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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories.
J Chem Inf Model
January 2025
Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States.
Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical data sets. Concurrently, our ability to perform long-time scale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially.
View Article and Find Full Text PDFStructural insights into the role of the prosegment binding loop in a papain-superfamily cysteine protease from Treponema denticola.
Acta Crystallogr F Struct Biol Commun
February 2025
Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA.
Periodontal diseases afflict 20-50% of the global population and carry serious health and economic burdens. Chronic periodontitis is characterized by inflammation of the periodontal pocket caused by dysbiosis. This dysbiosis is coupled with an increase in the population of Treponema denticola, a spirochete bacterium with high mobility and invasivity mediated by a number of virulence factors.
View Article and Find Full Text PDFIntranasal iron administration induces iron deposition, immunoactivation, and cell-specific vulnerability in the olfactory bulb of C57BL/6 mice.
Zool Res
January 2025
School of Basic Medicine, Institute of Brain Science and Disease, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Brain Diseases, Qingdao University, Qingdao, Shandong, 266071, China. E-mail:
Iron is the most abundant transition metal in the brain and is essential for brain development and neuronal function; however, its abnormal accumulation is also implicated in various neurological disorders. The olfactory bulb (OB), an early target in neurodegenerative diseases, acts as a gateway for environmental toxins and contains diverse neuronal populations with distinct roles. This study explored the cell-specific vulnerability to iron in the OB using a mouse model of intranasal administration of ferric ammonium citrate (FAC).
View Article and Find Full Text PDFCorrelation of zero echo time functional MRI with neuronal activity in rats.
J Cereb Blood Flow Metab
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A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Zero echo time (zero-TE) pulse sequences provide a quiet and artifact-free alternative to conventional functional magnetic resonance imaging (fMRI) pulse sequences. The fast readouts (<1 ms) utilized in zero-TE fMRI produce an image contrast with negligible contributions from blood oxygenation level-dependent (BOLD) mechanisms, yet the zero-TE contrast is highly sensitive to brain function. However, the precise relationship between the zero-TE contrast and neuronal activity has not been determined.
View Article and Find Full Text PDFImpact of glioma metabolism-related gene ALPK1 on tumor immune heterogeneity and the regulation of the TGF-β pathway.
Front Immunol
January 2025
Department of Neurological Care Unit, The First Affiliated Hospital of YangTze University, Jingzhou, Hubei, China.
Background: Recent years have seen persistently poor prognoses for glioma patients. Therefore, exploring the molecular subtyping of gliomas, identifying novel prognostic biomarkers, and understanding the characteristics of their immune microenvironments are crucial for improving treatment strategies and patient outcomes.
Methods: We integrated glioma datasets from multiple sources, employing Non-negative Matrix Factorization (NMF) to cluster samples and filter for differentially expressed metabolic genes.
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