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In situ detection of individual classical MHC-I gene products in cancer.
Cancer Immunol Res
January 2025
Vanderbilt University, Nashville, TN, United States.
Tumor-specific HLA class I expression is required for cytotoxic T-cell elimination of cancer cells expressing tumor-associated or neo-antigens. Cancers downregulate antigen presentation to avoid adaptive immunity. The highly polymorphic nature of the genes encoding these proteins, coupled with quaternary-structure changes after formalin fixation, complicate detection by immunohistochemistry.
View Article and Find Full Text PDFPHIStruct: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings.
Bioinformatics
January 2025
Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, 1004, Philippines.
Motivation: Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.
Results: We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera.
EnrichRBP: an automated and interpretable computational platform for predicting and analyzing RNA-binding protein events.
Bioinformatics
January 2025
School of Artificial Intelligence, Jilin University, Jilin, China.
Motivation: Predicting RNA-binding proteins (RBPs) is central to understanding post-transcriptional regulatory mechanisms. Here, we introduce EnrichRBP, an automated and interpretable computational platform specifically designed for the comprehensive analysis of RBP interactions with RNA.
Results: EnrichRBP is a web service that enables researchers to develop original deep learning and machine learning architectures to explore the complex dynamics of RNA-binding proteins.
Single Extracellular VEsicle Nanoscopy-Universal Protocol (SEVEN-UP): Accessible Imaging Platform for Quantitative Characterization of Single Extracellular Vesicles.
Anal Chem
January 2025
Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, United States.
Extracellular vesicles (EVs), membrane-encapsulated nanoparticles shed from all cells, are tightly involved in critical cellular functions. Moreover, EVs have recently emerged as exciting therapeutic modalities, delivery vectors, and biomarker sources. However, EVs are difficult to characterize, because they are typically small and heterogeneous in size, origin, and molecular content.
View Article and Find Full Text PDFGlobal Prevalence of Sexual Violence Against Children: A Systematic Review and Meta-Analysis.
JAMA Pediatr
January 2025
Health Psychology Unit, Institute of Psychology, University of Klagenfurt, Klagenfurt, Austria.
Importance: Sexual violence against children is a global concern, yet worldwide figures of its prevalence are scant.
Objective: To estimate the global prevalence of sexual violence against children using national-level population-based studies.
Data Sources: We searched the PubMed, Embase, CINAHL, Web of Science, PsycINFO, ERIC, and APA PsycArticles databases from their respective inceptions to March 2022.
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