ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task.

Unsupervised spatially embedded deep representation of spatial transcriptomics.

Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-supervised learning mechanism to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. SEDR achieved higher clustering performance on manually annotated 10 × Visium datasets and better scalability on high-resolution spatial transcriptomics datasets than existing methods.

Neutrophil Extracellular Traps Formation and Citrullinated Histones 3 Levels in Patients with Kawasaki Disease.

Background: Kawasaki disease (KD) is a vasculitis associated with vascular injury and autoimmune response. Inflammatory factors stimulate neutrophils to produce web-like structures called neutrophil extracellular traps (NETs). Citrullinated histone 3 (H3Cit) is one of the main protein components of neutrophil extracellular traps involved in the process of NETosis.

Resistance-proof antimicrobial drug discovery to combat global antimicrobial resistance threat.

Drug resistance is well-defined as a serious problem in our living world. To survive, microbes develop defense strategies against antimicrobial drugs. Drugs exhibit less or no effective results against microbes after the emergence of resistance because they are unable to cross the microbial membrane, in order to alter enzymatic systems, and/or upregulate efflux pumps, etc.

Comparison of O, UV/O, and UV/O/PS processes for marine oily wastewater treatment: Degradation performance, toxicity evaluation, and flocs analysis.

Efficient on-site treatment technology is crucial for mitigating marine oily wastewater pollution. This work investigates the ozone (O), ultraviolet (UV)/O, UV/O/persulfate (PS) processes for the treatment of marine oily wastewater, including degradation performance, acute toxicity evaluation, and oil flocs analysis in a benchtop circulating flow photoozonation reactor. Degradation performances have been studied by measuring the degradation rate of total oil concentrations, specific oil components (n-alkanes and polycyclic aromatic hydrocarbons (PAHs)), and total organic carbon (TOC).

Prediction of Cancer Treatment Using Advancements in Machine Learning.

Many cancer patients die due to their treatment failing because of their disease's resistance to chemotherapy and other forms of radiation therapy. Resistance may develop at any stage of therapy, even at the beginning. Several factors influence current therapy, including the type of cancer and the existence of genetic abnormalities.

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes.

The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4 T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota.

Development of advanced oil/water separation technologies to enhance the effectiveness of mechanical oil recovery operations at sea: Potential and challenges.

Mechanical oil recovery (i.e., booming and skimming) is the most common tool for oil spill response.

Ischemic-Trained Monocytes Improve Arteriogenesis in a Mouse Model of Hindlimb Ischemia.

Objective: Monocytes, which play an important role in arteriogenesis, can build immunologic memory by a functional reprogramming that modifies their response to a second challenge. This process, called trained immunity, is evoked by insults that shift monocyte metabolism, increasing HIF (hypoxia-inducible factor)-1α levels. Since ischemia enhances HIF-1α, we evaluate whether ischemia can lead to a functional reprogramming of monocytes, which would contribute to arteriogenesis after hindlimb ischemia.

DISCO: a database of Deeply Integrated human Single-Cell Omics data.

The ability to study cellular heterogeneity at single cell resolution is making single-cell sequencing increasingly popular. However, there is no publicly available resource that offers an integrated cell atlas with harmonized metadata that users can integrate new data with. Here, we present DISCO (https://www.

Cx32 inhibits the autophagic effect of Nur77 in SH-SY5Y cells and rat brain with ischemic stroke.

The pathogenesis of cerebral ischemia-reperfusion (I/R) is complex. Cx32 expression has been reported to be up-regulated in ischemic lesions of aged human brain. Nevertheless, the function of Cx32 during cerebral I/R is poorly understood.

A critical review on the environmental application of lipopeptide micelles.

The importance of lipopeptide micelles in environmental applications has been highlighted. These vessels exhibit various sizes, shapes, and surface properties under different environmental conditions. An in-depth understanding of the tunable assembling behavior of biosurfactant micelles is of great importance for their applications.

Access-dispersion-recovery strategy for enhanced mitigation of heavy crude oil pollution using magnetic nanoparticles decorated bacteria.

Heavy crude oil (HCO) pollution has gained global attention, but traditional bioremediating practices demonstrate limited effectiveness. This study developed magnetic nanoparticles decorated bacteria (MNPB) using an oil-degrading and biosurfactant-producing Rhodococcus erythropolis species and identified a novel access-dispersion-recovery strategy for enhanced HCO pollution mitigation. The strategy entails (1) magnetic navigation of the MNPB towards HCO layer, (2) enhanced oil dispersion and formation of suspended oil-bacteria aggregates, and (3) magnetic recovery of these aggregates.

Fish Waste Based Lipopeptide Production and the Potential Application as a Bio-Dispersant for Oil Spill Control.

There is a growing acceptance worldwide for the application of dispersants as a marine oil spill response strategy. The development of more effective dispersants with less toxicity and higher biodegradability would be a step forward in improving public acceptance and regulatory approvals for their use. By applying advances in environmental biotechnology, a bio-dispersant agent with a lipopeptide biosurfactant produced by N3-1P as the key component was formulated in this study.

Discovery of coumarin-derived imino sulfonates as a novel class of potential cardioprotective agents.

The burst of reactive oxygen species (ROS) contributes to and exacerbates cardiac injury. Exogenous supplementation of antioxidants or upregulation of endogenous antioxidant defense genes should be the potential therapies for cardiovascular disease. Sixteen coumarin-derived imino sulfonates compounds were synthesized with the ability of attenuating oxidative stress directly by reducing intracellular ROS level via promoting Nrf2 pathway.

A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity.

A substantial fraction of eukaryotic proteins is folded and modified in the endoplasmic reticulum (ER) prior to export and secretion. Proteins that enter the ER but fail to fold correctly must be degraded, mostly in a process termed ER-associated degradation (ERAD). Both protein folding in the ER and ERAD are essential for proper immune function.

Fly ash based robust biocatalyst generation: a sustainable strategy towards enhanced green biosurfactant production and waste utilization.

Biosurfactants have been well recognized as an environmentally friendly alternative to chemical surfactants. However, their production remains challenging due to low productivity, short-term microbe stability and the potentially toxic by-products generated in the growth media. To overcome these challenges, the emerging biofilm-based biosynthesis was investigated in this study.

Immunometabolism features of metabolic deregulation and cancer.

Immunometabolism is a branch dealing at the interface of immune functionalities and metabolic regulations. Considered as a bidirectional trafficking, metabolic contents and their precursors bring a considerable change in immune cells signal transductions which as a result affect the metabolic organs and states as an implication. Lipid metabolic ingredients form a major chunk of daily diet and have a proven contribution in immune cells induction, which then undergo metabolic pathway shuffling inside their ownself.

Targeted Delivery of Cyclotides via Conjugation to a Nanobody.

Many naturally occurring peptides have poor proteolytic stability, which limits their therapeutic applications. Cyclotides are plant-derived cyclic peptides that resist proteolysis due to their highly constrained structure, comprising a head-to-tail cyclic backbone and three disulfide bonds that form a cystine-knotted core. This structure makes them useful as scaffolds onto which peptide sequences (epitopes) can be grafted.

Nanobody-Antigen Conjugates Elicit HPV-Specific Antitumor Immune Responses.

High-risk human papillomavirus-associated cancers express viral oncoproteins (e.g., E6 and E7) that induce and maintain the malignant phenotype.

IL-17 induces cellular stress microenvironment of melanocytes to promote autophagic cell apoptosis in vitiligo.

Vitiligo is a depigmentary disorder that develops as a result of the progressive disappearance of epidermal melanocytes. Stress can precipitate or exacerbate a skin disease through psychosomatic mechanisms. Stress exposure induces vitiligo-like symptoms in mice, as cellular damage to melanocytes causes synthetic pigment loss.

Targeted antigen delivery by an anti-class II MHC VHH elicits focused αMUC1(Tn) immunity.

Unusual patterns of glycosylation on the surface of transformed cells contribute to immune modulation and metastasis of malignant tumors. Active immunization against them requires effective antigen presentation, which is complicated by a lack of access to tumor-specific posttranslational modifications through standard genetic approaches and by the low efficiency of passive antigen sampling. We found that antigen targeted to antigen presenting cells class II MHC products can elicit a robust immune response against MUC1(Tn) bearing a defined tumor-associated glycoform, Tn.

An RNA nanoparticle vaccine against Zika virus elicits antibody and CD8+ T cell responses in a mouse model.

The Zika virus (ZIKV) outbreak in the Americas and South Pacific poses a significant burden on human health because of ZIKV's neurotropic effects in the course of fetal development. Vaccine candidates against ZIKV are coming online, but immunological tools to study anti-ZIKV responses in preclinical models, particularly T cell responses, remain sparse. We deployed RNA nanoparticle technology to create a vaccine candidate that elicited ZIKV E protein-specific IgG responses in C57BL/6 mice as assayed by ELISA.

Synthesis and biological evaluation of nitric oxide (NO)-hydrogen sulfide (HS) releasing derivatives of (S)-3-n-butylphthalide as potential antiplatelet agents.

In the present study, a series of novel nitric oxide-hydrogen sulfide releasing derivatives of (S)-3-n-butylphthalide ((S)-NBP) were designed, synthesized, and evaluated as potential antiplatelet agents. Compound NOSH-NBP-5 displayed the strongest activity in inhibiting the arachidonic acid (AA)- and adenosine diphosphate (ADP)-induced platelet aggregation in vitro, with 3.8- and 7.

Neurokinin-1 receptor is a novel positive regulator of Wnt/ β-catenin signaling in melanogenesis.

Wnt/β-catenin signaling is essential for melanogenesis in melanocytes. Neurokinin-1 receptor (NK-1R) has recently been demonstrated to be involved in melanin production. However, the cross talk between NK-1R and Wnt/β-catenin is poorly understood.