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112 results on '"THOMAS, C. L. PAUL"'

1. Fast and automated biomarker detection in breath samples with machine learning

Author

Skarysz, Angelika, Salman, Dahlia, Eddleston, Michael, Sykora, Martin, Hunsicker, Eugenie, Nailon, William H, Darnley, Kareen, McLaren, Duncan B, Thomas, C L Paul, and Soltoggio, Andrea

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Signal Processing
Abstract

Volatile organic compounds (VOCs) in human breath can reveal a large spectrum of health conditions and can be used for fast, accurate and non-invasive diagnostics. Gas chromatography-mass spectrometry (GC-MS) is used to measure VOCs, but its application is limited by expert-driven data analysis that is time-consuming, subjective and may introduce errors. We propose a system to perform GC-MS data analysis that exploits deep learning pattern recognition ability to learn and automatically detect VOCs directly from raw data, thus bypassing expert-led processing. The new proposed approach showed to outperform the expert-led analysis by detecting a significantly higher number of VOCs in just a fraction of time while maintaining high specificity. These results suggest that the proposed method can help the large-scale deployment of breath-based diagnosis by reducing time and cost, and increasing accuracy and consistency.

Published
2020

2. IABR Symposium 2021 meeting report: breath standardization, sampling, and testing in a time of COVID-19.

Author

Schmidt, Alexander J, Salman, Dahlia, Pleil, Joachim, Thomas, C L Paul, and Davis, Cristina E

Subjects
Breath Tests, COVID-19, Humans, Reference Standards, SARS-CoV-2
Abstract

Due to COVID-19 travel disruptions, the International Association of Breath Research hosted the planned 2021 Breath Summit virtually as a symposium with oral and poster presentations. The event was comprised of a week-long social media asynchronous online event for sharing research abstracts, posters and discussions. Subsequently, there were two days of real-time webinar platform interactions each featuring three technical presentations, open forum questions, answers, and commentary. The symposium was well attended and well received. It allowed the breath community to share new research and to reconnect with colleagues and friends. This report presents an overview of the topics presented and various salient discussion points.

Published
2021

4. Contributors

Author

Abegg, Sebastian, primary, Ahmed, Waqar, additional, Alkhalifah, Yaser, additional, Apolonski, Alexander, additional, Bean, Heather D., additional, Beauchamp, Jonathan D., additional, Beck, Olof, additional, Berna, Amalia Z., additional, Bikov, Andras, additional, Borras, Eva, additional, Brinkman, Paul, additional, Brodrick, Emma, additional, Corradi, Massimo, additional, Cristescu, Simona M., additional, Cumeras, Raquel, additional, Davis, Cristina E., additional, Davis, Michael D., additional, de Lacy Costello, Ben, additional, Di Natale, Corrado, additional, Dragonieri, Silvano, additional, Dweik, Raed, additional, Egeghy, Peter P., additional, Eiceman, Gary A., additional, Focant, Jean-François, additional, Fowler, Stephen, additional, Frank, Matthias, additional, Geer Wallace, M. Ariel, additional, Ghorbani, Ramin, additional, Gierschner, Peter, additional, Giese, Roger, additional, Gould, Oliver, additional, Güntner, Andreas T., additional, Hackner, Klaus, additional, Haick, Hossam, additional, Hamm, Peter, additional, Hanna, George B., additional, Herbig, Jens, additional, Hill, Jane E., additional, Högman, Marieann, additional, Hohlfeld, Jens M., additional, Holz, Olaf, additional, Jones, Alan W., additional, King, Julian, additional, Köhler, Heike U., additional, Küntzel, Anne, additional, Lan, Jiayi, additional, Lazar, Zsofia, additional, Lehtimäki, Lauri, additional, Madden, Michael C., additional, Malinovschi, Andrei, additional, Marco, Santiago, additional, Mayhew, Christopher A., additional, McCartney, Mitchell M., additional, McCord, James P., additional, Metsälä, Markus, additional, Michils, Alain, additional, Miekisch, Wolfram, additional, Miller, Justin J., additional, Mochalski, Paweł, additional, Modak, Anil S., additional, Nakhleh, Morad K., additional, Nylander-French, Leena A., additional, Odom John, Audrey R., additional, Parte, Francisco Blanco, additional, Pleil, Joachim D., additional, Ranzieri, Silvia, additional, Ratcliffe, Norman M., additional, Reinhold, Petra E., additional, Risby, Terence H., additional, Ruszkiewicz, Dorota, additional, Ruzsanyi, Veronika, additional, Ryter, Stefan W., additional, Salman, Dahlia, additional, Schivo, Michael, additional, Schmidt, Florian M., additional, Schubert, Jochen K., additional, Schwarz, Katharina, additional, Smith, David, additional, Smolinska, Agnieszka, additional, Sobus, Jon R., additional, Solga, Steven F., additional, Spacek, Lisa A., additional, Španěl, Patrik, additional, Stavropoulos, Georgios, additional, Stefanuto, Pierre-Hugues, additional, Stiegel, Matthew A., additional, Teschl, Gerald, additional, Teschl, Susanne, additional, Thomas, C. L. Paul, additional, Unterkofler, Karl, additional, van der Schee, Marc P., additional, van Schooten, Frederik-Jan, additional, Vidal-de-Miguel, Guillermo, additional, Vishinkin, Rotem, additional, Wiesenhofer, Helmut, additional, Williams, Antony J., additional, Yeates, Laura C., additional, Zanella, Delphine, additional, and Zenobi, Renato, additional

Published
2020
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5. Urban search and rescue

Author

Ruzsanyi, Veronika, primary, Wiesenhofer, Helmut, additional, Salman, Dahlia, additional, Thomas, C. L. Paul, additional, Hamm, Peter, additional, Mochalski, Pawe, additional, and Mayhew, Christopher A., additional

Published
2020
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6. Ion mobility spectrometry

Author

Salman, Dahlia, primary, Eiceman, Gary A., additional, Ruszkiewicz, Dorota, additional, Ruzsanyi, Veronika, additional, Brodrick, Emma, additional, and Thomas, C. L. Paul, additional

Published
2020
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7. Peppermint protocol: first results for gas chromatography-ion mobility spectrometry

Author

Ruszkiewicz, Dorota M, primary, Myers, Renelle, additional, Henderson, Ben, additional, Yusof, Hazim, additional, Meister, Austin, additional, Moreno, Sergi, additional, Eddleston, Michael, additional, Darnley, Kareen, additional, Nailon, William H, additional, McLaren, Duncan, additional, Lao, Yvonne E, additional, Hovda, Knut Erik, additional, Lam, Stephen, additional, Cristescu, Simona M, additional, and Thomas, C L Paul, additional

Published
2022
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11. The variability of volatile organic compounds in the indoor air of clinical environments

Author

Salman, Dahlia, primary, Ibrahim, Wadah, additional, Kanabar, Amisha, additional, Joyce, Abigail, additional, Zhao, Bo, additional, Singapuri, Amisha, additional, Wilde, Michael, additional, Cordell, Rebecca L, additional, McNally, Teresa, additional, Ruszkiewicz, Dorota, additional, Hadjithekli, Andria, additional, Free, Robert, additional, Greening, Neil, additional, Gaillard, Erol A, additional, Beardsmore, Caroline, additional, Monks, Paul, additional, Brightling, Chris, additional, Siddiqui, Salman, additional, and Thomas, C L Paul, additional

Published
2021
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16. Breath markers for therapeutic radiation

Author

Salman, Dahlia, primary, Eddleston, Michael, additional, Darnley, Kareen, additional, Nailon, William H, additional, McLaren, Duncan B, additional, Hadjithelki, Andria, additional, Ruszkiewicz, Dorota, additional, Langejuergen, Jens, additional, Alkhalifa, Yaser, additional, Phillips, Iain, additional, and Thomas, C L Paul, additional

Published
2020
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17. A benchmarking protocol for breath analysis: the peppermint experiment

Author

Henderson, Ben, primary, Ruszkiewicz, Dorota M, additional, Wilkinson, Max, additional, Beauchamp, Jonathan D, additional, Cristescu, Simona M, additional, Fowler, Stephen J, additional, Salman, Dahlia, additional, Francesco, Fabio Di, additional, Koppen, Gudrun, additional, Langejürgen, Jens, additional, Holz, Olaf, additional, Hadjithekli, Andria, additional, Moreno, Sergi, additional, Pedrotti, Michele, additional, Sinues, Pablo, additional, Slingers, Gitte, additional, Wilde, Michael, additional, Lomonaco, Tommaso, additional, Zanella, Delphine, additional, Zenobi, Renato, additional, Focant, Jean-François, additional, Grassin-Delyle, Stanislas, additional, Franchina, Flavio Antonio, additional, Malásková, Michaela, additional, Stefanuto, Pierre-Hugues, additional, Pugliese, Giovanni, additional, Mayhew, Christopher, additional, and Thomas, C L Paul, additional

Published
2020
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18. A benchmarking protocol for breath analysis: the peppermint experiment

Author

Ruszkiewicz, Dorota M., Wilkinson, Max, Beauchamp, Jonathan D., Cristescu, Simona M., Fowler, Stephen J., Salman, Dahlia, Di Francesco, Fabio, Koppen, Gudrun, Langejürgen, Jens, Holz, Olaf, Hadjithekli, Andria, Moreno, Sergi, Pedrotti, Michele, Sinues, Pablo, Slingers, Gitte, Wilde, Michael, Lomonaco, Tommaso, Zanella, Delphine, Zenobi, Renato, Focant, Jean-François, Grassin-Delyle, Stanislas, Franchina, Flavio Antonio, Màlàskova, Michaela, Stefanuto, Pierre-Hugues, Pugliese, Giovanni, Mayhew, Christopher, and Thomas, C. L. Paul

Subjects
Peppermint, Repeated sampling, Standardization, Breathomics, Pharmacokinetics, Benchmark
Abstract

Sampling of volatile organic compounds (VOCs) has shown promise for detection of a range of diseases but results have proved hard to replicate due to a lack of standardization. In this work we introduce the 'Peppermint Initiative'. The initiative seeks to disseminate a standardized experiment that allows comparison of breath sampling and data analysis methods. Further, it seeks to share a set of benchmark values for the measurement of VOCs in breath. Pilot data are presented to illustrate the standardized approach to the interpretation of results obtained from the Peppermint experiment. This pilot study was conducted to determine the washout profile of peppermint compounds in breath, identify appropriate sampling time points, and formalise the data analysis. Five and ten participants were recruited to undertake a standardized intervention by ingesting a peppermint oil capsule that engenders a predictable and controlled change in the VOC profile in exhaled breath. After collecting a pre-ingestion breath sample, five further samples are taken at 2, 4, 6, 8, and 10 h after ingestion. Samples were analysed using ion mobility spectrometry coupled to multi-capillary column and thermal desorption gas chromatography mass spectrometry. A regression analysis of the washout data was used to determine sampling times for the final peppermint protocol, and the time for the compound measurement to return to baseline levels was selected as a benchmark value. A measure of the quality of the data generated from a given technique is proposed by comparing data fidelity. This study protocol has been used for all subsequent measurements by the Peppermint Consortium (16 partners from seven countries). So far 1200 breath samples from 200 participants using a range of sampling and analytical techniques have been collected. The data from the consortium will be disseminated in subsequent technical notes focussing on results from individual platforms., Journal of Breath Research, 14 (4), ISSN:1752-7155, ISSN:1752-7163

Published
2020
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21. Breath markers for therapeutic radiation.

Author

Salman, Dahlia, Eddleston, Michael, Darnley, Kareen, Nailon, William H., McLaren, Duncan B., Hadjithelki, Andria, Ruszkiewicz, Dorota, Langejuergen, Jens, Alkhalifa, Yaser, Phillips, Iain, and Thomas, C. L. Paul

Published
2021
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23. VOCCluster: Untargeted Metabolomics Feature Clustering Approach for Clinical Breath Gas Chromatography/Mass Spectrometry Data

Author

Alkhalifah, Yaser, Phillips, Iain, Soltoggio, Andrea, Darnley, Kareen, Nailon, William H., McLaren, Duncan, Eddleston, Michael, Thomas, C. L. Paul, and Salman, Dahlia

Abstract

Metabolic profiling of breath analysis involves processing, alignment, scaling, and clustering of thousands of features extracted from gas chromatography/mass spectrometry (GC/MS) data from hundreds of participants. The multistep data processing is complicated, operator error-prone, and time-consuming. Automated algorithmic clustering methods that are able to cluster features in a fast and reliable way are necessary. These accelerate metabolic profiling and discovery platforms for next-generation medical diagnostic tools. Our unsupervised clustering technique, VOCCluster, prototyped in Python, handles features of deconvolved GC/MS breath data. VOCCluster was created from a heuristic ontology based on the observation of experts undertaking data processing with a suite of software packages. VOCCluster identifies and clusters groups of volatile organic compounds (VOCs) from deconvolved GC/MS breath with similar mass spectra and retention index profiles. VOCCluster was used to cluster more than 15 000 features extracted from 74 GC/MS clinical breath samples obtained from participants with cancer before and after a radiation therapy. Results were evaluated against a panel of ground truth compounds and compared to other clustering methods (DBSCAN and OPTICS) that were used in previous metabolomics studies. VOCCluster was able to cluster those features into 1081 groups (including endogenous and exogenous compounds and instrumental artifacts) with an accuracy rate of 96% (±0.04 at 95% confidence interval).

Published
2020
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24. Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles

Author

Stevens, Deborah, primary, Cornmell, Robert, additional, Taylor, David, additional, Grimshaw, Sally G., additional, Riazanskaia, Svetlana, additional, Arnold, David S., additional, Fernstad, Sara Johansson, additional, Smith, Adrian M., additional, Heaney, Liam M., additional, Reynolds, James C., additional, Thomas, C. L. Paul, additional, and Harker, Mark, additional

Published
2014
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46. The presumptive detection of benzene in water in the presence of phenol with an active membrane-UV photo-ionisation differential mobility spectrometer

Author

Kanu, Abu B. and Thomas, C. L. Paul

Abstract

Studies with a new technique, active membrane-differential mobility spectrometry, with aqueous standards of benzene and phenol are described. The atmospheric pressure photo-ionisation chemistries of benzene and phenol in the presence of oxygen are similar in that benzene forms phenol radicals that subsequently react to yield diphenylether and 4-phenoxyphenol products. Further phenol sequesters charge from benzene ions leading to a significant loss of sensitivity. This is an important consideration in the development of screening techniques for the presence of benzene in environmental water samples. This challenge was addressed by including a pre-separation stage prior to photo-ionisation, and a 10 cm long polydimethylsiloxane active membrane inlet using nitrogen as a carrier gas was used to sample, concentrate and deliver low resolution separations to the 10.6 eV UV-ionisation region of a differential mobility spectrometer. Acetone was also proposed as a charge carrier for the UV photo-ionisation source; to promote phenol protonation and inhibit charge sequestration from benzene. The responses of the system to aqueous standards of benzene and phenol with and without acetone doping at 10.2 mg m−3were evaluated and four to five-fold increases in sensitivity were obtained with acetone doping. With a sampling time of 60 s and a total measurement cycle of 180 s it was possible to obtain quantitative responses to single standards over the concentration range 6 to 177 µg cm−3with linear correlations with R2values ranging from 0.97 to 0.99. The effects of the heating rate of the membrane and the dispersion field strength of the differential mobility spectrometer on sensitivity and the differentiation of benzene from phenol responses were optimised, leading to a configuration where a voltage heating programme of 4.75 V s−1was applied to a 124 µm stainless steel wire heating element within the active membrane, and a dispersion field strength of 22 kV cm−1was used to test a mixture of benzene (14 µg cm−3) and phenol (6 µg cm−3) in water. The presence of benzene was identified through the presence of a peak corresponding to a benzene response, VC= −9 V FWHM = 1 V, that followed the thermal desorption profile of benzene.

Published
2006
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50. Breath testing for SARS-CoV-2 infection.

Author

Myers R, Ruszkiewicz DM, Meister A, Bartolomeu C, Atkar-Khattra S, Thomas CLP, and Lam S

Subjects
Humans, SARS-CoV-2, COVID-19 Testing, Pandemics, Prospective Studies, Breath Tests methods, COVID-19 diagnosis
Abstract

Background: From a public health perspective, the identification of individuals with mild respiratory symptoms due to SARS-CoV-2 infection is important to contain the spread of the disease. The objective of this study was to identify volatile organic compounds (VOCs) in exhaled breath common to infection with different variants of the SARS-CoV-2 virus to inform the development of a point-of-care breath test to detect infected individuals with mild symptoms., Methods: A prospective, real-world, observational study was conducted on mildly symptomatic out-patients presenting to community test-sites for RT-qPCR SARS-CoV-2 testing when the Alpha, Beta, and Delta variants were driving the COVID-19 pandemic. VOCs in exhaled breath were compared between PCR-positive and negative individuals using TD-GC-ToF-MS. Candidate VOCs were tested in an independent set of samples collected during the Omicron phase of the pandemic., Findings: Fifty breath samples from symptomatic RT-qPCR positive and 58 breath samples from test-negative, but symptomatic participants were compared. Of the 50 RT-qPCR-positive participants, 22 had breath sampling repeated 8-12 weeks later. PCA-X model yielded 12 distinct VOCs that discriminated SARS-CoV-2 active infection compared to recovery/convalescence period, with an area under the receiver operator characteristic curve (AUROC), of 0.862 (0.747-0.977), sensitivity, and specificity of 82% and 86%, respectively. PCA-X model from 50 RT-qPCR positive and 58 negative symptomatic participants, yielded 11 VOCs, with AUROC of 0.72 (0.604-0.803) and sensitivity of 72%, specificity 65.5%. The 11 VOCs were validated in a separate group of SARS-CoV-2 Omicron positive patients' vs healthy controls demonstrating an AUROC of 0.96 (95% CI 0.827-0.993) with sensitivity of 80% specificity of 90%., Interpretation: Exhaled breath analysis is a promising non-invasive, point-of-care method to detect mild COVID-19 infection., Funding: Funding for this study was a competitive grant awarded from the Vancouver Coastal Research Institute as well as funding from the BC Cancer Foundation., Competing Interests: Declaration of interests The authors have no conflict of interest., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Published
2023
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