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Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation.
Brief Bioinform
November 2024
School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P.R. China.
Single-cell RNA sequencing (scRNA-seq) offers remarkable insights into cellular development and differentiation by capturing the gene expression profiles of individual cells. The role of dimensionality reduction and visualization in the interpretation of scRNA-seq data has gained widely acceptance. However, current methods face several challenges, including incomplete structure-preserving strategies and high distortion in embeddings, which fail to effectively model complex cell trajectories with multiple branches.
View Article and Find Full Text PDFDeep learning-based design and experimental validation of a medicine-like human antibody library.
Brief Bioinform
November 2024
Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceutical Inc., 900 Ridgebury Road, Ridgefield, CT 06877, United States.
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain along with the advent of generative deep learning algorithms raises the possibility of computationally generating novel antibody sequences with desirable developability attributes. Here, we describe a deep learning model for computationally generating libraries of highly human antibody variable regions whose intrinsic physicochemical properties resemble those of the variable regions of the marketed antibody-based biotherapeutics (medicine-likeness).
View Article and Find Full Text PDFscMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics.
Brief Bioinform
November 2024
Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Great Bay University, No. 16 Daxue Rd, Songshanhu District, Dongguan, Guangdong, 523000, China.
Multimodal omics provide deeper insight into the biological processes and cellular functions, especially transcriptomics and proteomics. Computational methods have been proposed for the integration of single-cell multimodal omics of transcriptomics and proteomics. However, existing methods primarily concentrate on the alignment of different omics, overlooking the unique information inherent in each omics type.
View Article and Find Full Text PDFNovel Real-Time Fluoroscopic Assessment Method of Transcatheter Heart Valve Expansion Following Balloon-Expandable TAVR.
Circ Cardiovasc Interv
January 2025
Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, Canada. (A.H., J.J., S.O., K.M., J.A.L., P.B., D.A.W., S.L.S., J.G.W., J.S.).
Background: Transcatheter heart valve (THV) underexpansion after transcatheter aortic valve replacement may be associated with worse outcomes. THV expansion can be assessed fluoroscopically using a pigtail for calibration; however, the accuracy of this technique specific to transcatheter aortic valve replacement is unknown. We assessed the accuracy and reproducibility of a novel fluoroscopic method to assess THV expansion using the THV commissural post for calibration.
View Article and Find Full Text PDFPrevalence of High-Risk CTA-Based Carotid Plaque-RADS Subtypes in Patients With Embolic Stroke of Undetermined Source.
Stroke
January 2025
Department of Neurology, University of Pennsylvania, PA. (L.I., S.E.Z., S.E.K., B.L.C.).
Background: A modified computed tomography angiography (CTA)-based Carotid Plaque Reporting and Data System (Plaque-RADS) classification was applied to a cohort of patients with embolic stroke of undetermined source to test whether high-risk Plaque-RADS subtypes are more prevalent on the ipsilateral side of stroke. With the widespread use of CTA for stroke evaluation, a CTA-based Plaque-RADS would be valuable for generalizability.
Methods: A retrospective observational cross-sectional study was conducted at a single integrated health system comprised of 3 hospitals with a comprehensive stroke center between October 1, 2015, and April 1, 2017.
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