03/ /2005 Postdoctoral Research Fellow, Department of Physics, Clemson University, SC Research Field: Biomedical Optical Imaging.

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1 Zhen Yuan Curriculum Vitae Name: Zhen Yuan (Ph.D.) Position Title: Research Assistant Professor Postal Address: Room 289, 1275 Center Drive, JG56 BMS Building, POB , Gainesville, FL Tel: (O) Positions, Employment and Education 09/2007- Research Assistant Professor, Biomedical Engineering Department, University of Florida. Research Field: Biomedical Imaging and Biomedical Optics. 01/ /2007 Postdoctoral Research Associate, Biomedical Engineering Department, University of Florida, Gainesville, FL Research Field: Biomedical Imaging and Signal Processing. 03/ /2005 Postdoctoral Research Fellow, Department of Physics, Clemson University, SC Research Field: Biomedical Optical Imaging. 03/ /2004 Postdoctoral Research Scientist, Institute of High performance Computing, National University of Singapore, Singapore Research Field: BioMEMS. 06/2002 Ph.D., University of Science and Technology of China (USTC), Hefei , China. Major: Computational Engineering (Biomechanics). Professional Services Member of SPIE Senior Member of OSA Member of IEEE Member of Biomedical Engineering Society Reviewers of IEEE Transactions on Biomedical Engineering, IEEE Transactions on Biomedical Imaging, Applied Optics, Optics Letter, Optics Express, JOSA A, Medical Physics, Physics in Medicine & Biology, Arthritis & Rheumatism, Biomedical Optics Express, Journal of Biomedical Optics, Journal of X-ray Science & Technology Research Interest I: Biomedical Imaging and Signal Processing Diffuse Optical Imaging & Spectroscopy Photoacoustic Imaging & Spectroscopy EEG Source Localization and Signal Processing

2 X-ray image reconstruction techniques Molecular Imaging based on Fluorescent and Bioluminescent Tomography Multi-modality Imaging Photon Transport in Biological Tissues II: Neurosciences Neurovascular and Neurometabolic Coupling Brain Connectivity, Brain (Neuron) Network and Brain Plasticity Data Driven and Model Based Neural Signal Analysis Methods Neuroinformatics & Computational Informatics Epilepsy, Neurocognitive Processing III: Modeling and Simulation, Computational Engineering Inverse Problems, Optimization methods, Numerical Solution of Partial Differential Equations, Statistical Methods Reconstruction Algorithms and Signal Processing Methods High Performance Numerical Methods: Meshless Method, Incompatible and Hybrid Finite Element Methods, Boundary Element methods. Modeling and Simulation in Multiphysics High Performance Computing: Cluster-based Parallel Computation and CPU- GPU-based Parallel Computing Image Segmentation and Classification, Partial Correlation and Coherence Analysis, Partial Mutual Information Analysis, Granger Causality Analysis Structural, Functional and Effective Connectivity Methods Programming Skills Matlab, C++/C, Fortran, ANSYS, Autocad, PATRAN, Abaqus, NASTRAN Teaching Interests High Performance Numerical Methods, High Performance Computing Finite Element Method, Biostatistics Methods Biomedical Engineering Introduction, Biomedical Optics, Biomedical imaging and Signal Processing, Applied Optics, Biomedical Instrumentations, Neuroengineering Multivariate Signal Processing Method Academic Service Served as a member of the Supervisory Committee for 3 Ph. D candidates in Biomedical Engineering Dept. at the University of Florida 2009 Reviewed grant proposals for the National Medical Research Council (Singapore) Mentored 4 graduate students in Biomedical Engineering Dept. at University of Florida (Summer) Mentored 5 high school students in the Innovation program at the University of Florida Editorial board Editorial board member of Journal of Biosensors and Bioelectronics Guess Associate Editor of Medical Physics Guess Associate Editor of Applied Optics

3 Honors and Fellowships Lixue Pandeng Scholarship of Chinese Academy of Sciences Postdoctoral Fellowship of ASTAR (Singapore) University of Florida: High performance Computing Fellowship (2006) 2008, 2009, 2010 &2011 Who is Who in America 2009,2010 &2011 Who is Who in the World 2010,2011 Who is Who in Medicine 2011 Who is Who in Science and Engineering Professional Experience Research Assistant Professor Dates (July 07 present) Dept of Biomedical Engineering, University of Florida, Gainesville, FL ( Clinically investigated the combined optical and fluorescence imaging\spectroscopy of breast cancer with enhanced sensitivity and specificity Provided a new multi-modality imaging strategy for x-ray guided three-dimensional diffuse optical tomography\spectroscopy of osteoarthritis with improved resolution and contrast Combined EEG recording and optical tomography/spectroscopy for neurovascular and neurometabolic coupling Granger causality statistical software development for brain connectivity Photoacoustic tomography\spectroscopy of epilepsy with high imaging contrast and resolution Research report preparation, NIH research grant applications Multi-modality imaging setups development Postdoctoral Research Fellow Dates (Jan 05 July 07) Dept of Biomedical Engineering, University of Florida, Gainesville, FL ( Software development for quantitative photoacoustic tomography\spectroscopy Diffuse optical imaging software development based on photon transport equation Photoacoustic tomography for imaging nanoparticles Manages a team of 3 students for photoacoustic imaging system development Postdoctoral Research Associate Dates (March 04 Jan 05) Dept of Physics, Clemson University, Clemson, SC ( Reconstruction algorithm development for diffuse optical imaging of breast cancer Software development for diffuse optical spectroscopy of biological tissues Reconstruction algorithm development for bioluminescence tomography

4 Postdoctoral Research Scientist Dates (March 02 March 04) Institute of High Performance Computing, National University of Singapore, Singapore ( Model development and numerical simulation in multi-physics Biomaterials development and Biomechanics application in BioMEMS. Teaching Experience Courses Taught Spring Graduate course BME, titled Advanced Mathematics and High Performance Numerical Methods offered through the Department of Biomedical Engineering at University of Florida Courses Developed (Collaborate with Dr. Huabei Jiang) Spring , Biomedical Imaging, Graduate course in the Department of Biomedical Engineering at University of Florida Patent Hybrid Photoacoustic Tomography (PAT) and Diffuse Optical Tomography (DOT): Methods and Algorithms, International Application No. PCT/US2008/ METHOD AND APPARATUS FOR TOMOGRAPHIC IMAGING OF ABSOLUTE OPTICAL ABSORPTION COEFFICIENT IN TURBID MEDIA USING COMBINED PHOTOACOUSTIC AND DIFFUSING LIGHT MEASUREMENTS (WO/2009/011934) Book Chapters 1. Z. Yuan, H. Jiang, Photoacoustic tomography, Advances in Optical Imaging for Clinical Medicine by Dr. N.V. Iftimia, Dr. W. Brugge, and Dr. D.X. Hammer (John Wiley and Sons Ltd);( advances-in-optical-imaging-for-clinical-medicine,61860). 2. Z. Yuan, H. Jiang, Photoacoustic tomography for imaging nanoparticles, in Cancer Nanotechnology by Drs. Stephen R. Grobmyer and Brij Moudgil Z. Yuan, H. Jiang, Diffuse Optical Tomography of osteoarthritis, in Handbook of Biophotonics, Volume 2, Photonics for Health Care, Edited by Jurger Popp, Valery V. Tuchin, Arthur Chiou, and Stefan Heinemann. Published by Wiley-VCH (2011).

5 4. Z. Yuan, H. Jiang, Optical Methods and Instrumentation in Brain Imaging and Therapy, Invited Book Chapter by Springer. Selected Peer-Reviewed Articles Biomedical Imaging and Signal Processing 1. Z. Yuan, HB Jiang, Quantitative photoacoustic tomography: recovery of optical absorption coefficient maps of heterogeneous medium, Applied Physics Letters 88, APL 1-3 (2006). 2. Z. Yuan, H.Z. Zhao, C.F. Wu, H.B. Jiang, Imaging of small nanoparticle containing objects using finite element-based photoacoustic tomography, Optics Letters 30, (2005). 3. Z. Yuan, H. Jiang, Simultaneous recovery of tissue physiological and acoustic properties and the criteria for wavelength selection in multispectral photoacoustic tomography, Optics Letters 34, (2009). 4. Z. Yuan, Q. Zhang, H.B. Jiang, 3D diffuse optical tomography imaging of osteoarthritis: initial results in the finger joints, Journal of Biomedical Optics 12(3), (2007). 5. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang, Tomographic x-ray-guided 3D diffuse optical tomography imaging of osteoarthritis: Initial results in the finger joints, Journal of Biomedical Optics 13, (2008). 6. Z. Yuan, Q. Zhang, E. Sobel, H. Jaign, Comparison of diffusion approximation and higher order diffusion equation for optical tomography of osteoarthritis, Journal of Biomedical Optics 14, (2009). 7. Z. Yuan, Q. Wang, H. Jiang, Reconstruction of optical absorption coefficient maps of heterogeneous medium by photoacoustic tomography coupled with diffusion equation based regularized Newton Method, Optics Express 15, (2007). 8. Z. Yuan, Q. Zhang, H. Jiang, Simultaneous reconstruction optical and acoustic properties by quantitative photoacoustic tomography, Optics Express 14, (2006). 9. Z. Yuan, H.Z. Zhao, H.B. Jiang, Finite element-based photoacoustic tomography: phantom and chicken bone experiments, Applied Optics 45(13), (2006). 10. Z. Yuan, H.B. Jiang, An image reconstruction scheme that combines modified Newton method and efficient initial guess estimation for optical tomography of finger joints, Applied Optics 46, (2007). 11. Z. Yuan, H.B. Jiang, Three-dimensional finite element-based photoacoustic tomography: Reconstruction algorithm and simulations, Medical Physics 34(2), (2007). 12. Z. Yuan, H. Jiang, Quantitative photoacoustic tomography, Philosophical Transaction of the Royal Society A 367, (2009). 13. Z. Yuan, X. Hu, H. Jiang, A higher order diffusion model for three-dimensional photon migration and image reconstruction in optical tomography, Physics in Medicine and Biology 54,65-88(2009). 14. Z. Yuan, H. Jiang. High resolution x-ray guided three dimensional diffuse optical tomography of joint tissues in hand osteoarthritis: Morphological and functional assessments, Medical Physics, 37 (8), 2010.

6 15. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang, Image-guided optical spectroscopy in diagnosis of osteoarthritis: A clinical study, Biomedical Optics Express 1, 74-86(2010). 16. H.B. Jiang, Z. Yuan, X.J. Gu, Spatially varying optical and acoustic property reconstruction using finite element-based photoacoustic tomography, Journal of the Optical Society of America A 23(4), (2006). 17. J. Xiao, Z. Yuan, H. Jiang, Quantitative multispectral photoacoustic tomography and wavelength optimization, Journal of X-Ray Science and Technology, 02 (2010). 18. Q. Zhang, L. Yin, Y. Tan, Z. Yuan, H. Jiang, Quantitative bioluminescence tomography guided by diffuse optical tomography, Optics Express 16, (2008). 19. Z. Yuan, Recent advances in Nano imaging using photoacoustic measurements Nano express 2011 (invited paper). 20. Q. Zhang, Z. Liu, P. Camey, Z. Yuan, H. Jiang, Noninvasive imaging of epileptic seizure in vivo using photoacoustic tomography, Physics in Medicine and Biology 53(7), (2008). 21. J. Zhang, Z. Wang, Z. Yuan and H. Jiang, Computer aided classification of optical images for diagnosis of osteoarthritis in the finger joints, Journal of X- Ray Science and Technology, 2011 (accepted). 22. Z. Yuan, H. Jiang, A more vigorous quantitative photoacoustic tomography reconstruction method, Journal of Biomedical Optics Letters, 2011 (in review). 23. Z. Yuan, Q. Zhang, H. Jiang. X-ray guided three-dimensional diffuse optical imaging of the finger joints in osteoarthritis and psoriatic arthritis: A comparable study, Journal of Biomedical Optics (in review). Computational Bioengineering and Computational Engineering 24. H. Li, Z. Yuan, K.Y. Lam et al., Model development and numerical simulation of electric-stimulus-responsive hydrogels subject to external electric field, Biosensors and Bioelectronics19 (9), (2004). 25. H. Li, Z. Yuan, T.Y. Ng, K.Y. Lam, Constitutive model development and microstructural topology optimization for Nafion hydrogel membrane with ionic clustering, Journal of Biomaterials Science-Polymer Edition.14, (2003). 26. L. Yin, Z. Yuan, L.H. He, Model development and numerical simulation of temperature-sensitive hydrogels, Computational Materials Sciences 31, (2004). 27. Z. Yuan, C.C. Wu, Hua Li, Homogenized-based topology design for pure torsion of composite shafts, ACTA MECHANICA SINICA 19(3), (2003). 28. L. Yin, Z. Yuan et al., Model development and numerical simulation of biohydrogels in aqueous salt solutions, ACTA MECHANICA SINICA 37(3), (2005). 29. Z. Yuan, C.C. Wu, Topology optimization for microstructures of cross-section of composite torsional shafts, ACTA MECHANICA SINICA, 35(1): 39-42(2003). 30. Z. Yuan, C.C. Wu, Topology optimization of continuum structures using incompatible finite elements, ACTA MECHANICA SINICA 35(2), (2003). 31. Z. Yuan, C.C. Wu, Topology optimization for periodic linear elastic microstructures of composite materials, ACTA MECHANICA SOLIDA SINICA 24(1), 40-45(2003).

7 32. Z. Yuan, C.C. Wu, Numerical simulation of mechanical properties of prestress concrete members due to creep and shrinkage, ACTA MECHANICA SOLIDA SINICA 24, (2001). 33. Z. Yuan, Z.R. Li, C.C. Wu, Simulation of Mixed-mode Fatigue Crack Growth by Element Free Galerkin Method, Engineering Mechanics 19(1), 25-28(2002). 34. Z. Yuan, Y. Liu, Effective method for dynamic analysis of interaction of fluid and structure of mechanical equipment, Journal of Mechanical Strength (1), 16-17(2000). 35. Z. Yuan, C.C. Wu, Analytical respond sensitivity computation using incompatible elements, Journal of Mechanical Strength 24(1), 59-61(2002). 36. Z. Yuan, C.C. Wu, Topology optimization of continuum structure using hybrid elements and artificial material model, Journal of China University of Science and Technology 31 (6), (2001). (In Chinese with English Abstract) 37. S. Zhuang, C.C. Wu, Z. Yuan, Microscopic investigation of cellular materials mechanical properties based on homogenization theory, Materials Science and Engineering 19(4), 9-13(2001). (In Chinese with English Abstract) Neuroimaging and Neuroinformatics 38. J. Zhang, T. Guo and Z. Yuan, Analysis of fmri Data Using an Integrated Principal Component Analysis and Supervised Affinity Propagation Clustering Approach, IEEE Transaction on Biomedical Engineering,2011(8),PMID: Q. Zhang, Z. Liu, P. Camey, Z. Yuan, H. Jiang, Noninvasive imaging of epileptic seizure in vivo using photoacoustic tomography, Physics in Medicine and Biology 53(7), (2008). 40. Z. Yuan, H. Jiang, A nonlinear reconstruction method for EEG source locations, IEEE Transactions on Biomedical Imaging, 2011 (in review). 41. Z. Yuan, H. Jiang, Investigation of brain effective connectivity in epilepsy using diffuse optical measurement, ASE 2011 Conference. 42. R. Jiang, Z. Yuan, H. Jiang. Imaging the blood flow and cellular morphology in epilepsy with diffuse optical tomography, 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. Invited International Conference Presentations 1. Z. Yuan, H. Jiang. Three-dimensional finite element-based PAT: initial results, Proc. SPIE 6437, 64371A, Z. Yuan, L. Yin, H. Jiang. Numerical simulation of transient nonlinear behaviors of electric-sensitive hydrogel membrane under an external electric field, Proc. SPIE 6465, 64650W, Z. Yuan, Q. Zhang, Y. Sun, H. Jiang. Simultaneous reconstruction of acoustic and optical properties of in-vivo tissues by PAT, Proc. SPIE 6437, 64371V, Z. Yuan, Q. Zhang, H.B. Jiang. Diagnosis of osteoarthritis in the finger joints by three-dimensional diffuse optical tomography: Pilot clinical results Technical Digest of OSA Biomedical Optics Topical Meeting, Fort Lauderdale, Florida, USA, March 19 23, 2006.

8 5. Z. Yuan, Q. Zhang, Y. Sun, H. Jiang. Simultaneous reconstruction of acoustic and optical properties of in-vivo tissues by PAT, Proc. SPIE 6437, 64371V, Z. Yuan, H. Jiang. Simultaneous recovery of chromophore concentrations and ultrasound velocity by PAT. Proc. SPIE BO203, 63, Z. Yuan, H. Jiang. X-ray guided 3D DOT imaging of OA finger joints: a clinical study. Proc. SPIE BO110, 11, Z. Yuan, H. Jiang. Diffuse optical imaging of OA finger joints by higher-order diffuse equations. Proc. SPIE BO118, 68, H, Jiang, Z. Yuan. Quantitative photoacoustic tomography: recover of optical absorption coefficient maps of heterogeneous media, Proc. SPIE 6437, 64371S, Q. Zhang, Z. Yuan, H. Jiang, X-ray guided 3D diffuse optical tomography: in vivo study of osteoarthritis in the finger joints, Proc. SPIE 6431, , Z. Yuan, H. Li, Ng T. Y. and J. Chen. A coupled multi-field formulation for stimuli-responsive hydrogel subject to electric field, Proceeding of the International Conference on Scientific & Engineering Computation (IC- SEC): , Singapore, Z. Yuan, L. Yin, C.C. Wu et al. Topology optimization of continuum structures using high performance finite elements, Proceeding of the 4th International Conference on Nonlinear Mechanics: , Shanghai, China, Z. Yuan et al. Image-guided photoacoustic spectroscopy in diagnosis of osteoarthritis, 2011 Photonics West, SPIE, California. 14. Z. Yuan et al., The diffuse optical imaging of epilepsy network in small animal, ASE 2010, Texas. International Conference Papers 1. Z. Yuan, Q.Z. Zhang, H.B. Jiang. 3D diffuse optical tomography of finger joints based on globally convergent methods and enhanced initial values optimization scheme Technical Digest of OSA Biomedical Optics Topical Meeting, Fort Lauderdale, Florida, USA, March 19 23, Z. Yuan, Q. Wang, H.B. Jiang. Recovery of Absolute Absorption Coefficient Maps of Heterogeneous Media by Photoacoustic Tomography Coupled with Diffusion Optical Reconstruction Algorithm Technical Digest of OSA Biomedical Optics Topical Meeting, Florida, USA, March Z. Yuan, X. Hu, H. Jiang. A Simplified Spherical Harmonics Approximated Radiation Transport Model for Three Dimensional (3-D) Photon Migration in Small Volume Tissues Technical Digest of OSA Biomedical Optics Topical Meeting, Florida, USA, March Z. Yuan, Q.Z. Zhang, H.B. Jiang. A clinical investigation on x-ray guided three-dimensional diffuse optical imaging of osteoarthritis in the finger joints Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 5. Z. Yuan, H.B. Jiang. Diffusion approximation and higher-order diffusion equations for optical tomography of osteoarthritis: A comparable study Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 6. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang. Imaging molecular signatures for detection of osteoarthritis by combining spectral and spatial a-priori information.

9 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 7. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang. X-ray guided three-dimensional diffuse optical tomography of osteoarthritis and psoriatic arthritis in finger joints: A comparable study Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 8. Z. Yuan, H.B. Jiang. Simultaneous recovery of tissue physiological and acoustic properties and uniqueness in multi-spectral photoacoustic tomography Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 9. H, Jiang, Z. Yuan. Quantitative photoacoustic tomography: recover of optical absorption coefficient maps of heterogeneous media, Proc. SPIE 6437, 64371S, Q. Zhang, Z. Yuan, H. Jiang, X-ray guided 3D diffuse optical tomography: in vivo study of osteoarthritis in the finger joints, Proc. SPIE 6431, , Qizhi Zhang, Lu Yin, Yiyong Tan, Z. Yuan. Three-Dimensional Bioluminescence Tomography Assisted by Diffuse Optical Tomography Technical Digest of OSA Biomedical Optics Topical Meeting, Florida, USA, March Z. Yuan, C. Wu. Numerical problem study on structural topology optimization, Proceedings of the 11 th National Computational Mechanics Conference, Guangzhou, China, Q. Zhang, Z. Yuan. In vivo x-ray guided optical tomography of osteoarthritis in the knee joints, 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 14. R. Jiang, Z. Yuan, H. Jiang. Imaging the blood flow and cellular morphology in epilepsy with diffuse optical tomography, 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 15. Q. Zhang, Z. Yuan, H. Jiang. Diffuse Optical Tomography of large joints: a phantom study, 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida, USA. April. 16. Q. Zhang, Z. Yuan, H. Jiang. Imaging osteoarthritis in the knee joints using x- ray guided diffuse optical tomography, SPIE 7548, 2010.