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Locating Multiple Transition Pathways for Complex Biomolecules.
J Chem Inf Model
March 2025
School of Medicine and Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.
Locating the low free energy paths (LFEPs) connecting different conformational states is among the major tasks for the simulations of complex biomolecules as the pathways encode the physical essence and, therefore, the underlying mechanism for their functional dynamics. Finding the LFEPs is yet challenging due to the numerous degrees of freedom of the molecules and expensive force calculations. To alleviate this issue, we have previously introduced a Traveling-Salesman-based Automated Path Searching (TAPS) approach that requires minimal input information to locate the LFEP closest to a given initial guess path.
View Article and Find Full Text PDFNumerous computational approaches have been developed to infer cell state transition trajectories from snapshot single-cell data. Most approaches first require projecting high-dimensional data onto a low-dimensional representation, raising the question of whether the dynamics of the system become distorted. Using epithelial-to-mesenchymal transition (EMT) as a test system, we show that both biology-guided low-dimensional representations and stochastic trajectory simulations in high-dimensional state space, not representations obtained with dimension-reduction methods, reveal multiple distinct paths of TGF-β-induced EMT.
View Article and Find Full Text PDFExploring a Favorable Tradeoff for Finding Every Efficient Path in Large-Scale Networks.
IEEE Trans Cybern
February 2025
Multiobjective shortest path problem (MSPP) is one of the most critical issues in network optimization, aimed at identifying all efficient paths across conflicting objectives. Nowadays, existing methods face substantial bottlenecks in addressing the diverse preferences of decision makers and high spatiotemporal overhead caused by the calculation process, particularly in cases with large-scale networks. To overcome these obstacles, a generalized MSPP in large-scale networks is investigated with the aim of solving it with diverse preferences of decision makers satisfied and low spatiotemporal overhead.
View Article and Find Full Text PDFDecoding the Role of Neurotrophins in Glycogen Synthase Kinase 3-Beta Regulation in Alzheimer's Disease.
Mol Neurobiol
February 2025
Pharmacology and Toxicology Laboratory, Dietetics and Nutrition Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most prevalent contributor to dementia in elderly individuals. Numerous signalling pathways influencing AD pathophysiology, involving glycogen synthase kinase-3β (Gsk-3β), have been investigated extensively as potential therapeutic targets. Gsk-3β is a critical factor in AD pathogenesis that affects several key hallmarks of the disease notably tau phosphorylation, amyloid-β generation, cognition, neurogenesis, and synaptic integrity.
View Article and Find Full Text PDFThe Occurrence of sensu lato in Ticks Collected from Nature-Educational and Tourist Trails in the Poprad Landscape Park.
Pathogens
January 2025
Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19, 41-808 Zabrze, Poland.
Throughout Europe, including Poland, ticks are the main vector of numerous pathogenic agents that pose a serious threat to public health. Southern Poland attracts many tourists with its scenic landscapes and abundant recreational opportunities. These areas are ideal habitats for wild fauna, which serve as the main reservoirs and hosts for these pathogens and ticks.
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