You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: ["HealthCareActivity", "InjuryOrPoisoning", "BodySubstance", "IntellectualProduct", "AnatomicalStructure", "SpatialConcept", "Chemical", "Bacterium", "MedicalDevice", "Organization", "BiomedicalOccupationOrDiscipline", "Finding", "BiologicFunction", "Virus", "ResearchActivity", "ClinicalAttribute", "PopulationGroup", "Eukaryote", "BodySystem", "Food", "ProfessionalOrOccupationalGroup"].

Please return the output as a JSON object of the format: {"Virus": ["HIV", ...], "Bacterium": ["MRSA", ...], "AnatomicalStructure": ["Lung", ...], "BodySystem": ["CNS", ...], "BodySubstance": ["Serum", ...], "Finding": ["Headache", ...], "InjuryOrPoisoning": ["Fracture", ...], "BiologicFunction": ["Death", ...], "HealthCareActivity": ["Biopsy", ...], "ResearchActivity": ["Clinical trial", ...], "MedicalDevice": ["Lenses", ...], "SpatialConcept": ["Camps", ...], "BiomedicalOccupationOrDiscipline": ["Forensic medicine", ...], "Organization": ["WHO", ...], "ProfessionalOrOccupationalGroup": ["Provider", ...], "PopulationGroup": ["Swimmers", ...], "Chemical": ["Gold", ...], "Food": ["Rice", ...], "IntellectualProduct": ["RPAM", ...], "ClinicalAttribute": ["Biomarker", ...], "Eukaryote": ["Dogs", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].

Only output the JSON object and do not include any additional text.

Abstract:

The use of Oxford Nanopore native barcoding for complete genome assembly The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data. The strain we used, MHO_001, represents the important community-acquired methicillin resistant Staphylococcus aureus lineage USA300. Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long-read data represented only ~5-10% of an average MinION(TM) run (~7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss and gain of mobile genetic elements. Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short-read data, to fully complete a bacterial genome. The ability to complete multiple genomes, for which short-read data is already available, from a single MinION(TM) run is set to impact on our understanding of accessory genome content, plasmid diversity and genome rearrangements.
{"AnatomicalStructure": ["bacterial genomes", "USA300_FPR3757", "bacterial genome", "genomic", "genomes", "genome", "circular chromosome", "genome content", "multiplexed library"], "Bacterium": ["Staphylococcus aureus", "S. aureus"], "BiologicFunction": ["rearrangements", "understanding", "translocation"], "BiomedicalOccupationOrDiscipline": [], "BodySubstance": [], "BodySystem": [], "Chemical": ["mobile genetic elements", "plasmid", "plasmids"], "ClinicalAttribute": [], "Eukaryote": [], "Finding": ["available"], "Food": [], "HealthCareActivity": [], "InjuryOrPoisoning": [], "IntellectualProduct": ["report", "tools", "long-read data", "short-read data"], "MedicalDevice": ["MinION(TM)"], "Organization": ["Oxford Nanopore Technologies", "Oxford Nanopore"], "PopulationGroup": [], "ProfessionalOrOccupationalGroup": [], "ResearchActivity": ["barcoding", "closure"], "SpatialConcept": ["barcoded long read sequences", "single contig genome assembly", "long read sequences", "genome assembly", "assembly"], "Virus": []}