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A 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 PDFA model of care redesign within rheumatology: A mixed methods approach integrating nurse practitioners and physician assistants.
J Am Assoc Nurse Pract
January 2025
Division of Cardiology, Department of Medicine, Duke Health Integrated Practice, Duke University Health System, Durham, North Carolina.
Background: Increasing patient demand and clinician burnout in rheumatology practices have highlighted the need for more efficient models of care (MOC). Interprofessional collaboration is essential for improving patient outcomes and clinician satisfaction.
Local Problem: Our current MOC lacks standardization and formal integration of Nurse Practitioners (NPs) and Physician Assistants (PAs), resulting in reduced clinician satisfaction and limited patient access.
A new HCM heart sound classification method based on weighted bispectrum features.
Phys Eng Sci Med
January 2025
School of Electrical Engineering and Electronic Information, Xihua University, Chengdu, China.
Hypertrophic cardiomyopathy (HCM), including obstructive HCM and non-obstructive HCM, can lead to sudden cardiac arrest in adolescents and athletes. Early diagnosis and treatment through auscultation of different types of HCM can prevent the occurrence of malignant events. However, it is challenging to distinguish the pathological information of HCM related to differential left ventricular outflow tract pressure gradients.
View Article and Find Full Text PDFIncreasing the robustness of Escherichia coli for aromatic chemicals production through transcription factor engineering.
Adv Biotechnol (Singap)
April 2024
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Engineering microbial cell factories has been widely used to produce a variety of chemicals, including natural products, biofuels, and bulk chemicals. However, poor robustness limits microbial production on an industrial scale. Microbial robustness is essential to ensure reliable and sustainable production of targeted chemicals.
View Article and Find Full Text PDFAdvancements in delivery strategies and non-tissue culture regeneration systems for plant genetic transformation.
Adv Biotechnol (Singap)
September 2024
Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
Plant genetic transformation is a pivotal and essential step in modifying important agronomic traits using biotechnological tools, which primarily depend on the efficacy of transgene delivery and the plant regeneration system. Over the years, advancements in the development of delivery methods and regeneration systems have contributed to plant engineering and molecular breeding. Recent studies have demonstrated that the efficiency of plant transformation can be improved by simultaneously delivering meristem-developmental regulators, utilizing virus-mediated gene editing, and executing non-sterile in planta manipulations.
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