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Search Publications by: John T. Elliott (Fed)

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Displaying 1 - 25 of 75

An Infrastructure for Curating, Querying, and Augmenting Document Data: COVID-19 Case Study

August 8, 2023
Author(s)
Eswaran Subrahmanian, Guillaume Sousa Amaral, Talapady N. Bhat, Mary C. Brady, Kevin G. Brady, Jacob Collard, Sarra Chouder, Philippe Dessauw, Alden A. Dima, John T. Elliott, Walid Keyrouz, Nicolas Lelouche, Benjamin Long, Rachael Sexton, Ram D. Sriram
With the advent of the COVID-19 pandemic, there was the hope that data science approaches could help discover means for understanding, mitigating, and treating the disease. This manifested itself in the creation of the COVID-19 Open Research Dataset (CORD

Technical Framework for High Quality New Approach Methodologies (NAMs)

July 15, 2022
Author(s)
Elijah Petersen, John T. Elliott, John Gordon, Nicole Kleinstreuer, Emily Reinke, Matthias Roesslein, Blaza Toman
New approach methodologies (NAMs) are in vitro, in chemico, and computational approaches that can potentially be used to reduce animal testing. For NAMs that require laboratory experiments, it is critical that they provide consistent and reliable results

Characteristics to Consider when Selecting a Positive Control Material for an In Vitro Assay

September 29, 2021
Author(s)
Elijah Petersen, Andrew Nguyen, Jeffrey Brown, John T. Elliott, Amy Clippinger, John Gordon, Nicole Kleinstreuer, Matthias Roesslein
The use of in vitro assays to inform decision-making requires robust and reproducible results across studies, laboratories, and time. Experiments using positive control materials are an integral component of an assay procedure to demonstrate the extent to

Accurate and Robust Trypan Blue-Based Cell Viability Measurement Using Neural Networks

July 19, 2021
Author(s)
Adele Peskin, Steven Lund, Chenyi Ling, Laura Pierce, Sumona Sarkar, Firdavs Kurbanov, Michael Halter, Joe Chalfoun, John T. Elliott
Trypan blue dye exclusion-based cell viability measurements are highly dependent upon image quality and consistency. In order to make measurements repeatable, one must be able to reliably capture images at a consistent focal plane, and with signal-to-noise

Workshop 13: Building Measurement Assurance in Flow Cytometry

June 17, 2019
Author(s)
Lili Wang, Stephen Perfetto, Robert Hoffman, John T. Elliott, Sheng Lin-Gibson, Steven Bauer, Heba Degheidy, Judith Arcidiacono, Litwin Virginia
Two workshops were held to identify measurement challenges and potential solutions for building measurement assurance for flow cytometry. This report summarizes key findings, including the need for high quality reagents, reference standards or materials

Generating Domain Terminologies using Root- and Rule-Based Terms

December 21, 2018
Author(s)
Talapady N. Bhat, John T. Elliott, Ursula R. Kattner, Carelyn E. Campbell, Eswaran Subrahmanian, Ram D. Sriram, Jacob Collard, Monarch Ira
Motivated by the need for exible, intuitive, reusable, and normalized ter- minology for the semantic web, we present a general approach for generat- ing sets of such terminologies from nat- ural language documents. The terms that this approach generates

How measurement science can improve confidence in research results

April 23, 2018
Author(s)
Anne L. Plant, Chandler A. Becker, Robert J. Hanisch, Ronald F. Boisvert, Antonio M. Possolo, John T. Elliott
The concepts and methods of measurement science can help provide clarity in the definition of reproducibility and its role in the scientific process. The qualities of rigorous research include reproducibility as one component, but there are other important

Agglomeration of Escherichia coli with positively charged nanoparticles can lead to artifacts in a standard Caenorhabditis elegans toxicity assay

April 19, 2018
Author(s)
Shannon Hanna, Antonio Montoro Bustos, Alexander W. Peterson, Vytas Reipa, Leona D. Scanlan, Sanem Hosbas Coskun, Tae Joon Cho, Monique Johnson, Vincent A. Hackley, Bryant C. Nelson, Michael R. Winchester, John T. Elliott, Elijah Petersen
The increased use and incorporation of engineered nanoparticles (ENPs) in consumer products requires a robust assessment of their potential environmental implications. However, a lack of standardized methods for nanotoxicity testing has yielded results

Large Field of View Quantitative Phase Imaging of Induced Pluripotent Stem Cells and Optical Pathlength Reference Materials

February 23, 2018
Author(s)
Edward J. Kwee, Alexander W. Peterson, Jeffrey R. Stinson, Michael W. Halter, Liya Yu, Michael P. Majurski, Joe Chalfoun, Peter Bajcsy, John T. Elliott
Induced pluripotent stem cells (iPSCs) are reprogrammed cells that can have heterogeneous biological potential. Quality assurance metrics of reprogrammed iPSCs will be critical to ensure reliable use in cell therapies and personalized diagnostic tests. We

Counting Caenorhabditis elegans: Protocol Optimization and Applications for Population Growth and Toxicity Studies in Liquid Medium

January 17, 2018
Author(s)
Steven Lund, Sanem Hosbas Coskun, Monique Johnson, Christopher Sims, Elijah Petersen, John T. Elliott, Bryant C. Nelson, Leona D. Scanlan, Shannon K. Hanna, Karina Brignoni, Patricia Lapasett
The nematode Caenorhabditis elegans is used extensively in molecular, toxicological and genetics research. However, standardized methods for counting nematodes in liquid culture do not exist despite the wide use of nematodes and need for accurate

A novel measure and significance testing in data analysis of cell image segmentation

April 20, 2017
Author(s)
Jin Chu Wu, Michael W. Halter, Raghu N. Kacker, John T. Elliott, Anne L. Plant
Background: Cell image segmentation (CIS) is an essential part of quantitative imaging of biological cells. Designing a performance measure and conducting significance testing are critical for evaluating and comparing the CIS algorithms for image-based

Separation, Sizing, and Quantitation of Engineered Nanoparticles in an Organism Model Using Inductively Coupled Plasma Mass Spectrometry and Image Analysis

December 16, 2016
Author(s)
Monique E. Johnson, Shannon Hanna, Antonio R. Montoro Bustos, Christopher M. Sims, Lindsay C. Elliott, Babak Nikoobakht, John T. Elliott, Richard D. Holbrook, Keana C. Scott, Karen E. Murphy, Elijah J. Petersen, Lee L. Yu, Bryant C. Nelson, Akshay Lingayat, Adrian C. Johnston
For environmental studies assessing uptake of orally ingested engineered nanoparticles (ENPs), a key step in ensuring accurate quantification of ingested ENPs is efficient separation of the organism from ENPs that are either nonspecifically adsorbed to the

Toward Achieving Harmonization in a Nano-cytotoxicity Assay Measurement through an Interlaboratory Comparison Study

September 29, 2016
Author(s)
John T. Elliott, Matthias Roesslein, Nam W. Song, Blaza Toman, Agnieszka Kinsner-Ovaskainen, Rawiwan Maniratanachote, Marc L. Salit, Elijah J. Petersen, Fatima Sequeira, Jieun Lee, Francois Rossi, Cordula Hirsch, Harald Krug, Wongsakorn Suchaoin, Peter Wick
Design and development of reliable cell-based nanotoxicology assays is important for ranking of potential hazardous engineered nanomaterials. Challenges to producing a reliable assay protocol include working with nanoparticle dispersions and living cell

Surface plasmon resonance microscopy: achieving a quantitative optical response

September 8, 2016
Author(s)
Alexander W. Peterson, Michael W. Halter, Anne L. Plant, John T. Elliott
Surface plasmon resonance imaging (SPRI) allows real-time label-free imaging based on index of refraction, and changes in index of refraction at an interface. SPRI can be carried out on a microscope by launching light into a sample, and collecting

Design, sensitivity analysis, and testing of a Caenorhabditis elegans nanoecotoxicity assay

August 11, 2016
Author(s)
Shannon Hanna, Gregory A. Cooksey, Bryant C. Nelson, John T. Elliott, Elijah J. Petersen
Increasing production and usage of engineered nanomaterials (ENMs) has generated widespread interest in measuring their environmental and human health effects. However, the lack of standardized methods for these measurements has often led to contradictory