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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 PDFInvestigating Smartphone-Based Sensing Features for Depression Severity Prediction: Observation Study.
J Med Internet Res
January 2025
Department of Clinical Psychology and Psychotherapy, Institute of Psychology and Education, Ulm University, Ulm, Germany.
Background: Unobtrusively collected objective sensor data from everyday devices like smartphones provide a novel paradigm to infer mental health symptoms. This process, called smart sensing, allows a fine-grained assessment of various features (eg, time spent at home based on the GPS sensor). Based on its prevalence and impact, depression is a promising target for smart sensing.
View Article and Find Full Text PDFAssessment of the underreporting of rhinitis in patients with asthma: A MASK-air® real-world study.
Pulmonology
December 2025
Department of Allergology, Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
Rhinitis is a common comorbidity in patients with asthma. However, the frequency of underreported rhinitis in asthma is not known. In this study, we aimed to assess the characteristics of patients with self-reported asthma and no self-reported rhinitis, as well as the extent of the underreporting of rhinitis.
View Article and Find Full Text PDFrecovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences.
Microb Genom
January 2025
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Braunschweig, Germany.
Genomic data on from the African continent are currently lacking, resulting in the region being under-represented in global analyses of infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare isolates from diarrhoeic human patients (=142), livestock (=38), poultry manure (=5) and dogs (=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global population. In addition, selected isolates were tested for antimicrobial susceptibility (=33) and characterized by PCR ribotyping (=53).
View Article and Find Full Text PDFKnee kinematics during gait in patients with discoid lateral meniscus: a systematic review.
Minerva Pediatr (Torino)
January 2025
Transalpine Center of Pediatric Sports Medicine and Surgery, University of Milano-Bicocca, Monza, Monza-Brianza, Italy.
Introduction: The aim of this study was to evaluate the difference between symptomatic discoid lateral meniscus (DLM) and healthy knees in terms of gait analysis.
Evidence Acquisition: A systematic review was conducted from the electronic databases PubMed/MEDLINE, EMBASE and Scopus. The review was performed on studies that reported data on kinematics, gait analysis, biomechanics in discoid lateral meniscus, before and after surgery.
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