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Deciphering cellular microenvironments at atlas scale remains challenging because molecular identity, spatial context, and platform heterogeneity are tightly coupled. Here we present CellNiche, a scalable contrastive-learning framework that identifies and characterizes cellular microenvironments from spatial …
Read PDFSpatial transcriptomics (ST) facilitates the exploration of biological tissue structures and functions within spatial context. Slice alignment and integration are prevalent for analyzing ST data, and current algorithms either focus on adjacent slices or require …
Read PDFDurio zibethinus, commonly known as the "king of the fruits," is widely cultivated in Southeast Asia, contributing significantly to the region's economy. In addition to commercial cultivars, numerous local edible durian species are also found …
Read PDF<h4>Background</h4>Severe COVID-19 is associated with dysregulated immune responses. Immune responses heterogeneity was previously reported during the first waves of the pandemic. We aimed to characterise mucosal transcriptomic profiles in critically-ill patients during the Omicron era.<h4>Methods</h4>This …
Read PDFAlzheimer's Disease (AD) is a progressive neurodegenerative disorder and the leading cause of dementia. Neuroinflammation drives AD progression and therefore represents a promising target for diagnosis and therapy. In early AD, microglia polarize into pro-inflammatory …
Read PDFMeat quality is a complex and dynamic trait, resulting from the integration of biological, nutritional, environmental, and technological factors operating across the entire production chain, from primary production systems to consumer handling [...].
Read PDFSpatially resolved transcriptomics (SRT) measures transcriptomes of cells within intact biological tissues, providing unprecedented opportunities to investigate tissue micro-environments, where spatial domains are modeled as clusters of spatially neighboring cells. Current methods for the identification …
Read PDFSpatial omics technologies generate high-dimensional, spatially resolved molecular data across transcripts, proteins, metabolites and lipids, requiring computational models that account for tissue topology, multi-scale organization, and experimental noise. Although machine-learning (ML) and deep-learning (DL) methods …
Read PDFTherapeutic resistance in metastatic castration-resistant prostate cancer (mCRPC) is orchestrated not only by tumor-intrinsic genomic alterations but also by dynamic reprogramming of the tumor microenvironment (TME). This review introduces the tumor-immune spatiotemporal co-evolution paradigm, which …
Read PDFGranulocyte-macrophage colony-stimulating factor (GM-CSF) deficiency drives autoimmune pulmonary alveolar proteinosis (aPAP), a disease characterized by impaired macrophage-mediated clearance of pulmonary surfactants. Clinical data suggest that inhaled recombinant GM-CSF reduces symptoms in aPAP patients, providing a …
Read PDFThe clinical management of refractory pituitary neuroendocrine tumors (PitNETs) remains a formidable challenge due to pervasive resistance to traditional therapies. Current therapeutic failures appear closely associated with lineage-specific immune heterogeneity and the unique "hypovascular-fibrotic" physical …
Read PDFThe application of virtual histology in determining endometrial receptivity has been effectively demonstrated in a recent publication. This commentary aims to elucidate previous research in this area and highlight the essential conditions for optimizing this …
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