Departmental Papers (BE)

Departmental Papers (BE)

 
The Department of Bioengineering, one of the first nationally, was established in 1973 with graduate degrees offered since 1961. Rated one of the top Bioengineering programs in the country, the Department presents the strong intellectual interdisciplinary infrastructure and collaborative culture that links Engineering, Life Sciences and Medicine at the University of Pennsylvania.

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Papers from 2007

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Self-assembled monolayers of omega-functional silanes: A platform for understanding cellular adhesion at the molecular level, Mark H. Lee, David Boettiger, Paul Ducheyne, and Russell J. Composto

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Propogation of Surface Plasmons in Ordered and Disordered Chains of Metal Nanospheres, Vadim A. Markel and Andrey K. Sarychev

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Cascaded Segmentation of Brain Tumors Using Multi-Modality MR Profiles, Yangming Ou, Hongmin Cai, Seung-Koo Lee, Elias R. Melhem, Christos Davatzikos, and Ragini Verma

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Structural Changes in the Cervical Facet Capsular Ligament: Potential Contributions to Pain Following Subfailure Loading, Kyle P. Quinn, Kathryn E. Lee, Chukwunyere C. Ahaghotu, and Beth A. Winkelstein

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Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage, Ravi Radhakrishnan

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Hydrostatic Pressure Differentially Regulates Outer and Inner Annulus Fibrosus Cell Matrix Production in 3D Scaffolds, Anna T. Reza and Steven B. Nicoll

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Differential alkaline phosphatase responses of rat and human bone marrow derived mesenchymal stem cells to 45S5 bioactive glass, Gwendolyn C. Riley, Shula Radin, Andrew T. Chen, and Paul Ducheyne

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Chemical and mechanical nerve root insults induce differential behavioral sensitivity and glial activation that are enhanced in combination, Sarah M. Rothman and Beth A. Winkelstein

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RGDS peptides immobilized on titanium alloy stimulate bone cell attachment, differentiation and confer resistance to apoptosis, Antonino G. Secchi, V Grigoriou, Irving M. Shapiro, E. A. Cavalcanti-Adam, Russell J. Composto, Paul Ducheyne, and Christopher S. Adams

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Materials in particulate form for tissue engineering. 2. Applications in bone, Gabriela Silva, O. P. Coutinho, Paul Ducheyne, and R. L. Reis

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Materials in particulate form for tissue engineering. 1. Basic concepts, Gabriela Silva, Paul Ducheyne, and R. L. Reis

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Magnetic microposts as an approach to apply forces to living cells, Nathan J. Sniadecki, Alexandre Anguelouch, Michael T. Yang, Corinne M. Lamb, Zhijun Liu, Stuart B. Kirschner, Yaohua Liu, Daniel H. Reich, and Christopher S. Chen

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Strong Tip Effects in Near-field Scanning Optical Tomography, Jin Sun, P. Scott Carney, and John C. Schotland

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Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus, Ravindra Venkatramani and Ravi Radhakrishnan

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Simultaneous Estimation and Segmentation of T1 Map for Breast Parenchyma Measurement, Ye Xing, Yangming Ou, Sarah Englander, Mitchell D. Schnall, and Dinggang Shen

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Registering Histological and MR Images of Prostate for Image-based Cancer Detection, Yiqiang Zhan, Yangming Ou, Michael Feldman, John Tomaszewski, Christos Davatzikos, and Dinggang Shen

Papers from 2006

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Silicon Neurons that Inhibit to Synchronize, John V. Arthur and Kwabena Boahen

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Stretch Increases Alveolar Epithelial Permeability to Uncharged Micromolecules, Kenneth Joseph Cavanaugh, Taylor Sitarik Cohen, and Susan S. Margulies

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Detecting Cognitive States from fMRI Images by Machine Learning and Multivariante Classification, Yong Fan, Dinggang Shen, and Christos Davatzikos

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Quantitative Membrane Loading of Polymer Vesicles, P. Peter Ghoroghchian, John J. Lin, Aaron K. Brannon, Paul R. Frail, Frank S. Bates, Michael J. Therien, and Daniel A. Hammer

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Induction of osteoblast differentiation markers in human dermal fibroblasts: potential application to bone tissue engineering., Christopher K. Hee and Steven B. Nicoll

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Neuronal Ion-Channel Dynamics in Silicon, Kai M. Hynna and Kwabena Boahen

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Spectroscopic Studies of Fractal Aggregates of Silver Nanospheres Undergoing Local Restructuring, Sergei V. Karpov, Valeriy S. Gerasimov, Ivan L. Isaev, and Vadim A. Markel

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Characterizing and Analyzing Diffusion Tensor Images by Learning their Underlying Manifold Structure, Parmeshwar Khurd, Ragini Verma, and Christos Davatzikos

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Adhesive Dynamics Simulation of Neutrophil Arrest with Deterministic Activation, Ellen F. Krasik, Ka Lai Yee, and Daniel A. Hammer

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Autocatalytic Activation of Influenza Hemagglutinin, Jeong H. Lee, Mark Goulian, and Eric T. Boder

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Tensile Cervical Facet Capsule Ligament Mechanics: Failure and Subfailure Responses in the Rat, Kathryn E. Lee, Andrew N. Franklin, Martin B. Davis, and Beth A. Winkelstein

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E-cadherin engagement stimulates proliferation via Rac1, Wendy F. Liu, Celeste M. Nelson, Dana M. Pirone, and Christopher S. Chen

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A Multiscale Computational Approach to Dissect Early Events in the Erb Family Receptor Mediated Activation, Differential Signaling, and Relevance to Oncogenic Transformations, Yingting Liu, Jeremy Purvis, Andrew Shih, Joshua Weinstein, Neeraj Agrawal, and Ravi Radhakrishnan

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A Joint Transformation and Residual Image Descriptor for Morphometric Image Analysis using an Equivalence Class Formulation, Sokratis Makrogiannis, Ragini Verma, Bilge Karacali, and Christos Davatzikos

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Comment on "Optical Response of Strongly Coupled Metal Nanoparticles in Dimer Arrays", Vadim A. Markel

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Dynamic Computation in a Recurrent Network of Heterogeneous Silicon Neurons, Paul Merolla and Kwabena Boahen

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Nonlinear Inverse Scattering and Three-Dimensional Near-Field Optical Imaging, George Y. Panasyuk, Vadim A. Markel, P. Scott Carney, and John C. Schotland

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Cervical facet capsular ligament yield defines the threshold for injury and persistent joint-mediated cervical pain, Kyle P. Quinn and Beth A. Winkelstein

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Nanotechnology for Cell–Substrate Interactions, Nathan J. Sniadecki, Ravi A. Desai, Sami Alom Ruiz, and Christopher S. Chen

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Near-Field Scanning Optical Tomography: A Nondestructive Method for Three-Dimensional Nanoscale Imaging, Jin Sun, P. Scott Carney, and John C. Schotland

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Superparamagnetic Iron Oxide Nanoparticle Probes for Molecular Imaging, Daniel L. J Thorek, Antony K. Chen, Julie Czupryna, and Andrew Tsourkas

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Suicide Gene Delivery by Calcium Phosphate Nanoparticles: A Novel Method of Targeted Therapy for Gastric Cancer, Andrew Tsourkas and Julie Czupryna

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Silicon Neurons That Phase-Lock, John H. Wittig Jr and Kwabena Boahen

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A Silicon Retina that Reproduces Signals in the Optic Nerve, Kareem A. Zaghloul and Kwabena Boahen

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Numerical Modeling of Turbulent and Laminar Airflow and Odorant Transport during Sniffing in the Human and Rat Nose , Kai Zhao, Pamela Dalton, Geoffery C. Yang, and Peter W. Scherer

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Statistically-Constrained High-Dimensional Warping Using Wavelet-Based Priors, Zhong Zue, Dinggang Shen, and Christos Davatzikos

Papers from 2005

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Should Children Use Mobile Phones?, Tung Tommy Chau and Kenneth R. Foster

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Neuromorphic Implementation of Orientation Hypercolumns, Thomas Yu Wing Choi, Paul A. Merolla, John V. Arthur, Kwabena A. Boahen, and Bertram E. Shi

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Principal Component Analysis of Temporal and Spatial Information for Human Gait Recognition, Sandhitsu Das, Maciej Lazarewicz, and Leif H. Finkel

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The Effect of Cellular Receptor Diffusion on Receptor-Mediated Viral Binding Using Brownian Adhesive Dynamics (BRAD) Simulations, Thomas J. English and Daniel A. Hammer

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I-Domain of Lymphocyte Function-Associated Antigen-1 Mediates Rolling of Polystyrene Particles on ICAM-1 under Flow, A. Omolala Eniola, Ellen F. Krasik, Lee A. Smith, Gang Song, and Daniel A. Hammer

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Collateral Damage: American Science and the War on Terrorism, Kenneth R. Foster and Irving A. Lerch

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Self-organized cortical map formation by guiding connections, Stanley Y.M. Lam, Bertram E. Shi, and Kwabena A. Boahen

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Adhesion of Polymer Vesicles, John J. Lin, Frank S. Bates, Daniel A. Hammer, and James A. Silas

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Generalized optical theorem for reflection, transmission, and extinction of power for electromagnetic fields, D. R. Lytle II, P. Scott Carney, John C. Schotland, and Emil Wolf

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Balancing Guidance Range and Strength Optimizes Self-Organization by Silicon Growth Cones, Brian Taba and Kwabena Boahen

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Assembly of multicellular constructs and microarrays of cells using magnetic nanowires, Monica Tanase, Edward J. Felton, Darren S. Gray, Anne Hultgren, Christopher S. Chen, and Daniel H. Reich

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The Role of NMDA Currents in State Transitions of the Nucleus Accumbens Medium Spiny Neuron, John A. Wolf, Jason T. Moyer, and Leif H. Finkel

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Solution mediated effect of bioactive glass in poly (lactic-co-glycolic acid)-bioactive glass composites on osteogenesis of marrow stromal cells, Jun Yao, Shula Radin, Gwendolen Reilly, Phoebe S. Leboy, and Paul Ducheyne

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An ON–OFF Log Domain Circuit That Recreates Adaptive Filtering in the Retina, Kareem A. Zaghloul and Kwabena A. Boahen

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Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns, Ying Zhang, Daniel A. Hammer, and David J. Graves

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Eikonal Method for Calculation of Coherence Functions, Adam B. Zysk, P. Scott Carney, and John C. Schotland

Papers from 2004

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Recurrently Connected Silicon Neurons with Active Dendrites for One-Shot Learning, John V. Arthur and Kwabena A. Boahen

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A burst-mode word-serial address-event link--III: analysis and test results, Kwabena A. Boahen

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A burst-mode word-serial address-event link--II: receiver design, Kwabena A. Boahen

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A burst-mode word-serial address-event link--I: transmitter design, Kwabena A. Boahen

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Computational Lens for the Near Field, P. Scott Carney, Richard A. Frazin, Sergey I. Bozhevolnyi, Valentyn S. Volkov, Alexandra Boltasseva, and John C. Schotland

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Generalized optical theorem for reflection, transmission, and extinction of power for scalar fields, P. Scott Carney, John C. Schotland, and Emil Wolf

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An ON-OFF orientation selective address event representation image transceiver chip, Thomas Yu Wing Choi, Bertram E. Shi, and Kwabena A. Boahen

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A multi-chip implementation of cortical orientation hypercolumns, Thomas Y. W. Choi, Bertram E. Shi, and Kwabena A. Boahen

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LVAD as Destination Therapy - The Economic Dilemma, Pamela Douglas, Courtney Morgan, Heather Lee, and Kenneth R. Foster

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Brownian Adhesive Dynamics (BRAD) for Simulating the Receptor-Mediated Binding of Viruses, Thomas J. English and Daniel A. Hammer

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Modeling thermal responses in human subjects following extended exposure to radiofrequency energy , Kenneth R. Foster and Eleanor R. Adair

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A Semianalytic Model of Leukocyte Rolling, Ellen F. Krasik and Daniel A. Hammer

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Oligomerization of Fusogenic Peptides Promotes Membrane Fusion by Enhancing Membrane Destabilization, Wai Leung Lau, David S. Ege, James D. Lear, Daniel A. Hammer, and William F. DeGrado

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A novel rodent neck pain model of facet-mediated behavioral hypersensitivity: implications for persistent pain and whiplash injury, Kathryn E. Lee, John H. Thinnes, David S. Gokhin, and Beth A. Winkelstein

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Symmetries, inversion formulas, and image reconstruction for optical tomography, Vadim A. Markel and John C. Schotland

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Mechanical thresholds for initiation and persistence of pain following nerve root injury: mechanical and chemical contributions at injury, Beth A. Winkelstein and Joyce A. DeLeo

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Optic Nerve Signals in a Neuromorphic Chip II: Testing and Results, Kareem A. Zaghloul and Kwabena A. Boahen

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Optic Nerve Signals in a Neuromorphic Chip I: Outer and Inner Retina Models, Kareem A. Zaghloul and Kwabena A. Boahen

Papers from 2003

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Dynamic Simulations of Inflammatory Cell Recruitment: The State Diagram for Cell Adhesion Mediated by Two Receptors, Sujata K. Bhatia and Daniel A. Hammer

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The Shear Threshold Effect for Particle Adhesion to Bioreactive Surfaces: Influence of Receptor and Ligand Site Density, Sujata K. Bhatia and Daniel A. Hammer

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The State Diagram for Cell Adhesion Mediated by Two Receptors, Sujata K. Bhatia, Michael R. King, and Daniel A. Hammer

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An orientation selective 2D AER transceiver, Thomas Yu Wing Choi, Bertram E. Shi, and Kwabena A. Boahen

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A biomorphic digital image sensor, Eugenio Culurciello, Ralph Etienne-Cummings, and Kwabena A. Boahen

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HIV Viral Docking: Model Predictions for Bond Number and Trajectory, Thomas J. English and Daniel A. Hammer

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Interplay between Rolling and Firm Adhesion Elucidated with a Cell-Free System Engineered with Two Distinct Receptor-Ligand Pairs, A. Omolola Eniola, P. Jeanene Willcox, and Daniel A. Hammer

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Bioethics and the Brain, Kenneth R. Foster, Paul Root Wolpe, and Arthur L. Caplan

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Mapping Mechanical Strain of an Endogenous Cytoskeletal Network in Living Endothelial Cells, Brian P. Helmke, Amy B. Rosen, and Peter F. Davies

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A silicon implementation of the thalamic low threshold calcium current, Kai M. Hynna and Kwabena A. Boahen

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Hyperspectral Image Processing Using Locally Linear Embedding, David H. Kim and Leif H. Finkel

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A recurrent model of orientation maps with simple and complex cells, Paul Merolla and Kwabena A. Boahen

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Curvature Covariation as a Factor in Perceptual Salience, Thomas M. Murphy, Mark Matlin, and Leif H. Finkel

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Anthropomorphic Simulations of Falls, Shakes, and Inflicted Impacts in Infants, Michael Thomas Prange, Brittany Coats, Ann-Christine Duhaime, and Susan S. Margulies

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Nanostructural Control of Implantabale Xerogels for the Controlled Release of Biomolecules, Shula Radin and Paul Ducheyne

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Effect of surface activated poly(dimethylsiloxane) on fibronectin adsorption and cell function, George K. Toworfe, Russell J. Composto, Christopher S. Adams, Irving M. Shapiro, and Paul Ducheyne

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A linear cochlear model with active bi-directional coupling, Bo Wen and Kwabena A. Boahen

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Mechanisms of central sensitization, neuroimmunology and injury biomechanics in persistent pain : implications for musculoskeletal disorders, Beth A. Winkelstein

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A Computational Model of the Nucleus Accumbens: Network Properties and their Functional Implications, John A. Wolf and Leif H. Finkel

Papers from 2002

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Rolling Adhesion of Yeast Engineered to Express Cell Adhesion Molecules, Sujata K. Bhatia, Jeffrey S. Swers, Raymond T. Camphausen, K. Dane Wittrup, and Daniel A. Hammer

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Herman P. Schwan: A Scientist and Pioneer in Biomedical Engineering, Kenneth R. Foster

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The Precautionary Principle - Common Sense or Environmental Extremism?, Kenneth R. Foster

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Effect of Shear Stress on Platelet Activation via the Glycoprotein VI Receptor, Kendra L. Sarratt, Hong M. Chen, Mark L. Kahn, and Daniel A. Hammer

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Competitively coupled orientation selective cellular neural networks, Bertram E. Shi and Kwabena A. Boahen