2024
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Mullin S, McDougal R, Cheung K, Kilicoglu H, Beck A, Zeiss C. Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics. Journal Of Biomedical Semantics 2024, 15: 13. PMID: 39080729, PMCID: PMC11290083, DOI: 10.1186/s13326-024-00314-1.Peer-Reviewed Original ResearchConceptsEntity normalizationChemical mentionsNatural language modelDictionary-based methodsDictionary-based approachCRAFT corpusDownstream tasksLanguage modelChemical Entities of Biological InterestPubMedBERT modelDisambiguationChEBIDownstream applicationsArticle abstractsRelationship typesMentionsPubMedBERTOntologyDementia literatureTaskDementia CohortMethodEntitiesAccuracyDementiaAutomating literature screening and curation with applications to computational neuroscience
Ji Z, Guo S, Qiao Y, McDougal R. Automating literature screening and curation with applications to computational neuroscience. Journal Of The American Medical Informatics Association 2024, 31: 1463-1470. PMID: 38722233, PMCID: PMC11187430, DOI: 10.1093/jamia/ocae097.Peer-Reviewed Original ResearchComputational neuroscienceLanguage modeling techniquesNatural language processingDomain-specific resourcesComputational neuroscience approachNeuroscience workMetadata annotationsModel discoveryLanguage processingComputing elementsNeuron modelModelDBMetadataRelevant metadataStandardized metadataAuthor submissionLarge Language Model (GPT-4) Accurately Localizes Stroke Lesions (P8-4.002)
Lee J, Choi E, McDougal R, Lytton W. Large Language Model (GPT-4) Accurately Localizes Stroke Lesions (P8-4.002). Neurology 2024, 102 DOI: 10.1212/wnl.0000000000204601.Peer-Reviewed Original ResearchGPT-4 Performance for Neurologic Localization
Lee J, Choi E, McDougal R, Lytton W. GPT-4 Performance for Neurologic Localization. Neurology Clinical Practice 2024, 14: e200293. PMID: 38596779, PMCID: PMC11003355, DOI: 10.1212/cpj.0000000000200293.Peer-Reviewed Original ResearchGenerative Pretrained TransformerText classificationText datasetsClass labelsPretrained TransformerLanguage modelF1 scorePerformance metricsKnowledge baseMetricsInadequate knowledge baseClassificationReduce health care disparitiesClinical reasoningCapabilityPerformanceTextHealth care disparitiesDatasetSoftware
2023
Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories
Cudone E, Lower A, McDougal R. Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories. PLOS Computational Biology 2023, 19: e1011548. PMID: 37824576, PMCID: PMC10597496, DOI: 10.1371/journal.pcbi.1011548.Peer-Reviewed Original ResearchConceptsInitial conditionsDifferential equation modelMore biological detailUnknown initial conditionsLarge network modelsDifferential equationsMore computational resourcesCell state variablesData-driven modelingState variablesNeuron statesLarge systemsComputational resourcesModel time constantsModeling assumptionsModel statesEquationsNetwork modelModeling frameworkBiological detailsDetailed simulationsAdditional realismCellular biophysicsModerate numberInput historySUBCELLULAR TO TISSUE SCALE MODELING OF ISCHEMIA AND SPREADING DEPOLARIZATION
Newton A, Kelley C, Guo A, Wang J, Zink S, Distasio M, Mcdougal R, Lytton W. SUBCELLULAR TO TISSUE SCALE MODELING OF ISCHEMIA AND SPREADING DEPOLARIZATION. IBRO Neuroscience Reports 2023, 15: s792. DOI: 10.1016/j.ibneur.2023.08.1633.Peer-Reviewed Original ResearchTutorial: using NEURON for neuromechanical simulations
Fietkiewicz C, McDougal R, Marco D, Chiel H, Thomas P. Tutorial: using NEURON for neuromechanical simulations. Frontiers In Computational Neuroscience 2023, 17: 1143323. PMID: 37583894, PMCID: PMC10424731, DOI: 10.3389/fncom.2023.1143323.Peer-Reviewed Original ResearchUse of pointersCode modularityCode reuseSeparate specificationComplex adaptive behaviorSimulation platformDifferent computational modelsComplicated syntaxClosed-loop modelSimulation toolNeuromechanical modelingNeuron simulationsLevel of complexityComputational modelNeuromechanical simulationsTutorialPointersNon-smooth dynamicsPedagogical modelNeural dynamicsProgramming optionsBody dynamicsModelingAdaptive behaviorFirst stepA pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
Newton A, Chartash D, Kleinstein S, McDougal R. A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. BMC Bioinformatics 2023, 24: 292. PMID: 37474900, PMCID: PMC10357743, DOI: 10.1186/s12859-023-05397-8.Peer-Reviewed Original ResearchConceptsDomain-specific informationDocument embeddingsSVM classifierSemi-structured representationsTraining setWeb-based formKnowledge repositoryInformation modelAutomatic analysisClassifier predictionsClassifierSignature informationAutomated systemBiomedical publicationsPaper authorsEmbeddingIncomplete information modelLiterature miningIterative processSpecific informationSuch informationInformationLimited setSetQueries
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 mannerDysfunctionMultiscale Computer Modeling of Spreading Depolarization in Brain Slices
Kelley C, Newton AJH, Hrabetova S, McDougal RA, Lytton WW. Multiscale Computer Modeling of Spreading Depolarization in Brain Slices. ENeuro 2022, 9: eneuro.0082-22.2022. PMID: 35927026, PMCID: PMC9410770, DOI: 10.1523/eneuro.0082-22.2022.Peer-Reviewed Original ResearchConceptsBrain slicesNeuronal spike rateGreater neuronal densityExtracellular spaceEffects of hypoxiaNeuronal densityNeurologic conditionsNeuronal depolarizationNeuronal silenceNeuronal volumeRelative hypoxiaSD velocityPathologic cycleECS volumeECS shrinkageSD speedMore dendritesSpike rateSDConcentration homeostasisNeuronsDepolarizationHypoxiaSlicesMultiscale computer modelingModernizing the NEURON Simulator for Sustainability, Portability, and Performance
Awile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJH, Pereira F, Săvulescu A, Carnevale NT, Lytton WW, Hines ML, Schürmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers In Neuroinformatics 2022, 16: 884046. PMID: 35832575, PMCID: PMC9272742, DOI: 10.3389/fninf.2022.884046.Peer-Reviewed Original ResearchComputer architectureDomain-specific languageCloud platformSoftware distributionScientific workflowsDeveloper baseSource compilerHardware platformTime compilationBuild systemSimulation engineContinuous integrationSimulation platformComputational neuroscienceNew usersNEURON simulatorSimulation performanceBiological modelingUsersPlatformArchitectureWorkflowBetter documentationBackendGPUModelDB
McDougal R, Wang R, Morse T, Migliore M, Marenco L, Carnevale T, Hines M, Shepherd G. ModelDB. 2022, 2053-2056. DOI: 10.1007/978-1-0716-1006-0_158.Peer-Reviewed Original ResearchEfficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks
McDougal RA, Conte C, Eggleston L, Newton AJH, Galijasevic H. Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks. Frontiers In Neuroinformatics 2022, 16: 847108. PMID: 35655652, PMCID: PMC9152282, DOI: 10.3389/fninf.2022.847108.Peer-Reviewed Original ResearchFinite volume method simulationIrregular 3D geometryMethod simulationsDouglas-GunnDimensional simulationsHigh-dimensional simulationsWave curvatureEfficient simulationSimulationsParallel algorithmCylinderModels of neuronsNetwork modelNEURON simulatorReconstruction algorithmRegion of interestAccelerated versionConnected cylindersReaction diffusionReaction-diffusion kineticsElectrophysiological simulationsAlgorithmKineticsBioSimulators: a central registry of simulation engines and services for recommending specific tools.
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 2022 PMID: 35524558, PMCID: PMC9252793, DOI: 10.1093/nar/gkac331.Peer-Reviewed Original ResearchConditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity
Huertas MA, Newton AJH, McDougal RA, Sacktor TC, Shouval HZ. Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity. ENeuro 2022, 9: eneuro.0064-22.2022. PMID: 35443991, PMCID: PMC9087736, DOI: 10.1523/eneuro.0064-22.2022.Peer-Reviewed Original Research
2020
Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data
Neymotin SA, Daniels DS, Caldwell B, McDougal RA, Carnevale NT, Jas M, Moore CI, Hines ML, Hämäläinen M, Jones SR. Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data. ELife 2020, 9: e51214. PMID: 31967544, PMCID: PMC7018509, DOI: 10.7554/elife.51214.Peer-Reviewed Original ResearchConceptsGraphical user interfaceNew software toolUser interfaceMEG/EEGSoftware toolsMEG/EEG dataTranslational neuroscience researchNew therapiesNeural originReliable markerDisease statesEEG dataBrain rhythmsNetwork originBrain activityHuman brain activityElectro-encephalographyInformation processingEEGUsersNeuroscience research
2019
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron 2019, 103: 395-411.e5. PMID: 31201122, PMCID: PMC6693896, DOI: 10.1016/j.neuron.2019.05.019.Peer-Reviewed Original ResearchConceptsData-driven modelsReproducibility of modelsCollaborative interactionsCollaborative resourceExperimental resultsComputational modelAnalyzingReuseStandardized modelModel structureSpecialist knowledgeMultiple scalesComplex biological systemsSharingVisualizingToolInfrastructureNetworkNew modelPlatformPowerful toolSimulatingModelWider communityAdoptionNetPyNE, a tool for data-driven multiscale modeling of brain circuits
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife 2019, 8: e44494. PMID: 31025934, PMCID: PMC6534378, DOI: 10.7554/elife.44494.Peer-Reviewed Original ResearchConceptsInformation-theoretic measuresDeclarative languageImplementation codeGraphical interfaceNetPyNENetwork parametersTheoretic measuresNetwork modelNeuron networkStandardized formatUsersMillions of cellsConnectivity rulesExperimental datasetsNetworkRaster plotMultiscale network modelMultiple scalesDatasetToolModelersSpecificationModel parametersModelingVisualizationNeuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons
Shepherd GM, Marenco L, Hines ML, Migliore M, McDougal RA, Carnevale NT, Newton AJH, Surles-Zeigler M, Ascoli GA. Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons. Frontiers In Neuroanatomy 2019, 13: 25. PMID: 30949034, PMCID: PMC6437103, DOI: 10.3389/fnana.2019.00025.Peer-Reviewed Original Research
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