2025
ML-ROM wall shear stress prediction in patient-specific vascular pathologies under a limited clinical training data regime
Chatpattanasiri C, Ninno F, Stokes C, Dardik A, Strosberg D, Aboian E, von Tengg-Kobligk H, Díaz-Zuccarini V, Balabani S. ML-ROM wall shear stress prediction in patient-specific vascular pathologies under a limited clinical training data regime. PLOS ONE 2025, 20: e0325644. PMID: 40504795, PMCID: PMC12161591, DOI: 10.1371/journal.pone.0325644.Peer-Reviewed Original ResearchConceptsReduced order modelComputational fluid dynamicsWall shear stressWall shear stress dataWall shear stress predictionsShear stress predictionsStress predictionShear stressFluid dynamicsLong processing timeFlowrate waveformsComputational cost analysisML-ROMOrder modelNumerical simulationsSpeed-up ratioProcessing timeMapping modelComputational costComputational demandsComplex case studyCase studyData-driven approachCost analysisFlowLats1/2 Are Essential for Developmental Vascular Remodeling and Biomechanical Adaptation to Shear Stress.
Cowdin M, Pramanik T, Mohr-Allen S, Fu Y, Mills A, Spurgin S, Varner V, Davis G, Cleaver O. Lats1/2 Are Essential for Developmental Vascular Remodeling and Biomechanical Adaptation to Shear Stress. Arteriosclerosis Thrombosis And Vascular Biology 2025 PMID: 40501385, DOI: 10.1161/atvbaha.124.322258.Peer-Reviewed Original ResearchShear stressLaminar shear stressCultured endothelial cellsEndothelial cellsResponse to shear stressCell shapeBlood flowShearHemodynamic forcesHippo pathway kinasesHuman pulmonary artery endothelial cellsPrimary human pulmonary artery endothelial cellsPulmonary artery endothelial cellsResponse to blood flowBiomechanical cuesMechanical cuesIn vitroArtery endothelial cellsCytoskeletal rearrangementsPhenotype in vivoMurine endothelial cellsFlowEmbryonic lethalityMRNA expression analysisPathway kinasesFluid Shear Stress–Regulated Vascular Remodeling: Past, Present, and Future
Deng H, Eichmann A, Schwartz M. Fluid Shear Stress–Regulated Vascular Remodeling: Past, Present, and Future. Arteriosclerosis Thrombosis And Vascular Biology 2025, 45: 882-900. PMID: 40207366, PMCID: PMC12094896, DOI: 10.1161/atvbaha.125.322557.Peer-Reviewed Original ResearchConceptsFluid shear stressShear stressVascular remodelingVascular bedCapillary densityOutward remodelingIn vivo animal modelsPotential therapeutic interventionsDownstream vascular bedArterial toneTherapeutic strategiesAnimal modelsPerfusion of tissuesAdequate perfusionUpstream arteriesEndothelial cellsVascular diseaseBlood flowTherapeutic interventionsClinical implicationsBlood vesselsTreat vascular diseasesFlowMetabolic stressBloodChromium removal from concentrated ammonium-nitrate solution: Electrocoagulation with iron in a plug-flow reactor
Costigan E, Wu S, Eckelman M, Fernandez L, Mueller A, Alshawabkeh A, Larese-Casanova P. Chromium removal from concentrated ammonium-nitrate solution: Electrocoagulation with iron in a plug-flow reactor. Separation And Purification Technology 2025, 354: 129353. DOI: 10.1016/j.seppur.2024.129353.Peer-Reviewed Original ResearchFlow ratePlug flow reactorCr removalSolution flow rateFlow-through reactorSynthetic wastewaterRemoval efficiencySteady state conditionsDesign guidelinesReactorMetallic infrastructureReaction rate coefficientsChromium removalCoexisting ionsState conditionsElectrocoagulationWastewaterAnode lengthAdvection-dispersion-reaction modelAdvection-dispersion-reactionFlowAmmonium nitrateSolutionAnodeCr concentration
2024
Controversy in mechanotransduction – the role of endothelial cell–cell junctions in fluid shear stress sensing
X S, Aitken C, Mehta V, Tardajos-Ayllon B, Serbanovic-Canic J, Zhu J, Miao B, Tzima E, Evans P, Fang Y, Schwartz M. Controversy in mechanotransduction – the role of endothelial cell–cell junctions in fluid shear stress sensing. Journal Of Cell Science 2024, 137: jcs262348. PMID: 39143856, PMCID: PMC11423816, DOI: 10.1242/jcs.262348.Peer-Reviewed Original ResearchShear stress sensingFluid shear stressFluid flowCell-cell contactShear stressCell-cell adhesionStress sensingCell-cell junctionsEndothelial cell-cell junctionsEC alignmentRegulates vascular developmentAdhesion receptorsCell typesEndothelial cellsFlowSingle cellsVascular developmentShearAdhesionContactHemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis
Cheng S, Xia I, Wanner R, Abello J, Stratman A, Nicoli S. Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis. ELife 2024, 13 DOI: 10.7554/elife.94094.3.Peer-Reviewed Original ResearchVascular smooth muscle cellsVascular smooth muscle cell differentiationWall shear stressVSMC differentiationEndothelial cellsAnalysis of blood flowBlood flowShear stressBrain arteriesPulsatile flowCerebrovascular diseaseDedifferentiated vascular smooth muscle cellsRegulate cerebral blood flowSmooth muscle cellsRed blood cell velocityDedifferentiation of vascular smooth muscle cellsCerebral blood flowBlood cell velocityArterial muscularizationVenous plexusCell progenitorsMuscle cellsBlood flow activationArteryFlowHemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis
Cheng S, Xia I, Wanner R, Abello J, Stratman A, Nicoli S. Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis. ELife 2024, 13: rp94094. PMID: 38985140, PMCID: PMC11236418, DOI: 10.7554/elife.94094.Peer-Reviewed Original ResearchConceptsVascular smooth muscle cellsWall shear stressVascular smooth muscle cell differentiationVSMC differentiationEndothelial cellsAnalysis of blood flowBlood flowShear stressBrain arteriesPulsatile flowCerebrovascular diseaseDedifferentiated vascular smooth muscle cellsRegulate cerebral blood flowSmooth muscle cellsRed blood cell velocityDedifferentiation of vascular smooth muscle cellsCerebral blood flowBlood cell velocityArterial muscularizationVenous plexusCell progenitorsMuscle cellsBlood flow activationArteryFlowUnbalanced regularized optimal mass transport with applications to fluid flows in the brain
Chen X, Benveniste H, Tannenbaum A. Unbalanced regularized optimal mass transport with applications to fluid flows in the brain. Scientific Reports 2024, 14: 1111. PMID: 38212659, PMCID: PMC10784574, DOI: 10.1038/s41598-023-50874-y.Peer-Reviewed Original ResearchConceptsFluid flowMass transportEntire transport processNumerical solution procedureKinetic energyTotal kinetic energyImage trackingSolution procedureOptimal mass transportTransport processesMass transport approachTransport problemsMass configurationConstraint equationsFlowTransport approachApplicationsBenamouFormulationTransportTracking
2023
Visualizing Fluid Flows via Regularized Optimal Mass Transport with Applications to Neuroscience
Chen X, Tran A, Elkin R, Benveniste H, Tannenbaum A. Visualizing Fluid Flows via Regularized Optimal Mass Transport with Applications to Neuroscience. Journal Of Scientific Computing 2023, 97: 26. PMID: 38938875, PMCID: PMC11210720, DOI: 10.1007/s10915-023-02337-9.Peer-Reviewed Original ResearchMass transport problemFluid flowOptimal mass transport problemComputational fluid dynamicsTransport problemsFluid dynamicsMass transportPrevious numerical methodsDynamic formulationOptimal mass transportContinuity equationNumerical methodNumerical resultsDiffusion termPresent workComputational runtimeFlowEfficient implementationBrenierBenamou
2022
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference.
Huguet G, Magruder D, Tong A, Fasina O, Kuchroo M, Wolf G, Krishnaswamy S. Manifold Interpolating Optimal-Transport Flows for Trajectory Inference. Advances In Neural Information Processing Systems 2022, 35: 29705-29718. PMID: 37397786, PMCID: PMC10312391.Peer-Reviewed Original ResearchOptimal transportNeural ordinary differential equationsOrdinary differential equationsSchrödinger bridgesDifferential equationsData manifoldGeodesic distanceTrajectory inferenceDynamic modelManifold learningLatent spaceGenerative modelScRNA-seq dataPopulation snapshotsFlowEquationsManifoldSpace distanceBifurcationPopulation dynamicsGround distanceGeometryModelInferenceSpace
2021
Microvascular fluid flow in ex vivo and engineered lungs
Raredon MSB, Engler AJ, Yuan Y, Greaney AM, Niklason LE. Microvascular fluid flow in ex vivo and engineered lungs. Journal Of Applied Physiology 2021, 131: 1444-1459. PMID: 34554016, PMCID: PMC8616606, DOI: 10.1152/japplphysiol.00286.2020.Peer-Reviewed Original Research
2020
A passive, biocompatible microfluidic flow sensor to assess flows in a cerebral spinal fluid shunt
Garrett A, Soler G, Diluna M, Grant R, Zaveri H, Hoshino K. A passive, biocompatible microfluidic flow sensor to assess flows in a cerebral spinal fluid shunt. Sensors And Actuators A Physical 2020, 312: 112110. DOI: 10.1016/j.sna.2020.112110.Peer-Reviewed Original ResearchFlow rateMicrofluidic flow sensorNovel microfluidic sensorBiocompatible polydimethylsiloxaneMicrofluidic sensorFlow sensorSensor stabilityImplanted electronicsSensor systemOptical detection systemSensor positionsBiocompatible materialsSensorsCantileverPolydimethylsiloxaneOutput lightOptical systemCerebral spinal fluidFlowMaterialsFluidLight spotElectronicsManufacturingDetection systemInnovations in Vascular Ultrasound
Gettle LM, Revzin MV. Innovations in Vascular Ultrasound. Radiologic Clinics Of North America 2020, 58: 653-669. PMID: 32471536, DOI: 10.1016/j.rcl.2020.03.002.Peer-Reviewed Original ResearchTrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics.
Tong A, Huang J, Wolf G, van Dijk D, Krishnaswamy S. TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. Proceedings Of Machine Learning Research 2020, 119: 9526-9536. PMID: 34337419, PMCID: PMC8320749.Peer-Reviewed Original ResearchOptimal transportNormalizing FlowsOptimal transport networksContinuous dynamicsTarget distributionTransport-based modelContinuous pathPaths of pointsArbitrary pathTransport networkSingle-cell RNA sequencing technologyDynamicsIndividual trajectoriesCellular dynamicsFlowPathDistributionNon-linear pathPairwise matchingPointTrajectoriesDynamic processGlycocalyx‐Like Hydrogel Coatings for Small Diameter Vascular Grafts
Dimitrievska S, Wang J, Lin T, Weyers A, Bai H, Qin L, Li G, Cai C, Kypson A, Kristofik N, Gard A, Sundaram S, Yamamoto K, Wu W, Zhao L, Kural M, Yuan Y, Madri J, Kyriakides T, Linhardt R, Niklason L. Glycocalyx‐Like Hydrogel Coatings for Small Diameter Vascular Grafts. Advanced Functional Materials 2020, 30 DOI: 10.1002/adfm.201908963.Peer-Reviewed Original ResearchDevelopment of a single helical baffle to increase CO2 gas and microalgal solution mixing and Chlorella PY-ZU1 biomass yield
Ali Kubar A, Cheng J, Guo W, Kumar S, Song Y. Development of a single helical baffle to increase CO2 gas and microalgal solution mixing and Chlorella PY-ZU1 biomass yield. Bioresource Technology 2020, 307: 123253. PMID: 32244074, DOI: 10.1016/j.biortech.2020.123253.Peer-Reviewed Original Research
2019
Self-rotary propellers with clockwise/counterclockwise blades create spiral flow fields to improve mass transfer and promote microalgae growth
Kumar S, Cheng J, Guo W, Ali KA, Song Y. Self-rotary propellers with clockwise/counterclockwise blades create spiral flow fields to improve mass transfer and promote microalgae growth. Bioresource Technology 2019, 286: 121384. PMID: 31048263, DOI: 10.1016/j.biortech.2019.121384.Peer-Reviewed Original ResearchConceptsSpiral flow fieldFlow fieldGas-liquid mixingRaceway pondsMass transfer coefficientWall shear stressTransfer coefficientPropeller diameterOpen raceway pondsMass transferSpiral flowPropellerShear stressRotational flowBladesExternal powerA. platensis biomassMicroalgae growthFlowMicroalgal growthHelix pitchDiameterMixingPitchFieldFlow network tracking for spatiotemporal and periodic point matching: Applied to cardiac motion analysis
Parajuli N, Lu A, Ta K, Stendahl J, Boutagy N, Alkhalil I, Eberle M, Jeng GS, Zontak M, O'Donnell M, Sinusas AJ, Duncan JS. Flow network tracking for spatiotemporal and periodic point matching: Applied to cardiac motion analysis. Medical Image Analysis 2019, 55: 116-135. PMID: 31055125, PMCID: PMC6939679, DOI: 10.1016/j.media.2019.04.007.Peer-Reviewed Original ResearchConceptsDeformation/strainExcellent tracking accuracyEntire cardiac cycleTracking accuracyCardiac motion analysisAccurate estimationSurface pointsEchocardiographic image sequencesLV motionDisplacementMotion analysisImage sequencesCardiac cyclePoint matchingMotionConsecutive framesEstimationNetwork trackingImportant characteristicsSignificant promiseSchemeGood correlationFlow
2018
Reduced generation time and size of carbon dioxide bubbles in a volute aerator for improving Spirulina sp. growth
Cheng J, Miao Y, Guo W, Song Y, Tian J, Zhou J. Reduced generation time and size of carbon dioxide bubbles in a volute aerator for improving Spirulina sp. growth. Bioresource Technology 2018, 270: 352-358. PMID: 30243242, DOI: 10.1016/j.biortech.2018.09.067.Peer-Reviewed Original ResearchConceptsBubble generation timeGas inlet velocityHigh-purity COHigh-speed cameraMass transfer coefficientCarbon dioxide bubblesInlet velocityTransfer coefficientBubble diameterLevel set methodGas flowMass transferAeratorBubble evolutionShear forceCulture microalgaeSpirulina spDiameterCOBubblesVelocityFlowMicroalgae
2017
Alternatively permutated conic baffles generate vortex flow field to improve microalgal productivity in a raceway pond
Cheng J, Guo W, Cai C, Ye Q, Zhou J. Alternatively permutated conic baffles generate vortex flow field to improve microalgal productivity in a raceway pond. Bioresource Technology 2017, 249: 212-218. PMID: 29045924, DOI: 10.1016/j.biortech.2017.10.031.Peer-Reviewed Original ResearchConceptsConic bafflesVorticity magnitudeRaceway pondsVortex flowBubble generation timeBubble residence timeVortex flow fieldMass transfer coefficientTransfer coefficientFlow fieldClockwise vortexMass transferVertical cross sectionBafflesHorizontal cross sectionPerpendicular velocityPure COResidence timeMicroalgal productivityFlowRelative spacingVelocityBiomass productivityMain streamCross sections
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