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11. Non-invasive diagnostic test for lung cancer using biospectroscopy and variable selection techniques in saliva samples.

Author

Morais, Camilo L. M., Lima, Kássio M. G., Dickinson, Andrew W., Saba, Tarek, Bongers, Thomas, Singh, Maneesh N., Martin, Francis L., and Bury, Danielle

Subjects
ATTENUATED total reflectance, NONINVASIVE diagnostic tests, LUNG cancer, EARLY detection of cancer, CLASSIFICATION algorithms
Abstract

Lung cancer is one of the most commonly occurring malignant tumours worldwide. Although some reference methods such as X-ray, computed tomography or bronchoscope are widely used for clinical diagnosis of lung cancer, there is still a need to develop new methods for early detection of lung cancer. Especially needed are approaches that might be non-invasive and fast with high analytical precision and statistically reliable. Herein, we developed a swab "dip" test in saliva whereby swabs were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy harnessed to principal component analysis–quadratic discriminant analysis (QDA) and variable selection techniques employing successive projections algorithm (SPA) and genetic algorithm (GA) for feature selection/extraction combined with QDA. A total of 1944 saliva samples (56 designated as lung-cancer positive and 1888 designed as controls) were obtained in a lung cancer-screening programme being undertaken in North-West England. GA-QDA models achieved, for the test set, sensitivity and specificity values of 100.0% and 99.1%, respectively. Three wavenumbers (1422 cm−1, 1546 cm−1 and 1578 cm−1) were identified using the GA-QDA model to distinguish between lung cancer and controls, including ring C–C stretching, C＝N adenine, Amide II [δ(NH), ν(CN)] and νs(COO−) (polysaccharides, pectin). These findings highlight the potential of using biospectroscopy associated with multivariate classification algorithms to discriminate between benign saliva samples and those with underlying lung cancer. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Attenuated total reflection Fourier-transform infrared spectroscopy for the prediction of hormone concentrations in plants.

Author

Holden, Claire A., McAinsh, Martin R., Taylor, Jane E., Beckett, Paul, Albacete, Alfonso, Martínez-Andújar, Cristina, Morais, Camilo L. M., and Martin, Francis L.

Subjects
ATTENUATED total reflectance, PLANT hormones, PARTIAL least squares regression, INFRARED spectroscopy, FISHER discriminant analysis, PECTINS
Abstract

Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed (Reynoutria japonica) plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Differences in the carcinogenic evaluation of glyphosate between the International Agency for Research on Cancer (IARC) and the European Food Safety Authority (EFSA)

Author

Portier, Christopher J, Armstrong, Bruce K, Baguley, Bruce C, Baur, Xaver, Belyaev, Igor, Bellé, Robert, Belpoggi, Fiorella, Biggeri, Annibale, Bosland, Maarten C, Bruzzi, Paolo, Budnik, Lygia Therese, Bugge, Merete D, Burns, Kathleen, Calaf, Gloria M, Carpenter, David O, Carpenter, Hillary M, López-Carrillo, Lizbeth, Clapp, Richard, Cocco, Pierluigi, Consonni, Dario, Comba, Pietro, Craft, Elena, Dalvie, Mohamed Aqiel, Davis, Devra, Demers, Paul A, De Roos, Anneclaire J, DeWitt, Jamie, Forastiere, Francesco, Freedman, Jonathan H, Fritschi, Lin, Gaus, Caroline, Gohlke, Julia M, Goldberg, Marcel, Greiser, Eberhard, Hansen, Johnni, Hardell, Lennart, Hauptmann, Michael, Huang, Wei, Huff, James, James, Margaret O, Jameson, CW, Kortenkamp, Andreas, Kopp-Schneider, Annette, Kromhout, Hans, Larramendy, Marcelo L, Landrigan, Philip J, Lash, Lawrence H, Leszczynski, Dariusz, Lynch, Charles F, Magnani, Corrado, Mandrioli, Daniele, Martin, Francis L, Merler, Enzo, Michelozzi, Paola, Miligi, Lucia, Miller, Anthony B, Mirabelli, Dario, Mirer, Franklin E, Naidoo, Saloshni, Perry, Melissa J, Petronio, Maria Grazia, Pirastu, Roberta, Portier, Ralph J, Ramos, Kenneth S, Robertson, Larry W, Rodriguez, Theresa, Röösli, Martin, Ross, Matt K, Roy, Deodutta, Rusyn, Ivan, Saldiva, Paulo, Sass, Jennifer, Savolainen, Kai, Scheepers, Paul TJ, Sergi, Consolato, Silbergeld, Ellen K, Smith, Martyn T, Stewart, Bernard W, Sutton, Patrice, Tateo, Fabio, Terracini, Benedetto, Thielmann, Heinz W, Thomas, David B, Vainio, Harri, Vena, John E, Vineis, Paolo, Weiderpass, Elisabete, Weisenburger, Dennis D, Woodruff, Tracey J, Yorifuji, Takashi, Yu, Il Je, Zambon, Paola, Zeeb, Hajo, and Zhou, Shu-Feng

Subjects
Carcinogens, Consumer Product Safety, European Union, Food Safety, Glycine, Herbicides, Humans, International Agencies, Neoplasms, CANCER, ENVIRONMENTAL HEALTH, Environmental epidemiology, PUBLIC HEALTH POLICY, TOXICOLOGY
Published
2016

23. Near-Infrared Spectroscopy with Supervised Machine Learning as a Screening Tool for Neutropenia

Author

Raposo-Neto, José Joaquim, primary, Kowalski-Neto, Eduardo, additional, Luiz, Wilson Barros, additional, Fonseca, Estherlita Almeida, additional, Cedro, Anna Karla Costa Logrado, additional, Singh, Maneesh N., additional, Martin, Francis L., additional, Vassallo, Paula Frizera, additional, Campos, Luciene Cristina Gastalho, additional, and Barauna, Valerio Garrone, additional

Published
2023
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25. Fast screening using attenuated total reflectance- fourier transform infrared (ATR-FTIR) spectroscopy of patients based on D-dimer threshold value

Author

Brun, Bruna F., primary, Nascimento, Marcia H.C., additional, Dias, Pedro A.C., additional, Marcarini, Wena D., additional, Singh, Maneesh N., additional, Filgueiras, Paulo R., additional, Vassallo, Paula F., additional, Romão, Wanderson, additional, Mill, José G., additional, Martin, Francis L., additional, and Barauna, Valerio G., additional

Published
2023
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34. Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead

Author

Goodson, William H, Lowe, Leroy, Carpenter, David O, Gilbertson, Michael, Manaf Ali, Abdul, Lopez de Cerain Salsamendi, Adela, Lasfar, Ahmed, Carnero, Amancio, Azqueta, Amaya, Amedei, Amedeo, Charles, Amelia K, Collins, Andrew R, Ward, Andrew, Salzberg, Anna C, Colacci, Annamaria, Olsen, Ann-Karin, Berg, Arthur, Barclay, Barry J, Zhou, Binhua P, Blanco-Aparicio, Carmen, Baglole, Carolyn J, Dong, Chenfang, Mondello, Chiara, Hsu, Chia-Wen, Naus, Christian C, Yedjou, Clement, Curran, Colleen S, Laird, Dale W, Koch, Daniel C, Carlin, Danielle J, Felsher, Dean W, Roy, Debasish, Brown, Dustin G, Ratovitski, Edward, Ryan, Elizabeth P, Corsini, Emanuela, Rojas, Emilio, Moon, Eun-Yi, Laconi, Ezio, Marongiu, Fabio, Al-Mulla, Fahd, Chiaradonna, Ferdinando, Darroudi, Firouz, Martin, Francis L, Van Schooten, Frederik J, Goldberg, Gary S, Wagemaker, Gerard, Nangami, Gladys N, Calaf, Gloria M, Williams, Graeme, Wolf, Gregory T, Koppen, Gudrun, Brunborg, Gunnar, Lyerly, H Kim, Krishnan, Harini, Ab Hamid, Hasiah, Yasaei, Hemad, Sone, Hideko, Kondoh, Hiroshi, Salem, Hosni K, Hsu, Hsue-Yin, Park, Hyun Ho, Koturbash, Igor, Miousse, Isabelle R, Scovassi, A Ivana, Klaunig, James E, Vondráček, Jan, Raju, Jayadev, Roman, Jesse, Wise, John Pierce, Whitfield, Jonathan R, Woodrick, Jordan, Christopher, Joseph A, Ochieng, Josiah, Martinez-Leal, Juan Fernando, Weisz, Judith, Kravchenko, Julia, Sun, Jun, Prudhomme, Kalan R, Narayanan, Kannan Badri, Cohen-Solal, Karine A, Moorwood, Kim, Gonzalez, Laetitia, Soucek, Laura, Jian, Le, D'Abronzo, Leandro S, Lin, Liang-Tzung, Li, Lin, Gulliver, Linda, McCawley, Lisa J, Memeo, Lorenzo, Vermeulen, Louis, Leyns, Luc, Zhang, Luoping, Valverde, Mahara, Khatami, Mahin, Romano, Maria Fiammetta, Chapellier, Marion, Williams, Marc A, and Wade, Mark

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, 2.2 Factors relating to the physical environment, Animals, Carcinogenesis, Carcinogens, Environmental, Environmental Exposure, Hazardous Substances, Humans, Neoplasms, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology.

Published
2015

40. ATR-FTIR spectroscopy detects alterations induced by organotin(IV) carboxylates in MCF-7 cells at sub-cytotoxic/-genotoxic concentrations

Author

Ahmad, Muhammad S, Mirza, Bushra, Hussain, Mukhtiar, Hanif, Muhammad, Ali, Saqib, Walsh, Michael J, and Martin, Francis L

Subjects
Physics - Biological Physics
Abstract

The environmental impact of metal complexes such as organotin(IV) compounds is of increasing concern. Genotoxic effects of organotin(IV) compounds (0.01 microg/ml, 0.1 microg/ml or 1.0 microg/ml) were measured using the alkaline single-cell gel electrophoresis (comet) assay to measure DNA single-strand breaks (SSBs) and the cytokinesis-block micronucleus (CBMN) assay to determine micronucleus formation. Biochemical-cell signatures were also ascertained using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. In the comet assay, organotin(IV) carboxylates induced significantly-elevated levels of DNA SSBs. Elevated micronucleus-forming activities were also observed. Following interrogation using ATR-FTIR spectroscopy, infrared spectra in the biomolecular range (900 cm-1 - 1800 cm-1) derived from orga..., Comment: 19 pages, 7 figures

Published
2009
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43. Infrared spectroscopy as a new approach for Fabry disease screening

Author

Barretto, Carolina Teles, primary, Nascimento, Márcia Helena Cassago, additional, Brun, Bruna, additional, Silva, Tiago Barcelos da, additional, Dias, Pedro Augusto Costa, additional, Silva, Cassiano Augusto Braga, additional, Singh, Maneesh N., additional, de Martin, Francis L., additional, Filgueiras, Paulo Roberto, additional, Romão, Wanderson, additional, Campos, Luciene Cristina Gastalho, additional, and Barauna, Valerio Garrone, additional

Published
2023
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46. List of contributors

Author

Alvarez-Puebla, Ramon A., primary, Baker, Matthew J., additional, Baranska, Malgorzata, additional, Beattie, James W., additional, Bik, Ewelina, additional, Bonnier, Franck, additional, Bouř, Petr, additional, Bruno, Clément, additional, Butler, Holly J., additional, Byrne, Bernadette, additional, Byrne, Hugh J., additional, Cameron, James M., additional, Chrabaszcz, Karolina, additional, Czamara, Krzysztof, additional, Dorosz, Aleksandra, additional, Dybas, Jakub, additional, Guerrini, Luca, additional, Handen, Joseph, additional, Hudecová, Jana, additional, Ishigaki, Mika, additional, Iwasaki, Keita, additional, Jung, Young Mee, additional, Kandori, Hideki, additional, Katayama, Kota, additional, Kazarian, Sergei G., additional, Kneipp, Janina, additional, Kochan, Kamila, additional, Lednev, Igor K., additional, Lendl, Bernhard, additional, Lima, Kássio M.G., additional, Lipiec, Ewelina, additional, Majzner, Katarzyna, additional, Malek, Kamilla, additional, Martin, Francis L., additional, Marzec, Katarzyna M., additional, Miller, Lisa M., additional, Mizutani, Yasuhisa, additional, Morais, Camilo L.M., additional, Noda, Isao, additional, Noothalapati, Hemanth, additional, Ozaki, Yukihiro, additional, Pacia, Marta Z., additional, Pan, Zhijun, additional, Parachalil, Drishya Rajan, additional, Park, Yeonju, additional, Santos, Marfran C.D., additional, Schlücker, Sebastian, additional, Schwaighofer, Andreas, additional, Song, Cai Li, additional, Wang, Yuling, additional, Wiercigroch, Ewelina, additional, Wislocka, Adrianna, additional, Wood, Bayden R., additional, Yamamoto, Tatsuyuki, additional, Zhang, Yuying, additional, and Zhuang, Wei, additional

Published
2020
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