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| http://dx.doi.org/10.1136/ewjm.173.2.119 | DOI Listing |
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Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways.
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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 PDFA comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFSaving coral reefs: significance and biotechnological approaches for coral conservation.
Adv Biotechnol (Singap)
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Department of Molecular Biosciences & Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
Coral reefs are highly productive ecosystems that provide valuable services to coastal communities worldwide. However, both local and global anthropogenic stressors, threaten the coral-algal symbiosis that enables reef formation. This breakdown of the symbiotic relationship, known as bleaching, is often triggered by cumulative cell damage.
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South Med J
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the Department of Public Health Sciences.
Objectives: Sickle cell disease (SCD), which disproportionately affects minorities, increases complications during pregnancy. Severe maternal mortality is increased in women with SCD, including morbidity related to the disease and other nondisease-related complications. It also can have devastating complications for fetuses, with increases in premature birth and low birth weight.
View Article and Find Full Text PDFEffect of Remote Ischemic Conditioning on the Form and Function of Red Blood Cells in Patients With Acute Ischemic Stroke.
Stroke
January 2025
Department of Neurology, Medical College of Georgia, Augusta University. (M.B.K., B.B., D.C.H.).
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