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Depressed mood and anhedonia, the core symptoms of major depressive disorder (MDD), are linked to dysfunction in the brain's reward and emotion regulation circuits. To develop a predictive model for treatment remission in MDD based on pre-treatment neurocircuitry and clinical features. A total of 279 untreated MDD patients were analyzed, treated with selective serotonin reuptake inhibitors for 8-12 weeks, and assigned to training, internal validation, and external validation datasets. A hierarchical local-global imaging and clinical feature fusion graph neural network model was constructed. The model achieved 76.21% accuracy (AUC = 0.78) in predicting remission. Validation on the internal and external independent datasets yielded similar performance (accuracy = 72.73%, AUC = 0.74; accuracy = 71.43%, AUC = 0.72). Key contributing brain regions included the right globus pallidus, bilateral putamen, left hippocampus, bilateral thalamus, and bilateral anterior cingulate gyrus. These findings highlight the role of specific circuits in guiding antidepressant treatment.
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http://dx.doi.org/10.1038/s41746-025-01912-8 | DOI Listing |
Bioinformatics
September 2025
Centre National de Recherche en Génomique Humaine, Institut François Jacob CEA Université Paris-Saclay.
Motivation: Graph Neural Network (GNN) models have emerged in many fields and notably for biological networks constituted by genes or proteins and their interactions. The majority of enrichment study methods apply over-representation analysis and gene/protein set scores according to the existing overlap between pathways. Such methods neglect knowledges coming from the interactions between the gene/protein sets.
View Article and Find Full Text PDFBrief Bioinform
August 2025
State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China.
The systematic identification of human-virus protein-protein interactions (PPIs) is a critical step toward elucidating the underlying mechanisms of viral infection, directly informing the development of targeted interventions against existing and emerging viral threats. In this work, we presented DeepGNHV, an end-to-end framework that integrated a pretrained protein language model with structural features derived from AlphaFold2 and leveraged graph attention networks to predict human-virus PPIs. In comparison to other state-of-the-art approaches, DeepGNHV exhibited superior predictive performance, especially when applied to viral proteins absent from the training process, indicating its strong generalization capability for detecting newly emerging virus-related PPIs.
View Article and Find Full Text PDFBrief Bioinform
August 2025
School of Information and Artificial Intelligence, Anhui Agricultural University, 130 Changjiang Road, Shushan District, Hefei, Anhui 230036, China.
Protein-nucleic acid binding sites play a crucial role in biological processes such as gene expression, signal transduction, replication, and transcription. In recent years, with the development of artificial intelligence, protein language models, graph neural networks, and transformer architectures have been adopted to develop both structure-based and sequence-based predictive models. Structure-based methods benefit from the spatial relationship between residues and have shown promising performance.
View Article and Find Full Text PDFJ Comput Soc Sci
September 2025
Chair of Research Methods in Developmental and Educational Sciences, Institute of Education, University of Zurich, Zurich, Switzerland.
School curricula guide the daily learning activities of millions of students. They embody the understanding of the education experts who designed them of how to organize the knowledge that students should acquire in a way that is optimal for learning. This can be viewed as a learning 'theory' which is, nevertheless, rarely put to the test.
View Article and Find Full Text PDFRSC Med Chem
August 2025
Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University 4.5 Km the Ring Road Ismailia 41522 Egypt.
Protein kinases are central regulators of cell signaling and play pivotal roles in a wide array of diseases, most notably cancer and autoimmune disorders. The clinical success of kinase inhibitors-such as imatinib and osimertinib-has firmly established kinases as valuable drug targets. However, the development of selective, potent inhibitors remains challenging due to the conserved nature of the ATP-binding site, off-target effects, resistance mutations, and patient-specific variability.
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