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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 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 PDFThe diagnostic performance and optimal strategy of cone beam CT-assisted bronchoscopy for peripheral pulmonary lesions: A systematic review and meta-analysis.
Pulmonology
December 2025
Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
Cone-beam computed tomography (CBCT) assisted bronchoscopy shows prospective advantages in diagnosing peripheral pulmonary lesions (PPLs), but its diagnostic value and potential influencing factors remain unclear. What is the clinical value and optimal strategy of CBCT-assisted bronchoscopy in diagnosing PPLs? The references were searched from PubMed, EmBase, and Web of Science. Studies reporting diagnostic yield and potential influencing factors of CBCT-assisted bronchoscopy were included.
View Article and Find Full Text PDFPsychometric properties and post-hoc CAT analysis of the pediatric PROMIS® item banks anxiety and depressive symptoms in a combined Swedish Child and Adolescent Psychiatry and School sample.
Qual Life Res
January 2025
Department of Clinical Science, Child- and Adolescent Psychiatry, Umeå University, 90185, Umeå, Sweden.
Purpose: The objective of this study is to assess the psychometric properties and reliability of the Swedish Patient-Reported Outcomes Measurement Information System (PROMIS) item banks for anxiety and depressive symptoms with item response theory analysis and post-hoc computerized adaptive testing in a combined Swedish Child and Adolescent Psychiatry (CAP) and school sample.
Methods: Participants (n = 928, age 12-20) were recruited from junior and high schools and Child and Adolescent Psychiatry Clinics in the region of Västerbotten. Unidimensionality, local independence, and monotonicity was tested.
Real-world application of CCTA with CT-FFR for coronary assessment pre-TAVI: the CT2TAVI study.
Int J Cardiovasc Imaging
January 2025
Cardiology, Endeavor NorthShore Cardiovascular Institute, Evanston, IL, USA.
This study aims to evaluate the implementation of concomitant CAD assessment on pre-TAVI (transcatheter aortic valve implantation) planning CTA (CT angiography) aided by CT-FFR (CT-fractional flow reserve) [The CT2TAVI protocol] and investigates the incremental value of CT-FFR to coronary CT angiography (CCTA) alone in the evaluation of patients undergoing CT2TAVI. This is a prospective observational real-world cohort study at an academic health system on consecutive patients who underwent CTA for TAVI planning from 1/2021 to 6/2022. This represented a transition period in our health system, from not formally reporting CAD on pre-TAVI planning CTA (Group A) to routinely reporting CAD on pre-TAVI CTA (Group B; CT2TAVI protocol).
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