Departmental Papers (BE)
Papers from 2018
An Open-Source Plate Reader, Karol Szymula, Michael S. Magaraci, Michael Patterson, Andrew Clark, Sevile G. Mannickarottu, and Brian Y. Chow
Papers from 2016
Optogenetic Control of Calcium Oscillation Waveform Defines NFAT as an Integrator of Calcium Load, Pimkhuan Hannanta-anan and Brian Y. Chow
Toolbox for Exploring Modular Gene Regulation in Synthetic Biology Training, Michael S. Magaraci, Jessica G. Bermudez, Deeksha Yogish, Daniel H. Pak, Viktor Mollov, Josh Tycko, David Issadore, Sevile G. Mannickarottu, and Brian Y. Chow
Papers from 2015
Noninvasive Metrics for Identification of Brain Injury Deficits in Piglets, Samer A. Jaber, Sarah Sullivan, and Susan S. Margulies
Peripheral Blood Mitochondrial DNA as a Biomarker of Cerebral Mitochondrial Dysfunction Following Traumatic Brain Injury in a Porcine Model, Todd Kilbaugh, Maria Lvova, Michael Karlsson, Zhe Zhang, Jeremy Leipzig, Douglas C. Wallace, and Susan S. Margulies
Persistently Altered Brain Mitochondrial Bioenergetics After Apparently Successful Resuscitation From Cardiac Arrest, Todd Kilbaugh, Robert M. Sutton, Michael Karlsson, Magnus J. Hansson, Maryam Y. Naim, Ryan W. Morgan, George Bratinov, Joshua Willard Lampe, Vinay Nadkarni, Lance Becker, Susan S. Margulies, and Robert A. Berg
Establishing a Clinically Relevant Large Animal Model Platform for TBI Therapy Development: Using Cyclosporin A as a Case Study, Susan S. Margulies, Todd Kilbaugh, Sarah Sullivan, Colin Smtih, Kathleen J. Propert, Melissa Byro, Kristen Saliga, Beth A. Costine, and Ann-Christine Duhaime
Papers from 2013
The Anesthetic Effects on Vasopressor Modulation of Cerebral Blood Flow in an Immature Swine Model, Benjamin Bruins, Todd Kilbaugh, Susan S. Margulies, and Stuart H. Friess
Papers from 2012
Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation, Pamela A. Barendt, Najaf A. Shah, Gregory A. Barendt, and Casim A. Sarkar
Ischemia Induces P-Selectin-Mediated Selective Progenitor Cell Engraftment in the Isolated-Perfused Heart, Jason A. Burdick, Jeremy A. Elser, Brendan P. Purcell, Irshad A. Allana, and Kenneth B. Margulies
Scanner-Free and Wide-Field Endoscopic Imaging by Using a Single Multimode Optical Fiber, Youngwoon Choi, Changhyeong Yoon, Moonseok Kim, Taeseok Daniel Yang, Christopher Fang-Yen, Ramchandra R. Dasari, Kyoung Jin Lee, and Wonshik Choi
Finite Element Model Predictions of Intracranial Hemorrhage From Non-impact, Rapid Head Rotations in the Piglet, Brittany Coats, Stephanie A. Eucker, Sarah Sullivan, and Susan S. Margulies
Sepsis Enhances Epithelial Permeability With Stretch in an Actin Dependent Manner, Taylor Sitarik Cohen, Brian Christopher DiPaolo, Gladys Gray Lawrence, and Susan S. Margulies
Uses of Remnant Human Lung Tissue for Mechanical Stretch Studies, Nurit Davidovich, Peter Chhour, and Susan S. Margulies
Rho Kinase Signaling Pathways During Stretch in Primary Alveolar Epithelia, Brian Christopher DiPaolo and Susan S. Margulies
Effects of Size Polydispersity on the Extinction Spectra of Colloidal Nanoparticle Aggregates, Alexander E. Ershov, Ivan L. Isaev, Polina N. Semina, Vadim A. Markel, and Sergei V. Karpov
Premedication With Meloxicam Exacerbates Intracranial Hemorrhage in an Immature Swine Model of Non-impact Inertial Head Injury, Stuart H. Friess, Maryam Y. Naim, Todd Kilbaugh, Jill Ralston, and Susan S. Margulies
Early Cerebral Perfusion Pressure Augmentation With Phenylephrine After Traumatic Brain Injury May Be Neuroprotective in a Pediatric Swine Model, Stuart H. Friess, Colin Smith, Todd Kilbaugh, Suzanne G. Frangos, Jill Ralston, Mark A. Helfaer, and Susan S. Margulies
Influence of Age and Fall Type on Head Injuries in Infants and Toddlers, Nicole G. Ibrahim, Joanne Wood, Susan S. Margulies, and Cindy W. Christian
Three-dimensional differential interference contrast microscopy using synthetic aperture imaging, Moonseok Kim, Youngwoon Choi, Christopher Fang-Yen, Yongjin Sung, Kwanhyung Kim, Ramachandra R. Dasari, Michael S. Feld, and Wonshik Choi
Comment on “Green’s function theory for infinite and semi-infinite particle chains”, Vadim A. Markel and Andrey K. Sarychev
MicroRNA Modulate Alveolar Epithelial Response to Cyclic Stretch, Nadir Yehya, Adi Yerrapureddy, John Tobias, and Susan S. Margulies
Spin-Labeling Magnetic Resonance Imaging Detects Increased Myocardial Blood Flow After Endothelial Cell Transplantation in the Infarcted Heart, HuaLei Zhang, Hui Qiao, Rachel S. Frank, Bin Huang, Kathleen J. Propert, Susan S. Margulies, Victor A. Ferrari, Jonathan A. Epstein, and Rong Zhou
Papers from 2011
Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise, Uma Balakrishnan, T. N. Swaminathan, Portonovo S. Ayyaswamy, David M. Eckmann, and Ravi Radhakrishnan
Schwann Cell Proliferation and Macrophage Infiltration Are Evident at Day 14 after Painful Cervical Nerve Root Compression in the Rat, Yu-Wen Chang and Beth A. Winkelstein
Overcoming the Diffraction Limit Using Multiple Light Scattering in a Highly Disordered Medium, Youngwoon Choi, Taeseok Daniel Yang, Christopher Fang-Yen, Pilsung Kang, Kyoung Jin Lee, Ramachandra R. Dasari, Michael S. Feld, and Wonshik Choi
Physiological and Histopathological Responses Following Closed Rotational Head Injury Depend on Direction of Head Motion, Stephanie A. Eucker
Neurocritical Care Monitoring Correlates with Neuropathology in a Swine Model of Pediatric Traumatic Brain Injury, Stuart H. Friess, Jill Ralston, Stephanie A. Eucker, Mark A. Helfaer, Colin Smith, and Susan S. Margulies
Robust Network Topologies for Generating Switch-Like Cellular Responses, Najaf A. Shah and Casim A. Sarkar
Papers from 2010
Inverse Scattering and Acousto-Optic Imaging, Giullaume Bal and John C. Schotland
Radiometric Bimolecular Beacons for Sensitive Detection of RNA in Single Living Cells, Antony K. Chen, Olga Davydenko, Mark A. Behlke, and Andrew Tsourkas
MAPk Activation Modulates Permeability of Isolated Rat Alveolar Epithelial Cell Monolayers Following Cyclic Stretch, Taylor Sitarik Cohen, Galadys Gray Lawrence, Amit Khasgiwala, and Susan S. Margulies
Cultured Alveolar Epithelial Cells From Septic Rats Mimic in Vivo Septic Lung, Taylor Sitarik Cohen, Gladys Gray Lawrence, and Susan S. Margulies
Polymer - Xerogel Composites for Controlled Release Wound Dressings, Marius C. Costache, Haibo Qu, Paul Ducheyne, and David Devore
Stretch Magnitude and Frequency-Dependent Actin Cytoskeleton Remodeling in Alveolar Epithelia, Brian Christopher DiPaolo; Guillaume Lenormand,; Jeffrey J. Fredberg; and Susan S. Margulies
MicroRNA-10a Regulation of Proinflammatory Phenotype in Athero-susceptible Endothelium in Vivo and in Vitro, Yun Fang, Congzhu Shi, Elisabetta Manduchi, Mete Civelek, and Peter F. Davies
Single-scattering Optical Tomography: Simultaneous Reconstruction of Scattering and Absorption, Lucia Florescu, Vadim A. Markel, and John C. Schotland
The Rho Pathway Mediates Transition to an Alveolar Type I Cell Phenotype During Static Stretch of Alveolar Type II Cells, Cherie D. Foster, Linda S. Varghese, Linda W. Gonzales, Susan S. Margulies, and Susan H. Guttentag
Biomechanics of the Toddler Head During Low-height Falls: An Anthropomorphic Dummy Analysis Laboratory Investigation, Nicole G. Ibrahim and Susan S. Margulies
Biomechanics of Toddler Head During Low-height Falls: An Anthorpomorphic Dummy Analysis, Nicole G. Ibrahim and Susan S. Margulies
Injectable Hydrogel Properties Influence Infarct Expansion and Extent of Postinfarction Left Ventricular Remodeling in an Ovine Model, Jamie L. Ifkovits, Elena Tous, Masahito Minakawa, J. Daniel Robb, Kevin J. Koomalsingh, Joseph H. Gorman III, Robert C. Gorman, and Jason A. Burdick
Mechanical Tugging Force Regulates the Size of Cell-Cell Junctions, Zhijun Liu, John L. Tan, Daniel M. Cohen, Michael T. Yang, Nathan J. Sniadecki, Sami Alom Ruiz, Celeste M. Nelson, and Christopher S. Chen
Detecting Mutually-Salient Landmark Pairs with MRF Regularization, Yangming Ou, Ahmed Besbes, Michel Bilello, Mohamed Mansour, Christos Davatzikos, and Nikos Paragios
Quantum Imaging and Inverse Scattering, John C. Schotland
The ErbB3/HER3 Intracellular Domain is Competent to Bind ATP and Catalyze Autophosphorylation, Fumin Shi, Shannon Telesco, Yingting Liu, Ravi Radhakrishnan, and Mark Lemmon
Mining Terabytes of Submillimeter-resolution ECoG Datasets for Neurophysiologic Biomarkers, Jonathan Viventi, Justin Blanco, and Brian Litt
Papers from 2009
Calculation of free energies in fluid membranes subject to heterogeneous curvature fields, Neeraj J. Agrawal and Ravi Radhakrishnan
Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons, Anthony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Single-scattering optical tomography, Lucia Florescu, John C. Schotland, and Vadim A. Markel
Phaseless Three-Dimensional Optical Nanoimaging, Alexander A. Govyadinov, George Y. Panasyuk, and John C. Schotland
Novel nano-composite biomaterials that respond to light, Kolin C. Hribar, Robert B. Metter, and Jason A. Burdick
Tuning hydrogel properties for applications in tissue engineering, Sudhir Khetan, Cindy Chung, and Jason A. Burdick
Ketamine Modulates Theta and Gamma Oscillations, Maciej T. Lazarewicz, Richard S. Ehrilichman, Christina R. Maxwell, Michael J. Gandal, Leif H. Finkel, and Steven J. Siegel
DRAMMS: deformable registration via attribute matching and mutual-saliency weighting, Yangming Ou and Christos Davatzikos
Non-Rigid Registration between Histological and MR Images of the Prostate: A Joint Segmentation and Registration Framework, Yangming Ou, Dinggang Shen, Michael Feldman, John Tomaszewski, and Christos Davatzikos
Sampling the spatial patterns of cancer: Optimized biopsy procedures for estimating prostate cancer volume and Gleason Score, Yangming Ou, Dinggang Shen, Jianchao Zeng, Leon Sun, Judd Moul, and Christos Davatzikos
Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior, Jeremy E. Purvis, Ravi Radhakrishnan, and Scott L. Diamond
Vector Correlation Technique for Pixel-wise Detection of Collagen Fiber Realignment During Injurious Tensile Loading, Kyle P. Quinn and Beth A. Winkelstein
Nanoscale Optical Tomography using Volume-scanning Near-field Microscopy, Jin Sun, John C. Schotland, Rainer Hillenbrand, and P. Scott Carney
Calpain mediates proteolysis of the voltage-gated sodium channel alpha-subunit, Catherine R. von Reyn, Jennifer M. Spaethling, Mahlet N. Mesfin, Marek Ma, Robert W. Neumar, Douglas H. Smith, Robert Siman, and David F. Meaney
Parallel Hopfield Networks, Robert C. Wilson
Diffuse optical monitoring of hemodynamic changes in piglet brain with closed head injury, Chao Zhou, Stephanie A. Eucker, Turgut Durduran, Guoqiang Yu, Jill Ralston, Stuart H. Friess, Rebecca N. Ichord, Susan S. Margulies, and Arjun G. Yodh
Diffuse Optical Monitoring of Hemodynamic Changes in Piglet Brain With Closed Head Injury, Chao Zhou, Stephanie A. Eucker, Turgut Durduran, Guoqiang Yu, Jill Ralston, Stuart H. Friess, Rebecca N. Ichord, Susan S. Margulies, and Arjun G. Yodh
Papers from 2008
Geometry of mediating protein affects the probability of loop formation in DNA., Neeraj J. Agrawal, Ravi Radhakrishnan, and Prashant K. Purohit
The inhibition of Staphylococcus epidermidis biofilm formation by vancomycinmodified titanium alloy and implications for the treatment of periprosthetic infection, Valentin Antoci Jr., Christopher S. Adams, Javad Parvizi, Helen M. Davidson, Russell J. Composto, Theresa A. Freeman, Eric Wickstrom, Paul Ducheyne, Donald Jungkind, Irving M. Shapiro, and Noreen J. Hickok
Cytoplasmic BKCa channel intron-containing mRNAs contribute to the intrinsic excitability of hippocampal neurons, Thomas J. Bell, Kevin Y. Miyashiro, Jai-Yoon Sul, Ronald McCullough, Peter T. Buckley, Jeanine Jochems, David F. Meaney, Phil Haydon, Charles R. Cantor, Thomas D. Parsons, and James Eberwine
Sequential Effects on the Detectability of a Tone Added to a Multitone Masker, Xiang Cao, Rong Huang, and Virginia M. Richards
Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA, Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Potential for Head Injuries in Infants From Low-Height Falls Laboratory Investigation, Brittany Coats and Susan S. Margulies
Potential for head injuries in infants from low-height falls: Laboratory investigation, Brittany Coats and Susan S. Margulies
Response to: Closer but not there yet: models in child injury research, Brittany Coats and Susan S. Margulies
The Bad Truth about Laplace's Transform, Charles L. Epstein and John C. Schotland
Adhesive Dynamics Simulations of the Shear Threshold Effect for Leukocytes, Kelly Kaputo, Dooyoung Lee, Michael R. King, and Daniel A. Hammer
Effect of rapidly resorbable bone substitute materials on the temporal expression of the osteoblastic phenotype in vitro, C. Knabe, A. Houshmand, G. Berger, Paul Ducheyne, R. Gildenhaar, I. Kranz, and M. Stiller
Validation of a novel device to objectively measure adherence to long-term oxygen therapy, Sun-Kai V. Lin, Daniel K. Bogen, and Samuel T. Kuna
In vitro surface reaction layer formation and dissolution of calcium phosphate cement – bioactive glass composites, Changsheng Liu, Chien-Wen Chen, and Paul Ducheyne
Rigid model-based 3D segmentation of the bones of joints in MR and CT images for motion analysis, Jiamin Liu, Jayaram K. Udupa, Punam K. Saha, Dewey Odhner, Bruce E. Hirsch, Sorin Seigler, Scott Simon, and Beth A. Winkelstein
Can the Imaginary Part of Permeability be Negative?, Vadim A. Markel
Optimized biopsy procedures for estimating Gleason Score and prostate cancer volume, Yangming Ou, Dinggang Shen, Yong Fan, Jianchao Zeng, Leon Sun, and Christos Davatzikos
Classical Theory of Optical Nonlinearity in Conducting Nanoparticles, George Y. Panasyuk, John C. Schotland, and Vadim A. Markel
The controlled release of drugs from emulsified, sol gel processed silica microspheres, Shula Radin, Paul Ducheyne, and Tiffany Chen
Emergence of Patterned Stem Cell Differentiation Within Multicellular Structures, Sami Alom Ruiz and Christopher S. Chen
Geometrical optics limit of stochastic electromagnetic fields, Robert W. Schoonover, Adam M. Zysk, P. Scott Carney, John C. Schotland, and Emil Wolfe
Molecular Systems Biology of ErbB1 Signaling: Bridging the Gap through Multiscale Modeling and High-Performance Computing, Andrew Shih, Jeremy Purvis, and Ravi Radhakrishnan
Magnetic microposts for mechanical stimulation of biological cells: Fabrication, characterization, and analysis, Nathan J. Sniadecki, Corinne M. Lamb, Yaohua Liu, Christopher S. Chen, and Daniel H. Reich
Size, charge and concentration dependent uptake of iron oxide particles by non-phagocytic cells, Daniel L.J. Thorek and Andrew Tsourkas
Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase, Ravindra Venkatramani and Ravi Radhakrishnan
The effect of oxidatively damaged DNA on the active site pre-organization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus, Ravindra Venkatramani and Ravi Radhakrishnan
Multiparametric Tissue Characterization of Brain Neoplasms and Their Recurrence Using Pattern Classification of MR Images, Raginia Verma, Evangelia I. Zacharaki, Yangming Ou, Hongmin Cai, Sanjeev Chawla, Seung-Koo Lee, Elias R. Melhem, Ronald Wolf, and Christos Davatzikos
Integrin-mediated signalling through the MAP-kinase pathway, Ka Lai Yee, V. M. Weaver, and Daniel A. Hammer
Papers from 2007
Probabilistic Segmentation of Brain Tumors Based on Multi-Modality Magnetic Resonance Images, Hongmin Cai, Ragini Verma, Yangming Ou, Seung-Koo Lee, Elias R. Melhem, and Christos Davatzikos
Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells, Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Separate but not equal: Differential mechanical roles for myosin isoforms, Christopher S. Chen
Polymorphic Variation in Human Meiotic Recombination, Vivian G. Cheung, Joshua T. Burdick, Deborah Hirschmann, and Michael Morley
mGluR5 stimulates gliotransmission in the nucleus accumbens., Marcello D'Ascenzo, Tommaso Fellin, Miho Terunuma, Raquel Revilla-Sanchez, David F. Meaney, Yves P. Auberson, Stephen J. Moss, and Philip G. Haydon
Enhanced Astrocytic Ca2+ Signals Contribute to Neuronal Excitotoxicity after Status Epilepticus, Shinghua Ding, Tommaso Fellin, Yingzi Zhu, So-Young Lee, Yves P. Auberson, David F. Meaney, Douglas A. Coulter, Giorgio Carmignoto, and Philip G. Haydon
Photoacoustic effect for multiply scattered light, Andrew R. Fisher, Andrew J. Schissler, and John C. Schotland
RFID Inside: The Murky Ethics of Implanted Chips, Kenneth R. Foster and Jan Jaeger
Hyaluronic acid hydrogel for controlled self-renewal and differentiation of human embryonic stem cells, Sharon Gerecht, Jason A. Burdick, Lino S. Ferreira, Seth A. Townsend, Robert Langer, and Gordana Vunjak-Novakovic
Transient Cervical Nerve Root Compression Modulates Pain: Load Thresholds for Allodynia and Sustained Changes in Spinal Neuropeptide Expression, Raymond D. Hubbard, Zen Chen, and Beth A. Winkelstein