cluster

PURPOSE: Immune tumor microenvironment (iTME) determines ovarian cancer development. This study investigates changes in HLA-I expression, CD8+/Foxp3 ratio, CD8+ cells and coregulators density at diagnosis and upon neoadjuvant chemotherapy (NACT), correlating changes with clinical outcomes. EXPERIMENTAL DESIGN: Multiplexed immune profiling and cell clustering analysis was performed on paired matched OC samples to characterize the iTME at diagnosis and under NACT from patients enrolled in the CHIVA trial (NCT01583322)...

Antimicrobial resistance (AMR) is a great threat to animal and public health. Here, we conducted a surveillance of Escherichia coli isolated from healthy chickens during 2009-2014 to identify the characteristics of AMR. A total of 351 (95.64%) E. coli isolates were obtained from 367 healthy chicken fecal samples collected from 6 farms located in Shandong Province, China. The susceptibility to 10 antimicrobials, the prevalence of antibiotic resistance genes (ARGs), phylogenetic clustering, and multilocus sequence typing were evaluated...

We have used a scanning tunneling microscope operated under ultrahigh vacuum conditions to investigate an oxo-vanadium-salen complex V(O)salen, that has potential applications as qubits in future quantum-based technologies. The adsorption and self-assembly of V(O)salen on a range of single crystal metal surfaces and nanoislands and the influence of substrate morphology and reactivity has been measured. On the close-packed flat Ag(111) and Cu(111) surfaces, the molecules adsorb isolated or form small clusters arranged randomly on the surface, whereas structured adsorption occurs on two types of Co nanoislands; Co grown on Ag(111) and Ag capped Co islands grown on Cu(111), both forming a Moiré pattern at the surface...

The emergence and development of single-cell RNA sequencing (scRNA-seq) techniques enable researchers to perform large-scale analysis of the transcriptomic profiling at cell-specific resolution. Unsupervised clustering of scRNA-seq data is central for most studies, which is essential to identify novel cell types and their gene expression logics. Although an increasing number of algorithms and tools are available for scRNA-seq analysis, a practical guide for users to navigate the landscape remains underrepresented...

PURPOSE: The relationship between vitamin intake and cancer risk in the chronic kidney disease (CKD) population is unknown. For this reason, we investigated the relationship between dietary vitamin intake and cancer risk in CKD patients and looked for effective vitamin dietary patterns. METHODS: This study included 3518 CKD patients from 2007 to 2018 National Health and Nutrition Examination Survey database. All participants were categorized into four groups based on vitamin intake by K-mean clustering...

BACKGROUND: The prevalence and mortality of bladder cancer (BLCA) present a significant medical challenge. While the function of senescence-related genes in tumor development is recognized, their prognostic significance in BLCA has not been thoroughly explored. METHODS: BLCA transcriptome datasets were sourced from the TCGA and GEO repositories. Gene groupings were determined through differential gene expression and non-negative matrix factorization (NMF) methodologies...

Hepatocellular carcinoma (HCC), one of the most prevalent cancers globally, is closely associated with tumor-associated macrophages (TAMs), including monocyte-derived macrophages and liver-resident Kupffer cells. Understanding TAM heterogeneity at the cellular level is crucial for developing effective HCC prevention and treatment strategies. In this study, we conducted an integrated single-cell analysis of four cohorts (GSE140228, GSE125449, GSE149614 and GSE156625) to elucidate the TAM landscape in HCC. We identified 284 gene markers, termed Panmyeloid markers, that characterize myeloid cells within this context...

In view of the extensive potential applications of chitinase (ChiA) in various fields such as agriculture, environmental protection, medicine, and biotechnology, the development of a high-yielding strain capable of producing chitinase with enhanced activity holds significant importance. The objective of this study was to utilize the extracellular chitinase from Bacillus thuringiensis as the target, and Bacillus licheniformis as the expression host to achieve heterologous expression of ChiA with enhanced activity...

Core histones in the nucleosome are subject to a wide variety of posttranslational modifications (PTMs), such as methylation, phosphorylation, ubiquitylation, and acetylation, all of which are crucial in shaping the structure of the chromatin and the expression of the target genes. A putative histone methyltransferase LaeA/Lae1, which is conserved in numerous filamentous fungi, functions as a global regulator of fungal growth, virulence, secondary metabolite formation, and the production of extracellular glycoside hydrolases (GHs)...

The search for low-diffusion barriers and high-capacity anode materials is considered a key step in boosting the efficiency of metal-ion batteries. Herein, we investigate the impact of a series of conducting polymers (CPs), namely, polyacetylene (PA), polypyrrole (PP), poly- p -phenylene (PPPh), and polythiophene (PT), on enhancing the material design and anodic performance of boron nitride nanosheet (BNNS)-based Li-ion and Na-ion batteries. For this purpose, first principle DFT simulations, utilizing both clustered and periodic models, are systematically performed to assess the stability of such nanostructures and their electronic behavior as potential anodic materials...

A Gram-stain-negative bacterium, designated LG-4T , was isolated from sediment of Qiantang River in Zhejiang Province, PR China. Cells were strictly aerobic, non-spore-forming, non-motile and short-rod-shaped (1.0-1.2 µm long and 0.7-0.8 µm wide). Growth occurred at 15-42 °C (optimum, 30 °C), at pH 5.0-9.0 (pH 7.0) and at 0-2.0 % (w/v) NaCl (optimum, 0.5 % NaCl). Strain LG-4T showed 95.75-96.90 % 16S rRNA gene sequence similarity to various type strains of the genera Tabrizicola , Pseudotabrizicola , Phaeovulum , Rhodobacter and Wagnerdoeblera of the family Paracoccaceae , and the most closely related strain was Tabrizicola soli ZQBWT (96...

Two novel meroterpenoids, alliisativins A and B ( 1 , 2 ) were discovered through a genome-based exploration of the biosynthetic gene clusters of the deep-sea-derived fungus Penicillium allii-sativi MCCC entry 3A00580. Extensive spectroscopic analysis, quantum calculations, chemical derivatization, and biogenetic considerations were utilized to establish their structures. Alliisativins A and B ( 1 , 2 ) possess a unique carbon skeleton featuring a drimane sesquiterpene with a highly oxidized polyketide. Noteworthily, alliisativin A ( 1 ) showed dual activity in promoting osteogenesis and inhibiting osteoclast, indicating an antiosteoporosis potential...

The design and synthesis of stable porous materials capable of removing both hard and soft metal ions pose a significant challenge. In this study, a novel metal-organic framework (MOF) adsorbent named CdK- m -COTTTB was developed. This MOF material was constructed using sulfur-rich m -cyclooctatetrathiophene-tetrabenzoate ( m -H4 COTTTB) as the organic ligand and oxygen-rich bimetallic clusters as the inorganic nodes. The incorporation of both soft and hard base units within the MOF structure enables effective removal of various heavy metal ions, including both soft and hard acid species...

Amphotericin B is a popular antifungal antibiotic, but the exact way it works is still a matter of debate. Here, we used monolayers composed of phosphatidylcholine with ergosterol as a model of fungal lipid membranes to study drug incorporation from the aqueous phase and analyze the molecular reorganization of membranes underlying the biological activity of the antibiotic. The results show that the internalization of antibiotic molecules into membranes occurs only in the presence of ergosterol in the lipid phase...

Two Gram-negative bacterial strains designated MMS20-SJTN17T and MMS20-SJTR3T were isolated from a grassland soil sample, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence analysis indicates that both strains belong to the genus Paraburkholderia of the class Betaproteobacteria , with strain MMS20-SJTN17T being mostly related to Paraburkholderia sprentiae WSM5005T (96.45 % sequence similarity) and strain MMS20-SJTR3T to Paraburkholderia tuberum STM678T (98.59 % sequence similarity)...

Botulinum toxin type-A (BoNT-A) has emerged as a key therapeutic agent for the management of spasticity. This paper presents a comprehensive bibliometric and visual analysis of research concerning BoNT-A treatment of spasticity to elucidate current trends and future directions in this research area. A search was conducted in the Web of Science database for articles focused on the use of BoNT-A in spasticity published between 2000 and 2022. We extracted various metrics, including counts of publications and contributions from different countries, institutions, authors, and journals...

Despite ongoing efforts for elimination, malaria continues to be a major public health problem in the Republic of Panama. For effective elimination, it is key that malaria foci and areas of high transmission are identified in a timely manner. Here, we study malaria transmission records for the 2015-2022 period, a time when cases have increased by a factor of ten. Using several methods to study spatial and spatiotemporal malaria confirmed case clusters at the level of localities, including LISA and scan, we found that cases are clustered across indigenous villages located within the autonomous indigenous regions of Ngäbe-Buglé, Guna Yala, and Embera, with the latter on the eastern border of Panama (with Colombia)...

BACKGROUND: International migration is a global phenomenon with significant implications on the health-disease process due to exposures along transit routes and local/destination epidemiological indicators. We aimed to analyze the transmission and spread of tuberculosis among international migrants and refugees from a spatiotemporal perspective and the associated factors. METHOD: This was an ecological study of cases of tuberculosis in international migrants in Brazil, between 2010 and 2021...

Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation...

Sugarcane ( Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane yield. However, other constituents in sugarcane remain largely unutilized in sugarcane breeding programs. This study aims to establish a data-driven approach to analyze agronomic characteristics from breeding programs...