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Successful management of a multi-species outbreak of carbapenem-resistant organisms in Fiji: a prospective genomics-enhanced investigation and response.
Lancet Reg Health West Pac
December 2024
WHO Collaborating Centre for Antimicrobial Resistance, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Background: Fiji is a Pacific Island nation grappling with the increasing threat of antimicrobial resistance (AMR). While genomic technologies are increasingly utilised to understand the emergence and spread of AMR globally, its application to inform outbreak responses in low- and middle-income settings has not been reported.
Methods: Through an established capacity building program, suspected carbapenem-resistant organisms (CRO) identified at Colonial War Memorial Hospital in Fiji (Jan 2022-Oct 2023) underwent whole genome sequencing and analysis.
The "limbic network," comprising orbitofrontal and anterior temporal cortex, is part of an extended default network: Evidence from multi-echo fMRI.
Netw Neurosci
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Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
Resting-state functional magnetic resonance imaging (fMRI) investigations have provided a view of the default network (DN) as composed of a specific set of frontal, parietal, and temporal cortical regions. This spatial topography is typically defined with reference to an influential network parcellation scheme that designated the DN as one of seven large-scale networks (Yeo et al., 2011).
View Article and Find Full Text PDFTowards multi-modal, multi-species brain atlases: part two.
Brain Struct Funct
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Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany.
DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.
Nucleic Acids Res
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Department of Surgery, Brown University, 69 Brown St Box 1822, 02912 RI, USA.
It was previously shown that DNA breathing, thermodynamic stability, as well as transcriptional activity and transcription factor (TF) bindings are functionally correlated. To ascertain the precise relationship between TF binding and DNA breathing, we developed the multi-modal deep learning model EPBDxDNABERT-2, which is based on the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA dynamics model. To train our EPBDxDNABERT-2, we used chromatin immunoprecipitation sequencing (ChIP-Seq) data comprising 690 ChIP-seq experimental results encompassing 161 distinct TFs and 91 human cell types.
View Article and Find Full Text PDFCactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis.
Genomics
July 2024
Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden. Electronic address:
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly.
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