2022
Joint spectral quantification of MR spectroscopic imaging using linear tangent space alignment‐based manifold learning
Ma C, Han P, Zhuo Y, Djebra Y, Marin T, Fakhri G. Joint spectral quantification of MR spectroscopic imaging using linear tangent space alignment‐based manifold learning. Magnetic Resonance In Medicine 2022, 89: 1297-1313. PMID: 36404676, PMCID: PMC9892363, DOI: 10.1002/mrm.29526.Peer-Reviewed Original ResearchConceptsSubspace-based methodsManifold learningIntrinsic low-dimensional structureGlobal coordinationLearning-based methodsNumerical simulation dataSpatial smoothness constraintSparsity constraintSpace alignmentSubspace modelSmoothness constraintSuperior performanceRoot mean square errorLinear transformationMechanical simulationsLow-dimensionalSquare errorSubspaceExperimental dataSpectroscopic imagingQuantum mechanical simulationsCoordinate alignmentMR spectroscopic imagingSpectral quantificationSimulated data
2021
Free‐breathing 3D cardiac T1 mapping with transmit B1 correction at 3T
Han P, Marin T, Djebra Y, Landes V, Zhuo Y, Fakhri G, Ma C. Free‐breathing 3D cardiac T1 mapping with transmit B1 correction at 3T. Magnetic Resonance In Medicine 2021, 87: 1832-1845. PMID: 34812547, PMCID: PMC8810588, DOI: 10.1002/mrm.29097.Peer-Reviewed Original ResearchConceptsFlip-angle estimationCardiac T<sub>1</sub> mappingGradient echo readoutThrough-plane spatial resolutionImaging timePractical imaging timesFree breathingPhantom studyB1 correctionAccelerated imagingIn-planeT)-spaceMyocardial T<sub>1</sub> valuesSubspace-based methodsSpatial resolutionImaging experimentsAcquisition schemeT)-space dataSubject-specific timeCorrectionModified Look-Locker inversion recoveryLook-Locker inversion recoveryTime of data acquisitionAverage imaging timeInversion-recovery sequenceDeep learning-based GTV contouring modeling inter- and intra- observer variability in sarcomas
Marin T, Zhuo Y, Lahoud R, Tian F, Ma X, Xing F, Moteabbed M, Liu X, Grogg K, Shusharina N, Woo J, Lim R, Ma C, Chen Y, El Fakhri G. Deep learning-based GTV contouring modeling inter- and intra- observer variability in sarcomas. Radiotherapy And Oncology 2021, 167: 269-276. PMID: 34808228, PMCID: PMC8934266, DOI: 10.1016/j.radonc.2021.09.034.Peer-Reviewed Original ResearchConceptsGross tumor volumeRadiation therapy treatment planningGross tumor volume contoursGross tumor volume delineationTherapy treatment planningIntra-observer variabilityConsensus contoursGTV contoursPre-operative CT imagesSoft tissue sarcomasRadiation oncologistsTumor volumeBone sarcomasTreatment planningAccurate contoursCT imagesDelineation procedureSarcomaSoft tissueConfidence levelRadiationPatientsHausdorff distanceMultiple contoursX-ray
2015
Subcellular and Dynamic Coordination between Src Activity and Cell Protrusion in Microenvironment
Zhuo Y, Qian T, Wu Y, Seong J, Gong Y, Ma H, Wang Y, Lu S. Subcellular and Dynamic Coordination between Src Activity and Cell Protrusion in Microenvironment. Scientific Reports 2015, 5: 12963. PMID: 26261043, PMCID: PMC4531316, DOI: 10.1038/srep12963.Peer-Reviewed Original ResearchConceptsSrc kinase activitySrc activationKinase activityFluorescence resonance energy transfer (FRET)-based biosensorsInitiation of cell migrationNon-polarized cellsCoordinated molecular eventsAutomated computer image analysisMembrane protrusionsCell protrusionsCell polarityProtrusive edgesPolarized cellsMigration of endothelial cellsCell migrationSrcEndothelial cellsMolecular eventsSpatiotemporal coordinationSpatiotemporal controlEndothelial migrationCellsComputer image analysisCell edgeTumor micro-environment
2013
The Effect of Differentiation Induction on FAK and Src Activity in Live HMSCs Visualized by FRET
Liao X, Lu S, Wu Y, Xu W, Zhuo Y, Peng Q, Li B, Zhang L, Wang Y. The Effect of Differentiation Induction on FAK and Src Activity in Live HMSCs Visualized by FRET. PLOS ONE 2013, 8: e72233. PMID: 24015220, PMCID: PMC3754985, DOI: 10.1371/journal.pone.0072233.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCells, CulturedCSK Tyrosine-Protein KinaseEnzyme ActivationFeedback, PhysiologicalFluorescence Resonance Energy TransferFocal Adhesion Kinase 1HumansMesenchymal Stem CellsProto-Oncogene ProteinsProto-Oncogene Proteins p21(ras)Ras ProteinsSignal TransductionSrc-Family KinasesTissue EngineeringConceptsSrc activationCell differentiationStem cell differentiationInhibiting FAK activityStages of stem cell differentiationPlasma membrane of human mesenchymal stem cellsSrc biosensorFAK activationActivated FAKActivated SrcFate decisionsInduction reagentsFAKSrc signalingKinase activityPlasma membraneSrcRegulation mechanismLiving human mesenchymal stem cellsUp-regulatedHuman mesenchymal stem cellsDifferentiation inductionNeural inductionDifferentiationCellsAntagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2
Sun J, Lu S, Ouyang M, Lin L, Zhuo Y, Liu B, Chien S, Neel B, Wang Y. Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2. Nature Communications 2013, 4: 2037. PMID: 23792876, PMCID: PMC3777412, DOI: 10.1038/ncomms3037.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesEmbryo, MammalianExtracellular Signal-Regulated MAP KinasesFibroblastsFluorescence Resonance Energy TransferGenes, ReporterGRB2 Adaptor ProteinHEK293 CellsHumansKineticsMiceMolecular Sequence DataMutant ProteinsMutationPeptidesPhosphorylationPhosphotyrosineProtein BindingProtein ConformationProtein Tyrosine Phosphatase, Non-Receptor Type 11ConceptsCis-interactionsSH2 domainC-terminal phosphotyrosinesProtein tyrosine phosphatase SHP2Amino acid sequenceTyrosine phosphatase SHP2Adaptor proteinModular domainsModular proteinsTrans-regulationAcid sequenceProtein functionPhosphatase SHP2Evolutionary dynamicsBinding site affinityPhosphotyrosineConformational dynamicsProteinGrb2SH2SequenceSHP2Site affinityAntagonist combinationDominant form
2012
Visualization of Src and FAK Activity during the Differentiation Process from HMSCs to Osteoblasts
Liao X, Lu S, Zhuo Y, Winter C, Xu W, Wang Y. Visualization of Src and FAK Activity during the Differentiation Process from HMSCs to Osteoblasts. PLOS ONE 2012, 7: e42709. PMID: 22900044, PMCID: PMC3416797, DOI: 10.1371/journal.pone.0042709.Peer-Reviewed Original ResearchConceptsSrc activationFluorescence resonance energy transferFAK activationDifferentiation processActivation of FAKRegulates cellular adhesionSrc biosensorKinase FAKInduction of differentiationResonance energy transferFAKBiochemical signalsSrcCellular adhesionLiving cellsStem cellsOsteoblast differentiation processDifferentiationCellsBone cellsSrc/FAKInductionMesenchymal stem cellsActivityGenetics
2009
Iterative Image Reconstruction Model Including Susceptibility Gradients Combined with Z-shimming Gradients in fMRI
Zhuo Y, Sutton B. Iterative Image Reconstruction Model Including Susceptibility Gradients Combined with Z-shimming Gradients in fMRI. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2009, 2009: 5721-5724. PMID: 19963915, DOI: 10.1109/iembs.2009.5332669.Peer-Reviewed Original ResearchConceptsSusceptibility-induced magnetic field gradientsMagnetic field gradientField gradientEffects of magnetic field gradientNear air/tissue interfacesField inhomogeneity effectsIterative reconstruction algorithmSignal lossSpiral-inIncreasing acquisition timeZ-shimMagnetic fieldAir/tissue interfacesMR signal modelMagnetic field distortionFunctional magnetic resonance imagingMagnetic susceptibility artifactsBlood oxygen levelAcquisition timeSusceptibility artifactsReconstruction algorithmField distortionImage distortionData acquisition techniquesSignal distortionEffect on BOLD Sensitivity Due to Susceptibility-induced Echo Time Shift in Spiral-in Based Functional MRI
Zhuo Y, Sutton B. Effect on BOLD Sensitivity Due to Susceptibility-induced Echo Time Shift in Spiral-in Based Functional MRI. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2009, 2009: 4449-4452. PMID: 19964630, DOI: 10.1109/iembs.2009.5333815.Peer-Reviewed Original ResearchConceptsEffective echo timeBOLD sensitivityEcho time shiftsSusceptibility gradientsSpiral-in trajectoryMagnetic field inhomogeneityBOLD functional magnetic resonance imagingEcho timeSusceptibility artifactsSpiral-inAir/tissue interfacesField inhomogeneityFunctional magnetic resonance imagingIn-planeBlood oxygen levelReconstructed imagesGeometric distortionSignal lossTime shiftsVentral brainBOLDInhomogeneityShiftOrbitofrontal cortex