Resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) analysis has illuminated brain network interactions across many neuropsychiatric disorders. A common analysis approach involves using hard clustering methods to identify transitory states of brain activity, and in response to this, other methods have been developed to quantify the importance of specific dFNC interactions to identified states. Some of these methods involve perturbing individual features and examining the number of samples that switch states. However, only a minority of samples switch states. As such, these methods actually identify the importance of dFNC features to the clustering of a subset of samples rather than the overall clustering. In this study, we present a novel approach that more capably identifies the importance of each feature to the overall clustering. Our approach uses fuzzy clustering to output probabilities of each sample belonging to states and then measures their Kullback-Leibler divergence after perturbation. We show the viability of our approach in the context of schizophrenia (SZ) default mode network analysis, identifying significant differences in state dynamics between individuals with SZ and healthy controls. We further compare our approach with an existing approach, showing that it captures the effects of perturbation upon most samples. We also find that interactions between the posterior cingulate cortex (PCC) and the anterior cingulate cortex and the PCC and precuneus are important across methods. We expect that our novel explainable clustering approach will enable further progress in rs-fMRI analysis and to other clustering applications.
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http://dx.doi.org/10.1109/EMBC40787.2023.10340173 | DOI Listing |
Microbiome
January 2025
Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, Jena, 07745, Germany.
Background: The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.
Results: Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis.
Genome Biol
January 2025
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
Background: Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.
Results: We perform pangenome analysis on 2371 Streptomyces genomes, including approximately 1200 complete assemblies.
Sci Rep
January 2025
Department of Basic Sciences, Faculty of Dentistry, Universidad de Antioquia U de A, Medellín, 050010, Colombia.
The NLRP3 inflammasome, regulated by TLR4, plays a pivotal role in periodontitis by mediating inflammatory cytokine release and bone loss induced by Porphyromonas gingivalis. Periodontal disease creates a hypoxic environment, favoring anaerobic bacteria survival and exacerbating inflammation. The NLRP3 inflammasome triggers pyroptosis, a programmed cell death that amplifies inflammation and tissue damage.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Chemistry, Federal University of Paraná, Curitiba, 81531-980, Brazil.
Gold-based (Au) nanostructures are efficient catalysts for CO oxidation, hydrogen evolution (HER), and oxygen evolution (OER) reactions, but stabilizing them on graphene (Gr) is challenging due to weak affinity from delocalized [Formula: see text] carbon orbitals. This study investigates forming metal alloys to enhance stability and catalytic performance of Au-based nanocatalysts. Using ab initio density functional theory, we characterize [Formula: see text] sub-nanoclusters (M = Ni, Pd, Pt, Cu, and Ag) with atomicities [Formula: see text], both in gas-phase and supported on Gr.
View Article and Find Full Text PDFMedicine (Baltimore)
November 2024
Department of Infectious Diseases, Nantong Clinical Medical College of Integrated Traditional Chinese and Western Medicine of Nanjing University of Chinese Medicine, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China.
Background: To investigate global trends and current research on post-traumatic osteoarthritis (PTOA) from 2010 to 2024 using bibliometric and visualization techniques.
Methods: A bibliometric analysis was conducted using data from the Web of Science Core Collection. The study examined publication trends, author contributions, institutional collaborations, keyword co-occurrence, and citation patterns, employing CiteSpace software to analyze key metrics such as publication frequency, centrality, and clustering.
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