as the template. The morphology, structure, and composition of the samples were characterized by SEM, TEM, XRD, and XPS, and the physical properties of the samples were tested by N adsorption-desorption curve. The results showed that the mesoporous ZnO nanosheets presented a flower-like appearance.

Revealing the Mutation Patterns of Drug-Resistant Reverse Transcriptase Variants of Human Immunodeficiency Virus through Proteochemometric Modeling.

Drug-resistant cases of human immunodeficiency virus (HIV) nucleoside reverse transcriptase inhibitors (NRTI) are constantly accumulating due to the frequent mutations of the reverse transcriptase (RT). Predicting the potential drug resistance of HIV-1 NRTIs could provide instructions for the proper clinical use of available drugs. In this study, a novel proteochemometric (PCM) model was constructed to predict the drug resistance between six NRTIs against different variants of RT.

Double-layer capsule of mesoporous ZnO@SnO for sensitive detection of triethylamine.

To overcome obstacles such as low response and poor selectivity of pure ZnO and SnO gas sensors, the ZnO@SnO sensor was synthesized by hydrothermal synthesis. The samples were characterized by XRD, XPS, SEM, HRTEM, N adsorption-desorption and other techniques. The results show that ZnO@SnO forms an n-n-type heterostructure and presents a double-layer capsule with a size of 0.

Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens.

Attenuated Listeria monocytogenes could be a potential vaccine vector for the immunotherapy of tumors or pathogens. However, the lack of reliable promoters has limited its ability to express foreign antigens. In the present study, 21 promoters were identified from Listeria monocytogenes through RNA-seq analysis under two pH conditions of pH 7.

Raman spectroscopy combined with machine learning for rapid detection of food-borne pathogens at the single-cell level.

Rapid detection of food-borne pathogens in early food contamination is a permanent topic to ensure food safety and prevent public health problems. Raman spectroscopy, a label-free, highly sensitive and dependable technology has attracted more and more attention in the field of diagnosing food-borne pathogens in recent years. In the research, 15,890 single-cell Raman spectra of 23 common strains from 7 genera were obtained at the single cell level.

Development overview of Raman-activated cell sorting devoted to bacterial detection at single-cell level.

Understanding the metabolic interactions between bacteria in natural habitat at the single-cell level and the contribution of individual cell to their functions is essential for exploring the dark matter of uncultured bacteria. The combination of Raman-activated cell sorting (RACS) and single-cell Raman spectra (SCRS) with unique fingerprint characteristics makes it possible for research in the field of microbiology to enter the single cell era. This review presents an overview of current knowledge about the research progress of recognition and assessment of single bacterium cell based on RACS and further research perspectives.

A Novel Design of Multi-epitope Vaccine Against by Immunoinformatics Approach.

Unlabelled: () is a gram-negative spiral bacterium that caused infections in half of the world's population and had been identified as type I carcinogen by the World Health Organization. Compared with antibiotic treatment which could result in drug resistance, the vaccine therapy is becoming a promising immunotherapy option against . Further, the multi-epitope vaccine could provoke a wider immune protection to control infection.

Hydrangea-like mesoporous WO nanoflowers with crystalline framework for 3-hydroxy-2-butanone sensing.

In this study, a simple and efficient strategy for the construction of hydrangea-like mesoporous WO nanoflowers templated using diblock copolymer PS-PtBA was developed. The nanoflower shows good gas sensing properties, especially for 3-hydroxy-2-butanone (3H-2B), which is the signature metabolite of Listeria monocytogenes (L. monocytogenes).