2024
Local-structure-preservation and redundancy-removal-based feature selection method and its application to the identification of biomarkers for schizophrenia
Xing Y, Pearlson G, Kochunov P, Calhoun V, Du Y. Local-structure-preservation and redundancy-removal-based feature selection method and its application to the identification of biomarkers for schizophrenia. NeuroImage 2024, 299: 120839. PMID: 39251116, DOI: 10.1016/j.neuroimage.2024.120839.Peer-Reviewed Original ResearchConceptsSelection methodClassification accuracy gainsGraph-based regularizationHigh-dimensional dataFeature selection methodLocal structural informationSparse regularizationAblation studiesFeature subsetPublic datasetsFeature selectionClassification accuracyExperimental evaluationAccuracy gainsSelection techniquesNetwork connectivityData transformationSuperior performanceDatasetConvergence analysisStructural informationClassificationRegularizationFeaturesDisorder predictionNeurodevelopmental subtypes of functional brain organization in the ABCD study using a rigorous analytic framework
DeRosa J, Friedman N, Calhoun V, Banich M. Neurodevelopmental subtypes of functional brain organization in the ABCD study using a rigorous analytic framework. NeuroImage 2024, 299: 120827. PMID: 39245397, DOI: 10.1016/j.neuroimage.2024.120827.Peer-Reviewed Original ResearchConceptsResting-state functional connectivityAdolescent Brain Cognitive DevelopmentIndividual’s resting-state functional connectivityAdolescent Brain Cognitive Development StudyFunctional brain organizationMental health profilesMental health characteristicsRsFC dataBrain organizationFunctional connectivityDevelopmental trajectoriesChildren aged 9Emotional functioningCognitive developmentLate childhoodAged 9SubtypesAdolescentsHealth characteristicsHealth profileChildhoodJoint multi-site domain adaptation and multi-modality feature selection for the diagnosis of psychiatric disorders
Ji Y, Silva R, Adali T, Wen X, Zhu Q, Jiang R, Zhang D, Qi S, Calhoun V. Joint multi-site domain adaptation and multi-modality feature selection for the diagnosis of psychiatric disorders. NeuroImage Clinical 2024, 43: 103663. PMID: 39226701, DOI: 10.1016/j.nicl.2024.103663.Peer-Reviewed Original ResearchAssociations of alcohol and tobacco use with psychotic, depressive and developmental disorders revealed via multimodal neuroimaging
Qiu L, Liang C, Kochunov P, Hutchison K, Sui J, Jiang R, Zhi D, Vergara V, Yang X, Zhang D, Fu Z, Bustillo J, Qi S, Calhoun V. Associations of alcohol and tobacco use with psychotic, depressive and developmental disorders revealed via multimodal neuroimaging. Translational Psychiatry 2024, 14: 326. PMID: 39112461, PMCID: PMC11306356, DOI: 10.1038/s41398-024-03035-2.Peer-Reviewed Original ResearchConceptsFronto-limbic networkSalience networkAssociated with cognitionFronto-basal gangliaDevelopmental disordersBrain networksLimbic systemAlcohol useAssociated with alcohol useMultimodal brain networksTobacco useAssociation of alcoholPsychiatric disordersMultimodal neuroimagingDMNBrain featuresCognitionAlcohol/tobacco useDisordersAssociated with tobacco useDepressionSymptomsFunctional abnormalitiesAlcoholBrain4D dynamic spatial brain networks at rest linked to cognition show atypical variability and coupling in schizophrenia
Pusuluri K, Fu Z, Miller R, Pearlson G, Kochunov P, Van Erp T, Iraji A, Calhoun V. 4D dynamic spatial brain networks at rest linked to cognition show atypical variability and coupling in schizophrenia. Human Brain Mapping 2024, 45: e26773. PMID: 39045900, PMCID: PMC11267451, DOI: 10.1002/hbm.26773.Peer-Reviewed Original ResearchConceptsBrain networksFunctional magnetic resonance imagingAssociated with cognitive performanceDynamics of functional brain networksAssociated with cognitionFunctional brain networksVoxel-wise changesVolumetric couplingDynamical variablesCognitive performanceTypical controlsSchizophreniaCognitive impairmentNetwork pairsMagnetic resonance imagingPair of networksCognitionAtypical variabilityResonance imagingCouplingNetwork connectivityNetwork growthImpairmentBrainStatic networksEffects of endogenous testosterone on oscillatory activity during verbal working memory in youth
Killanin A, Ward T, Embury C, Calhoun V, Wang Y, Stephen J, Picci G, Heinrichs‐Graham E, Wilson T. Effects of endogenous testosterone on oscillatory activity during verbal working memory in youth. Human Brain Mapping 2024, 45: e26774. PMID: 38949599, PMCID: PMC11215982, DOI: 10.1002/hbm.26774.Peer-Reviewed Original ResearchConceptsVerbal working memoryVerbal working memory processingWorking memory processesWorking memoryEffects of chronological ageEndogenous testosterone levelsMemory processesOscillatory activitySternberg verbal working memory taskEffects of testosteroneLeft-lateralized language networkVerbal working memory taskAlpha oscillationsSalivary testosterone samplesWorking memory encodingWorking memory taskLeft temporal cortexRight cerebellar cortexNeural oscillatory activitySignificant oscillatory responsesNeural oscillatory dynamicsHuman brain structureCerebellar cortexYouth aged 6Chronological ageEstimation of complete mutual information exploiting nonlinear magnitude-phase dependence: Application to spatial FNC for complex-valued fMRI data
Li W, Lin Q, Zhang C, Han Y, Li H, Calhoun V. Estimation of complete mutual information exploiting nonlinear magnitude-phase dependence: Application to spatial FNC for complex-valued fMRI data. Journal Of Neuroscience Methods 2024, 409: 110207. PMID: 38944128, DOI: 10.1016/j.jneumeth.2024.110207.Peer-Reviewed Original ResearchConceptsComplex-valued fMRI dataMutual informationJoint entropyNetwork connectivityComplex-valued signalsFunctional network connectivityMagnitude-phase dependenceDensity estimation methodMI estimationHistogram-basedKernel density estimation methodFMRI dataEstimation accuracyProbability density functionJoint probability density functionSimulated signalsChain rulePhase dependenceEstimation methodHigh-orderDensity functionControl networkInaccurate estimationNonlinear dependenceDependenceA survey of brain functional network extraction methods using fMRI data
Du Y, Fang S, He X, Calhoun V. A survey of brain functional network extraction methods using fMRI data. Trends In Neurosciences 2024, 47: 608-621. PMID: 38906797, DOI: 10.1016/j.tins.2024.05.011.Peer-Reviewed Original ResearchThe brain structure, inflammatory, and genetic mechanisms mediate the association between physical frailty and depression
Jiang R, Noble S, Rosenblatt M, Dai W, Ye J, Liu S, Qi S, Calhoun V, Sui J, Scheinost D. The brain structure, inflammatory, and genetic mechanisms mediate the association between physical frailty and depression. Nature Communications 2024, 15: 4411. PMID: 38782943, PMCID: PMC11116547, DOI: 10.1038/s41467-024-48827-8.Peer-Reviewed Original ResearchConceptsIncident depressionPre-frailPhysical frailtyFrail individualsPopulation attributable fraction analysisRisk factors of depressionMendelian randomization analysisFactors of depressionPotential causal effectModifiable risk factorsNon-frail individualsCross-sectional studyEffect of frailtyHigher disease burdenUK BiobankRandomization analysisBrain volumeDepression casesDisease burdenFrailtyRegional brain volumesIncreased riskDepressionHigh riskFollow-upA confounder controlled machine learning approach: Group analysis and classification of schizophrenia and Alzheimer’s disease using resting-state functional network connectivity
Hassanzadeh R, Abrol A, Pearlson G, Turner J, Calhoun V. A confounder controlled machine learning approach: Group analysis and classification of schizophrenia and Alzheimer’s disease using resting-state functional network connectivity. PLOS ONE 2024, 19: e0293053. PMID: 38768123, PMCID: PMC11104643, DOI: 10.1371/journal.pone.0293053.Peer-Reviewed Original ResearchConceptsResting-state functional network connectivityFunctional network connectivityResting-state functional magnetic resonance imagingFunctional magnetic resonance imagingAlzheimer's diseaseClassification of schizophreniaNetwork pairsPatients to healthy controlsSchizophrenia patientsNeurobiological mechanismsSZ patientsSubcortical networksCerebellum networkSchizophreniaRs-fMRIDisorder developmentMotor networkCompare patient groupsSubcortical domainSZ disorderHealthy controlsMagnetic resonance imagingDisordersNetwork connectivityFunctional abnormalitiesSearching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities
Fu Z, Batta I, Wu L, Abrol A, Agcaoglu O, Salman M, Du Y, Iraji A, Shultz S, Sui J, Calhoun V. Searching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities. NeuroImage 2024, 292: 120617. PMID: 38636639, PMCID: PMC11416721, DOI: 10.1016/j.neuroimage.2024.120617.Peer-Reviewed Original ResearchConceptsFunctional MRIStructural MRIResting-state scanSpatial similarity analysisMental health researchBrain markersDiffusion MRIAge differencesBrain featuresNeuromarkersBrain disordersYoung adult cohortBrain developmentWell-replicatedHuman brainBrainDiffusion MRI dataData-driven analysisDisordersSimilarity analysisAge cohortsGeneralizabilityPopulation-based researchAdult cohortAge-specific adaptationInterpretable Cognitive Ability Prediction: A Comprehensive Gated Graph Transformer Framework for Analyzing Functional Brain Networks
Qu G, Orlichenko A, Wang J, Zhang G, Xiao L, Zhang K, Wilson T, Stephen J, Calhoun V, Wang Y. Interpretable Cognitive Ability Prediction: A Comprehensive Gated Graph Transformer Framework for Analyzing Functional Brain Networks. IEEE Transactions On Medical Imaging 2024, 43: 1568-1578. PMID: 38109241, PMCID: PMC11090410, DOI: 10.1109/tmi.2023.3343365.Peer-Reviewed Original ResearchConceptsGraph transformation frameworkBrain imaging datasetsFunctional brain networksPhiladelphia Neurodevelopmental CohortConvolutional deep learningFeature embeddingPropagation weightsGraph embeddingHuman Connectome ProjectAttention mechanismImage datasetsDeep learningGraph transformationFunctional connectivityAnalyze functional brain networksTransformation frameworkDiffusion strategyBrain networksPositional encodingSpatial knowledgePrediction accuracyIndividual cognitive abilitiesEmbeddingNetworkGraphMultimodal active subspace analysis for computing assessment oriented subspaces from neuroimaging data
Batta I, Abrol A, Calhoun V, Initiative A. Multimodal active subspace analysis for computing assessment oriented subspaces from neuroimaging data. Journal Of Neuroscience Methods 2024, 406: 110109. PMID: 38494061, PMCID: PMC11100582, DOI: 10.1016/j.jneumeth.2024.110109.Peer-Reviewed Original ResearchConceptsBrain subspacesStandard machine learning algorithmsHigh-dimensional neuroimaging dataTrain machine learning modelsUnsupervised decompositionMachine learning algorithmsMachine learning modelsFunctional sub-systemsSubspace analysisSubspace componentsLearning algorithmsSupervised approachBiological traitsLearning modelsSub-systemsAlzheimer's diseaseSubspaceComputational frameworkActive subspaceCross-validation procedureNeuroimaging dataAD-related brain regionsAutomated identificationPredictive performanceOrientation subspacesSMART (Splitting-Merging Assisted Reliable) Independent Component Analysis for Extracting Accurate Brain Functional Networks
He X, Calhoun V, Du Y. SMART (Splitting-Merging Assisted Reliable) Independent Component Analysis for Extracting Accurate Brain Functional Networks. Neuroscience Bulletin 2024, 40: 905-920. PMID: 38491231, DOI: 10.1007/s12264-024-01184-4.Peer-Reviewed Original ResearchConceptsIndependent component analysisFunctional magnetic resonance imagingClustering independent componentsFunctional networksIndependent component analysis methodMulti-subject fMRI dataIndependent componentsBrain functional networksFMRI dataSubject-specific functional networksFunctional magnetic resonance imaging dataOptimal model orderSmartComponent analysisReconfiguration of Structural and Functional Connectivity Coupling in Patient Subgroups With Adolescent Depression
Xu M, Li X, Teng T, Huang Y, Liu M, Long Y, Lv F, Zhi D, Li X, Feng A, Yu S, Calhoun V, Zhou X, Sui J. Reconfiguration of Structural and Functional Connectivity Coupling in Patient Subgroups With Adolescent Depression. JAMA Network Open 2024, 7: e241933. PMID: 38470418, PMCID: PMC10933730, DOI: 10.1001/jamanetworkopen.2024.1933.Peer-Reviewed Original ResearchConceptsAdolescent major depressive disorderMajor depressive disorderSC-FC couplingIncreased SC-FC couplingSC-FCMode networkSuicide attemptsFirst-episode major depressive disorderVisual networkMDD subgroupsNonsuicidal self-injurious behaviorRates of self-injuryHealthy controlsResting-state functional MRI dataMagnetic resonance imagingCross-sectional studySelf-injurious behaviorOutpatient psychiatry clinicFunctional MRI dataMajor life eventsFirst Affiliated Hospital of Chongqing Medical UniversityDepressive disorderNeurobiological mechanismsChildhood traumaSelf-injuryA whole-brain neuromark resting-state fMRI analysis of first-episode and early psychosis: Evidence of aberrant cortical-subcortical-cerebellar functional circuitry
Jensen K, Calhoun V, Fu Z, Yang K, Faria A, Ishizuka K, Sawa A, Andrés-Camazón P, Coffman B, Seebold D, Turner J, Salisbury D, Iraji A. A whole-brain neuromark resting-state fMRI analysis of first-episode and early psychosis: Evidence of aberrant cortical-subcortical-cerebellar functional circuitry. NeuroImage Clinical 2024, 41: 103584. PMID: 38422833, PMCID: PMC10944191, DOI: 10.1016/j.nicl.2024.103584.Peer-Reviewed Original ResearchConceptsFunctional network connectivityFirst-episodeEarly psychosisAberrant functional network connectivityResting-state functional magnetic resonance imagingFunctional magnetic resonance imagingCorrelates of psychosisResting-state fMRI analysisWhole-brain approachPsychiatric disordersPsychiatric illnessSubcortical regionsCerebellar regionsFMRI analysisPsychosisControl participantsCognitive functionRs-fMRICerebellar connectivityMulti-site datasetFunctional circuitryMagnetic resonance imagingCircuitryResonance imagingProminent patternStriatum- and Cerebellum-Modulated Epileptic Networks Varying Across States with and without Interictal Epileptic Discharges
Jiang S, Pei H, Chen J, Li H, Liu Z, Wang Y, Gong J, Wang S, Li Q, Duan M, Calhoun V, Yao D, Luo C. Striatum- and Cerebellum-Modulated Epileptic Networks Varying Across States with and without Interictal Epileptic Discharges. International Journal Of Neural Systems 2024, 34: 2450017. PMID: 38372049, DOI: 10.1142/s0129065724500175.Peer-Reviewed Original ResearchConceptsSalience networkSensorimotor cortexFunctional magnetic resonance imaging dataModerating effectInterictal epileptic dischargesIdiopathic generalized epilepsyMagnetic resonance imaging dataInteraction of regionsDecreased connectivityStriatumDMNThalamocortical circuitsCortical interactionsSimultaneous electroencephalogramCortical targetsEpileptic dischargesCerebellumThalamusHierarchical connectionEpileptic networkNeuromodulation techniquesIndirect moderating effectStateCryptogenic etiologyIntra-Atlas Node Size Effects on Graph Metrics in fMRI Data: Implications for Alzheimer’s Disease and Cognitive Impairment
Kolla S, Falakshahi H, Abrol A, Fu Z, Calhoun V. Intra-Atlas Node Size Effects on Graph Metrics in fMRI Data: Implications for Alzheimer’s Disease and Cognitive Impairment. Sensors 2024, 24: 814. PMID: 38339531, PMCID: PMC10857295, DOI: 10.3390/s24030814.Peer-Reviewed Original ResearchConceptsGraph metricsFunctional network connectivityIndependent component analysisResting state fMRI dataData-driven methodologyNetwork connectivityNovel metricFunctional nodesNode sizeNodesLocal graph metricsMetricsNode dimensionsGraphAlzheimer's diseaseMild cognitive impairmentNetwork neuroscienceNeuroimaging researchNeuroimaging investigationsRevealing complex functional topology brain network correspondences between humans and marmosets
Li Q, Calhoun V, Iraji A. Revealing complex functional topology brain network correspondences between humans and marmosets. Neuroscience Letters 2024, 822: 137624. PMID: 38218321, DOI: 10.1016/j.neulet.2024.137624.Peer-Reviewed Original ResearchConceptsWhole-brain functional connectivityFunctional brain connectivityDorsal attention networkFunctional connectivity patternsBrain connectivityMarmoset monkey brainBrain networksTopological characteristicsMode networkFunctional connectivityCognitive functionVisual networkNon-human primatesMonkey brainAttention networkConnectivity patternsNeural connectionsBrainFunctional correspondenceConnectome
2023
Dynamic functional network connectivity based on spatial source phase maps of complex-valued fMRI data: Application to schizophrenia
Li W, Lin Q, Zhao B, Kuang L, Zhang C, Han Y, Calhoun V. Dynamic functional network connectivity based on spatial source phase maps of complex-valued fMRI data: Application to schizophrenia. Journal Of Neuroscience Methods 2023, 403: 110049. PMID: 38151187, DOI: 10.1016/j.jneumeth.2023.110049.Peer-Reviewed Original ResearchConceptsSchizophrenia patientsFMRI dataFunctional network connectivityHealthy controlsDynamic functional network connectivityPsychotic diagnosesMental disordersSchizophreniaComplex-valued fMRI dataPotential imaging biomarkersDetect functional alterationsFMRIState transitionsNetwork connectivityPhase informationFunctional alterationsComplex valuesBrain informationMutual informationDynamicsPhase