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

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Submissions from 2014

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Microwave Tomographic Imaging Utilizing Low-Profile, Rotating, Right Angle-Bent Monopole Antennas, N. R. Epstein, P. M. Meaney, and K. D. Paulsen

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A Sustainable Design Method Acting As An Innovation Tool, Jeremy Faludi

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Advances in Optics for Biotechnology, Medicine and Surgery, Maryann Fitzmaurice, Brian W. Pogue, Guillermo J. Tearney, and James W. Tunnell

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A Review of the Pinned Photodiode for CCD and CMOS Image Sensors, Eric R. Fossum and Donald B. Hondongwa

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Extraction of Intrinsic Fluorescence from Single Fiber Fluorescence Measurements on a Turbid Medium: Experimental Validation, U. A. Gamm, C. L. Hoy, F. van Leeuwen - van Zaane, H. J. C. M. Sterenborg, S. C. Kanick, D J. Robinson, and A. Amelink

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Correspondence of Electroencephalography and Near-Infrared Spectroscopy Sensitivities to the Cerebral Cortex using a High-Density Layout, Paolo Giacometti and Solomon G. Diamond

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Plastic Faulting in Saltwater Ice, Narayana Golding, Scott A. Snyder, Erland M. Schulson, and Carl E. Renshaw

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Impact of Physical Properties and Accumulation Rate on Pore Close-Off in Layered Firn, S. A. Gregory, M. R. Albert, and I. Baker

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The Exometabolome of Clostridium Thermocellum Reveals Overflow Metabolism at High Cellulose Loading, Evert K. Holwerda, Philip G. Thorne, Daniel G. Olson, Daniel Amador-Noguez, Nancy L. Engle, Timothy J. Tschaplinski, Johannes P. van Dijken, and Lee R. Lynd

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Dual-Channel Red/Blue Fluorescence Dosimetry with Broadband Reflectance Spectroscopic Correction Measures Protoporphyrin IX Production during Photodynamic Therapy of Actinic Keratosis, Stephen Chad Kanick, Scott C. Davis, Yan Zhao, Tayyaba Hasan, Edward V. Maytin, Brian W. Pogue, and M Shane Chapman

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Sub-Diffusive Scattering Parameter Maps Recovered Using Wide-Field High-Frequency Structured Light Imaging, Stephen C. Kanick, David M. McClatchy, Venkataramanan Krishnaswamy, Jonathan T. Elliott, Keith D. Paulsen, and Brian W. Pogue

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Pixel-Based Absorption Correction for Dual-Tracer Fluorescence Imaging of Receptor Binding Potential, Stephen C. Kanick, Kenneth M. Tichauer, Jason Gunn, Kimberley S. Samkoe, and Brian W. Pogue

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Climate Change and Forest Fires Synergistically Drive Widespread Melt Events of the Greenland Ice Sheet, Kaitlin M. Keegan, Mary R. Albert, Joseph R. McConnell, and Ian Baker

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The Impact of Ice Layers on Gas Transport through Firn at the North Greenland Eemian Ice Drilling (Neem) Site, Greenland, K. Keegan, M. R. Albert, and I. Baker

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Structured Light Scatteroscopy, Venkataramanan Krishnaswamy, Jonathan T. Elliott, David M. McClatchy, Richard J. Barth Jr., Wendy A. Wells, Brian W. Pogue, and Keith D. Paulsen

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Comparative Efficiency and Driving Range of Light- and Heavy-Duty Vehicles Powered with Biomass Energy Stored in Liquid Fuels or Batteries, Mark Laser and Lee R. R. Lynd

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Ionospheric Control of Magnetotail Reconnection, William Lotko, Ryan H. Smith, Binzheng Zhang, Jeremy E. Ouellette, Oliver J. Brambles, and John G. Lyon

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Sensitivity of MRI-Guided Near-Infrared Spectroscopy Clinical Breast Exam Data and Its Impact on Diagnostic Performance, Michael A. Mastanduno, Junqing Xu, Fadi El-Ghussein, Shudong Jiang, Hong Yin, Yan Zhao, Kelly E. Michaelson, Ke Wang, Fang Ren, Brian W. Pogue, and Keith D. Paulsen

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Anthropomorphic Breast Phantoms with Physiological Water, Lipid, and Hemoglobin Content for Near-Infrared Spectral Tomography, Kelly E. Michaelsen, Venkataramanan Krishnaswamy, Adele Shenoy, Emily Jordan, Brian W. Pogue, and Keith D. Paulsen

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Preface to the 13th Physics and Chemistry of Ice Conference (PCI-2014), Rachel Obbard and Ian Baker

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Global warming releases microplastic legacy frozen in Arctic Sea ice, Rachel Obbard, Saeed Sadri, Ying Qi Wong, Alexandra A. Khitun, Ian Baker, and Richard C. Thompson

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T1 Magnetic Resonance Imaging Head Segmentation for Diffuse Optical Tomography and Electroencephalography, Katherine L. Perdue and Solomon G. Diamond

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Predicting the Risk of Suicide by Analyzing the Text of Clinical Notes, Chris Poulin, Brian Shiner, Paul Thompson, Linas Vepstas, Yinong Young-Xu, Benjamin Goertzel, Bradley Watts, Laura Flashman, and Thomas McAllister

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Spatial Frequency Analysis of Anisotropic Drug Transport in Tumor Samples, Stewart Russell, Kimberley S. Samkoe, Jason R. Gunn, P Jack Hoopes, Thienan A. Nguyen, Milo J. Russell, Robert R. Alfano, and Brian W. Pogue

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Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment, José A. Siles, Caio T.C.C Rachid, Inmaculada Sampedro, Inmaculada García-Romera, and James M. Tiedje

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Gene and Protein Sequence Optimization for High-Level Production of Fully Active and Aglycosylated Lysostaphin in Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, and Karl E. Griswold

Submissions from 2013

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Enhanced Phagocytic Activity of HIV-Specific Antibodies Correlates with Natural Production of Immunoglobulins with Skewed Affinity for FcγR2a and FcγR2b, Margaret E. Ackerman, Anne-Sophie Dugast, Elizabeth G. McAndrew, and Stephen Tsoukas

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Impact of Treatment Response Metrics on Photodynamic Therapy Planning and Outcomes in a Three-Dimensional Model of Ovarian Cancer, Sriram Anbil, Imran Rizvi, Jonathan P. Celli, Nermina Alagic, Brian W. Pogue, and Tayyaba Hasan

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Interactions of Peptide Triazole Thiols with Env gp120 Induce Irreversible Breakdown and Inactivation of HIV-1 Virions, Arangassery Bastian, Mark Contarino, Lauren D. Bailey, Rachna Aneja, Diogo Rodrigo Magalhaes Moreira, Kevin Freedman, Karyn McFadden, Caitlin Duffy, and Ali Emileh

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Growing a Sustainable Biofuels Industry: Economics, Environmental Considerations, and the Role of the Conservation Reserve Program, Christopher M. Clark, Yolanda Lin, Britta G. Bierwagen, Laurence M. Eaton, Matthew H. Langholtz, Philip Morefield, Caroline E. Ridley, Laura Vimmerstedt, Steve Peterson, and Brian W. Bush

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Functional Heterologous Expression of an Engineered Full Length Cipa from Clostridium Thermocellum in Thermoanaerobacterium Saccharolyticum, Devin H. Currie, Christopher D. Herring, Adam M. Guss, Daniel G. Olson, David A. Hogsett, and Lee R. Rynd

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Dynamic Dual-Tracer MRI-Guided Fluorescence Tomography to Quantify Receptor Density In Vivo, Scott C. Davis, Kimberley S. Samkoe, Kenneth M. Tichauer, Kristian J. Sexton, Jason R. Gunn, Sophie J. Deharvengt, Tayyaba Hasan, and Brian W. Pogue

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Effects of Spatial Pattern Scale of Brain Activity on the Sensitivity of DOT, fMRI, EEG and MEG, Solomon Gilbert Diamond and Katherine L. Perdue

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Tracking the Cellulolytic Activity of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon M. Wolfaardt, David Allen, Steven N. Liss, and Lee R. Lynd

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Direct Identification of Breast Cancer Pathologies Using Blind Separation of Label-Free Localized Reflectance Measurements, Alma Eguizabal, Ashley M. Laughney, Pilar Beatriz García-Allende, Venkataramanan Krishnaswamy, Wendy A. Wells, Keith D. Paulsen, Brian W. Pogue, Jose M. Lopez-Higuera, and Olga M. Conde

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Sustainable Design Education through a Self-Directed Online System, Jeremy Faludi and Adam Menter

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White Light-Informed Optical Properties Improve Ultrasound-Guided Fluorescence Tomography of Photoactive Protoporphyrin IX, Brendan P. Flynn, Alisha V. DSouza, Stephen C. Kanick, Scott C. Davis, and Brian W. Pogue

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Nonlinear optics in daily life, Elsa Garmire

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Compliant Head Probe for Positioning Electroencephalography Electrodes and Near-Infrared Spectroscopy Optodes, Paolo Giacometti and Solomon G. Diamond

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A GAMOS Plug-In for GEANT4 Based Monte Carlo Simulation of Radiation-Induced Light Transport in Biological Media, Adam K. Glaser, Stephen C. Kanick, Rongxiao Zhang, Pedro Arce, and Brian W. Pogue

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Fast Segmentation and High-Quality Three-Dimensional Volume Mesh Creation from Medical Images for Diffuse Optical Tomography, Michael Jermyn, Hamid Ghadyani, Michael A. Mastanduno, Wes Turner, Scott C. Davis, Hamid Dehghani, and Brian W. Pogue

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Pilot Study Assessment of Dynamic Vascular Changes in Breast Cancer with Near-Infrared Tomography from Prospectively Targeted Manipulations of Inspired End-Tidal Partial Pressure of Oxygen and Carbon Dioxide, Shudong Jiang, Brian W. Pogue, Kelly E. Michaelsen, Michael Jermyn, Michael A. Mastanduno, Tracy E. Frazee, Peter A. Kaufman, and Keith D. Paulsen

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Scanning in Situ Spectroscopy Pplatform for Imaging Surgical Breast Tissue Specimens, Venkataramanan Krishnaswamy, Ashley M. Laughney, Wendy A. Wells, Keith D. Paulsen, and Brian W. Pogue

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Alginate Lyase Exhibits Catalysis-Independent Biofilm Dispersion and Antibiotic Synergy, John W. Lamppa and Karl E. Griswold

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System Analysis of Spatial Frequency Domain Imaging for Quantitative Mapping of Surgically Resected Breast Tissues, Ashley M. Laughney, Venkataramanan Krishnaswamy, Tyler B. Rice, and David J. Cuccia

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Microwave Imaging for Neoadjuvant Chemotherapy Monitoring: Initial Clinical Experience, Paul M. Meaney, Peter A. Kaufman, Lori S. Muffly, Michael Click, Stephen P. Poplack, Wendy A. Wells, Gary N. Schwartz, Roberta M. di Florio-Alexander, Tor Tosteson, Zhongze Li, Shireen D. Geimer, Margaret W. Fanning, Tian Zhou, Neil R. Epstein, and Keith D. Paulsen

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Role of the CipA Scaffoldin Protein in Cellulose Solubilization, as Determined by Targeted Gene Deletion and Complementation in Clostridium thermocellum, Daniel G. Olson, Richard J. Giannone, Robert L. Hettich, and Lee R. Lynd

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Discontinuities and Alfvenic Fluctuations in the Solar Wind, G. Paschmann, S. Haaland, B. Sonnerup, and T. Knetter

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Contrast Enhanced-Magnetic Resonance Imaging as a Surrogate to Map Verteporfin Delivery in Photodynamic Therapy, Kimberley S. Samkoe, Amber Bryant, Jason R. Gunn, Stephen P. Pereira, Tayyaba Hasan, and Brian W. Pogue

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Fluorescent Affibody Peptide Penetration in Glioma Margin Is Superior to Full Antibody, Kristian Sexton, Kenneth Tichauer, Kimberley S. Samkoe, Jason Gunn, P. Jack Hoopes, and Brian W. Pogue

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Continuous Correction of Differential Path Length Factor in Near-Infrared Spectroscopy, Tanveer Talukdar, Jason H. Moore, and Solomon G. Diamond

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Bioengineered Lysozyme Reduces Bacterial Burden and Inflammation in a Murine Model of Mucoid Pseudomonas aeruginosa Lung Infection, Charlotte C. Teneback, Thomas C. Scanlon, Matthew J. Wargo, Jenna L. Bement, Karl E. Griswold, and Laurie W. Leclair

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Dual-Tracer Background Subtraction Approach for Fluorescent Molecular Tomography, Kenneth M. Tichauer, Robert W. Holt, Fadi El-Ghussein, Scott C. Davis, Kimberly S. Samkoe, Jason R. Gunn, Frederic Leblond, and Brian W. Pogue

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Modeling Biofuel Expansion Effects on Land Use Change Dynamics, Ethan Warner, Daniel Inman, Benjamin Kunstman, Brian Bush, Laura Vimmerstedt, and Steve Peterson

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Real-time in vivo Cherenkoscopy Imaging During External Beam Radiation Therapy, Rongxiao Zhang, David J. Gladstone, Lesley A. Jarvis, Rendall R. Strawbridge, P Jack Hoopes, Oscar D. Friedman, Adam K. Glaser, and Brian W. Pogue

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Atypical Glycolysis in Clostridium Thermocellum, Jilai Zhou, Daniel G. Olson, D. Aaron Argyros, Yu Deng, Walter M. van Gulik, Johannes P. van Dijken, and Lee R. Lynd

Submissions from 2012

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Integrated Analysis of Hydrothermal Flow through Pretreatment, Veronique Archambault-Leger, Xiongjun Shao, and Lee R. Lynd

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Quantitative Cherenkov Emission Spectroscopy for Tissue Oxygenation Assessment, Johan Axelsson, Adam K. Glaser, David J. Gladstone, and Brian W. Pogue

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Multichannel Diffuse Optical Raman Tomography for Bone Characterization In Vivo: a Phantom Study, Jennifer-Lynn H. Demers, Scott C. Davis, Brian W. Pogue, and Michael D. Morris

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Form and Function of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon Wolfaardt, Grant Allen, Steven N. Liss, and Lee R. Lynd

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Using Life Cycle Assessment Methods to Guide Architectural Decision-Making for Sustainable Prefabricated Modular Buildings, Jeremy Faludi, Michael Lepech, and George Loisos

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Image-Based Quantification of Benzoporphyrin Derivative Uptake, Localization, and Photobleaching in 3D Tumor Models, for Optimization of PDT Parameters, Michael D. Glidden, Jonathan P. Celli, Iqbal Massodi, Imran Rizvi, Brian Pogue, and Tayyaba Hasan

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Weighted multiple testing procedures for genomic studies, Jiang Gui, Tor Tosteson, and Mark Borsuk

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Dcm Methylation is Detrimental to Plasmid Transformation in Clostridium Thermocellum, Adam M. Guss, Daniel G. Olson, Nicky C. Caiazza, and Lee R. Lynd

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More about arc-polarized structures in the solar wind, S A. Haaland, B Sonnerup, and G Paschmann

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Transition in the Fractal Geometry of Arctic Melt Ponds, C. Hohenegger, B. Alali, K. R. Steffen, D. K. Perovich, and K. M. Golden

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Complete Genome Sequence of Clostridium clariflavum DSM 19732, Javier A. Izquierdo, Lynne Goodwin, Karen W. Davenport, and Hazuki Teshima

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Scattering phase Function Spectrum Makes Reflectance Spectrum Measured from Intralipid phantoms and Tissue Sensitive to the Device Detection Geometry, S. C. Kanick, V. Krishnaswamy, U. A. Gamm, H. J.C.M Sterenborg, D. J. Robinson, A. Amelink, and B. W. Pogue

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Spatial Frequency Domain Tomography of Protoporphyrin IX Fluorescence in Preclinical Glioma Models, Soren D. Konecky, Chris M. Owen, Tyler Rice, Pablo A. Valdés, Chris M. Owen, Pablo A. Valdes, David W. Roberts, Kolbein Kolste, Frederic Leblond, Keith D. Paulsen, and Brian C. Wilson

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A Digital X-Ray Tomosynthesis Coupled Near Infrared Spectral Tomography System for Dual-Modality Breast Imaging, Venkataramanan Krishnaswamy, Kelly E. Michaelsen, Brian W. Pogue, Steven P. Poplack, Ian Shaw, Ken Defrietas, Ken Brooks, and Keith D. Paulsen

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Minimum Cost of Transport in Asian Elephants: Do We Really Need a Bigger Elephant?, V. A. Langman, M. F. Rowe, T. J. Roberts, N. V. Langman, and C. R. Taylor

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Automatic And Robust Calibration of Optical Detector Arrays for Biomedical Diffuse Optical Spectroscopy, Michael A. Mastanduno, Shudong Jiang, Roberta DiFlorio-Alexander, Brian W. Pogue, and Keith Paulsen

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Formation and Characterization of Non-Growth States in Clostridium Thermocellum: Spores and L-Forms, Elizabeth B. Mearls, Javier A. Izquierdo, and Lee R. Lynd

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New shortwave infrared albedo measurements for snow specific surface area retrieval, Benoit Montpetit, A Royer, A Langlois, P Cliché, A Roy, N Champollion, G Picard, F Domine, and Rachel Obbard

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New Shortwave Infrared Albedo Measurements for Snow Specific Surface Area Retrieval, B. Montpetit, A. Royer, A. Langlois, P. Cliche, A. Roy, N. Champollion, G. Picard, F. Domine, and R. Obbard

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Computational Design and Characterization of a Temperature-Sensitive Plasmid Replicon for Gram Positive Thermophiles, Daniel G. Olson and Lee R. Lynd

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Characterization of Xylan Utilization and Discovery of a New Endoxylanase in Thermoanaerobacterium Saccharolyticum through Targeted Gene Deletions, Kara K. Podkaminer, Adam M. Guss, Heather L. Trajano, David A. Hogsett, and Lee R. Lynd

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Ethanol and Anaerobic Conditions Reversibly Inhibit Commercial Cellulase Activity in Thermophilic Simultaneous Saccharification and Fermentation (tSSF), Kara K. Podkaminer, William R. Kenealy, Christopher D. Herring, David A. Hogsett, and Lee R. Lynd

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Joint Diagonalization Applied to the Detection and Discrimination of Unexploded Ordnance, Fridon Shubitidze, Juan Pablo Fernández, Irma Shamatava, Benjamin Barrowes, and Kevin O’Neill

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Improved Tumor Contrast Achieved by Single Time Point Dual-Reporter Fluorescence Imaging, Kenneth M. Tichauer, Kimberley S. Samkoe, Kristian J. Sexton, Jason R. Gunn, Tayyaba Hasan, and Brian W. Pogue

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Quantitative, Spectrally-Resolved Intraoperative Fluorescence Imaging, Pablo A. Valdés, Frederic Leblond, Valerie L. Jacobs, Brian C. Wilson, Keith D. Paulsen, and David W. Roberts

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Developing Unique Engineering Solutions to Improve Patient Safety, Bradley Watts, Douglas Van Citters, Brian Shiner, and Peter Mills

Submissions from 2011

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High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, and Nicky C. Caiazza

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Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium Thermocellum, Steven D. Brown, Adam M. Guss, Tatiana V. Karpinets, and Jerry M. Parks

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Does the Normal Stress Parallel to the Sliding Plane Affect the Friction of Ice upon Ice?, Andrew L. Fortt and Erland M. Schulson

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Resource Letter NO-1: Nonlinear Optics, Elsa Garmire

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Crystal Structure of a Charge Engineered Human Lysozyme Having Enhanced Bactericidal Activity, Avinash Gill, Thomas C. Scanlon, Daniel C. Osipovitch, Dean R. Madden, and Karl E. Griswold

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Current Review of In Nivo GBM Rodent Models: Emphasis on the CNS-1 Tumour Model, Valerie L. Jacobs, Pablo A. Valdes, William F. Hickey, and Joyce A. De Leo

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Genetically Engineered Alginate Lyase-PEG Conjugates Exhibit Enhanced Catalytic Function and Reduced Immunoreactivity, John W. Lamppa, Margaret E. Ackerman, Jennifer I. Lai, Thomas C. Scanlon, and Karl E. Griswold

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Dual-Channel Imaging System for Singlet Oxygen and Photosensitizer for PDT, Seonkyung Lee, Martin E. Isabelle, Kristin L. Gabally-Kinney, Brian W. Pogue, and Steven J. Davis

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Protein-Protein Fusion Catalyzed by Sortase A, David A. Levary, Ranganath Parthasarathy, Eric T. Boder, and Margaret E. Ackerman

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Approach to Accurately Measuring the Speed of Optical Precursors, Chuan-Feng Li, Zong-Quan Zhou, Heejeong Jeong, and Guang-Can Guo

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Remote Positioning Optical Breast Magnetic Resonance Coil for Slice-Selection During Image-Guided Near-Infrared Spectroscopy of Breast Cancer, Michael A. Mastanduno, Shudong Jiang, Brian W. Pogue, Keith D. Paulsen, and Roberta DiFlorio-Alexander

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A scanning electron microscope technique for identifying the mineralogy of dust in ice cores, Rachel Obbard, Ian Baker, and David Prior

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A scanning electron microscope technique for identifying the mineralogy of dust in ice cores, Rachel Obbard, Ian Baker, and David Prior

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Microstructural evolution in the fine-grained region of the Sip le Dome (Antarctica) ice core, Rachel Obbard, K E. Sieg, Ian Baker, D Meese, and G A. Catania

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Using Borehole Logging and Electron Backscatter Diffraction to Orient an Ice Core from Upper Fremont Glacier, Wyoming, USA, R. W. Obbard, T. Cassano, K. Aho, G. Troderman, and I. Baker

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Arctic sea-ice melt in 2008 and the role of solar heating, Donald K. Perovich, Jacqueline A. Richter-Menge, Kathleen F. Jones, and Bonnie Light

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Seasonal ice mass-balance buoys: adapting tools to the changing Arctic, Chris Polashenski, Don Perovich, Jackie Richter-Menge, and Bruce Elder

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Frost flowers in the laboratory: Growth, characteristics, aerosol, and the underlying sea ice, H K. Roscoe, B Brooks, A V. Jackson, M H. Smith, S J. Walker, Rachel Obbard, and E W. Wolff