2022
PLD3 affects axonal spheroids and network defects in Alzheimer’s disease
Yuan P, Zhang M, Tong L, Morse T, McDougal R, Ding H, Chan D, Cai Y, Grutzendler J. PLD3 affects axonal spheroids and network defects in Alzheimer’s disease. Nature 2022, 612: 328-337. PMID: 36450991, PMCID: PMC9729106, DOI: 10.1038/s41586-022-05491-6.Peer-Reviewed Original ResearchConceptsAxonal spheroidsAlzheimer's diseaseConduction blockadeNeural circuit abnormalitiesNeural network dysfunctionAmyloid removalCircuit abnormalitiesAge-dependent accumulationNetwork dysfunctionEndolysosomal vesiclesMouse modelNeuronal overexpressionCognitive declineAxonal connectivityDiseasePrecise mechanismBlockadePLD3Neural network functionSpheroid growthSevere disruptionCurrent sinkVoltage imagingSize-dependent mannerDysfunction
2018
Automated Metadata Suggestion During Repository Submission
McDougal RA, Dalal I, Morse TM, Shepherd GM. Automated Metadata Suggestion During Repository Submission. Neuroinformatics 2018, 17: 361-371. PMID: 30382537, PMCID: PMC6494730, DOI: 10.1007/s12021-018-9403-z.Peer-Reviewed Original ResearchConceptsMetadata annotationMetadata tagsData providersAmount of dataDifferent text sourcesUser data entryData uploaderKnowledge discoveryText sourcesRelevant metadataMetadataHigh recallInformatics resourcesAnnotation schemeResearch communityData entryAnnotationBioinformatics resourcesDiscovery resourcesLow precisionMinimal costResourcesTagsModelDBUpload
2016
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database 2016, 2016: baw132. PMID: 27694208, PMCID: PMC5045865, DOI: 10.1093/database/baw132.Peer-Reviewed Original Research
2015
Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex
Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW. Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 2015, 316: 344-366. PMID: 26746357, PMCID: PMC4724569, DOI: 10.1016/j.neuroscience.2015.12.043.Peer-Reviewed Original ResearchConceptsHCN channelsExcitation/inhibition balancePersistent activityMetabotropic glutamate receptorsCalcium regulationNeuronal persistent activityEndoplasmic reticulum storesIonotropic inputsGABAB receptorsGlutamate receptorsInhibition balanceMultiple pathwaysCell excitabilityCortical layersMembrane depolarizationCompartmental neuronsInositol triphosphateIP3 receptorReceptorsNeuronsActivationMolecular eventsNeocortical modelsDepolarizationPathwayModelView for ModelDB: Online Presentation of Model Structure
McDougal RA, Morse TM, Hines ML, Shepherd GM. ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 2015, 13: 459-470. PMID: 25896640, PMCID: PMC4618280, DOI: 10.1007/s12021-015-9269-2.Peer-Reviewed Original ResearchConceptsSource codeModel source codeComputational neuroscience modelsWeb applicationModel reuseUser interfaceVisualization algorithmsWeb presentationCode sharingGraphical viewModelDBContextual informationSearchable repositoryManual curationModel structureNeuroscience modelsOnline presentationCodeNecessary dataData analysisKey featuresUsersRepositoryStructures of hundredsSharingNeuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer Model
Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW. Neuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer Model. Neural Computation 2015, 27: 898-924. PMID: 25734493, PMCID: PMC4386758, DOI: 10.1162/neco_a_00712.Peer-Reviewed Original Research
2013
Water-tight membranes from neuronal morphology files
McDougal RA, Hines ML, Lytton WW. Water-tight membranes from neuronal morphology files. Journal Of Neuroscience Methods 2013, 220: 167-178. PMID: 24091136, PMCID: PMC4197804, DOI: 10.1016/j.jneumeth.2013.09.011.Peer-Reviewed Original ResearchConceptsConstructive solid geometryFull shapeGeometry algorithmsSolid geometryElectrophysiology simulationsTriangular meshesMulti-scale modelSuch modelsReaction-diffusion simulationsElectrophysiological simulationsSimple interpretationGeometryAlgorithmSurface trianglesSimulationsList of pointsSpace constantsMorphology descriptionDistance calculationNeuronal geometryThree-dimensional shapeSmall objects