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das Chagas E Silva de Carvalho LF, de Lima Morais TM, Nogueira MS. Providing potential solutions by using FT-IR spectroscopy for biofluid analysis: Clinical impact of optical screening and diagnostic tests. Photodiagnosis Photodyn Ther 2023; 44:103753. [PMID: 37597683 DOI: 10.1016/j.pdpdt.2023.103753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Currently, the potential of FT-IR spectroscopy for rapid diagnosis of many pathologies has been demonstrated by numerous research studies including those targeting COVID-19 detection. However, the number of clinicians aware of this potential and who are willing to use spectroscopy in their clinics and hospitals is still negligible. In addition, lack of awareness creates a huge gap between clinicians and researchers involved in clinical translation of current FT-IR technology hence hindering initiatives to bring basic and applied research together for the direct benefit of patients. METHODS Knowledge and medical training on FT-IR on the side of clinicians should be one of the first steps to be able to integrate it into the list of complementary exams which may be requested by health professionals. Countless FT-IR applications could have a life-changing impact on patients' lives, especially screening and diagnostic tests involving biofluids such as blood, saliva and urine which are routinely non-invasively or minimally-invasively. RESULTS Blood may be the most difficult to obtain by the invasive method of collection, but much can be evaluated in its components, and areas such as hematology, infectiology, oncology and endocrinology can be directly benefited. Urine with a relatively simple collection method can provide pertinent information from the entire urinary system, including the actual condition of the kidneys. Saliva collection can be simpler for the patient and can provide information on diseases affecting the mouth and digestive system and can be used to diagnose diseases such as oral cancer in its early-stages. An unavoidable second step is the active involvement of industries to design robust and portable instruments for specific purposes, as the medical community requires user-friendly instruments of advanced computational algorithms. A third step resides in the legal situation involving the global use of the technique as a new diagnostic modality. CONCLUSIONS It is important to note that decentralized funds for variety of technologies hinders the training of clinical and medical professionals for the use of newly arising technologies and affect the engagement of these professionals with technology developers. As a result of decentralized funding, research efforts are spread out over a range of technologies which take a long time to get validated and translated to the clinic. Partnership over similar groups of technologies and efforts to test the same technologies while overcoming barriers posed to technology validation in different areas around the globe may benefit the clinical/medical, research and industry community globally.
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Affiliation(s)
| | | | - Marcelo Saito Nogueira
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork T12 R5CP, Ireland; Department of Physics, University College Cork, College Road, Cork T12 K8AF, Ireland.
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Kim S, Choi J, Park H, Yoon T, Do H. Gas composition measurements in randomly distributed and fast moving gas bubbles in two-phase fluids. OPTICS EXPRESS 2023; 31:14255-14264. [PMID: 37157293 DOI: 10.1364/oe.487036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Gas composition in randomly distributed and fast-moving bubbles was optically measured aided by laser-induced breakdown spectroscopy (LIBS). Laser pulses were focused at a point in a stream of bubbles to induce plasmas for the LIBS measurements. The distance between the laser focal point and liquid-gas interface, or 'depth,' plays a major role in determining the plasma emission spectrum in two-phase fluids. However, the 'depth' effect has not been investigated in previous studies. Therefore, we evaluated the 'depth' effect in a calibration experiment near a still and flat liquid-gas interface using proper orthogonal decomposition, and a support vector regression model was trained to exclude the influence of the interfacing liquid and extract gas composition information from the spectra. The gaseous molecular oxygen mole fraction in the bubbles was accurately measured under realistic two-phase fluid conditions.
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Insights into Biochemical Sources and Diffuse Reflectance Spectral Features for Colorectal Cancer Detection and Localization. Cancers (Basel) 2022; 14:cancers14225715. [PMID: 36428806 PMCID: PMC9688116 DOI: 10.3390/cancers14225715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common and second most deadly type of cancer worldwide. Early detection not only reduces mortality but also improves patient prognosis by allowing the use of minimally invasive techniques to remove cancer while avoiding major surgery. Expanding the use of microsurgical techniques requires accurate diagnosis and delineation of the tumor margins in order to allow complete excision of cancer. We have used diffuse reflectance spectroscopy (DRS) to identify the main optical CRC biomarkers and to optimize parameters for the integration of such technologies into medical devices. A total number of 2889 diffuse reflectance spectra were collected in ex vivo specimens from 47 patients. Short source-detector distance (SDD) and long-SDD fiber-optic probes were employed to measure tissue layers from 0.5 to 1 mm and from 0.5 to 1.9 mm deep, respectively. The most important biomolecules contributing to differentiating DRS between tissue types were oxy- and deoxy-hemoglobin (Hb and HbO2), followed by water and lipid. Accurate tissue classification and potential DRS device miniaturization using Hb, HbO2, lipid and water data were achieved particularly well within the wavelength ranges 350-590 nm and 600-1230 nm for the short-SDD probe, and 380-400 nm, 420-610 nm, and 650-950 nm for the long-SDD probe.
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Nogueira MS, Leal LB, Marcarini WD, Pimentel RL, Muller M, Vassallo PF, Campos LCG, Dos Santos L, Luiz WB, Mill JG, Barauna VG, de Carvalho LFDCES. Rapid diagnosis of COVID-19 using FT-IR ATR spectroscopy and machine learning. Sci Rep 2021; 11:15409. [PMID: 34635702 PMCID: PMC8505540 DOI: 10.1038/s41598-021-93511-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Early diagnosis of COVID-19 in suspected patients is essential for contagion control and damage reduction strategies. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in oropharyngeal swab suspension fluid to predict COVID-19 positive samples. The study included samples of 243 patients from two Brazilian States. Samples were transported by using different viral transport mediums (liquid 1 or 2). Clinical COVID-19 diagnosis was performed by the RT-PCR. We built a classification model based on partial least squares (PLS) associated with cosine k-nearest neighbours (KNN). Our analysis led to 84% and 87% sensitivity, 66% and 64% specificity, and 76.9% and 78.4% accuracy for samples of liquids 1 and 2, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective solution for high-throughput screening of suspect patients for COVID-19 in health care centres and emergency departments.
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Affiliation(s)
- Marcelo Saito Nogueira
- Tyndall National Institute, University College Cork, Lee Maltings Complex, Dyke Parade, Cork, T12R5CP, Ireland.
| | - Leonardo Barbosa Leal
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Wena Dantas Marcarini
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil.,Faculdade Vale do Cricaré, São Matheus, Brazil
| | - Raquel Lemos Pimentel
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Matheus Muller
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | | | | | - Leonardo Dos Santos
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Wilson Barros Luiz
- Department of Biological Science, Santa Cruz State University, Ilhéus, BA, Brazil
| | - José Geraldo Mill
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Valerio Garrone Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
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5
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Nogueira MS, Leal LB, Marcarini WD, Pimentel RL, Muller M, Vassallo PF, Campos LCG, Dos Santos L, Luiz WB, Mill JG, Barauna VG, de Carvalho LFDCES. Rapid diagnosis of COVID-19 using FT-IR ATR spectroscopy and machine learning. Sci Rep 2021. [PMID: 34635702 DOI: 10.1038/s41598-021-93511-] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023] Open
Abstract
Early diagnosis of COVID-19 in suspected patients is essential for contagion control and damage reduction strategies. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in oropharyngeal swab suspension fluid to predict COVID-19 positive samples. The study included samples of 243 patients from two Brazilian States. Samples were transported by using different viral transport mediums (liquid 1 or 2). Clinical COVID-19 diagnosis was performed by the RT-PCR. We built a classification model based on partial least squares (PLS) associated with cosine k-nearest neighbours (KNN). Our analysis led to 84% and 87% sensitivity, 66% and 64% specificity, and 76.9% and 78.4% accuracy for samples of liquids 1 and 2, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective solution for high-throughput screening of suspect patients for COVID-19 in health care centres and emergency departments.
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Affiliation(s)
- Marcelo Saito Nogueira
- Tyndall National Institute, University College Cork, Lee Maltings Complex, Dyke Parade, Cork, T12R5CP, Ireland.
| | - Leonardo Barbosa Leal
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Wena Dantas Marcarini
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
- Faculdade Vale do Cricaré, São Matheus, Brazil
| | - Raquel Lemos Pimentel
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Matheus Muller
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | | | | | - Leonardo Dos Santos
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Wilson Barros Luiz
- Department of Biological Science, Santa Cruz State University, Ilhéus, BA, Brazil
| | - José Geraldo Mill
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
| | - Valerio Garrone Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Vitória, Brazil
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6
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Leal LB, Nogueira MS, Mageski JGA, Martini TP, Barauna VG, Dos Santos L, de Carvalho LFDCES. Diagnosis of Systemic Diseases Using Infrared Spectroscopy: Detection of Iron Overload in Plasma-Preliminary Study. Biol Trace Elem Res 2021; 199:3737-3751. [PMID: 33415581 DOI: 10.1007/s12011-020-02510-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
Despite the important role of iron in cellular homeostasis, iron overload (IO) is associated with systemic and tissue deposits which damage several organs. In order to reduce the impact caused by IO, invasive diagnosis exams (e.g., biopsies) and minimally invasive methods were developed including computed tomography and magnetic resonance imaging. However, current diagnostic methods are still time-consuming and expensive. A cost-effective solution is using Fourier-transform infrared spectroscopy (FTIR) for real-time and molecular-sensitive biofluid analysis during conventional laboratory exams. In this study, we performed the first evaluation of the accuracy of FTIR for IO diagnosis. The study was performed by collecting FTIR spectra of plasma samples of five rats intravenously injected with iron-dextran and five control rats. We developed a classification model based on principal component analysis and supervised methods including J48, random forest, multilayer perceptron, and radial basis function network. We achieved 100% accuracy for the classification of the IO status and provided a list of possible biomolecules related to the vibrational modes detected. In this preliminary study, we give a first step towards real-time diagnosis for acute IO or intoxication. Furthermore, we have expanded the literature knowledge regarding the pathophysiological changes induced by iron overload.
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Affiliation(s)
- Leonardo Barbosa Leal
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, Vitória, Espírito Santo, 29040-090, Brazil.
| | - Marcelo Saito Nogueira
- Tyndall National Institute/University College Cork - Lee Maltings Complex, Dyke Parade, Cork, T12R5CP, Ireland
| | - Jandinay Gonzaga Alexandre Mageski
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, Vitória, Espírito Santo, 29040-090, Brazil
| | - Thiago Pereira Martini
- Institute of Science and Technology, Federal University of Sao Paulo, São José dos Campos, Brazil
| | - Valério Garrone Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, Vitória, Espírito Santo, 29040-090, Brazil
| | - Leonardo Dos Santos
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, Vitória, Espírito Santo, 29040-090, Brazil
| | - Luis Felipe das Chagas E Silva de Carvalho
- Universidade de Taubaté. R. dos Operários, 09 - Centro, Taubaté, São Paulo, 12020-340, Brazil
- Centro Universitário Braz Cubas, Av. Francisco Rodrigues Filho, 1233 - Vila Mogilar, Mogi das Cruzes, São Paulo, Brazil
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7
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Schie IW, Placzek F, Knorr F, Cordero E, Wurster LM, Hermann GG, Mogensen K, Hasselager T, Drexler W, Popp J, Leitgeb RA. Morpho-molecular signal correlation between optical coherence tomography and Raman spectroscopy for superior image interpretation and clinical diagnosis. Sci Rep 2021; 11:9951. [PMID: 33976274 PMCID: PMC8113482 DOI: 10.1038/s41598-021-89188-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/16/2021] [Indexed: 01/16/2023] Open
Abstract
The combination of manifold optical imaging modalities resulting in multimodal optical systems allows to discover a larger number of biomarkers than using a single modality. The goal of multimodal imaging systems is to increase the diagnostic performance through the combination of complementary modalities, e.g. optical coherence tomography (OCT) and Raman spectroscopy (RS). The physical signal origins of OCT and RS are distinctly different, i.e. in OCT it is elastic back scattering of photons, due to a change in refractive index, while in RS it is the inelastic scattering between photons and molecules. Despite those diverse characteristics both modalities are also linked via scattering properties and molecular composition of tissue. Here, we investigate for the first time the relation of co-registered OCT and RS signals of human bladder tissue, to demonstrate that the signals of these complementary modalities are inherently intertwined, enabling a direct but more importantly improved interpretation and better understanding of the other modality. This work demonstrates that the benefit for using two complementary imaging approaches is, not only the increased diagnostic value, but the increased information and better understanding of the signal origins of both modalities. This evaluation confirms the advantages for using multimodal imaging systems and also paves the way for significant further improved understanding and clinically interpretation of both modalities in the future.
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Affiliation(s)
- Iwan W Schie
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, Jena, 07745, Germany.
- Department of Medical Engineering and Biotechnology, University of Applied Sciences-Jena, Carl-Zeiss-Promenade 2, 07745, Jena, Germany.
| | - Fabian Placzek
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20 / 4L, 1090, Vienna, Austria
| | - Florian Knorr
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, Jena, 07745, Germany
| | - Eliana Cordero
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, Jena, 07745, Germany
| | - Lara M Wurster
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20 / 4L, 1090, Vienna, Austria
| | - Gregers G Hermann
- Department of Urology, Copenhagen University, Herlev/Gentofte Hospital, Borgmester Ib Juuls Vej 23A, 2730, Herlev/Copenhagen, Denmark
| | - Karin Mogensen
- Department of Urology, Copenhagen University, Herlev/Gentofte Hospital, Borgmester Ib Juuls Vej 23A, 2730, Herlev/Copenhagen, Denmark
| | - Thomas Hasselager
- Department of Pathology, Copenhagen University, Herlev/Gentofte Hospital, Borgmester Ib Juuls Vej 23A, 2730, Herlev/Copenhagen, Denmark
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20 / 4L, 1090, Vienna, Austria
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, Jena, 07745, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Rainer A Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20 / 4L, 1090, Vienna, Austria
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8
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Pinto GC, Leal LB, Magalhães NC, Pereira MF, Vassallo PF, Pereira TM, Barauna VG, Byrne HJ, Carvalho LFCS. The potential of FT-IR spectroscopy for improving healthcare in sepsis - An animal model study. Photodiagnosis Photodyn Ther 2021; 34:102312. [PMID: 33930577 DOI: 10.1016/j.pdpdt.2021.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/07/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
Fourier Transform-Infrared (FT-IR) absorption spectroscopy has been used to investigate pathophysiological changes caused by sepsis. Sepsis has been defined as a potentially fatal organic dysfunction caused by a dysregulated host response to infection and can lead a patient to risk of death. This study used samples consisting of the blood plasma of mice which were induced to sepsis state, compared to a healthy group using FT-IR associated with attenuated total reflectance (ATR) spectroscopy. For statistical analysis, principal components analysis (PCA) and linear discriminant analysis (LDA) were applied, independently, to the second derivative spectra of both the fingerprint (900-1800 cm-1) and the high wavenumber (2800-3100 cm-1) regions. The technique efficiently differentiated the blood plasma of the two groups, sepsis and healthy mice, the analysis indicating that fatty acids and lipids in the blood samples could be an important biomarker of sepsis.
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Affiliation(s)
- G C Pinto
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - L B Leal
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil.
| | - N C Magalhães
- Universidade de Taubaté. R. dos Operários, 09 - Centro, Taubaté, SP, 12020-340, Brazil
| | - M F Pereira
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - P F Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil; Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - T M Pereira
- Universidade Federal do Estado de São Paulo. R. Talim, 330 - Vila Nair, São José dos Campos, SP, 12231-0, Brazil
| | - V G Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - H J Byrne
- FOCAS Research Institute, Technological University Dublin, Kevin Street, Dublin 8, Ireland
| | - L F C S Carvalho
- Universidade de Taubaté. R. dos Operários, 09 - Centro, Taubaté, SP, 12020-340, Brazil; Centro Universitário Braz Cubas. Av. Francisco Rodrigues Filho, 1233 - Vila Mogilar, Mogi das Cruzes, SP, 08773-380, Brazil
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Nogueira MS, Brugnera Junior A, Bagnato VS, Panhóca VH. Evaluation of the Whitening Effectiveness of Violet Illumination Alone or Combined with Hydrogen Peroxide Gel. Photobiomodul Photomed Laser Surg 2021; 39:395-402. [PMID: 33439765 DOI: 10.1089/photob.2020.4846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective: To evaluate the effectiveness of the whitening and washing steps of a treatment using violet illumination (VI) alone or combined with hydrogen peroxide gel. In addition, we evaluated the color change after cleaning the tooth with and without mineral oil. Methods: First, 16 bovine teeth were extracted and stored in 5% thymol solution. Next, the teeth were collected and cleaned. Then, the teeth were stained with instant coffee solution for 24 h. The teeth were divided in four groups: control, VI without 35% hydrogen peroxide gel (VI), VI with 35% hydrogen peroxide gel (VI + gel), and VI without 35% hydrogen peroxide gel and cleaned with mineral oil before washing (VI + oil). Results: The whitening treatment VI + gel was able to completely restore the teeth whiteness and make the teeth 31.2% less yellow than prior coffee staining. The VI + oil treatment led to about 3.7 times the whiteness and yellowness changes observed in the VI treatment and restored 51% of the whiteness lost by staining. Conclusions: The VI + gel treatment can be recommended against coffee stains and should be further investigated for other types of tooth stains. In addition, cleaning the tooth surface with mineral oil could be an alternative to increase the performance of whitening treatments.
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Affiliation(s)
| | - Aldo Brugnera Junior
- Physics Institute of São Carlos, University of Sao Paulo, São Carlos, Brazil.,Department of Dental Science, Faculty of Medicine, Emdola, University in Liège, Liège, Belgium
| | | | - Vitor Hugo Panhóca
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
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10
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Nogueira MS, Maryam S, Amissah M, Lu H, Lynch N, Killeen S, O'Riordain M, Andersson-Engels S. Evaluation of wavelength ranges and tissue depth probed by diffuse reflectance spectroscopy for colorectal cancer detection. Sci Rep 2021; 11:798. [PMID: 33436684 PMCID: PMC7804163 DOI: 10.1038/s41598-020-79517-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common type of cancer worldwide and the second most deadly. Recent research efforts have focused on developing non-invasive techniques for CRC detection. In this study, we evaluated the diagnostic capabilities of diffuse reflectance spectroscopy (DRS) for CRC detection by building 6 classification models based on support vector machines (SVMs). Our dataset consists of 2889 diffuse reflectance spectra collected from freshly excised ex vivo tissues of 47 patients over wavelengths ranging from 350 and 1919 nm with source-detector distances of 630-µm and 2500-µm to probe different depths. Quadratic SVMs were used and performance was evaluated using twofold cross-validation on 10 iterations of randomized training and test sets. We achieved (93.5 ± 2.4)% sensitivity, (94.0 ± 1.7)% specificity AUC by probing the superficial colorectal tissue and (96.1 ± 1.8)% sensitivity, (95.7 ± 0.6)% specificity AUC by sampling deeper tissue layers. To the best of our knowledge, this is the first DRS study to investigate the potential of probing deeper tissue layers using larger SDD probes for CRC detection in the luminal wall. The data analysis showed that using a broader spectrum and longer near-infrared wavelengths can improve the diagnostic accuracy of CRC as well as probing deeper tissue layers.
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Affiliation(s)
- Marcelo Saito Nogueira
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork, Ireland.
- Department of Physics, University College Cork, College Road, Cork, Ireland.
| | - Siddra Maryam
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork, Ireland
- Department of Physics, University College Cork, College Road, Cork, Ireland
| | - Michael Amissah
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork, Ireland
- Department of Physics, University College Cork, College Road, Cork, Ireland
| | - Huihui Lu
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork, Ireland
| | - Noel Lynch
- Department of Surgery, Mercy University Hospital, Cork, Ireland
| | - Shane Killeen
- Department of Surgery, Mercy University Hospital, Cork, Ireland
| | | | - Stefan Andersson-Engels
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork, Ireland
- Department of Physics, University College Cork, College Road, Cork, Ireland
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Placzek F, Cordero Bautista E, Kretschmer S, Wurster LM, Knorr F, González-Cerdas G, Erkkilä MT, Stein P, Ataman Ç, Hermann GG, Mogensen K, Hasselager T, Andersen PE, Zappe H, Popp J, Drexler W, Leitgeb RA, Schie IW. Morpho-molecular ex vivo detection and grading of non-muscle-invasive bladder cancer using forward imaging probe based multimodal optical coherence tomography and Raman spectroscopy. Analyst 2020; 145:1445-1456. [PMID: 31867582 DOI: 10.1039/c9an01911a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Non-muscle-invasive bladder cancer affects millions of people worldwide, resulting in significant discomfort to the patient and potential death. Today, cystoscopy is the gold standard for bladder cancer assessment, using white light endoscopy to detect tumor suspected lesion areas, followed by resection of these areas and subsequent histopathological evaluation. Not only does the pathological examination take days, but due to the invasive nature, the performed biopsy can result in significant harm to the patient. Nowadays, optical modalities, such as optical coherence tomography (OCT) and Raman spectroscopy (RS), have proven to detect cancer in real time and can provide more detailed clinical information of a lesion, e.g. its penetration depth (stage) and the differentiation of the cells (grade). In this paper, we present an ex vivo study performed with a combined piezoelectric tube-based OCT-probe and fiber optic RS-probe imaging system that allows large field-of-view imaging of bladder biopsies, using both modalities and co-registered visualization, detection and grading of cancerous bladder lesions. In the present study, 119 examined biopsies were characterized, showing that fiber-optic based OCT provides a sensitivity of 78% and a specificity of 69% for the detection of non-muscle-invasive bladder cancer, while RS, on the other hand, provides a sensitivity of 81% and a specificity of 61% for the grading of low- and high-grade tissues. Moreover, the study shows that a piezoelectric tube-based OCT probe can have significant endurance, suitable for future long-lasting in vivo applications. These results also indicate that combined OCT and RS fiber probe-based characterization offers an exciting possibility for label-free and morpho-chemical optical biopsies for bladder cancer diagnostics.
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Affiliation(s)
- Fabian Placzek
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 4L, 1090 Vienna, Austria
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Gunaratne R, Goncalves J, Monteath I, Sheh R, Kapfer M, Chipper R, Robertson B, Khan R, Fick D, Ironside CN. Wavelength weightings in machine learning for ovine joint tissue differentiation using diffuse reflectance spectroscopy (DRS). BIOMEDICAL OPTICS EXPRESS 2020; 11:5122-5131. [PMID: 33014603 PMCID: PMC7510883 DOI: 10.1364/boe.397593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/02/2020] [Accepted: 08/09/2020] [Indexed: 05/03/2023]
Abstract
Objective: To investigate the DRS of ovine joint tissue to determine the optimal optical wavelengths for tissue differentiation and relate these wavelengths to the biomolecular composition of tissues. In this study, we combine machine learning with DRS for tissue classification and then look further at the weighting matrix of the classifier to further understand the key differentiating features. Methods: Supervised machine learning was used to analyse DRS data. After normalising the data, dimension reduction was achieved through multiclass Fisher's linear discriminant analysis (Multiclass FLDA) and classified with linear discriminant analysis (LDA). The classifier was first run with all the tissue types and the wavelength range 190 nm - 1081 nm. We analysed the weighting matrix of the classifier and then ran the classifier again, the first time using the ten highest weighted wavelengths and the second using only the single highest. Our method was applied to a dataset containing ovine joint tissue including cartilage, cortical and subchondral bone, fat, ligament, meniscus, and muscle. Results: It achieved a classification accuracy of 100% using the wavelength 190 nm - 1081 nm (2048 attributes) with an accuracy of 90% being present for 10 attributes with the exception of those with comparable compositions such as ligament and meniscus. An accuracy greater than 70% was achieved using a single wavelength, with the same exceptions. Conclusion: Multiclass FLDA combined with LDA is a viable technique for tissue identification from DRS data. The majority of differentiating features existed within the wavelength ranges 370-470 and 800-1010 nm. Focusing on key spectral regions means that a spectrometer with a narrower range can potentially be used, with less computational power needed for subsequent analysis.
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Affiliation(s)
| | - Joshua Goncalves
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | | | - Raymond Sheh
- Curtin University, Kent Street, Bentley 6102, Australia
| | - Michael Kapfer
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Richard Chipper
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Brett Robertson
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Riaz Khan
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
- The Joint Studio, 85 Monash Avenue, Nedlands 6009, Australia
- Department of Medicine, The University of Notre Dame, Fremantle, Australia
| | - Daniel Fick
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
- The Joint Studio, 85 Monash Avenue, Nedlands 6009, Australia
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Gonzaga AKG, Mafra RP, da Silva LP, de Almeida Freitas R, de Souza LB, Pinto LP. Actinic cheilitis: Morphometric parameters and its relationship with the degree of epithelial dysplasia. Acta Histochem 2020; 122:151452. [PMID: 31558280 DOI: 10.1016/j.acthis.2019.151452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022]
Abstract
Actinic cheilitis (AC) is a potentially malignant lesion caused by chronic sun exposure. This study aimed to evaluate the relationship between the degree of epithelial dysplasia and morphometric findings in AC. Sixty-eight slides of AC cases were selected and classified according to the grade of epithelial dysplasia, following morphologic criteria of World Health Organization. For morphometric analysis, the slides were scanned and images were analyzed using Pannoramic Viewer software. We obtained vertical measurements of the parameters: thicknesses of the keratin layer, lamina propria and zone of solar elastosis in three selected fields. Thirty-seven (54.4%) of the analyzed cases were classified as none/mild dysplasia and 31 (45.6%) as moderate/severe epithelial dysplasia. Cases with a moderate/severe dysplasia exhibited a thicker layer of keratin (median = 0.055 mm) than none/mild dysplasia (median = 0.045 mm) (p = 0.033). No significant differences in the thicknesses of lamina propria and zone of solar elastosis were observed according to the grade of epithelial dysplasia. A positive significant correlation between keratin layer and lamina propria thicknesses was found (p = 0.019). Based on our findings, rigorous clinical follow-up should be recommended for patients whose histopathological examination shows a greater thickness of the keratin layer.
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Gunaratne R, Monteath I, Goncalves J, Sheh R, Ironside CN, Kapfer M, Chipper R, Robertson B, Khan R, Fick D. Machine learning classification of human joint tissue from diffuse reflectance spectroscopy data. BIOMEDICAL OPTICS EXPRESS 2019; 10:3889-3898. [PMID: 31452982 PMCID: PMC6701523 DOI: 10.1364/boe.10.003889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 05/08/2023]
Abstract
Objective: To assess if incorporation of DRS sensing into real-time robotic surgery systems has merit. DRS as a technology is relatively simple, cost-effective and provides a non-contact approach to tissue differentiation. Methods: Supervised machine learning analysis of diffuse reflectance spectra was performed to classify human joint tissue that was collected from surgical procedures. Results: We have used supervised machine learning in the classification of a DRS human joint tissue data set and achieved classification accuracy in excess of 99%. Sensitivity for the various classes were; cartilage 99.7%, subchondral 99.2%, meniscus 100% and cancellous 100%. Full wavelength range is required for maximum classification accuracy. The wavelength resolution must be larger than 8nm. A SNR better than 10:1 was required to achieve a classification accuracy greater than 50%. The 800-900nm wavelength range gave the greatest accuracy amongst those investigated Conclusion: DRS is a viable method for differentiating human joint tissue and has the potential to be incorporated into robotic orthopaedic surgery.
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Affiliation(s)
| | | | - Joshua Goncalves
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Raymond Sheh
- Curtin University, Kent Street, Bentley 6102, Australia
| | | | - Michael Kapfer
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Richard Chipper
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Brett Robertson
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
| | - Riaz Khan
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
- The Joint Studio, 85 Monash Avenue, Nedlands 6009, Australia
- Department of Medicine, The University of Notre Dame, Fremantle, Australia
| | - Daniel Fick
- Australian Institute of Robotic Orthopaedics, 2 Centro Avenue, Subiaco 6008, Australia
- The Joint Studio, 85 Monash Avenue, Nedlands 6009, Australia
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Leal L, Nogueira M, Canevari R, Carvalho L. Vibration spectroscopy and body biofluids: Literature review for clinical applications. Photodiagnosis Photodyn Ther 2018; 24:237-244. [DOI: 10.1016/j.pdpdt.2018.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 12/19/2022]
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Carvalho LFCS, Nogueira MS, Neto LPM, Bhattacharjee TT, Martin AA. Erratum: Raman spectral post-processing for oral tissue discrimination - a step for an automatized diagnostic system: erratum. BIOMEDICAL OPTICS EXPRESS 2018; 9:649. [PMID: 29553144 PMCID: PMC5854067 DOI: 10.1364/boe.9.000649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 05/02/2023]
Abstract
[This corrects the article on p. 5218 in vol. 8, PMID: 29188115.].
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Affiliation(s)
- Luis Felipe C S Carvalho
- Univap/Instituto de Pesquisa e Desenvolvimento, Laboratório de Espectroscopia Vibracional Biomédica, Avenida Shishima Hifumi, 2911, São José dos Campos/SP, - CEP: 12244-000, Brazil
- Co-first authors with equal contribution
| | - Marcelo Saito Nogueira
- University of São Paulo/ São Carlos Institute Of Physics, Optics Group, Biophotonics Division, Avenida Trabalhador São Carlense, 400, São Carlos/SP, - CEP: 13566-590, Brazil
- Co-first authors with equal contribution
| | - Lázaro P M Neto
- Univap/Instituto de Pesquisa e Desenvolvimento, Laboratório de Espectroscopia Vibracional Biomédica, Avenida Shishima Hifumi, 2911, São José dos Campos/SP, - CEP: 12244-000, Brazil
| | - Tanmoy T Bhattacharjee
- Univap/Instituto de Pesquisa e Desenvolvimento, Laboratório de Espectroscopia Vibracional Biomédica, Avenida Shishima Hifumi, 2911, São José dos Campos/SP, - CEP: 12244-000, Brazil
| | - Airton A Martin
- Biomedical Engineering innovation Center - Biomedical Vibrational Spectroscopy Group. Universidade Brasil - UnBr - Rua Carolina Fonseca, 235 - 08230-030 - Itaquera São Paulo/SP/ Visiting Professor Universidade Federal do Piauí - UFPI - Campus Ministro Petrônio Portella Departamento de Física - CCN Bairro Ininga Teresina, PI, CEP: 64049-550, Brazil
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de Carvalho LFDCES, Saito Nogueira M. New insights of Raman spectroscopy for oral clinical applications. Analyst 2018; 143:6037-6048. [DOI: 10.1039/c8an01363b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oral injuries are currently diagnosed by histopathological analysis of biopsy, which is an invasive procedure and does not give immediate results.
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