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

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Submissions from 2022

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Reframe Patterns Lesson, Nitya Agarwala, Ava J. Ori, Anthony W. Fosu, and Rafe Steinhauer

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Pathways to Impact Lesson, Chukwuka V. Odigbo and Rafe Steinhauer

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Designing Handoffs Lesson, Ava J. Ori, Anthony W. Fosu, Nitya Agarwala, and Rafe H. Steinhauer

Submissions from 2021

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Color Cherenkov imaging of clinical radiation therapy, Daniel A. Alexander, Anthony Nomezine, Lesley A. Jarvis, David J. Gladstone, Brian W. Pogue, and Petr Bruza

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Simulating 50 kev x-ray photon detection in silicon with a down-conversion layer, Kaitlin M. Anagnost, Eldred Lee, Zhehui Wang, Jifeng Liu, and Eric R. Fossum

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OPTIMADE, an API for exchanging materials data, Casper W. Andersen, Rickard Armiento, Evgeny Blokhin, Gareth J. Conduit, Shyam Dwaraknath, Matthew L. Evans, Ádám Fekete, Abhijith Gopakumar, Saulius Gražulis, Andrius Merkys, Fawzi Mohamed, Corey Oses, Giovanni Pizzi, Gian Marco Rignanese, Markus Scheidgen, Leopold Talirz, Cormac Toher, Donald Winston, Rossella Aversa, and Kamal Choudhary

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Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings, Dhananjay Beri, Christopher D. Herring, Sofie Blahova, Suresh Poudel, Richard J. Giannone, Robert L. Hettich, and Lee R. Lynd

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Breath can discriminate tuberculosis from other lower respiratory illness in children, Carly A. Bobak, Lili Kang, Lesley Workman, Lindy Bateman, Mohammad S. Khan, Margaretha Prins, Lloyd May, Flavio A. Franchina, Cynthia Baard, Mark P. Nicol, Heather J. Zar, and Jane E. Hill

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Diverse antiviral IgG effector activities are predicted by unique biophysical antibody features, Hao D. Cheng, Karen G. Dowell, Chris Bailey-Kellogg, Brittany A. Goods, J. Christopher Love, Guido Ferrari, Galit Alter, Johannes Gach, Donald N. Forthal, George K. Lewis, Kelli Greene, Hongmei Gao, David C. Montefiori, and Margaret E. Ackerman

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Biophysical Evaluation of Rhesus Macaque Fc Gamma Receptors Reveals Similar IgG Fc Glycoform Preferences to Human Receptors, Andrew R. Crowley, Nana Yaw Osei-Owusu, Gillian Dekkers, Wenda Gao, Manfred Wuhrer, Diogo M. Magnani, Keith A. Reimann, Seth H. Pincus, Gestur Vidarsson, and Margaret E. Ackerman

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Materials property prediction for limited datasets enabled by feature selection and joint learning with MODNet, Pierre-Paul De Breuck, Geoffroy Hautier, and Gian Marco Rignanese

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Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter, Yijie Deng, Douglas Raymond Beahm, Steven Ionov, and Rahul Sarpeshkar

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Photodynamic priming with triple-receptor targeted nanoconjugates that trigger T cell-mediated immune responses in a 3D in vitro heterocellular model of pancreatic cancer, Pushpamali De Silva, Shazia Bano, Brian W. Pogue, Kenneth K. Wang, Edward V. Maytin, and Tayyaba Hasan

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Visualizing temperature-dependent phase stability in high entropy alloys, Daniel Evans, Jiadong Chen, George Bokas, Wei Chen, Geoffroy Hautier, and Wenhao Sun

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A bioimpedance-based monitor for real-time detection and identification of secondary brain injury, Alicia Everitt, Brandon Root, Daniel Calnan, Preston Manwaring, David Bauer, and Ryan Halter

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Design of gate-tunable graphene electro-optical reflectors based on an optical slot-antenna coupled cavity, Tao Fang, Xiaoxue Gao, Xiaoxin Wang, and Jifeng Liu

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Performance assessment of MRI guided continuous wave near-infrared spectral tomography for breast imaging, Jinchao Feng, Shudong Jiang, Brian W. Pogue, and Keith D. Paulsen

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Microstructures in a shear margin: Jarvis Glacier, Alaska, Christopher Gerbi, Stephanie Mills, Renée Clavette, Seth Campbell, Steven Bernsen, David Clemens-Sewall, Ian Lee, Robert Hawley, Karl Kreutz, and Kate Hruby

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Detecting supraglacial debris thickness with GPR under suboptimal conditions, Alexandra Giese, Steven Arcone, Robert Hawley, Gabriel Lewis, and Patrick Wagnon

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Revisiting an IgG Fc Loss-of-Function Experiment: The Role of Complement in HIV Broadly Neutralizing Antibody b12 Activity, Benjamin S. Goldberg, Chengzi I. Kaku, Jérémy Dufloo, Timothée Bruel, Olivier Schwartz, David A. Spencer, Ann J. Hessell, and Margaret E. Ackerman

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Sparsity-based recovery of three-dimensional photoacoustic images from compressed single-shot optical detection, Dylan Green, Anne Gelb, and Geoffrey P. Luke

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The influence of snow on sea ice as assessed from simulations of CESM2, Marika M. Holland, David Clemens-Sewall, Laura Landrum, Bonnie Light, Donald Perovich, Chris Polashenski, Madison Smith, and Melinda Webster

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Clinically relevant dual probe difference specimen imaging (DDSI) protocol for freshly resected breast cancer specimen staining, Broderick J. House, Marcus J. Kwon, Jasmin M. Schaefer, Connor W. Barth, Allison Solanki, Scott C. Davis, and Summer L. Gibbs

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Ultracompact fluorescence smartphone attachment using built-in optics for protoporphyrin-IX quantification in skin, Brady Hunt, Samuel S. Streeter, Alberto J. Ruiz, M. Shane Chapman, and Brian W. Pogue

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Influence of high road labor policies and practices on renewable energy costs, decarbonization pathways, and labor outcomes, Erin Mayfield and Jesse Jenkins

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The Crossroads of Glycoscience, Infection, and Immunology, Tanya R. McKitrick, Margaret E. Ackerman, Robert M. Anthony, Clay S. Bennett, Michael Demetriou, Gregory A. Hudalla, Katharina Ribbeck, Stefan Ruhl, Christina M. Woo, Loretta Yang, Seth J. Zost, Ronald L. Schnaar, and Tamara L. Doering

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Amagmatic hydrothermal systems on Mars from radiogenic heat, Lujendra Ojha, Suniti Karunatillake, Saman Karimi, and Jacob Buffo

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Meltwater sources and sinks for multiyear Arctic sea ice in summer, Don Perovich, Madison Smith, Bonnie Light, and Melinda Webster

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Dramatic reduction of distant pancreatic metastases using local light activation of verteporfin with nab-paclitaxel, Michael Pigula, Zhiming Mai, Sriram Anbil, Myung Gyu Choi, Kenneth Wang, Edward Maytin, Brian Pogue, and Tayyaba Hasan

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Optimization of in vivo Cherenkov imaging dosimetry via spectral choices for ambient background lights and filtering, Mahbubur Rahman, Petr Bruza, Rachael Hachadorian, Daniel Alexander, Xu Cao, Rongxiao Zhang, David J. Gladstone, and Brian W. Pogue

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CT for estimating adequacy of lymph node dissection in patients with squamous cell carcinoma of the head and neck, Christiaan A. Rees, Joshua H. Litchman, Xiaotian Wu, Mariah M. Servos, Darcy A. Kerr, Ryan J. Halter, David A. Pastel, and Joseph A. Paydarfar

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3D printing fluorescent material with tunable optical properties, Alberto J. Ruiz, Sadhya Garg, Samuel S. Streeter, Mia K. Giallorenzi, Ethan P.M. LaRochelle, Kimberley S. Samkoe, and Brian W. Pogue

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Usability Assessment of a Bluetooth-Enabled Resistance Exercise Band Among Young Adults, Lillian M. Seo, Curtis L. Peterson, Ryan J. Halter, David Kotz, Karen L. Fortuna, and John A. Batsis

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A Safety Factor Approach to Designing Urban Infrastructure for Dynamic Conditions, Sanjib Sharma, Ben Seiyon Lee, Robert E. Nicholas, and Klaus Keller

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Developing diagnostic assessment of breast lumpectomy tissues using radiomic and optical signatures, Samuel S. Streeter, Brady Hunt, Rebecca A. Zuurbier, Wendy A. Wells, Keith D. Paulsen, and Brian W. Pogue

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Rational design of on-chip gold plasmonic nanoparticles towards ctDNA screening, Amogha Tadimety, Ziqian Wu, John H. Molinski, Russell Beckerman, Congran Jin, Lauren Zhang, Timothy J. Palinski, and John X.J. Zhang

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Gaussian-preserved, non-volatile shape morphing in three-dimensional microstructures for dual-functional electronic devices, Ziao Tian, Borui Xu, Guangchao Wan, Xiaomin Han, Zengfeng Di, Zi Chen, and Yongfeng Mei

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Considering uncertainties expands the lower tail of maize yield projections, Haochen Ye, Robert E. Nicholas, Samantha Roth, and Klaus Keller

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Fabrication of monodisperse magnetic nanorods for improving hyperthermia efficacy, Shan Zhao, Nanjing Hao, John X.J. Zhang, P. Jack Hoopes, Fridon Shubitidze, and Zi Chen

Submissions from 2019

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Characterizing Short-Wave Infrared Fluorescence of Conventional Near-Infrared Fluorophores, Brook K. Byrd, Margaret R. Folaron, Joseph P. Leonor, Rendall R. Strawbridge, Xu Cao, Petr Bruza, and Scott C. Davis

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1/fNoise Modelling and Characterization for CMOS Quanta Image Sensors, Wei Deng and Eric R. Fossum

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Signal Intensity Analysis and Optimization for in Vivo Imaging of Cherenkov and Excited Luminescence., Ethan P. M. LaRochelle, Jennifer R. Shell, Jason R. Gunn, Scott C. Davis, and Brian W. Pogue

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Biomedical Engineering or Biomedical Optics: Will the Real Discipline Please Stand Up?, Brian W. Pogue

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Ensuring Scientific Publishing Credibility in Translational Biomedical Optics., Brian W. Pogue

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Diagnostic Performance of Receptor-Specific Surgical Specimen Staining Correlates with Receptor Expression Level, Jasmin M. Schaefer, Connor W. Barth, Scott C. Davis, and Summer L. Gibbs

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Characterization of a Non-Contact Imaging Scintillator-Based Dosimetry System for Total Skin Electron Therapy., Irwin I. Tendler, Petr Bruza, Michael Jermyn, Xu Cao, Benjamin B. Williams, Lesley A. Jarvis, Brian W. Pogue, and David J. Gladstone

Submissions from 2018

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Radiotherapy-Induced Cherenkov Luminescence Imaging in a Human Body Phantom, Syed Rakin Ahmed, Mengyu Jia, Petr Bruza, Sergei A. Vinogradov, Shudong Jiang, David J. Gladstone, Lesley A. Jarvis, and Brian W. Pogue

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Cherenkov Excited Short-Wavelength Infrared Fluorescence Imaging in vivo with External Beam Radiation, Xu Cao, Shudong Jiang, Mengyu Jeremy Jia, Jason R. Gunn, Tianshun Miao, Scott C. Davis, Petr Bruza, and Brian W. Pogue

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Tissue Oxygen Saturation Predicts Response to Breast Cancer Neoadjuvant Chemotherapy within 10 Days of Treatment, Jeffrey M. Cochran, David R. Busch, Anais Leproux, Zheng Zhang, Thomas D. O'Sullivan, Albert E. Cerussi, Philip M. Carpenter, Rita S. Mehta, Darren Roblyer, Wei Yang, Keith D. Paulsen, Brian Pogue, Shudong Jiang, and Peter A. Kaufman

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What Design Practices Do Professionals Use for Sustainability and Innovation?, Jeremy Faludi and Alice M. Agogino

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Novel Materials Can Radically Improve Whole-System Environmental Impacts of Additive Manufacturing, Jeremy Faludi, Cory M. Van Sice, Yuan Shi, Justin Bower, and Owen M.K Brooks

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Weighting Function Effects in a Direct Regularization Method for Image-Guided Near-Infrared Spectral Tomography of Breast Cancer., Jinchao Feng, Shudong Jiang, Brian W. Pogue, and Keith Paulsen

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Multi-Beam Scan Analysis with a Clinical LINAC for High Resolution Cherenkov-Excited Molecular Luminescence Imaging in Tissue., Mengyu Jeremy Jia, Peter Bruza, Lesley A. Jarvis, David J. Gladstone, and Brian W. Pogue

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Review of Methods for Intraoperative Margin Detection for Breast Conserving Surgery, Benjamin W. Maloney, David M. McClatchy, Brian W. Pogue, Keith D. Paulsen, Wendy A. Wells, and Richard J. Barth

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Optimal Wavelength Selection for Optical Spectroscopy of Hemoglobin and Water within a Simulated Light-Scattering Tissue, Mikael Marois, Stephen L. Jacques, and Keith D. Paulsen

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Light Scattering Measured with Spatial Frequency Domain Imaging can Predict Stromal Versus Epithelial Proportions in Surgically Resected Breast Tissue, David M. McClatchy, Elizabeth J. Rizzo, Wendy A. Wells, Candice C. Black, Keith D. Paulsen, Stephen C. Kanick, and Brian W. Pogue

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Calibration and Analysis of a Multimodal Micro-CT and Structured Light Imaging System for the Evaluation of Excised Breast Tissue., David M. McClatchy III, Elizabeth J. Rizzo, Jeff Meganck, Josh Kempner, Jared Vicory, Wendy A. Wells, Keith D. Paulsen, and Brian W. Pogue

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Micro-Computed Tomography Enables Rapid Surgical Margin Assessment During Breast Conserving Surgery (BCS): Correlation of Whole BCS Micro-CT Readings to Final Histopathology., David M. McClatchy III, Rebecca A. Zuurbier, Wendy A. Wells, Kieth D. Paulsen, and Brian W. Pogue

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Biomedical Optics Scientific Community, Brian W. Pogue

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Can Novel Technologies Improve Breast Conserving Surgery?, Brian W. Pogue

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Grant Funding Needs Parallel the Start-Up Venture: An Analogy for Translational Research Success, Brian W. Pogue

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Medical Perspective Articles to Stimulate the Field for Needs-Finding, Brian W. Pogue

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Perspective Review of what is Needed for Molecular-Specific Fluorescence-Guided Surgery, Brian W. Pogue, Eben L. Rosenthal, Samuel Achilefu, and Gooitzen M. van Dam

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Optical and X-Ray Technology Synergies Enabling Diagnostic and Therapeutic Applications in Medicine, Brian W. Pogue and Brian C. Wilson

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Correcting for Targeted and Control Agent Signal Differences in Paired-Agent Molecular Imaging of Cancer Cell-Surface Receptors, Negar Sadeghipour, Scott C. Davis, and Kenneth M. Tichauer

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Quantifying Cancer Cell Receptors with Paired-Agent Fluorescent Imaging: a Novel Method to Account for Tissue Optical Property Effects., Negar Sadeghipour, Scott C. Davis, and Kenneth M. Tichauer

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Application of Fluorescence-Guided Surgery to Subsurface Cancers Requiring Wide Local Excision: Literature Review and Novel Developments Toward Indirect Visualization., Kimberly S. Samkoe, Brent D. Bates, Jonathan T. Elliott, Ethan LaRochelle, Jason R. Gunn, Kayla Marra, Joachim Feldwisch, Dipak B. Ramkumar, David F. Bauer, Keith D. Paulsen, Brian W. Pogue, and Eric R. Henderson

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Algorithm Development for Intrafraction Radiotherapy Beam Edge Verification from Cherenkov Imaging., Clare Snyder, Brian W. Pogue, Michael Jermyn, and Irwin Tendler

Submissions from 2017

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Optimizing Fresh Specimen Staining for Rapid Identification of Tumor Biomarkers During Surgery., Connor W. Barth, Jasmin M. Schaefer, Vincent M. Rossi, Scott C. Davis, and Summer L. Gibbs

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Hyperspectral Data Processing Improves PpIX Contrast During Fluorescence Guided Surgery of Human Brain Tumors., Jaime J. Bravo, Jonathan D. Olson, Scott C. Davis, David W. Roberts, Keith D. Paulsen, and Stephen C. Kanick

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Single-crystal Ih Ice Surfaces Unveil Connection between Macroscopic and Molecular Structure, Alexandra Brumberg, Kevin Hammonds, Ian Baker, Ellen H.G Backus, Patrick J. Bisson, Mischa Bonn, Charles P. Daghlian, Markus Mezger, and Mary Jane Schultz

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Impact of MODIS sensor calibration updates on Greenland Ice Sheet surface reflectance and albedo trends, Kimberly A. Casey, Chris M. Polashenski, Justin Chen, and Marco Tedesco

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Apertureless Near-Field Scanning Probes Based on Graphene Plasmonics, Hamid T. Chorsi and John X. Zhang

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Development of a Core Clostridium Thermocellum Kinetic Metabolic Model Consistent with Multiple Genetic Perturbations, Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K. Holwerda, Daniel Olson, Lee Lynd, and Costas Maranas

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Assessing Daylight & Low-Dose Rate Photodynamic Therapy Efficacy, Using Biomarkers of Photophysical, Biochemical and Biological Damage Metrics in Situ., Ana Luiza Ribeiro de Souza, Ethan LaRochelle, Kayla Marra, Jason Gunn, Scott C. Davis, Kimberley S. Samoke, M. Shane Chapman, Edward V. Maytin, Tayyaba Hasan, and Brian W. Pogue

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Boosting of HIV Envelope Cd4 Binding Site Antibodies with Long Variable Heavy Third Complementarity Determining Region in the Randomized Double Blind Rv305 Hiv-1 Vaccine Trial, David Easterhoff, M. Anthony Moody, Daniela Fera, Hao Cheng, and Margaret Ackerman

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Simultaneous In Vivo Fluorescent Markers for Perfusion, Protoporphyrin Metabolism, and EGFR Expression for Optically Guided Identification of Orthotopic Glioma, Jonathon T. Elliot, Kayla Marra, Linton T. Evans, Scott C. Davis, Kimberly Samkoe, Joachim Feldwisch, Keith D. Paulsen, David W. Roberts, and Brian W. Pogue

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Golden Tools in Green Design: What Drives Sustainability, Innovation, and Value in Green Design Methods?, Jeremy Faludi

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Recommending Sustainable Design Practices by Characterizing Activities And Mindsets, Jeremy Faludi

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What Green Design Activities and Mindsets Drive Innovation and Sustainability in Student Teams?, Jeremy Faludi, Alice Agogino, Sara Beckman, and Alastair Isles

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Environmental Impacts of Selective Laser Melting: Do Printer, Powder, Or Power Dominate?, Jeremy Faludi, Martin Baumers, Ian Maskery, and Richard Hague

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Addition of T2-Guided Optical Tomography Improves Noncontrast Breast Magnetic Resonance Imaging Diagnosis., Jinchao Feng, Junqing Xu, Shudong Jiang, Hong Yin, Yan Zhao, Jiang Gui, Ke Wang, Xiuhua Lv, Fang Ren, Brian W. Pogue, and Keith D. Paulsen

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Streptomyces Exploration is Triggered by Fungal Interactions and Volatile Signals, Stephanie E. Jones, Louis Ho, Christiaan A. Rees, Jane E. Hill, Justin R. Nodwell, and Marie A. Elliot

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Performance Assessment of Diffuse Optical Spectroscopic Imaging Instruments in a 2-Year Multicenter Breast Cancer Trial, Anais Leproux, Thomas D.O. Sullivan, Albert E. Cerussi, Amanda Durkin, Brian Hill, Nola M. Hylton, Arjun G. Yodh, Stefan A. Carp, David A. Boas, Shudong Jiang, Keith D. Paulsen, Brian W. Pogue, Darren M. Roblyr, Wei T. Yang, and Bruce J. Tromberg

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Collagen Complexity Spatially Defines Microregions of Total Tissue Pressure in Pancreatic Cancer., Michael D. Nieskoski, Kayla Marra, Jason R. Gunn, P. Jack Hoopes, Marvin M. Doyley, Tayyaba Hasan, B. Stuart Trembly, and Brian W. Pogue

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MLFMM techniques for efficient analysis of random array configuration for Square Kilometer Array (SKA) radio telescope, S K. Padhi

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Generalized paired-agent kinetic model for in vivo quantification of cancer cell-surface receptors under receptor saturation conditions, N Sadeghipour, Scott Davis, and K M. Tichauer

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Development and Evaluation of a Connective Tissue Phantom Model for Subsurface Visualization of Cancers Requiring Wide Local Excision, Kimberly S. Samkoe, Brent D. Bates, Niki N. Tselepidakis, Alisha V. Dsouza, Jason R. Gunn, Dipak B. Ramkumar, Keith D. Paulsen, Brian W. Pogue, and Eric R. Henderson

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Optimization of Fluorescent Imaging in the Operating Room through Pulsed Acquisition and Gating to Ambient Background Cycling, Kristian J. Sexton, Yan Zhao, Scott C. Davis, Shudong Jiang, and Brian Pogue

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Optimization of fluorescent imaging in the operating room through pulsed acquisition and gating to ambient background cycling, Kristian Sexton, Yan Zhao, Scott Davis, Shudong Jiang, and Brian Pogue

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Preclinical Evaluation of Spatial Frequency Domain-Enabled Wide-Field Quantitative Imaging for Enhanced Glioma Resection, Mira Sibai, Carl Fisher, Israel Veilleux, Jonathan T. Elliot, Frederic Leblond, David W. Roberts, and Brian Wilson

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A numerical framework for interstitial fluid pressure imaging in poroelastic MRE, Likun Tan, Matthew McGarry, Elijah E. W. Van Houten, and Ming Ji

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A Hybrid Dynamic System Assessment Methodology for Multi-Modal Transportation-Electrification, Thomas J.T van der Wardt and Amro M. Farid

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Both adhE and a Separate NADPH-Dependent Alcohol Dehydrogenase Gene, adhA, Are Necessary for High Ethanol Production in Thermoanaerobacterium saccharolyticum, Tianyong Zheng, Daniel G. Olson, Sean J. Murphy, Xiongjun Shao, Liang Tian, and Lee Lynd

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Neurologic Correlates of Gait Abnormalities in Cerebral Palsy: Implications for Treatment, Joanne Zhou, Erin E. Butler, and Jessica Rose

Submissions from 2016

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Polyfunctional Hiv-Specific Antibody Responses Are Associated with Spontaneous Hiv Control, Margaret E. Ackerman, Anastassia Mikhailova, Eric P. Brown, Karen G. Dowell, Bruce D. Walker, Chris Bailey-Kellogg, Todd J. Suscovich, and Galit Alter

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Quantum Random Number Generation Using a Quanta Image Sensor, Emna Amri, Yacine Felk, Damien Stucki, Jiaju Ma, and Eric Fossum

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Biophysical and Functional Characterization of Rhesus Macaque IgG Subclasses, Austin W. Boesch, Nana Yaw Osei-Owusu, Andrew R. Crowley, Thach H. Chu, Ying Chan, Joshua Weiner, Pranay Bharadwaj, Rufus Hards, Mark Adamo, Scott Gerber, Sarah Cocklin, Joern Schmitz, Adam Miles, Joshua Eckman, Aaron J. Belli, Keith Reimann, and Margaret E. Ackerman

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Quantitative Multi-plexed Fluorescence Spectroscopy in the Presence of a Strong Fluorescent Marker, Jaime J. Bravo, Scott Davis, Keith D. Paulsen, David W. Roberts, and Stephen Kanick

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Mathematical model to interpret localized reflectance spectra measured in the presence of a strong fluorescence marker, Jamie J. Bravo, Scott C. Davis, David W. Roberts, Keith D. Paulsen, and Stephen Kanick