2025
Predicting tumor recurrence site after reirradiation in head and neck cancer: a retrospective external validation of a published [18F]-FDG PET radiomic signature
Beddok A, Grogg K, Nioche C, Rozenblum L, Orlhac F, Calugaru V, Crehange G, Shih H, Marin T, Buvat I, El Fakhri G. Predicting tumor recurrence site after reirradiation in head and neck cancer: a retrospective external validation of a published [18F]-FDG PET radiomic signature. La Radiologia Medica 2025, 1-10. PMID: 40833475, DOI: 10.1007/s11547-025-02072-1.Peer-Reviewed Original ResearchHead and neck cancerPET radiomics signaturePositive predictive valueNeck cancerRadiomics signatureRecurrent head and neck cancerExternal cohortTumor recurrence siteDose escalationLocoregional failurePET radiomicsRecurrence siteMassachusetts General HospitalLIFEx softwareIndependent cohortRadiomic featuresOriginal cutoffPatientsPredictive valuePublished cutoffsPurposeThis studyCohortGeneral HospitalRecurrenceConclusionThe studyClinical validation of a multi-modal Ataraxis AI platform for recurrence prediction in early-stage breast cancer across multiple patient cohorts.
Witowski J, Choucair K, Elayoubi J, Chiru E, Chan N, Kang Y, Howard F, Ostrovnaya I, Schnabel F, Abdulsattar W, Zong Y, Daoud L, Vetter M, Pan J, Laurinavičius A, Piening B, Bifulco C, Brufsky A, Esteva F, Pusztai L. Clinical validation of a multi-modal Ataraxis AI platform for recurrence prediction in early-stage breast cancer across multiple patient cohorts. Journal Of Clinical Oncology 2025, 43: 549-549. DOI: 10.1200/jco.2025.43.16_suppl.549.Peer-Reviewed Original ResearchDisease-free intervalOncotype DXBreast cancer recurrenceClinical characteristicsBreast cancerC-indexHazard ratioCancer recurrenceStage I–III BC patientsEarly-stage breast cancerMultiple patient cohortsHarrell's C-indexDuctal histologyER/PR/HER2 statusHER2+BC subtypesBC patientsPatient cohortValidation cohortTNM stagePrediction of breast cancer recurrenceClinical variablesExternal cohortH&E slidesMultivariate analysisCharacterizing the ADPKD-IFT140 Phenotypic Signature With Deep Learning and Advanced Imaging Biomarkers
Ghanem A, Debeh F, Borghol A, Zagorec N, Tapia A, Smith B, Paul S, Basit A, AlKhatib B, Nader N, Antoun M, Gregory A, Yang H, Schauer R, Dahl N, Hanna C, Torres V, Kline T, Harris P, Gall E, Chebib F. Characterizing the ADPKD-IFT140 Phenotypic Signature With Deep Learning and Advanced Imaging Biomarkers. Kidney International Reports 2025, 10: 2690-2707. PMID: 40814641, PMCID: PMC12348249, DOI: 10.1016/j.ekir.2025.04.062.Peer-Reviewed Original ResearchArea under the curveHeight-adjusted total kidney volumeAutosomal dominant polycystic kidney diseaseEstimated glomerular filtrationDisease-causing variantsDevelopment cohortAdvanced imaging biomarkersTotal kidney volumeDominant polycystic kidney diseaseRetrospective cohort studyPolycystic kidney diseaseClinical presentationCyst volumeKidney volumeCyst diameterCystic indexDiverse clinical settingsLiver cystsCohort studyExternal cohortKidney diseaseLarge cystsInternational cohortGlomerular filtrationPatients
2024
Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial
Rediti M, Venet D, Joaquin Garcia A, Maetens M, Vincent D, Majjaj S, El-Abed S, Di Cosimo S, Ueno T, Izquierdo M, Piccart M, Pusztai L, Loi S, Salgado R, Viale G, Rothé F, Sotiriou C. Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial. Nature Communications 2024, 15: 10402. PMID: 39613746, PMCID: PMC11607438, DOI: 10.1038/s41467-024-54621-3.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBiomarkers, TumorBreast NeoplasmsClinical Trials, Phase III as TopicFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMiddle AgedNeoplasm Recurrence, LocalPrognosisRandomized Controlled Trials as TopicReceptor, ErbB-2TrastuzumabTumor MicroenvironmentConceptsHER2-positive breast cancerMolecular subtypesBreast cancerRate of pathological complete responseSensitive to HER2-targeted therapiesClinical trialsRisk of distant recurrenceBreast cancer molecular subtypesPathological complete responseHER2-Targeted TherapyCancer molecular subtypesPotential clinical implicationsNeoALTTO trialDistant recurrenceComplete responseAdjuvant trastuzumabPrognostic/predictive valueHeterogeneous biologySurvival outcomesI-SPY2Clinical outcomesMicroenvironment featuresGene expression profilesExternal cohortTumor
2023
Time and event-specific deep learning for personalized risk assessment after cardiac perfusion imaging
Pieszko K, Shanbhag A, Singh A, Hauser M, Miller R, Liang J, Motwani M, Kwieciński J, Sharir T, Einstein A, Fish M, Ruddy T, Kaufmann P, Sinusas A, Miller E, Bateman T, Dorbala S, Di Carli M, Berman D, Dey D, Slomka P. Time and event-specific deep learning for personalized risk assessment after cardiac perfusion imaging. Npj Digital Medicine 2023, 6: 78. PMID: 37127660, PMCID: PMC10151323, DOI: 10.1038/s41746-023-00806-x.Peer-Reviewed Original ResearchAcute coronary syndromeMajor adverse cardiovascular eventsMyocardial perfusion imagingCause deathAdverse cardiovascular eventsModifiable risk factorsPrediction of deathPersonalized risk assessmentCardiovascular eventsCoronary syndromeClinical featuresPrognostic valueRisk factorsExternal cohortStandard clinical interpretationPerfusion imagingAbnormality measuresCardiac perfusionTime pointsPatients' explanationsClinical interpretationExternal validationDeathPatientsRisk assessmentUnsupervised learning to characterize patients with known coronary artery disease undergoing myocardial perfusion imaging
Williams M, Bednarski B, Pieszko K, Miller R, Kwiecinski J, Shanbhag A, Liang J, Huang C, Sharir T, Dorbala S, Di Carli M, Einstein A, Sinusas A, Miller E, Bateman T, Fish M, Ruddy T, Acampa W, Hauser M, Kaufmann P, Dey D, Berman D, Slomka P. Unsupervised learning to characterize patients with known coronary artery disease undergoing myocardial perfusion imaging. European Journal Of Nuclear Medicine And Molecular Imaging 2023, 50: 2656-2668. PMID: 37067586, PMCID: PMC10317876, DOI: 10.1007/s00259-023-06218-z.Peer-Reviewed Original ResearchConceptsCoronary artery diseaseMyocardial perfusion imagingCause mortalityTotal perfusion deficitArtery diseaseRisk stratificationPerfusion deficitsHigher Body Mass IndexTomography myocardial perfusion imagingMore diabetes mellitusSPECT myocardial perfusion imagingBetter risk stratificationRisk-stratify patientsBody mass indexREFINE SPECT registrySingle photon emissionDiabetes mellitusMass indexExternal cohortStress imagingMyocardial perfusionPatientsRisk phenotypePerfusion imagingImaging characteristicsDevelopment and external validation of machine learning algorithms for postnatal gestational age estimation using clinical data and metabolomic markers
Hawken S, Ducharme R, Murphy M, Olibris B, Bota A, Wilson L, Cheng W, Little J, Potter B, Denize K, Lamoureux M, Henderson M, Rittenhouse K, Price J, Mwape H, Vwalika B, Musonda P, Pervin J, Chowdhury A, Rahman A, Chakraborty P, Stringer J, Wilson K. Development and external validation of machine learning algorithms for postnatal gestational age estimation using clinical data and metabolomic markers. PLOS ONE 2023, 18: e0281074. PMID: 36877673, PMCID: PMC9987787, DOI: 10.1371/journal.pone.0281074.Peer-Reviewed Original ResearchConceptsGestational ageCord blood dataClinical dataBlood dataMetabolomic markersEarly pregnancy ultrasoundHeel-prick blood sampleProspective birth cohortMultivariable linear regressionBlood sample dataExternal validationGestational age estimationRetrospective cohortPregnancy ultrasoundHeel prickExternal cohortIndependent cohortBlood samplesBirth cohortNewbornsPostnatal gestational age estimationCohortUltrasound estimatesInternal model validationLow-income countries
2022
Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae
Thompson R, Simons N, Wilkins L, Cheng E, Del Valle D, Hoffman G, Cervia C, Fennessy B, Mouskas K, Francoeur N, Johnson J, Lepow L, Le Berichel J, Chang C, Beckmann A, Wang Y, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo M, Yuan D, Huckins L, Roussos P, Marron T, Glicksberg B, Nadkarni G, Heath J, Gonzalez-Kozlova E, Boyman O, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt E, Charney A, Beckmann N. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nature Medicine 2022, 29: 236-246. PMID: 36482101, PMCID: PMC9873574, DOI: 10.1038/s41591-022-02107-4.Peer-Reviewed Original ResearchConceptsImmunoglobulin-related genesPost-acute sequelaeAdaptive immune cellsTiter-dependent mannerLong-term sequelaeGene expression signaturesSARS-CoV-2 infectionAcute COVID-19Acute host responseImmune cellsAcute infectionSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2External cohortMultiple etiologiesSequelaePost-acute sequelae of severe acute respiratory syndrome coronavirus 2Molecular etiologyTranscriptome-wide investigationSyndrome coronavirus 2Expression signaturesHost responseAntibody productionGene expression patternsCT angiographic radiomics signature for risk stratification in anterior large vessel occlusion stroke
Avery EW, Behland J, Mak A, Haider SP, Zeevi T, Sanelli PC, Filippi CG, Malhotra A, Matouk CC, Griessenauer CJ, Zand R, Hendrix P, Abedi V, Falcone GJ, Petersen N, Sansing LH, Sheth KN, Payabvash S. CT angiographic radiomics signature for risk stratification in anterior large vessel occlusion stroke. NeuroImage Clinical 2022, 34: 103034. PMID: 35550243, PMCID: PMC9108990, DOI: 10.1016/j.nicl.2022.103034.Peer-Reviewed Original ResearchConceptsLarge vessel occlusion strokeIndependent cohortPrognostication toolsMechanical thrombectomyRisk stratificationOcclusion strokeExternal cohortAnterior circulation large vessel occlusion strokeOutcome predictionAcute stroke triageAnterior circulation territoryRadiomic featuresTime of admissionGeisinger Medical CenterLVO stroke patientsReliable clinical informationSignificant differencesAdmission CTAStroke patientsPrognostic informationFavorable outcomeStroke triageTreatment decisionsMedical CenterRadiomics signature
2021
Machine learning implicates the IL-18 signaling axis in severe asthma
Camiolo MJ, Zhou X, Wei Q, Bittar H, Kaminski N, Ray A, Wenzel S. Machine learning implicates the IL-18 signaling axis in severe asthma. JCI Insight 2021, 6: e149945. PMID: 34591794, PMCID: PMC8663569, DOI: 10.1172/jci.insight.149945.Peer-Reviewed Original ResearchConceptsLung functionIL-18NF-κBTranscriptional hallmarksExacerbation-prone asthmaSevere asthma pathogenesisSubgroup of patientsVariable natural historySevere Asthma Research Program (SARP) cohortDownstream NF-κBMixed inflammatory processActivator protein-1 (AP-1) activationPathobiological underpinningsCorticosteroid exposureSevere asthmaAsthma clustersAsthma pathogenesisPatient morbidityInflammatory processProtein-1 activationExternal cohortLung tissuePatient clustersAP-1 activityNatural historyProgressive immune dysfunction with advancing disease stage in renal cell carcinoma
Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell 2021, 39: 632-648.e8. PMID: 33711273, PMCID: PMC8138872, DOI: 10.1016/j.ccell.2021.02.013.Peer-Reviewed Original ResearchConceptsClear cell renal cell carcinomaM2-like macrophagesRenal cell carcinomaAdvanced diseaseExhausted CD8Cell carcinomaDisease stageAdvanced/metastaticImmune inhibitory pathwaysProgressive immune dysfunctionCell renal cell carcinomaAdjacent non-tumor tissuesTumor immune microenvironmentPro-inflammatory macrophagesM2-like polarizationNon-tumor tissuesMetastatic diseaseImmune dysfunctionWorse prognosisImmune microenvironmentImmune cellsCell dysfunctionExternal cohortInhibitory pathwaysMyeloid compartment
2020
PET/CT radiomics signature of human papilloma virus association in oropharyngeal squamous cell carcinoma
Haider SP, Mahajan A, Zeevi T, Baumeister P, Reichel C, Sharaf K, Forghani R, Kucukkaya AS, Kann BH, Judson BL, Prasad ML, Burtness B, Payabvash S. PET/CT radiomics signature of human papilloma virus association in oropharyngeal squamous cell carcinoma. European Journal Of Nuclear Medicine And Molecular Imaging 2020, 47: 2978-2991. PMID: 32399621, DOI: 10.1007/s00259-020-04839-2.Peer-Reviewed Original ResearchConceptsOropharyngeal squamous cell carcinomaMetastatic cervical lymph nodesCervical lymph nodesLymph nodesSquamous cell carcinomaPrimary tumorPET/CTHPV associationCell carcinomaRadiomics signatureVolume of interestHuman papilloma virus associationHuman papillomavirus associationMulti-national cohortNon-contrast CTHPV statusFDG-PETExternal cohortVirus associationFinal modelTumorsRadiomic featuresCTSignificant differencesLesion features
2017
White Blood Count, Albumin, and BMI Enhance VACS Index Prognostic Model, but Nadir CD4 and CD8 Metrics Do Not
Tate J, Brown S, Gibert C, Goetz M, Marconi V, Oursler K, Rimland D, Rodriguez-Barradas M, Justice A. White Blood Count, Albumin, and BMI Enhance VACS Index Prognostic Model, but Nadir CD4 and CD8 Metrics Do Not. Open Forum Infectious Diseases 2017, 4: s210-s210. PMCID: PMC5631891, DOI: 10.1093/ofid/ofx163.415.Peer-Reviewed Original ResearchWhite blood countAbsolute neutrophil countBody mass indexNadir CD4VACS IndexBlood countC-statisticVeterans Aging Cohort Study (VACS) IndexCD4/CD8 ratioLong-term viral suppressionKaplan-Meier plotsAvailable clinical dataDeciles of riskART initiationCD8 ratioViral suppressionNeutrophil countMass indexVA careClinical managementDisease burdenClinical dataExternal cohortLaboratory valuesRisk score
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