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Predicting transcriptional changes induced by molecules with MiTCP.
Brief Bioinform
November 2024
Department of Automation, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.
View Article and Find Full Text PDFIntegrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis.
Ann Med
December 2025
Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, PR China.
Objective: This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.
Methods: Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes.
Structural insights into glucose-6-phosphate recognition and hydrolysis by human G6PC1.
Proc Natl Acad Sci U S A
January 2025
Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
The glucose-6-phosphatase (G6Pase) is an integral membrane protein that catalyzes the hydrolysis of glucose-6-phosphate (G6P) in the endoplasmic reticulum lumen and plays a vital role in glucose homeostasis. Dysregulation or genetic mutations of G6Pase are associated with diabetes and glycogen storage disease 1a (GSD-1a). Studies have characterized the biophysical and biochemical properties of G6Pase; however, the structure and substrate recognition mechanism of G6Pase remain unclear.
View Article and Find Full Text PDFChallenges when Combining Expertise to Provide Integrated Care for Youth At-Risk and Their Family: A Qualitative Study.
Adm Policy Ment Health
January 2025
LUMC Curium - Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Post Box 15, Leiden, 2300 AA, the Netherlands.
The needs of youth at-risk and their families, facing multiple problems and serious mental health issues, exceed the expertise and possibilities of a single stakeholder (professional, organization, municipality). These youngsters require care in which the expertise of different professionals and organizations is integrated. However, combining various types of expertise to provide integrated care to youth at-risk is challenging.
View Article and Find Full Text PDF[A case of atopic dermatitis-the biopsychosocial view].
Dermatologie (Heidelb)
January 2025
Psychoneuroimmunologie Labor, Klinik für Psychosomatik und Psychotherapie, Justus-Liebig-Universität Gießen, Aulweg 123, 35385, Gießen, Deutschland.
Background: Atopic dermatitis is perhaps the most comprehensively studied skin disease in psychosomatic medicine and psychoneuroimmunology. Its biopsychosocial conceptualization incorporates psychodynamic as well as behavioral and systemic considerations. At the same time, there is also extensive biological knowledge of the neuroendocrine-immune control of barrier and immune function, characterized through animal experiments and translational clinical studies.
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