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Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways.
Brief Bioinform
November 2024
School of Artificial Intelligence, Jilin University, Qianjin Street 2699, 130010 Changchun, China.
Imaging-based spatial transcriptomics (iST), such as MERFISH, CosMx SMI, and Xenium, quantify gene expression level across cells in space, but more importantly, they directly reveal the subcellular distribution of RNA transcripts at the single-molecule resolution. The subcellular localization of RNA molecules plays a crucial role in the compartmentalization-dependent regulation of genes within individual cells. Understanding the intracellular spatial distribution of RNA for a particular cell type thus not only improves the characterization of cell identity but also is of paramount importance in elucidating unique subcellular regulatory mechanisms specific to the cell type.
View Article and Find Full Text PDFrecovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences.
Microb Genom
January 2025
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Braunschweig, Germany.
Genomic data on from the African continent are currently lacking, resulting in the region being under-represented in global analyses of infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare isolates from diarrhoeic human patients (=142), livestock (=38), poultry manure (=5) and dogs (=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global population. In addition, selected isolates were tested for antimicrobial susceptibility (=33) and characterized by PCR ribotyping (=53).
View Article and Find Full Text PDFMapping Key Populations to Develop Improved HIV and AIDS Interventions: Multiphase Cross-Sectional Observational Mapping Study Using a District and City Approach.
JMIR Public Health Surveill
January 2025
Monitoring, Evaluation, and Learning Platform USAID, Jakarta, Indonesia.
Background: Indonesia's vast archipelago and substantial population size present unique challenges in addressing its multifaceted HIV epidemic, with 90% of its 514 districts and cities reporting cases. Identifying key populations (KPs) is essential for effectively targeting interventions and allocating resources to address the changing dynamics of the epidemic.
Objective: We examine the 2022 mapping of Indonesia's KPs to develop improved HIV and AIDS interventions.
Association of multidimensional schizotypy with cognitive-behavioral disorganization in daily life: An experience sampling methodology study.
Personal Disord
January 2025
Department of Psychology, University of Illinois at Urbana-Champaign.
Schizotypy is a multidimensional construct that is composed of positive, negative, and disorganized dimensions. Historically, disorganized schizotypy, which involves disruptions in thoughts, speech, behavior, and affect, has been relatively understudied and less clearly operationalized than the other dimensions. The present study employed experience sampling methodology to examine the associations of positive, negative, and disorganized schizotypy, as measured by the Multidimensional Schizotypy Scale, with daily life experiences.
View Article and Find Full Text PDFGlobal identification and regulatory network analysis reveal the significant roles of lncRNAs during anther and pollen development in Arabidopsis.
Plant Cell Rep
January 2025
Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.
A high-throughput sequencing identified 1283 lncRNAs in anthers at different stages in Arabidopsis and their relationship with protein-coding genes and miRNAs during anther and pollen development were analyzed. Long non-coding RNAs (lncRNAs) are important regulatory molecules involved in various biological processes. However, their roles in male reproductive development and interactions with miRNAs remained elusive.
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