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| http://dx.doi.org/10.1007/s13224-023-01776-6 | DOI Listing |
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DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.
Bioinformatics
January 2025
Biocomputing Group, University of Bologna, Italy.
Motivation: The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimental approaches and allow a fast screening of large datasets of variations.
Results: In this work we present DDGemb, a novel method combining protein language model embeddings and transformer architectures to predict protein ΔΔG upon both single- and multi-point variations.
Beyond the Horizon: Rethinking Prostate Cancer Treatment Through Innovation and Alternative Strategies.
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December 2024
Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA.
For nearly a century, fundamental observations that prostate cancer (PCa) cells nearly always require AR stimulation for sustained proliferation have led to a unidirectional quest to abrogate such a pathway. Similarly focused have been efforts to understand AR-driven processes in the context of elevated expression of its target genes, and much less so on products that become overexpressed when AR signaling is suppressed. Treatment with ARSI results in an increased expression of the TLK1B splice variant via a 'translational' derepression driven by the compensatory mTOR activation and consequent activation of the TLK1 > NEK1 > ATR > Chk1 and NEK1 > YAP axes.
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Department of Nephrocardiology, Medical University of Lodz, 90-549 Lodz, Poland.
This narrative review explores the benefits and risks of cannabinoids in kidney health, particularly in individuals with pre-existing renal conditions. It discusses the roles of cannabinoid receptor ligands (phytocannabinoids, synthetic cannabinoids, and endocannabinoids) in kidney physiology. The metabolism and excretion of these substances are also highlighted, with partial elimination occurring via the kidneys.
View Article and Find Full Text PDFWhole-Exome Sequencing: Discovering Genetic Causes of Granulomatous Mastitis.
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Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, 34093 Istanbul, Türkiye.
Granulomatous mastitis (GM) is a rare, benign, but chronic and recurrent inflammatory breast disease that significantly impacts physical and psychological well-being. It often presents symptoms such as pain, swelling, and discharge, leading to diagnostic confusion with malignancy. The etiology of GM remains unclear, though autoimmune and multifactorial components are suspected.
View Article and Find Full Text PDFAssociation of Novel Pathogenic Variant (p. Ile366Asn) in Gene with Infantile Neuroaxonal Dystrophy.
Int J Mol Sci
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Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA.
A couple presented to the office with an apparently healthy infant for a thorough clinical assessment, as they had previously lost two male children to a neurodegenerative disorder. They also reported the death of a male cousin abroad with a comparable condition. We aimed to evaluate a novel coding pathogenic variant c.
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