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1. Detection and characterization of nonspecific, sparsely-populated binding modes for conformational selection in the early stages of complexation
Published: 3/18/2015
Authors: Antonio Cardone, Aaron Bornstein, Harish C. Pant, Mary C Brady, Ram D Sriram, Sergio Hassan
Abstract: A method is proposed to study protein-ligand binding in a system governed by specific and non-specific interactions. Strong associations lead to narrow conformational distributions in the proteins configuration space; weak and ultra-weak associations ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=917286

2. Background Intensity Correction for Terabyte-Sized Time-Lapse Images
Published: 12/30/2014
Authors: Joe Chalfoun, Michael P Majurski, Kiran Bhadriraju, Steven P Lund, Peter Bajcsy, Mary C Brady
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=915208

3. Calibrating multiple microscopes with a smartphone
Published: 4/1/2014
Authors: Peter Bajcsy, Mary C Brady, Jacob Siegel
Abstract: Summary: The iPhone liquid crystal displays allows efficient and accurate calibration of an inexpensive array of handheld microscopes for measuring microscopic dynamic events over a large field of view. How does one build an inexpensive array of ha ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914722

4. Depicting Web Images for the Blind and Visually Impaired
Published: 12/9/2013
Authors: Andrea Bajcsy, YaShian Li-Baboud, Mary C Brady
Abstract: A prototype to translate web graph and map images into 3D printed models in order to give the blind and visually impaired access to voting and election information.
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914629

5. Ontology for Big Systems: The Ontology Summit 2012 Communique
Published: 10/16/2013
Authors: Ram D Sriram, Mary C Brady
Abstract: The Ontology Summit 2012 explored the current and potential uses of ontology, its methods and paradigms, in big systems and big data: How ontology can be used to design, develop, and operate such systems. The systems addressed were not just software ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=911587

6. Re-projection of Terabyte-Sized Images
Published: 10/7/2013
Authors: Peter Bajcsy, Antoine Vandecreme, Mary C Brady
Abstract: This work addresses the problem of re-projecting a terabyte-sized 3D data set represented as a set of 2D Deep Zoom pyramids. In general, a re-projection for small 3D data sets is executed directly in RAM. However, RAM becomes a limiting factor for te ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914488

7. Terabyte Size Image Computations on Hadoop Cluster Platforms
Published: 10/7/2013
Authors: Peter Bajcsy, Antoine Vandecreme, Julien M. Amelot, Phuong Thi Thu Nguyen, Joe Chalfoun, Mary C Brady
Abstract: We present a characterization of four basic terabyte size image computations on a Hadoop cluster in terms of their relative efficiency according to the modified Amdahl‰s law. The work is motivated by the fact that there is a lack of standard benchmar ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914001

8. Parallel Geometric Classification of Stem Cells by Their 3D Morphology
Published: 7/1/2013
Authors: Derek Juba, Antonio Cardone, Cheuk Yiu Ip, Carl George Simon Jr., Christopher K. Tison, Girish Kumar, Mary C Brady
Abstract: Autologous stem cells show great promise for tissue engineering as they can regenerate diseased or damaged tissue, without requiring an organ donor or causing immune rejection. A primary goal of regenerative medicine is to identify methods for contr ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=912852

9. A Hybrid CPU-GPU System for Fourier-Based Stitching of Optical Microscopy Images
Published: 3/15/2013
Authors: Walid Keyrouz, Bertrand Clement Stivalet, Timothy J Blattner, Shujia Zhou, Joe Chalfoun, Mary C Brady
Abstract: We present a high performance hybrid CPU-GPU implementation that accelerates the Fourier-based stitching of 2D optical microscopy images to less than 1-minute (end-to-end execution times). This implementation takes advantage of coarse-grained parall ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913080

10. A Hybrid CPU-GPU Approach to Fourier-Based Image Stitching of Optical Microscopy Images
Published: 3/3/2013
Authors: Walid Keyrouz, Timothy J Blattner, Bertrand Clement Stivalet, Joe Chalfoun, Mary C Brady, Shujia Zhou
Abstract: We present a hybrid CPU-GPU approach for the Fourier-based stitching of optical microscopy images. This system achieves sub-minute stitching rates with large grids; it stitches a grid of 59x42 tiles in 26 seconds on a two-CPU (8 physical cores) & two ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913305



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