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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 PDFThe clinical meaning of the UIP pattern in fibrotic hypersensitivity pneumonitis on cryobiopsy: A multicentre retrospective study.
Pulmonology
December 2025
Department of Medical Specialities, Pulmonology Unit, GB Morgagni-L. Pierantoni Hospital, Forlì, Italy.
Fibrotic hypersensitivity pneumonitis (f-HP) is an interstitial lung disease in which various antigens in susceptible individuals may play a pathogenetic role. This study evaluates the role of transbronchial lung cryobiopsy (TBLC) and bronchoalveolar lavage (BAL) in identifying a UIP-like pattern and its association with fibrosis progression. We conducted a multicentre retrospective cohort study of patients diagnosed with f-HP who underwent BAL and TBLC between 2011 and 2023.
View Article and Find Full Text PDFUltrathin bronchoscopy-guided small airway biopsy for diagnosing sarcoidosis: A prospective study.
Pulmonology
December 2025
Department of Cardiovascular and Pulmonary Sciences, Catholic University of the Sacred Hearth, Rome, Italy.
New ultrathin bronchoscopes (UTBs) enable the inspection and biopsy of small airways, potentially offering diagnostic advantages in sarcoidosis. In this prospective study, patients with suspected sarcoidosis underwent airway inspection with a UTB. Observed airway abnormalities were categorised into six predefined patterns.
View Article and Find Full Text PDFGlia control experience-dependent plasticity in an olfactory critical period.
Elife
January 2025
Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, United States.
Sensory experience during developmental critical periods has lifelong consequences for circuit function and behavior, but the molecular and cellular mechanisms through which experience causes these changes are not well understood. The antennal lobe houses synapses between olfactory sensory neurons (OSNs) and downstream projection neurons (PNs) in stereotyped glomeruli. Many glomeruli exhibit structural plasticity in response to early-life odor exposure, indicating a general sensitivity of the fly olfactory circuitry to early sensory experience.
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).
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