This collection contains works by faculty from the Thayer School of Engineering.

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Submissions from 2011

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A Contrast Source Inversion Algorithm Formulated Using the Log-Phase Formulation, Tonny Rubæk, Paul M. Meaney, and Keith D. Paulsen

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Protoporphyrin IX Fluorescence Contrast in Invasive Glioblastomas is Linearly Correlated with Gd Enhanced Magnetic Resonance Image Contrast but has Higher Diagnostic Accuracy, Kimberley S. Samkoe, Summer L. Gibbs-Strauss, Harold H. Yang, S. Khan Hekmatyar, P. Jack Hoopes, Julia A. O'Hara, Risto A. Kauppinen, and Brian W. Pogue

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Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, and L. R. Lynd

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Excitation of zero-frequency magnetic field-aligned currents by ionospheric heating, A V. Streltsov and T R. Pedersen

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Combined Fluorescence and Reflectance Spectroscopy for In Vivo Quantification of Cancer Biomarkers in Low- and High-Grade Glioma Surgery, Pablo A. Valdés, Anthony Kim, Keith D. Paulsen, Frederic Leblond, Olga M. Conde, Brent T. Harris, and David W. Roberts

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Enhanced Microbial Utilization of Recalcitrant Cellulose by an Ex Vivo Cellulosome-Microbe Complex, Chun You, Xiao-Zhou Zhang, Noppadon Sathitsuksanoh, and Lee R. Lynd

Submissions from 2010

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Inspired Gas-Induced Vascular Change in Tumors with Magnetic-Resonance-Guided Near-Infrared Imaging: Human Breast Pilot Study, Colin M. Carpenter, Rebecca Rakow-Penner, Shudong Jiang, Bruce L. Daniel, Brian W. Pogue, Gary H. Glover, and Keith D. Paulsen

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Quantitative Imaging Reveals Heterogeneous Growth Dynamics and Treatment-Dependent Residual Tumor Distributions in a Three-Dimensional Ovarian Cancer Model, Jonathan P. Celli, Imran Rizvi, Conor L. Evans, Adnan O. Abu-Yousif, and Tayyaba Hasan

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Comparing Implementations of Magnetic-Resonance-Guided Fluorescence Molecular Tomography for Diagnostic Classification of Brain Tumors, Scott C. Davis, Kimberley S. Samkoe, Julia A. O’Hara, Summer L. Gibbs-Strauss, Keith D. Paulsen, and Brian W. Pogue

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Characterization of an Implicitly Resistively-Loaded Monopole Antenna in Lossy Liquid Media, Colleen J. Fox, Paul M. Meaney, Fridon Shubitidze, Lincoln Potwin, and Keith D. Paulsen

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Characterizing Accuracy of Total Hemoglobin Recovery Using Contrast-Detail Analysis in 3D Image-Guided Near Infrared Spectroscopy with the Boundary Element Method, Hamid R. Ghadyani, Subhadra Srinivasan, Brian W. Pogue, and Keith D. Paulsen

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System Development for High Frequency Ultrasound-Guided Fluorescence Quantification of Skin Layers, Josiah D. Gruber, Akshat Paliwal, Venkataramanan Krishnaswamy, and Hamid Ghadyani

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Importance of Phase Unwrapping for the Reconstruction of Microwave Tomographic Images, Tomasz M. Grzegorczyk, Paul M. Meaney, Soon Ik Jeon, Shireen D. Geimer, and Keith D. Paulsen

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Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost, Javier A. Izquierdo, Maria V. Sizova, and Lee R. Lynd

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Empirical Geographic Modeling of Switchgrass Yields in the United States, Henriette I. Jager, Latha M. Baskaran, Craig C. Brandt, and Ethan B. Davis

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Automated Classification of Breast Pathology using Local Measures of Broadband Reflectance, Ashley M. Laughney, Venkataramanan Krishnaswamy, Pilar Beatriz Garcia-Allende, Olga M. Conde, Wendy A. Wells, Keith D. Paulsen, and Brian W. Pogue

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Singular Value Decomposition Metrics show Limitations of Detector Design in Diffuse Fluorescence Tomography, Frederic Leblond, Kenneth M. Tichauer, and Brian W. Pogue

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Nonlinear Circuit Analysis via Perturbation Methods and Hardware Prototyping, Kofi Odame and P. E. Hasler

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Deletion of the Cel48S cellulase from Clostridium thermocellum, Daniel G. Olson, Shital A. Tripathi, Richard J. Giannone, Jonathan Lo, Nicky C. Caiazza, David A. Hogsett, Robert L. Hettich, Adam M. Guss, Genia Dubrovsky, and Lee R. Lynd

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Imaging Targeted-Agent Binding In Vivo with Two Probes, Brian W. Pogue, Kimberley S. Samkoe, Shannon Hextrum, Julia A. O'Hara, Michael Jermyn, Subhadra Srinivasan, and Tayyaba Hasan

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Natural Competence in Thermoanaerobacter and Thermoanaerobacterium Species, A Joe Shaw, David A. Hogsett, and Lee R. Lynd

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On arc-polarized structures in the solar wind, B U. Sonnerup, S E. Haaland, and G Paschmann

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A New Technique for Firn Grain-Size Measurement Using Sem Image Analysis, N.E. Spaulding, D.A. Meese, I. Baker, and P.A. Mayewski

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Image Guided Near-Infrared Spectroscopy of Breast Tissue In Vivo Using Boundary Element Method, Subhadra Srinivasan, Colin M. Carpenter, Hamid R. Ghadyani, Senate J. Taka, Peter A. Kaufman, Roberta M. diFlorio-Alexander, Wendy A. Wells, Brian W. Pogue, and Keith D. Paulsen

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A Coupled Finite Element-Boundary Element Method for Modeling Diffusion Equation in 3d Multi-Modality Optical Imaging, Subhadra Srinivasan, Hamid R. Ghadyani, Brian W. Pogue, and Keith D. Paulsen

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Resistive MHD reconstruction of two-dimensional coherent structures in space, W L. Teh, B U. Sonnerup, J Birn, and R E. Denton

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Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium Thermocellum and Creation of a pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. McCool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, and Nicky C. Caiazza

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Noninvasive Fluorescence Monitoring of Protoporphyrin IX Production and Clinical Outcomes in Actinic Keratoses Following Short-Contact Application of 5-Aminolevulinate, Christine B. Warren, Sara Lohser, Lauren C. Wene, Brian W. Pogue, Philip Bailin, and Edward Maytin

Submissions from 2009

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Vesicles in Poiseuille Flow, Gerrit Danker, Petia M. Vlahovska, and Chaouqi Misbah

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In Vitro Ovarian Tumor Growth and Treatment Response Dynamics Visualized with Time-Lapse OCT Imaging, Conor L. Evans, Imran Rizvi, Tayyaba Hasan, and Johannes F. de Boer

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Automated Identification of Tumor Microscopic Morphology based on Macroscopically Measured Scatter Signatures, Pilar Beatriz Garcia-Allende, Venkataramanan Krishnaswamy, P Jack Hoopes, Kimberley S. Samkoe, Olga M. Conde, and Brian W. Pogue

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Noninvasive Measurement of Aminolevulinic Acid-Induced Protoporphyrin IX Fluorescence Allowing Detection of Murine Glioma In Vivo, Summer L. Gibbs-Strauss, Julia A. O'Hara, P Jack Hoopes, Tayyaba Hasan, and Brian W. Pogue

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Automatic Exposure Control and Estimation of Effective System Noise in Diffuse Fluorescence Tomography, Dax L. Kepshire, Hamid Dehghani, Frederic Leblond, and Brian W. Pogue

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Imaging of Glioma Tumor with Endogenous Fluorescence Tomography, Dax S. Kepshire, Summer L. Gibbs-Strauss, Julia A. O'Hara, Michael Hutchins, Niculae Mincu, Frederic Leblond, Mario Khayat, Hamid Dehghani, Subhadra Srinivasan, and Brian W. Pogue

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Quantitative Imaging of Scattering Changes Associated with Epithelial Proliferation, Necrosis and Fibrosis in Tumors Using Microsampling Reflectance Spectroscopy, Venkataramanan Krishnaswamy, P Jack Hoopes, Kimberley S. Samkoe, Julia A. O'Hara, Tayyaba Hasan, and Brian W. Pogue

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Video-Rate Near Infrared Tomography to Image Pulsatile Absorption Properties in Thick Tissue, Zhiqiu Li, Venkataramanan Krishnaswamy, Scott C. Davis, Subhadra Srinivasan, Keith D. Paulsen, and Brian W. Pogue

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Imaging brine and air inclusions in sea ice using micro-X-ray computed tomography, Rachel Obbard, Gregory Troderman, and Ian Baker

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Quantifying and Resolving Multiple Vector Transformants in S. cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, and Karl E. Griswold

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Identification of the [FeFe]-Hydrogenase Responsible for Hydrogen Generation in Thermoanaerobacterium saccharolyticum and Demonstration of Increased Ethanol Yield via Hydrogenase Knockout, A. Joe Shaw, David A. Hogsett, and Lee R. Lynd

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Reconstruction of a Large-Scale Reconnection Exhaust Structure in the Solar Wind, W.-L. Teh, B. U. Ö Sonnerup, Q. Hu, and C. J. Farrugia

Submissions from 2008

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Methodology Development for Three-Dimensional MR-Guided Near Infrared Spectroscopy of Breast Tumors, Colin M. Carpenter, Subhadra Srinivasan, Brian W. Pogue, and Keith D. Paulsen

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Wavelength Band Optimization in Spectral Near-Infrared Optical Tomography Improves Accuracy while Reducing Data Acquisition and Computational Burden, Matthew E. Eames, Jia Wang, Brian W. Pogue, and Hamid Dehghani

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Direct Estimation of Evoked Hemoglobin Changes by Multimodality Fusion Imaging, Theodore J. Huppert, Solomon G. Diamond, and David A. Boas

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Effects of Impurities and their Redistribution during Recrystallization of Ice Crystals, D. Iliescu and I. Baker

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Fluorescence Tomography Characterization for Sub-Surface Imaging with Protoporphyrin IX, Dax Kepshire, Scott C. Davis, Hamid Dehghani, Keith D. Paulsen, and Brian W. Pogue

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Protoporphyrin IX Fluorescence Photobleaching Increases with the Use of Fractionated Irradiation in the Esophagus, Brian W.Q. Pogue, Chao Sheng, Juan Benevides, David Forcione, Bill Puricelli, Norman S. Nishioka, and Tayyaba Hasan

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Non-Invasive Raman Tomographic Imaging of Canine Bone Tissue, Matthew V. Schulmerich, Jacqueline H. Cole, Kathryn A. Dooley, Michael D. Morris, Jaclynn M. Kreider, Steven A. Goldstein, Subhadra Srinivasan, and Brian W. Pogue

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Transient and Localized Processes in the Magnetotail: A Review, A. S. Sharma, R. Nakamura, A. Runov, E. E. Grigorenko, H. Hasegawa, M. Hoshino, P. Louarn, C. J. Owen, A. Petrukovich, J.A. Sauvaud, V. S. Semenov, V. A. Sergeev, J. A. Slavin, B.U. O. Sonnerup, L. M. Zelenyi, G. Fruit, S. Haaland, H. Malova, and K. Snekvik

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Metabolic Engineering of a Thermophilic Bacterium to Produce Ethanol at High Yield, A. Joe Shaw, Kara K. Podkaminer, Sunil G. Desai, John S. Bardsley, Stephen R. Rogers, Philip G. Thorne, David A. Hogsett, and Lee R. Lynd

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The Effect of Particles on Creep Rate and Microstructures of Granular Ice, Min Song, Ian Baker, and David M. Cole

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Image-Guided Raman Spectroscopic Recovery of Canine Cortical Bone Contrast in Situ, Subhadra Srinivasan, Matthew Schulmerich, Jacqueline H. Cole, Kathryn Dooley, Jaclynn M. Kreider, and Brian W. Pogue

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First results from ideal 2-D MHD reconstruction: magnetopause reconnection event seen by Cluster, W. L. Teh and B. U. O. Sonnerup

Submissions from 2007

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Image-Guided Diffuse Optical Fluorescence Tomography Implemented with Laplacian-Type Regularization, Scott C. Davis, Hamid Dehghani, Jia Wang, Shudong Jiang, Brian W. Pogue, and Keith D. Paulsen

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Do Loading Path and Specimen Thickness Affect the Brittle Compressive Failure of Ice?, A. L. Fortt and E. M. Schulson

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N-Glycan Modification in Aspergillus Species, Elke Kainz, Andreas Gallmetzer, Christian Hatzl, Juergen H. Nett, Huijuan Li, Thorsten Schinko, Robert Pachlinger, Harald Berger, Yazmid Reyes-Dominguez, Andreas Bernreiter, Tillmann Gerngross, Stefan Wildt, and Joseph Strauss

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Receiver Operating Characteristic and Location Analysis of Simulated Near-Infrared Tomography Images, Xiaomei Song, Brian W. Pogue, Hamid Dehghani, Shudong Jiang, Keith D. Paulsen, and Tor D. Tosteson

Submissions from 2006

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Imaging Breast Adipose and Fibroglandular Tissue Molecular Signatures by Using Hybrid MRI-Guided Near-Infrared Spectral Tomography, Ben Brooksby, Brian W. Pogue, Shudong Jiang, Hamid Dehghani, Subhadra Srinivasan, Christine Kogel, Tor D. Tosteson, John Weaver, Steven P. Poplack, and Keith D. Paulsen

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The structure of flux transfer events recovered from Cluster data, H Hasegawa, B U. Ö Sonnerup, C J. Owen, B Klecker, G Paschmann, A Balogh, and H Re`me

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Enzyme–microbe Synergy During Cellulose Hydrolysis by Clostridium Thermocellum, Yanpin Lu, Yi-Heng P. Zhang, and Lee R. Lynd

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The microstructure of meteoric ice from Vostok, Antarctica, Rachel Obbard and Ian Baker

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Using Electron Backscatter Diffraction Patterns to Examine Recrystallization in Polar Ice Sheets, Rachel Obbard, Ian Baker, and Katherine Sieg

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Brittle Compressive Failure of Ice: Proportional Straining vs Proportional Loading, E. M. Schulson and D. Iliescu

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Orientation of Optically Trapped Nonspherical Birefringent Particles, Wolfgang Singer, Timo A. Nieminen, Ursula J. Gibson, and Norman R. Heckenberg

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Critical Computational Aspects of Near Infrared Circular Tomographic Imaging: Analysis of Measurement Number, Mesh Resolution and Reconstruction Basis, Phaneendra K. Yalavarthy, Hamid Dehghani, Brian W. Pogue, and Keit D. Paulsen

Submissions from 2005

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Microstructural characterization of ice cores, Ian Baker, Daniel Iliescu, Rachel Obbard, Hui Chang, Benjamin Bostick, and Charles Daghlian

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Integrated Recombinant Protein Expression and Purification Platform Based on Ralstonia eutropha, Gavin C. Barnard, Jesse D. McCool, David W. Wood, and Tillman U. Gerngross

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Survey of Energetic O + Ions Near the Dayside Mid-Latitude Magnetopause with Cluster, M. Bouhram, B. Klecker, G. Paschmann, S. Haaland, H. Hasegawa, A. Blagau, H. Reme, J.A. Sauvaud, L. M. Kistler, and A. Balogh

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Contrast-Detail Analysis Characterizing Diffuse Optical Fluorescence Tomography Image Reconstruction, Scott C. Davis, Brian W. Pogue, Hamid Dehghani, and Keith D. Paulsen

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Optimal reconstruction of magnetopause structures from Cluster data, H Hasegawa, B U. Ö Sonnerup, B Klecker, and G Paschmann

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Automated Migration Analysis Based on Cell Texture: Method & Reliability, Jianfeng Qin, Thomas W. Chittenden, Ling Gao, and Justin D D. Pearlman

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The Effect of Particles on Dynamic Recrystallization and Fabric Development of Granular Ice during Creep, Min Song, Ian Baker, and David M. Cole

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Creep of Granular Ice With and Without Dispersed Particles, Min Song, David M. Cole, and Ian Baker

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Near-Infrared Characterization of Breast Tumors In Vivo using Spectrally-Constrained Reconstruction, Subhadra Srinivasan, Brian W. Pogue, Ben Brooksby, Shudong Jiang, Hamid Dehghani, Christine Kogel, Wendy A. Wells, Steven P. Poplack, and Keith D. Paulsen

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Role of Spontaneous Current Oscillations during High-Efficiency Electrotransformation of Thermophilic Anaerobes, Michael V. Tyurin, Charles R. Sullivan, and Lee R. Lynd

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Cellulose Utilization by Clostridium Thermocellum: Bioenergetics and Hydrolysis Product Assimilation, Yi-Heng P. Zhang and Lee R. Lynd

Submissions from 2004

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Four-Spacecraft Determination of Magnetopause Orientation, Motion and Thickness: Comparison with Results from Single-Spacecraft Methods, S. E. Haaland, B. U. Ö. Sonnerup, M. W. Dunlop, A. Balogh, E. Georgescu, H. Hasegawa, B. Klecker, G. Paschmann, P. Puhl-Quinn, H. Vaith, and A. Vaivads

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Reconstruction of Two-Dimensional Magnetopause Structures From Cluster Observations: Verification of Method, H. Hasegawa, B. U. Ö Sonnerup, M. W. Dunlop, A. Balogh, S. E. Haaland, B. Klecker, G. Paschmann, B. Lavraud, I. Dandouras, and H. Reme

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A study of Pc-5 ULF oscillations, M K. Hudson, R E. Denton, M R. Lessard, E G. Miftakhova, and R R. Anderson

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Characterization of Hemoglobin, Water, and NIR Scattering in Breast Tissue: Analysis of Intersubject Variability and Menstrual Cycle Changes, Brian W. Pogue, Shudong Jiang, Hamid Dehghani, Christine Kogel, Sandra Soho, Subhadra Srinivasan, Xiaomei Song, Tor D. Tosteson, Steven P. Poplack, and Keith D. Paulsen

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Simulations of resonant Alfvén waves generated by artificial HF heating of the auroral ionosphere, D Pokhotelov, W Lotko, and A V. Streltsov

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Improved Quantification of Small Objects in Near-Infrared Diffuse Optical Tomography, Subhadra Srinivasan, Brian W. Pogue, Hamid Dehghani, Shudong Jiang, Xiaomei Song, and Keith D. Paulsen

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Electrotransformation of Clostridium thermocellum, Michael V. Tyurin, Sunil G. Desai, and Lee R. Lynd

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Kinetics and Relative Importance of Phosphorolytic and Hydrolytic Cleavage of Cellodextrins and Cellobiose in Cell Extracts of Clostridium thermocellum, Yie.-Heng P. Zhang and Lee R. Lynd

Submissions from 2003

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SEM/EDS Observations of Impurities in Polar Ice: Artifacts or Not?, Ian Baker and Daniel Cullen

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Use of Combinatorial Genetic Libraries to Humanize N-Linked Glycosylation in the Yeast Pichia Pastoris, Byung-Kwon Choi, Piotr Bobrowicz, Robert C. Davidson, Stephen R. Hamilton, David Kung, Huijuan Li, Robert Miele, Juergen Nett, Stefan Wildt, and Tillman Gerngross

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Converting Plant Biomass to Fuels and Commodity Chemicals in South Africa: a Third Chapter?, L R. Lynd, H H von Blottnitz, B Tait, J de Boer, I S. Pretorius, K Rumbold, and W H. van Zyl

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On Friction and Surface Cracking During Sliding of Ice on Ice, Maurine Montagnat and Erland M. Schulson

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Incommensurate Spin Density Waves in Iron Aluminides, D. R. Noakes, A. S. Arrott, M. G. Belk, and S. C. Deevi

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Interpreting Hemoglobin and Water Concentration, Oxygen Saturation, and Scattering Measured In Vivo by Near-Infrared Breast Tomography, Subhadra Srinivasan, Brian W. Pogue, Shudong Jiang, Hamid Dehghani, Christine Kogel, Sandra Soho, Jennifer J. Gibson, Tor D. Tosteson, Steven P. Poplack, and Keith D. Paulsen

Submissions from 2002

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Genome-Wide Screening for Trait Conferring Genes Using DNA Microarrays, R. T. Gill, S. Wildt, Y. T. Yang, S. Ziesman, and G. Stephanopoulos

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Microbial Cellulose Utilization: Fundamentals and Biotechnology, Lee R. Lynd, Paul J. Weimer, Willem H. van Zyl, and Isak S. Pretorius

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A Novel High-Cell-Density Protein Expression System Based on Ralstonia eutropha, Sriram Srinivasan, Gavin C. Barnard, and Tillman U. Gerngross

Submissions from 2001

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Compressional Pc5 type pulsations in the morningside plasma sheet, A. Vaivads, W. Baumjohann, G. Haerendel, R. Nakamura, H. Kucharek, B. Klecker, M. R. Lessard, L. M. Kistler, T. Mukai, and A. Nishida

Submissions from 2000

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The Effects of Sulfuric Acid on the Mechanical Properties of Ice Single Crystals, Y. L. Trickett, I. Baker, and P. M.S Pradhan

Submissions from 1999

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Ruby films as surface temperature and pressure sensors, Ursula J. Gibson and Maxim Chernuschenko

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Comparison of imaging geometries for diffuse optical tomography of tissue, Brian W. Pogue, Troy O. McBride, Ulf L. Osterberg, and Keith D. Paulsen

Submissions from 1997

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On the Strain-Rate Sensitivity of Columnar Ice, M. E. Manley and E. M. Schulson

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Across-Column Cracks and Axial Splits in S2 Saline Ice under Compression, E. M. Schulson, S. Qi, J. S. Melton, and E. T. Gratz

Submissions from 1994

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Ductile Saline Ice, G. A. Kuehn and E. M. Schulson

Submissions from 1993

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Brittle Compressive Failure of Salt-Water Columnar Ice Under Biaxial Loading, T. R. Smith and E. M. Schulson