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Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants.
View Article and Find Full Text PDFRole of Prothrombin and Methylenetetrahydrofolate Reductase Gene Polymorphisms as well as Thrombophilia Markers, as Risk Factors for Unexplained Recurrent Miscarriage: A Case-Control Study.
Int J Fertil Steril
January 2025
Clinical Pathology Department, Faculty of Medicine, Assiut University, Assiut, Egypt.
Background: Unexplained recurrent miscarriage (RM) is still an unsolved reproductive health problem. Inherited thrombophilias have been one of the causes. Mutation in genes encoding coagulation proteins, including prothrombin (PT G20210A) and methylenetetrahydrofolate reductase (MTHFR) genes, increase tendency for venous thromboembolism.
View Article and Find Full Text PDFQuantitative Determination of a Series of Oxysterols by an Optimized LC-MS/MS Analysis in Different Tissue Types.
Int J Mol Sci
December 2024
School of Public Health, Capital Medical University, Beijing 100069, China.
Oxysterols, as metabolites of cholesterol, play a key role in cholesterol homeostasis, autophagosome formation, and regulation of immune responses. Disorders in oxysterol metabolism are closely related to the pathogenesis of neurodegenerative diseases. To systematically investigate the profound molecular regulatory mechanisms of neurodegenerative diseases, it is necessary to quantify oxysterols and their metabolites in central and peripheral biospecimens simultaneously and accurately.
View Article and Find Full Text PDFReconstructing Waddington Landscape from Cell Migration and Proliferation.
Interdiscip Sci
January 2025
School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.
The Waddington landscape was initially proposed to depict cell differentiation, and has been extended to explain phenomena such as reprogramming. The landscape serves as a concrete representation of cellular differentiation potential, yet the precise representation of this potential remains an unsolved problem, posing significant challenges to reconstructing the Waddington landscape. The characterization of cellular differentiation potential relies on transcriptomic signatures of known markers typically.
View Article and Find Full Text PDF'Stuck or unstable': partnerships between GPs and patients with complex chronic conditions. A qualitative study.
BJGP Open
January 2025
The Research Unit for General Practice & Section for General Practice, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
Background: In chronic care, patient-GP collaboration is essential, but might be challenging if patients have complex health problems due to multimorbidity, psychosocial predicaments and addiction problems. To understand and manage these challenges, it is important to explore how patients' and GPs' attempt to collaborate, to maintain and achieve an alliance in order to gain good quality of care.
Aim: To explore how dyads of GPs and patients that GPs deem have complex health problems and difficulties following treatment perceive and manage challenges in their chronic care partnership.
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