2022
Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study
Nguyen N, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai P, Boland B, Mahadevan U, Sandborn W, Ohno-Machado L, McGovern D, Singh S. Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Clinical Gastroenterology And Hepatology 2022, 21: 173-181.e5. PMID: 35644340, PMCID: PMC9701245, DOI: 10.1016/j.cgh.2022.05.008.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseNon-Hispanic patientsBiologic-treated patientsHispanic patientsSerious infectionsBiologic therapyBowel diseasePropensity score-matched cohortBurden of inflammationRisk of hospitalizationHigh ratePropensity-score matchingCause hospitalizationAdult patientsBiologic initiationCohort studyBiologic agentsMedication useHigh burdenHigh riskHospitalizationPatientsSurvival analysisSurgeryAbstractTextProtein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis
Povero D, Tameda M, Eguchi A, Ren W, Kim J, Myers R, Goodman Z, Harrison S, Sanyal A, Bosch J, Ohno-Machado L, Feldstein A. Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. Scientific Reports 2022, 12: 3027. PMID: 35194091, PMCID: PMC8863778, DOI: 10.1038/s41598-022-06809-0.Peer-Reviewed Original ResearchConceptsSmall non-coding RNAsExtracellular vesiclesNon-coding RNAsNovel miRNAsControl subjectsFurther molecular characterizationMiRNA sequence analysisLiver-specific markersProtein profilingMiRNA cargoMolecular characterizationHuman diseasesCurrent serum markersNovel surrogate biomarkersPrimary sclerosing cholangitisCholestatic liver diseaseHealthy control subjectsMiRNA profilesProteinCell specificityDifferential centrifugationMiRNAsPSC patientsSclerosing cholangitisLiver disease
2021
Privacy-protecting, reliable response data discovery using COVID-19 patient observations
Kim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.Peer-Reviewed Original ResearchKawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic Profiles
Jackson H, Menikou S, Hamilton S, McArdle A, Shimizu C, Galassini R, Huang H, Kim J, Tremoulet A, Thorne A, Fischer R, de Jonge M, Kuijpers T, Wright V, Burns J, Casals-Pascual C, Herberg J, Levin M, Kaforou M, On Behalf Of The Perform Consortium. Kawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic Profiles. International Journal Of Molecular Sciences 2021, 22: 5655. PMID: 34073389, PMCID: PMC8198135, DOI: 10.3390/ijms22115655.Peer-Reviewed Original ResearchConceptsKawasaki diseaseViral infectionHost responseKD patientsAcute inflammatory disordersAnti-bacterial responsePathway analysisBacterial patientsInflammatory disordersInflammatory responsePatient stratificationCommon triggerPatientsKD samplesHost transcriptomicsInfectionProteomic profilesOmics profilesDifferent triggersDiagnostic signatureResponseInflammationTriggersLevelsEtiologyPredictive Analytics for Glaucoma Using Data From the All of Us Research Program
Baxter S, Saseendrakumar B, Paul P, Kim J, Bonomi L, Kuo T, Loperena R, Ratsimbazafy F, Boerwinkle E, Cicek M, Clark C, Cohn E, Gebo K, Mayo K, Mockrin S, Schully S, Ramirez A, Ohno-Machado L, Investigators A. Predictive Analytics for Glaucoma Using Data From the All of Us Research Program. American Journal Of Ophthalmology 2021, 227: 74-86. PMID: 33497675, PMCID: PMC8184631, DOI: 10.1016/j.ajo.2021.01.008.Peer-Reviewed Original ResearchConceptsGlaucoma surgeryPrimary open-angle glaucomaOphthalmic researchSingle-center cohortElectronic health record dataMultivariable logistic regressionSingle-center dataOpen-angle glaucomaHealth record dataMean ageClaims dataUs Research ProgramLogistic regressionSurgeryRecord dataOphthalmic imagingCharacteristic curveExternal validationGlaucomaCohortAUCSingle-center model
2020
Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1
Rawat P, Brummel S, Singh K, Kim J, Frazer K, Nichols S, Seage G, Williams P, Van Dyke R, Harismendy O, Trout R, Spector S. Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1. The Journal Of Infectious Diseases 2020, 224: 870-880. PMID: 33373444, PMCID: PMC8408770, DOI: 10.1093/infdis/jiaa792.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsChildChild, PreschoolFemaleGenome-Wide Association StudyGenomicsHIV InfectionsHIV-1HumansInfantInfectious Disease Transmission, VerticalInflammasomesInflammationIntracellular Signaling Peptides and ProteinsMaleMembrane ProteinsMicrogliaNeurocognitive DisordersReceptors, CCRConceptsWhole-exome sequencingValidation cohortNeurocognitive impairmentOdds ratioRisk of NCIHuman immunodeficiency virus type 1Immunodeficiency virus type 1Single nucleotide variantsAdjusted odds ratioIL-1β releaseVirus type 1Microglial releaseIL-1βHuman microgliaDecreased oddsType 1Logistic regressionCognitive scoresCCRL2MicrogliaFurther studiesHIVInflammationCsACohortNo benefit of continuing vs stopping 5‐aminosalicylates in patients with ulcerative colitis escalated to anti‐metabolite therapy
Singh S, Kim J, Zhu W, Dulai P, Sandborn W, Jairath V. No benefit of continuing vs stopping 5‐aminosalicylates in patients with ulcerative colitis escalated to anti‐metabolite therapy. Alimentary Pharmacology & Therapeutics 2020, 52: 481-491. PMID: 32573825, PMCID: PMC8015755, DOI: 10.1111/apt.15876.Peer-Reviewed Original ResearchConceptsAnti-metabolite therapyUlcerative colitisCorticosteroid useRisk of UCCox proportional hazards analysisAdministrative claims databaseEmergency department visitsProportional hazards analysisComorbidity burdenTreatment escalationBiologic therapyAbdominal surgeryDepartment visitsClinical benefitClaims databaseResidual confoundingHigh riskPatientsDisease severityMonotherapyTherapyHospitalisationColitisSurgeryMonthsComprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice
Eguchi A, Yan R, Pan S, Wu R, Kim J, Chen Y, Ansong C, Smith R, Tempaku M, Ohno-Machado L, Takei Y, Feldstein A, Tsukamoto H. Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice. Journal Of Molecular Medicine 2020, 98: 1021-1034. PMID: 32556367, PMCID: PMC7810220, DOI: 10.1007/s00109-020-01926-7.Peer-Reviewed Original ResearchConceptsHepatic stellate cellsAlcoholic liver diseaseAlcoholic hepatitisAH miceIL-1βHepatic macrophagesStellate cellsExtracellular vesiclesPrimary hepatic stellate cellsIL-17 upregulationIL-17 productionUpregulated IL-1βHepatocyte-derived extracellular vesiclesNovel murine modelTLR9-dependent mannerMacrophage IL-1βHepatitis miceIL-17Liver diseaseControl miceCytokine productionLiver pathologyLiver fibrogenesisMurine modelΑ-SMA
2019
Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research
Kim J, Kim H, Bell E, Bath T, Paul P, Pham A, Jiang X, Zheng K, Ohno-Machado L. Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research. JAMA Network Open 2019, 2: e199550. PMID: 31433479, PMCID: PMC6707015, DOI: 10.1001/jamanetworkopen.2019.9550.Peer-Reviewed Original ResearchHuman induced pluripotent stem cell-derived extracellular vesicles reduce hepatic stellate cell activation and liver fibrosis
Povero D, Pinatel E, Leszczynska A, Goyal N, Nishio T, Kim J, Kneiber D, de Araujo Horcel L, Eguchi A, Ordonez P, Kisseleva T, Feldstein A. Human induced pluripotent stem cell-derived extracellular vesicles reduce hepatic stellate cell activation and liver fibrosis. JCI Insight 2019, 5 PMID: 31184999, PMCID: PMC6675559, DOI: 10.1172/jci.insight.125652.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisCell MovementCell ProliferationChemical and Drug Induced Liver InjuryChemotaxisDisease Models, AnimalExtracellular VesiclesHepatic Stellate CellsHumansInduced Pluripotent Stem CellsLiverLiver CirrhosisMaleMiceMice, Inbred C57BLMicroRNAsTranscriptomeTransforming Growth Factor betaConceptsHepatic stellate cell activationChronic liver diseaseAnti-fibrotic effectsStellate cell activationLiver fibrosisLiver diseaseExtracellular vesiclesInduced pluripotent stem cellsCell activationDuct ligation-induced liver fibrosisFlow cytometryAnti-fibrotic approachesDevelopment of cirrhosisPro-fibrogenic responseProgression of fibrosisStem cell-derived extracellular vesiclesAnti-fibrotic strategiesCharacterization of iPSCsGreatest unmet needCell-derived extracellular vesiclesMiR-92a-3pWound healing responseStem cellsIPSC-EVsLiver injury
2018
Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki disease
Oyamada J, Shimizu C, Kim J, Williams M, Png E, Hibberd M, Tremoulet A, Perry J, Burns J. Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki disease. Congenital Heart Disease 2018, 14: 213-220. PMID: 30395415, DOI: 10.1111/chd.12696.Peer-Reviewed Original ResearchConceptsBifid T wavesKawasaki diseaseT-wave morphologyKD subjectsT waveIndependent cohortKD susceptibilityAcute KD subjectsAcute Kawasaki diseaseSelf-limited vasculitisSubunit geneGenetic variantsGenotype/phenotype association studiesWide association study dataGenome-wide association study dataIntracellular calcium signalingPhenotype association studiesWave morphologyAssociation study dataCalcium channel geneCommon causeCardiac repolarizationMyocardial repolarizationCardiac diseaseAbnormal repolarization
2017
A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries
Gabriel R, Waterman R, Kim J, Ohno-Machado L. A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries. Anesthesia & Analgesia 2017, 124: 1529-1536. PMID: 28079580, DOI: 10.1213/ane.0000000000001827.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAge FactorsAgedAged, 80 and overAmbulatory Surgical ProceduresAnesthesiaChildChild, PreschoolCritical CareFemaleForecastingHumansHypertensionInfantInfant, NewbornIntensive Care UnitsLength of StayLogistic ModelsMaleMiddle AgedModels, StatisticalObesity, MorbidPostoperative CareRisk FactorsROC CurveYoung AdultConceptsPACU lengthPostanesthesia care unit lengthPrimary anesthesia typePostanesthesia care unitHosmer-Lemeshow testLogistic regression modelsAnesthesia typeMorbid obesityCare unitHL testOutpatient surgeryOutpatient procedureSingle institutionHigher oddsNonsignificant P valuesStayPatientsSurgical specialtiesROC curveGood calibrationCharacteristic curveExcellent discriminationAUC valuesP-valueBackward eliminationA risk prediction score for acute kidney injury in the intensive care unit
Malhotra R, Kashani K, Macedo E, Kim J, Bouchard J, Wynn S, Li G, Ohno-Machado L, Mehta R. A risk prediction score for acute kidney injury in the intensive care unit. Nephrology Dialysis Transplantation 2017, 32: 814-822. PMID: 28402551, DOI: 10.1093/ndt/gfx026.Peer-Reviewed Original ResearchConceptsAcute kidney injuryIntensive care unitAcute risk factorsRisk score modelICU admissionKidney injuryCare unitValidation cohortKidney diseaseRisk factorsTest cohortTreatment of AKIAtherosclerotic coronary vascular diseaseMulticenter prospective cohort studyGlobal Outcomes criteriaChronic kidney diseaseHigh-risk patientsProspective cohort studyChronic liver diseaseCongestive heart failureTime of screeningCoronary vascular diseaseRisk prediction scoreEarly therapeutic interventionExternal validation cohortWhole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
Kim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.Peer-Reviewed Original ResearchConceptsWhole genome sequencesGenome-wide association studiesToll-like receptor 6Single nucleotide variantsCommon disease-rare variant hypothesisExpression quantitative trait loci (eQTL) analysisDifferential expressionQuantitative trait locus (QTL) analysisCommon disease–common variantPathogen-associated molecular pattern recognitionIntegrative genomics approachIntronic single nucleotide variantsComplex genetic diseasesSequence quality scoresMolecular pattern recognitionWhole-genome sequencingGenomic approachesTranscriptome dataGenome sequenceSequence variationLocus analysisGenome sequencingAssociation studiesFunction of genotypeNucleotide variants
2016
iCONCUR: informed consent for clinical data and bio-sample use for research
Kim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe S, Ohno-Machado L. iCONCUR: informed consent for clinical data and bio-sample use for research. Journal Of The American Medical Informatics Association 2016, 24: 380-387. PMID: 27589942, PMCID: PMC5391727, DOI: 10.1093/jamia/ocw115.Peer-Reviewed Original ResearchConceptsPatient preferencesClinical dataHuman immunodeficiency virus clinicInternal medicine clinicElectronic health record dataHealth record dataAcademic medical centerElectronic health recordsDe-identified dataOutpatient clinicMedicine clinicFamily historyMedical CenterInformed Consent ToolClinical settingClinicHealth recordsRecord dataInformed consent systemPatientsConsent toolRecipientsConsentE-consentParticipants
2015
Safety and efficacy of pharmacological thromboprophylaxis for hospitalized patients with cirrhosis: a single‐center retrospective cohort study
Shatzel J, Dulai P, Harbin D, Cheung H, Reid T, Kim J, James S, Khine H, Batman S, Whyman J, Dickson R, Ornstein D. Safety and efficacy of pharmacological thromboprophylaxis for hospitalized patients with cirrhosis: a single‐center retrospective cohort study. Journal Of Thrombosis And Haemostasis 2015, 13: 1245-1253. PMID: 25955079, PMCID: PMC6658183, DOI: 10.1111/jth.13000.Peer-Reviewed Original ResearchMeSH KeywordsAcademic Medical CentersAgedAnticoagulantsDrug Administration ScheduleFemaleGastrointestinal HemorrhageHeparin, Low-Molecular-WeightHospitalizationHumansLength of StayLiver CirrhosisMaleMiddle AgedNew HampshireOdds RatioRetrospective StudiesRisk FactorsTertiary Care CentersTime FactorsTreatment OutcomeVenous ThromboembolismConceptsLow molecular weight heparinHospital bleeding eventsRetrospective cohort studyMolecular weight heparinVTE prophylaxisVenous thromboembolismBleeding eventsPharmacological thromboprophylaxisCirrhotic patientsCohort studyUnfractionated heparinWeight heparinSingle-center retrospective cohort studyEnd-stage liver disease (MELD) scoreAcademic tertiary care referral centerRate of VTETertiary care referral centerRisk of VTEGastrointestinal bleeding eventsHospitalized cirrhotic patientsNew VTE eventsPharmacological VTE prophylaxisLiver Disease scoreHospital bleedingVTE events
2014
Reducing Communication Delays and Improving Quality of Care with a Tuberculosis Laboratory Information System in Resource Poor Environments: A Cluster Randomized Controlled Trial
Blaya J, Shin S, Yagui M, Contreras C, Cegielski P, Yale G, Suarez C, Asencios L, Bayona J, Kim J, Fraser H. Reducing Communication Delays and Improving Quality of Care with a Tuberculosis Laboratory Information System in Resource Poor Environments: A Cluster Randomized Controlled Trial. PLOS ONE 2014, 9: e90110. PMID: 24721980, PMCID: PMC3982951, DOI: 10.1371/journal.pone.0090110.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAntitubercular AgentsClinical Laboratory Information SystemsCommunicationDatabases, FactualDeveloping CountriesFemaleHumansLaboratoriesMaleMedical ErrorsMicrobial Sensitivity TestsMiddle AgedPeruPovertyProportional Hazards ModelsProspective StudiesQuality ImprovementQuality of Health CareResearch DesignTreatment OutcomeTuberculosisTuberculosis, Multidrug-ResistantYoung AdultConceptsIntervention health centersHealth centersDrug susceptibility testLaboratory information systemMDR-TB risk factorsMulti-drug resistant tuberculosisMDR-TB patientsPrimary health centersMain outcome measuresCulture convertCulture conversionResistant tuberculosisRisk factorsPatient outcomesClinical impactOutcome measuresDays less timePatientsPatient treatmentStudy designSusceptibility testsBaseline dataTrialsOnly studyTreatment
2013
Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)
Lin K, Tharp M, Conway M, Hsieh A, Ross M, Kim J, Kim H. Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP). PLOS ONE 2013, 8: e76384. PMID: 24058713, PMCID: PMC3776754, DOI: 10.1371/journal.pone.0076384.Peer-Reviewed Original ResearchComparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis.
Thawait S, Kim J, Klufas R, Morrison W, Flanders A, Carrino J, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. American Journal Of Roentgenology 2013, 200: 493-502. PMID: 23436836, DOI: 10.2214/ajr.11.7192.Peer-Reviewed Original ResearchAdultAgedAged, 80 and overAlgorithmsCohort StudiesComputer SimulationDiagnosis, DifferentialFemaleFractures, CompressionHumansImage EnhancementImage Interpretation, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedModels, BiologicalNeoplasmsPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySpinal FracturesYoung Adult
2010
Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer.
Sadow C, Wheeler S, Kim J, Ohno-Machado L, Silverman S. Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer. American Journal Of Roentgenology 2010, 195: w337-43. PMID: 20966298, DOI: 10.2214/ajr.09.4147.Peer-Reviewed Original ResearchConceptsUpper tract urothelial cancerPositive predictive valueUrothelial cancerUrine cytologyCT urographyPredictive valueUrographic examinationUrothelial thickeningExact testUpper tract urothelial malignanciesMultivariate logistic regression analysisPositive urine cytologyRecords of patientsSignificant univariate predictorsLogistic regression analysisFisher's exact testT-testStudent's t-testEffect of ageFollowup imagingRetrospective reviewPathologic examinationUrothelial malignancyUnivariate predictorsMimic cancer