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Bian H, Wang P, Wang N, Tian Y, Bai P, Jiang H, Gao J. Dual-model analysis for improving the discrimination performance of human and nonhuman blood based on Raman spectroscopy. Biomed Opt Express 2018; 9:3512-3522. [PMID: 30338136 PMCID: PMC6191633 DOI: 10.1364/boe.9.003512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 05/28/2023]
Abstract
The discrimination accuracy for human and nonhuman blood is important for customs inspection and forensic applications. Recently, Raman spectroscopy has shown effectiveness in analyzing blood droplets and stains with an excitation wavelength of 785 nm. However, the discrimination of liquid whole blood in a vacuum blood tube using Raman spectroscopy, which is a form of noncontact and nondestructive detection, has not been achieved. An excitation wavelength of 532 nm was chosen to avoid the fluorescent background of the blood tube, at the cost of reduced spectroscopic information and discrimination accuracy. To improve the accuracy and true positive rate (TPR) for human blood, a dual-model analysis method is proposed. First, model 1 was used to discriminate human-unlike nonhuman blood. Model 2 was then used to discriminate human-like nonhuman blood from the "human blood" obtained by model 1. A total of 332 Raman spectra from 10 species were used to build and validate the model. A blind test and external validation demonstrated the effectiveness of the model. Compared with the results obtained by the single partial least-squares model, the discrimination performance was improved. The total accuracy and TPR, which are highly important for practical applications, increased to 99.1% and 97.4% from 87.2% and 90.6%, respectively.
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Affiliation(s)
- Haiyi Bian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Schott Glass Technologies (Suzhou) Co., Ltd., Suzhou 215009, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Ning Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yubing Tian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Pengli Bai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Jiangsu 215163, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jing Gao
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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2
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Li X, Yang T, Li CS, Jin L, Lou H, Song Y. Prenatal detection of thalassemia by cell-free fetal DNA (cffDNA) in maternal plasma using surface enhanced Raman spectroscopy combined with PCR. Biomed Opt Express 2018; 9:3167-3176. [PMID: 29984090 PMCID: PMC6033558 DOI: 10.1364/boe.9.003167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/04/2018] [Accepted: 02/09/2018] [Indexed: 05/30/2023]
Abstract
Thalassemias are widely occurring genetic hemoglobin disorders; patients with severe thalassemia often require regular blood transfusions for survival. Prenatal detection of thalassemia is currently invasive and carries the risk of miscarriage and infection. A polymerase chain reaction (PCR)-based surface enhanced Raman spectroscopy (SERS) technique was investigated in this paper for the purpose of detecting prenatal α-thalassemia Southeast Asian (SEA) type deletion using maternal plasma. Couples with the same SEA thalassemia (-SEA/αα) were selected, and the quantification of SEA and wild type (WT) alleles in the maternal plasma sample predicted the fetal genotype. PCR was performed using two pairs of fluorescence tag-labeled primers to produce tag-labeled PCR products for both the SEA (labeled with R6G) and WT (labeled with Cy3) alleles. Then, the labeled PCR products containing the two fluorescence tags were measured by SERS. The ratios between the R6G and Cy3 tags were obtained using multiple linear regressions (MLR), and these ratios corresponded with the physical ratio of WT and SEA concentrations in maternal plasma. After verifying this technique on DNA mixtures with known SEA and WT ratios, the plasma from 24 pregnant women was screened. An accuracy of 91.7% was achieved for detecting the fetal genotypes of Hb Bart's, alpha-trait, and normal trait. The results indicated that the simple PCR-SERS method may be sensitive enough for use on cell free fetal DNA (cffDNA) in maternal plasma for non-invasive prenatal detection (NIPD).
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Affiliation(s)
- Xiaozhou Li
- School of Science, Shenyang Ligong University, Shenyang 110159, China
- College of Environmental Sciences, Liaoning University, Shenyang 110036, China
| | - Tianyue Yang
- School of Science, Shenyang Ligong University, Shenyang 110159, China
| | - Caesar Siqi Li
- College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Lili Jin
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Hong Lou
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Youtao Song
- College of Environmental Sciences, Liaoning University, Shenyang 110036, China
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3
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Sohail A, Khan S, Ullah R, Qureshi SA, Bilal M, Khan A. Analysis of hepatitis C infection using Raman spectroscopy and proximity based classification in the transformed domain. Biomed Opt Express 2018; 9:2041-2055. [PMID: 29760968 PMCID: PMC5946769 DOI: 10.1364/boe.9.002041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 05/25/2023]
Abstract
This work presents a diagnostic system for the hepatitis C infection using Raman spectroscopy and proximity based classification. The proposed method exploits transformed Raman spectra using the proximity based machine learning technique and is denoted as RS-PCA-Prox. First, Raman spectral data is baseline corrected by subtracting noise and low intensity background. After this, a feature transformation of Raman spectra is adopted, not only to reduce the feature's dimensionality but also to learn different deviations in Raman shifts. The proposed RS-PCA-Prox shows significant diagnostic power in terms of accuracy, sensitivity, and specificity as 95%, 0.97 and 0.94 in PCA based transformed domain. The comparison of the RS-PCA-Prox with linear and ensemble based classifiers shows that proximity based classification performs better for the discrimination of HCV infected individuals and is able to differentiate the infected individuals from normal ones on the basis of molecular spectral information. Furthermore, it is observed that characteristic spectral changes are due to variation in the intensity of lectin, chitin, lipids, ammonia and viral protein as a consequence of the HCV infection.
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Affiliation(s)
- Anabia Sohail
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Saranjam Khan
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
| | - Rahat Ullah
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
| | - Shahzad Ahmad Qureshi
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Bilal
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
- Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Asifullah Khan
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
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4
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Ahmed R, Law AWL, Cheung TW, Lau C. Raman spectroscopy of bone composition during healing of subcritical calvarial defects. Biomed Opt Express 2018; 9:1704-1716. [PMID: 29675312 PMCID: PMC5905916 DOI: 10.1364/boe.9.001704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 05/20/2023]
Abstract
Subcritical calvarial defects heal spontaneously and optical methods can study the healing without mechanically perturbing the bone. In this study, 1mm defects were created on the skulls (in vivo) of Sprague-Dawley rats (n = 14). After 7 (n = 7) and 14 days (n = 7) of healing, the subjects were sacrificed and additional defects were similarly created (control). Raman spectroscopy (785nm) was performed at the two time points and defect types. Spectra were quantified by the mineral/matrix ratio, carbonate/phosphate ratio and crystallinity. Mineral/matrix of in vivo defects is lower than that of controls by ~34% after 7 days and ~21% after 14 days. Carbonate/phosphate is 8% and 5% higher while crystallinity is 7% and 3% lower, respectively. Optical profiling shows that the surface roughness increases 1.2% from controls to in vivo after 7 days, then decreases 13% after 14 days. Overall, the results show maturation of mineral crystals during healing and agree with microscopic assessment.
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Ullah R, Khan S, Javaid S, Ali H, Bilal M, Saleem M. Raman spectroscopy combined with a support vector machine for differentiating between feeding male and female infants mother's milk. Biomed Opt Express 2018; 9:844-851. [PMID: 29552417 PMCID: PMC5854083 DOI: 10.1364/boe.9.000844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 05/22/2023]
Abstract
This study presents differentiation in milk samples of mother's feeding male and female infants using Raman spectroscopy combined with a support vector machine (SVM). Major differences have been observed in the Raman spectra of both types of milk based on their chemical compositions. Overall, it has been found that milk samples of mother's having a female infant are richer in fatty acids, phospholipids, and tryptophan. In contrast, milk samples of mother's having a male infant contain more carotenoids and saccharides. Principal component analysis and SVM further highlighted the differences between the two groups on the basis of differentiating features obtained from their Raman spectra. The SVM model with two different kernels, i.e. polynomial kernel function (order-2) and Gaussian radial basis function (RBF sigma-2), are used for gender based milk differentiations. The performance of the proposed model in terms of accuracy, precision, sensitivity, and specificity using the polynomial kernel function of order-2 have been found to be 86%, 88%, 85% and 88%, respectively.
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Affiliation(s)
- Rahat Ullah
- Agri-Biophotonics Division, National Institute of Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Saranjam Khan
- Agri-Biophotonics Division, National Institute of Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Samina Javaid
- Department of Biotechnology, International Islamic University Islamabad (IIUI), Pakistan
| | - Hina Ali
- Agri-Biophotonics Division, National Institute of Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Muhammad Bilal
- Agri-Biophotonics Division, National Institute of Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Muhammad Saleem
- Agri-Biophotonics Division, National Institute of Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
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6
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Boitor R, Kong K, Shipp D, Varma S, Koloydenko A, Kulkarni K, Elsheikh S, Schut TB, Caspers P, Puppels G, van der Wolf M, Sokolova E, Nijsten TEC, Salence B, Williams H, Notingher I. Automated multimodal spectral histopathology for quantitative diagnosis of residual tumour during basal cell carcinoma surgery. Biomed Opt Express 2017; 8:5749-5766. [PMID: 29296502 PMCID: PMC5745117 DOI: 10.1364/boe.8.005749] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 05/11/2023]
Abstract
Multimodal spectral histopathology (MSH), an optical technique combining tissue auto-fluorescence (AF) imaging and Raman micro-spectroscopy (RMS), was previously proposed for detection of residual basal cell carcinoma (BCC) at the surface of surgically-resected skin tissue. Here we report the development of a fully-automated prototype instrument based on MSH designed to be used in the clinic and operated by a non-specialist spectroscopy user. The algorithms for the AF image processing and Raman spectroscopy classification had been first optimised on a manually-operated laboratory instrument and then validated on the automated prototype using skin samples from independent patients. We present results on a range of skin samples excised during Mohs micrographic surgery, and demonstrate consistent diagnosis obtained in repeat test measurement, in agreement with the reference histopathology diagnosis. We also show that the prototype instrument can be operated by clinical users (a skin surgeon and a core medical trainee, after only 1-8 hours of training) to obtain consistent results in agreement with histopathology. The development of the new automated prototype and demonstration of inter-instrument transferability of the diagnosis models are important steps on the clinical translation path: it allows the testing of the MSH technology in a relevant clinical environment in order to evaluate its performance on a sufficiently large number of patients.
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Affiliation(s)
- Radu Boitor
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Kenny Kong
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dustin Shipp
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sandeep Varma
- Circle Nottingham Ltd NHS Treatment Centre, Lister Road, Nottingham NG7 2FT, UK
| | - Alexey Koloydenko
- Mathematics Department, Royal Holloway University of London, Egham, TW20 OEX, UK
| | - Kusum Kulkarni
- Department of Pathology, Nottingham University Hospitals NHS Trust, QMC Campus, Derby Road, Nottingham, NG7 2UH, UK
| | - Somaia Elsheikh
- Department of Pathology, Nottingham University Hospitals NHS Trust, QMC Campus, Derby Road, Nottingham, NG7 2UH, UK
| | - Tom Bakker Schut
- Erasmus-University Medical Center Rotterdam, Department of Dermatology, The Netherlands
- RiverD International, Marconistraat 16, Rotterdam 3029 AK, The Netherlands
| | - Peter Caspers
- Erasmus-University Medical Center Rotterdam, Department of Dermatology, The Netherlands
- RiverD International, Marconistraat 16, Rotterdam 3029 AK, The Netherlands
| | - Gerwin Puppels
- Erasmus-University Medical Center Rotterdam, Department of Dermatology, The Netherlands
- RiverD International, Marconistraat 16, Rotterdam 3029 AK, The Netherlands
| | | | - Elena Sokolova
- RiverD International, Marconistraat 16, Rotterdam 3029 AK, The Netherlands
| | - T. E. C. Nijsten
- Erasmus-University Medical Center Rotterdam, Department of Dermatology, The Netherlands
| | | | - Hywel Williams
- Centre of Evidence-Based Dermatology, Nottingham University Hospital NHS Trust, QMC Campus, Derby Road, NG7 2UH, UK
| | - Ioan Notingher
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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7
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Feng X, Moy AJ, Nguyen HTM, Zhang J, Fox MC, Sebastian KR, Reichenberg JS, Markey MK, Tunnell JW. Raman active components of skin cancer. Biomed Opt Express 2017; 8:2835-2850. [PMID: 28663910 PMCID: PMC5480433 DOI: 10.1364/boe.8.002835] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 05/05/2023]
Abstract
Raman spectroscopy (RS) has shown great potential in noninvasive cancer screening. Statistically based algorithms, such as principal component analysis, are commonly employed to provide tissue classification; however, they are difficult to relate to the chemical and morphological basis of the spectroscopic features and underlying disease. As a result, we propose the first Raman biophysical model applied to in vivo skin cancer screening data. We expand upon previous models by utilizing in situ skin constituents as the building blocks, and validate the model using previous clinical screening data collected from a Raman optical fiber probe. We built an 830nm confocal Raman microscope integrated with a confocal laser-scanning microscope. Raman imaging was performed on skin sections spanning various disease states, and multivariate curve resolution (MCR) analysis was used to resolve the Raman spectra of individual in situ skin constituents. The basis spectra of the most relevant skin constituents were combined linearly to fit in vivo human skin spectra. Our results suggest collagen, elastin, keratin, cell nucleus, triolein, ceramide, melanin and water are the most important model components. We make available for download (see supplemental information) a database of Raman spectra for these eight components for others to use as a reference. Our model reveals the biochemical and structural makeup of normal, nonmelanoma and melanoma skin cancers, and precancers and paves the way for future development of this approach to noninvasive skin cancer diagnosis.
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Affiliation(s)
- Xu Feng
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
| | - Austin J Moy
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
| | - Hieu T. M. Nguyen
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
| | - Jason Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
| | - Matthew C. Fox
- Medicine, Dell Medical School, The University of Texas at Austin, 1400 N IH-35 Suite C2-470, Austin, TX 78701, USA
| | - Katherine R. Sebastian
- Medicine, Dell Medical School, The University of Texas at Austin, 1400 N IH-35 Suite C2-470, Austin, TX 78701, USA
| | - Jason S. Reichenberg
- Medicine, Dell Medical School, The University of Texas at Austin, 1400 N IH-35 Suite C2-470, Austin, TX 78701, USA
| | - Mia K. Markey
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
| | - James W. Tunnell
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton Street C0800, Austin, TX 78712, USA
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Law AWL, Ahmed R, Cheung TW, Mak CY, Lau C. In situ cellular level Raman spectroscopy of the thyroid. Biomed Opt Express 2017; 8:670-678. [PMID: 28270975 PMCID: PMC5330565 DOI: 10.1364/boe.8.000670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/27/2016] [Accepted: 01/02/2017] [Indexed: 05/07/2023]
Abstract
We report a novel Raman spectroscopy method for in situ cellular level analysis of the thyroid. Thyroids are harvested from control and lithium treated mice. Lithium is used to treat bipolar disorder, but affects thyroid function. Raman spectra are acquired with a confocal setup (514 nm laser, 20 µm spot) focused on a follicular lumen. Raman peaks are observed at 1440, 1656, and 1746 cm-1, corresponding to tyrosine, an important amino acid for protein synthesis. Peaks are also observed at 563, 1087, 1265 and 1301 cm-1. With lithium, the tyrosine peaks increase, indicating tyrosine buildup. Raman spectroscopy can study the impact of many exogenous treatments on thyroid biochemistry.
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Sfakis L, Sharikova A, Tuschel D, Costa FX, Larsen M, Khmaladze A, Castracane J. Core/shell nanofiber characterization by Raman scanning microscopy. Biomed Opt Express 2017; 8:1025-1035. [PMID: 28271000 PMCID: PMC5330587 DOI: 10.1364/boe.8.001025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
Core/shell nanofibers are becoming increasingly popular for applications in tissue engineering. Nanofibers alone provide surface topography and increased surface area that promote cellular attachment; however, core/shell nanofibers provide the versatility of incorporating two materials with different properties into one. Such synthetic materials can provide the mechanical and degradation properties required to make a construct that mimics in vivo tissue. Many variations of these fibers can be produced. The challenge lies in the ability to characterize and quantify these nanofibers post fabrication. We developed a non-invasive method for the composition characterization and quantification at the nanoscale level of fibers using Confocal Raman microscopy. The biodegradable/biocompatible nanofibers, Poly (glycerol-sebacate)/Poly (lactic-co-glycolic) (PGS/PLGA), were characterized as a part of a fiber scaffold to quickly and efficiently analyze the quality of the substrate used for tissue engineering.
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Affiliation(s)
- Lauren Sfakis
- SUNY Polytechnic Institute, Nanobioscience Constellation, Albany NY, USA
| | - Anna Sharikova
- University at Albany, SUNY, Department of Physics, Albany, NY, USA
| | - David Tuschel
- HORIBA Scientific, 3880 Park Avenue, Edison, NJ, USA
| | - Felipe Xavier Costa
- University at Albany, SUNY, Department of Physics, Albany, NY, USA; Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Melinda Larsen
- University at Albany, SUNY, Department of Biological Sciences, Albany, NY, USA
| | - Alexander Khmaladze
- University at Albany, SUNY, Department of Physics, Albany, NY, USA; Dr. Alexander Khmaladze
| | - James Castracane
- SUNY Polytechnic Institute, Nanobioscience Constellation, Albany NY, USA; Dr. James Castracane
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Bilal M, Ullah R, Khan S, Ali H, Saleem M, Ahmed M. Lactate based optical screening of dengue virus infection in human sera using Raman spectroscopy. Biomed Opt Express 2017; 8:1250-1256. [PMID: 28271015 PMCID: PMC5330547 DOI: 10.1364/boe.8.001250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/19/2017] [Accepted: 01/22/2017] [Indexed: 05/27/2023]
Abstract
This study presents the screening of dengue virus (DENV) infection in human blood sera based on lactate concentration using Raman spectroscopy. A total of 70 samples, 50 from confirmed DENV infected patients and 20 from healthy volunteers have been used in this study. Raman spectra of all these samples have been acquired in the spectral range from 600 cm-1 to 1800 cm-1 using a 532 nm laser as an excitation source. Spectra of all these samples have been analyzed for assessing the biochemical changes resulting from infection. In DENV infected samples three prominent Raman peaks have been found at 750, 830 and 1450 cm-1. These peaks are most probably attributed to an elevated level of lactate due to an impaired function of different body organs in dengue infected patients. This has been proven by an addition of lactic acid solution to the healthy serum in a controlled manner. By the addition of lactic acid solution, the intense Raman bands at 1003, 1156 and 1516 cm-1 found in the spectrum of healthy serum got suppressed when the new peaks appeared around 750, 830, 925, 950, 1123, 1333, 1450, 1580 and 1730 cm-1. The current study predicts that lactate may possibly be a potential biomarker for the diagnosis of DENV infection.
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Affiliation(s)
- Muhammad Bilal
- Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Rahat Ullah
- Agri. & Biophtonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad, 45650, Pakistan
| | - Saranjam Khan
- Agri. & Biophtonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad, 45650, Pakistan
| | - Hina Ali
- Agri. & Biophtonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Saleem
- Agri. & Biophtonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad, 45650, Pakistan
| | - Mushtaq Ahmed
- Agri. & Biophtonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad, 45650, Pakistan
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11
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Sinjab F, Kong K, Gibson G, Varma S, Williams H, Padgett M, Notingher I. Tissue diagnosis using power-sharing multifocal Raman micro-spectroscopy and auto-fluorescence imaging. Biomed Opt Express 2016; 7:2993-3006. [PMID: 27570692 PMCID: PMC4986808 DOI: 10.1364/boe.7.002993] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/24/2016] [Accepted: 06/07/2016] [Indexed: 05/05/2023]
Abstract
We describe a multifocal Raman micro-spectroscopy detection method based on a digital micromirror device, which allows for simultaneous "power-sharing" acquisition of Raman spectra from ad hoc sampling points. As the locations of the points can be rapidly updated in real-time via software control of a liquid-crystal spatial light modulator (LC-SLM), this technique is compatible with automated adaptive- and selective-sampling Raman spectroscopy techniques, the latter of which has previously been demonstrated for fast diagnosis of skin cancer tissue resections. We describe the performance of this instrument and show examples of multiplexed measurements on a range of test samples. Following this, we show the feasibility of reducing measurement time for power-shared multifocal Raman measurements combined with confocal auto-fluorescence imaging to provide guided diagnosis of tumours in human skin samples.
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Affiliation(s)
- Faris Sinjab
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Kenny Kong
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Graham Gibson
- School of Physics and Astronomy, University of Glasgow, Kelvin Building, Glasgow G12 8QQ, UK
| | - Sandeep Varma
- Circle Nottingham Ltd NHS Treatment Centre, Lister Road, Nottingham NG7 2FT, UK
| | - Hywel Williams
- Centre of Evidence-Based Dermatology, Nottingham University Hospital NHS Trust, QMC Campus, Derby Road, NG7 2UH, UK
| | - Miles Padgett
- School of Physics and Astronomy, University of Glasgow, Kelvin Building, Glasgow G12 8QQ, UK
| | - Ioan Notingher
- School of Physics and Astronomy, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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12
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Cepeda-Pérez E, López-Luke T, Salas P, Plascencia-Villa G, Ponce A, Vivero-Escoto J, José-Yacamán M, de la Rosa E. SERS-active Au/SiO2 clouds in powder for rapid ex vivo breast adenocarcinoma diagnosis. Biomed Opt Express 2016; 7:2407-18. [PMID: 27375955 PMCID: PMC4918593 DOI: 10.1364/boe.7.002407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 05/26/2023]
Abstract
In the present work, we report a dry-based application technique of Au/SiO2 clouds in powder for rapid ex vivo adenocarcinoma diagnosis through surface-enhanced Raman scattering (SERS); using low laser power and an integration time of one second. Several characteristic Raman peaks frequently used for the diagnosis of breast adenocarcinoma in the range of the amide III are successfully enhanced by breading the tissue with Au/SiO2 powder. The SERS activity of these Au/SiO2 powders is attributed to their rapid rehydration upon contact with the wet tissues, which promotes the formation of gold nanoparticle aggregates. The propensity of the Au/SiO2 cloud structures to adsorb biomolecules in the vicinity of the gold nanoparticle clusters promotes the necessary conditions for SERS detection. In addition, electron microscopy, together with elemental analysis, have been used to confirm the structure of the new Au/SiO2 cloud material and to investigate its distribution in breast tissues.
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Affiliation(s)
| | | | - Pedro Salas
- Universidad Nacional Autónoma de México, Centro de Física Aplicada y Tecnología Avanzada, Querétaro 76000, Mexico
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, USA
| | - Arturo Ponce
- Department of Physics and Astronomy, The University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, USA
| | - Juan Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, 9201 University City Blvd. Charlotte, NC 28223, USA
| | - Miguel José-Yacamán
- Department of Physics and Astronomy, The University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, USA
| | - Elder de la Rosa
- Centro de Investigaciones en Óptica, León, Gto., C.P. 37150, Mexico
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13
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Khan S, Ullah R, Khan A, Wahab N, Bilal M, Ahmed M. Analysis of dengue infection based on Raman spectroscopy and support vector machine (SVM). Biomed Opt Express 2016; 7:2249-56. [PMID: 27375941 PMCID: PMC4918579 DOI: 10.1364/boe.7.002249] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 05/02/2023]
Abstract
The current study presents the use of Raman spectroscopy combined with support vector machine (SVM) for the classification of dengue suspected human blood sera. Raman spectra for 84 clinically dengue suspected patients acquired from Holy Family Hospital, Rawalpindi, Pakistan, have been used in this study.The spectral differences between dengue positive and normal sera have been exploited by using effective machine learning techniques. In this regard, SVM models built on the basis of three different kernel functions including Gaussian radial basis function (RBF), polynomial function and linear functionhave been employed to classify the human blood sera based on features obtained from Raman Spectra.The classification model have been evaluated with the 10-fold cross validation method. In the present study, the best performance has been achieved for the polynomial kernel of order 1. A diagnostic accuracy of about 85% with the precision of 90%, sensitivity of 73% and specificity of 93% has been achieved under these conditions.
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Affiliation(s)
- Saranjam Khan
- Agri-Biophotonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Rahat Ullah
- Agri-Biophotonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Asifullah Khan
- Pattern Recognition Lab, DCIS, Pakistan Institutes of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad 45650, Pakistan
| | - Noorul Wahab
- Pattern Recognition Lab, DCIS, Pakistan Institutes of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad 45650, Pakistan
| | - Muhammad Bilal
- Agri-Biophotonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
| | - Mushtaq Ahmed
- Agri-Biophotonics Division, National Institute for Lasers and Optronics (NILOP), Nilore, Islamabad 45650, Pakistan
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14
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Vardaki MZ, Matousek P, Stone N. Characterisation of signal enhancements achieved when utilizing a photon diode in deep Raman spectroscopy of tissue. Biomed Opt Express 2016; 7:2130-2141. [PMID: 27375932 PMCID: PMC4918570 DOI: 10.1364/boe.7.002130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 06/06/2023]
Abstract
We characterise the performance of a beam enhancing element ('photon diode') for use in deep Raman spectroscopy (DRS) of biological tissues. The optical component enhances the number of laser photons coupled into a tissue sample by returning escaping photons back into it at the illumination zone. The method is compatible with transmission Raman spectroscopy, a deep Raman spectroscopy concept, and its implementation leads to considerable enhancement of detected Raman photon rates. In the past, the enhancement concept was demonstrated with a variety of samples (pharmaceutical tablets, tissue, etc) but it was not systematically characterized with biological tissues. In this study, we investigate the enhancing properties of the photon diode in the transmission Raman geometry as a function of: a) the depth and b) the optical properties of tissue samples. Liquid tissue phantoms were employed to facilitate systematic variation of optical properties. These were chosen to mimic optical properties of human tissues, including breast and prostate. The obtained results evidence that a photon diode can enhance Raman signals of tissues by a maximum of × 2.4, although it can also decrease the signals created towards the back of samples that exhibit high scattering or absorption properties.
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Affiliation(s)
- Martha Z Vardaki
- School of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QL, UK
| | - Pavel Matousek
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, OX11 0QX, UK;
| | - Nicholas Stone
- School of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QL, UK;
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15
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Rocha-Mendoza I, Licea-Rodriguez J, Marro M, Olarte OE, Plata-Sanchez M, Loza-Alvarez P. Rapid spontaneous Raman light sheet microscopy using cw-lasers and tunable filters. Biomed Opt Express 2015; 6:3449-61. [PMID: 26417514 PMCID: PMC4574670 DOI: 10.1364/boe.6.003449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 05/25/2023]
Abstract
We perform rapid spontaneous Raman 2D imaging in light-sheet microscopy using continuous wave lasers and interferometric tunable filters. By angularly tuning the filter, the cut-on/off edge transitions are scanned along the excited Stokes wavelengths. This allows obtaining cumulative intensity profiles of the scanned vibrational bands, which are recorded on image stacks; resembling a spectral version of the knife-edge technique to measure intensity profiles. A further differentiation of the stack retrieves the Raman spectra at each pixel of the image which inherits the 3D resolution of the host light sheet system. We demonstrate this technique using solvent solutions and composites of polystyrene beads and lipid droplets immersed in agar and by imaging the C-H (2800-3100cm(-1)) region in a C. elegans worm. The image acquisition time results in 4 orders of magnitude faster than confocal point scanning Raman systems, allowing the possibility of performing fast spontaneous Raman·3D-imaging on biological samples.
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Affiliation(s)
- Israel Rocha-Mendoza
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, 22860 Ensenada B.C., Mexico ;
| | - Jacob Licea-Rodriguez
- ICFO-Institut de Ciencies Fotoniques, Av. Carl Friedrich Gauss, 3 08860 Castelldefels (Barcelona), Spain
| | - Mónica Marro
- ICFO-Institut de Ciencies Fotoniques, Av. Carl Friedrich Gauss, 3 08860 Castelldefels (Barcelona), Spain
| | - Omar E Olarte
- ICFO-Institut de Ciencies Fotoniques, Av. Carl Friedrich Gauss, 3 08860 Castelldefels (Barcelona), Spain
| | - Marcos Plata-Sanchez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, 22860 Ensenada B.C., Mexico
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, Av. Carl Friedrich Gauss, 3 08860 Castelldefels (Barcelona), Spain ;
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16
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Huang X, Irmak S, Lu YF, Pipinos I, Casale G, Subbiah J. Spontaneous and coherent anti-Stokes Raman spectroscopy of human gastrocnemius muscle biopsies in CH-stretching region for discrimination of peripheral artery disease. Biomed Opt Express 2015; 6:2766-2777. [PMID: 26309742 PMCID: PMC4541506 DOI: 10.1364/boe.6.002766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 06/04/2023]
Abstract
Peripheral Artery Disease (PAD) is a common manifestation of atherosclerosis, characterized by lower leg ischemia and myopathy in association with leg dysfunction. In the present study, Spontaneous and coherent anti-Stokes Raman scattering (CARS) spectroscopic techniques in CH-stretching spectral region were evaluated for discriminating healthy and diseased tissues of human gastrocnemius biopsies of control and PAD patients. Since Raman signatures of the tissues in the fingerprint region are highly complex and CH containing moieties are dense, CH-stretching limited spectral range was used to classify the diseased tissues. A total of 181 Raman spectra from 9 patients and 122 CARS spectra from 12 patients were acquired. Due to the high dimensionality of the data in Raman and CARS measurements, principal component analysis (PCA) was first performed to reduce the dimensionality of the data (6 and 9 principal scores for Raman and CARS, respectively) in the CH-stretching region, followed by a discriminant function analysis (DFA) to classify the samples into different categories based on disease severity. The CH2 and CH3 vibrational signatures were observed in the Raman and CARS spectroscopy. Raman and CARS data in conjunction with PCA-DFA analysis were capable of differentiating healthy and PAD gastrocnemius with an accuracy of 85.6% and 78.7%, respectively.
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Affiliation(s)
- X. Huang
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - S. Irmak
- Biological Systems Engineering, University of Nebraska, Lincoln, NE 68583-0726, USA
| | - Y. F. Lu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - I. Pipinos
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE 68198-5182, USA
| | - G. Casale
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE 68198-5182, USA
| | - J. Subbiah
- Biological Systems Engineering, University of Nebraska, Lincoln, NE 68583-0726, USA
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17
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Jung GB, Nam SW, Choi S, Lee GJ, Park HK. Evaluation of antibiotic effects on Pseudomonas aeruginosa biofilm using Raman spectroscopy and multivariate analysis. Biomed Opt Express 2014; 5:3238-51. [PMID: 25401035 PMCID: PMC4230853 DOI: 10.1364/boe.5.003238] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 06/08/2014] [Accepted: 08/19/2014] [Indexed: 05/22/2023]
Abstract
We investigate the mode of action and classification of antibiotic agents (ceftazidime, patulin, and epigallocatechin gallate; EGCG) on Pseudomonas aeruginosa (P. aeruginosa) biofilm using Raman spectroscopy with multivariate analysis, including support vector machine (SVM) and principal component analysis (PCA). This method allows for quantitative, label-free, non-invasive and rapid monitoring of biochemical changes in complex biofilm matrices with high sensitivity and specificity. In this study, the biofilms were grown and treated with various agents in the microfluidic device, and then transferred onto gold-coated substrates for Raman measurement. Here, we show changes in biochemical properties, and this technology can be used to distinguish between changes induced in P. aeruginosa biofilms using three antibiotic agents. The Raman band intensities associated with DNA and proteins were decreased, compared to control biofilms, when the biofilms were treated with antibiotics. Unlike with exposure to ceftazidime and patulin, the Raman spectrum of biofilms exposed to EGCG showed a shift in the spectral position of the CH deformation stretch band from 1313 cm(-1) to 1333 cm(-1), and there was no difference in the band intensity at 1530 cm(-1) (C = C stretching, carotenoids). The PCA-SVM analysis results show that antibiotic-treated biofilms can be detected with high sensitivity of 93.33%, a specificity of 100% and an accuracy of 98.33%. This method also discriminated the three antibiotic agents based on the cellular biochemical and structural changes induced by antibiotics with high sensitivity and specificity of 100%. This study suggests that Raman spectroscopy with PCA-SVM is potentially useful for the rapid identification and classification of clinically-relevant antibiotics of bacteria biofilm. Furthermore, this method could be a powerful approach for the development and screening of new antibiotics.
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Affiliation(s)
- Gyeong Bok Jung
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- These authors contributed equally to this work
| | - Seong Won Nam
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- These authors contributed equally to this work
| | - Samjin Choi
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
| | - Gi-Ja Lee
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
| | - Hun-Kuk Park
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
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18
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Li Q, Gao Q, Zhang G. Classification for breast cancer diagnosis with Raman spectroscopy. Biomed Opt Express 2014; 5:2435-45. [PMID: 25071976 PMCID: PMC4102376 DOI: 10.1364/boe.5.002435] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 05/21/2023]
Abstract
In order to promote the development of the portable, low-cost and in vivo cancer diagnosis instrument, a miniature laser Raman spectrometer was employed to acquire the conventional Raman spectra for breast cancer detection in this paper. But it is difficult to achieve high discrimination accuracy. Then a novel method of adaptive weight k-local hyperplane (AWKH) is proposed to increase the classification accuracy. AWKH is an extension and improvement of K-local hyperplane distance nearest-neighbor (HKNN). It considers the features weights of the training data in the nearest neighbor selection and local hyperplane construction stage, which resolve the basic shortcoming of HKNN works well only for small values of the nearest-neighbor. Experimental results on Raman spectra of breast tissues in vitro show the proposed method can realize high classification accuracy.
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19
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Xie R, Su J, Rentchler EC, Zhang Z, Johnson CK, Shi H, Hui R. Multi-modal label-free imaging based on a femtosecond fiber laser. Biomed Opt Express 2014; 5:2390-6. [PMID: 25071972 PMCID: PMC4102372 DOI: 10.1364/boe.5.002390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/19/2014] [Accepted: 05/31/2014] [Indexed: 05/11/2023]
Abstract
We demonstrate multi-mode microscopy based on a single femtosecond fiber laser. Coherent anti-Stokes Raman scattering (CARS), stimulated Raman scattering (SRS) and photothermal images can be obtained simultaneously with this simplified setup. Distributions of lipid and hemoglobin in sliced mouse brain samples and blood cells are imaged. The dependency of signal amplitude on the pump power and pump modulation frequency is characterized, which allows to isolate the impact from different contributions.
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Affiliation(s)
- Ruxin Xie
- Department Electrical Engineering & Computer Science, University of Kansas, Lawrence, KS, 66045, USA
| | - Jue Su
- Department Electrical Engineering & Computer Science, University of Kansas, Lawrence, KS, 66045, USA
| | - Eric C. Rentchler
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA
| | - Ziyan Zhang
- Department of Pharmacology & Toxicology, University of Kansas, Lawrence, KS, 66045, USA
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA
| | - Honglian Shi
- Department of Pharmacology & Toxicology, University of Kansas, Lawrence, KS, 66045, USA
| | - Rongqing Hui
- Department Electrical Engineering & Computer Science, University of Kansas, Lawrence, KS, 66045, USA
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20
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Li N, Chen D, Xu Y, Liu S, Zhang H. Confocal Raman micro-spectroscopy for rapid and label-free detection of maleic acid-induced variations in human sperm. Biomed Opt Express 2014; 5:1690-9. [PMID: 24877025 PMCID: PMC4026909 DOI: 10.1364/boe.5.001690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 05/11/2023]
Abstract
Confocal Raman microspectroscopy is a valuable analytical tool in biological and medical research, allowing the detection of sample variations without external labels or extensive preparation. To determine whether this method can assess the effect of maleic acid on sperm, we prepared human sperm samples incubated in different concentrations of maleic acid, after which Raman spectra from the various regions of sperm cells were recorded. Following the maleic acid treatment, Raman spectra indicated significant changes. Combined with other means, we found that the structures and chemical compositions of sperm membranes were damaged, and even the sperm DNA was damaged by the incorporation of maleic acid. Thus, this technique can be used for detection and identification of maleic acid-induced changes in human sperm at a molecular level. Although this particular application of Raman microspectroscopy still requires further validation, it has potentially promise as a diagnostic tool for reproductive medicine.
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Affiliation(s)
- Ning Li
- Southern Institute of Pharmaceutical Research, South China Normal University, Guangzhou, 510631, China
- School of Information and Optoelectronic Science and Engineering, South China Normal University, Guangzhou, 510006, China
| | - Diling Chen
- Southern Institute of Pharmaceutical Research, South China Normal University, Guangzhou, 510631, China
| | - Yan Xu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Songhao Liu
- School of Information and Optoelectronic Science and Engineering, South China Normal University, Guangzhou, 510006, China
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Heming Zhang
- Southern Institute of Pharmaceutical Research, South China Normal University, Guangzhou, 510631, China
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21
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Agenant M, Grimbergen M, Draga R, Marple E, Bosch R, van Swol C. Clinical superficial Raman probe aimed for epithelial tumor detection: Phantom model results. Biomed Opt Express 2014; 5:1203-16. [PMID: 24761301 PMCID: PMC3985982 DOI: 10.1364/boe.5.001203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 05/04/2023]
Abstract
A novel clinical Raman probe for sampling superficial tissue to improve in vivo detection of epithelial malignancies is compared to a non-superficial probe regarding depth response function and signal-to-noise ratio. Depth response measurements were performed in a phantom tissue model consisting of a polyethylene terephthalate disc in an 20%-Intralipid(®) solution. Sampling ranges of 0-200 and 0-300 μm were obtained for the superficial and non-superficial probe, respectively. The mean signal-to-noise ratio of the superficial probe increased by a factor of 2 compared with the non-superficial probe. This newly developed superficial Raman probe is expected to improve epithelial cancer detection in vivo.
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Affiliation(s)
- Michelle Agenant
- Department of Medical Physics & Instrumentation, St. Antonius Hospital, PO Box 2500, 3430 EM Nieuwegein, The Netherlands
- Department of Urology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Matthijs Grimbergen
- Department of Medical Physics & Instrumentation, St. Antonius Hospital, PO Box 2500, 3430 EM Nieuwegein, The Netherlands
| | - Ronald Draga
- Department of Urology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Eric Marple
- EmVision LLC, 1471 F Road, Loxahatchee, Florida 33470, USA
| | - Ruud Bosch
- Department of Urology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Christiaan van Swol
- Department of Medical Physics & Instrumentation, St. Antonius Hospital, PO Box 2500, 3430 EM Nieuwegein, The Netherlands
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22
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Jung GB, Lee YJ, Lee G, Park HK. A simple and rapid detection of tissue adhesive-induced biochemical changes in cells and DNA using Raman spectroscopy. Biomed Opt Express 2013; 4:2673-82. [PMID: 24298425 PMCID: PMC3829560 DOI: 10.1364/boe.4.002673] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/27/2013] [Accepted: 09/27/2013] [Indexed: 05/24/2023]
Abstract
We demonstrate a cytotoxicity evaluation of tissue adhesive using Raman spectroscopy. This method allows for quantitative, label-free, non-invasive and rapid monitoring of the biochemical changes of cells following tissue adhesive treatment. Here, we show the biochemical property changes in mouse fibroblast L929 cells and cellular DNA following tissue adhesive (Dermabond) treatment using Raman spectroscopy. The Raman band intensities were significantly decreased when the cells were treated with Dermabond as compared to control cells. These results suggest denaturation and conformational changes in proteins and degradation of DNA related to cell death. To support these conclusions, conventional cytotoxicity assays such as WST, LIVE/DEAD, and TUNEL were carried out, and the results were in agreement with the Raman results. Thus, Raman spectroscopy analysis not only distinguishes between viable and damaged cells, but can also be used for identification and quantification of a cytotoxicity of tissue adhesive, which based on the cellular biochemical and structural changes at a molecular level. Therefore, we suggest that this method could be used for cytotoxic evaluation of tissue adhesives by rapid and sensitive detection of cellular changes.
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Affiliation(s)
- Gyeong Bok Jung
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
| | - Young Ju Lee
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
| | - Gihyun Lee
- Department of Physiology, College of Korean Medicine, Kyung Hee University, 1 Hoeki-Dong, Dongdaemoon-gu, Seoul 130-701, South Korea
| | - Hun-Kuk Park
- Department of Biomedical Engineering & Healthcare Industry Research Institute, College of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, South Korea
- Program of Medical Engineering, Kyung Hee University, Seoul 130-701, South Korea
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23
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Hamasha K, Mohaidat QI, Putnam RA, Woodman RC, Palchaudhuri S, Rehse SJ. Sensitive and specific discrimination of pathogenic and nonpathogenic Escherichia coli using Raman spectroscopy-a comparison of two multivariate analysis techniques. Biomed Opt Express 2013; 4:481-9. [PMID: 23577283 PMCID: PMC3617710 DOI: 10.1364/boe.4.000481] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 05/22/2023]
Abstract
The determination of bacterial identity at the strain level is still a complex and time-consuming endeavor. In this study, visible wavelength spontaneous Raman spectroscopy has been used for the discrimination of four closely related Escherichia coli strains: pathogenic enterohemorrhagic E. coli O157:H7 and non-pathogenic E. coli C, E. coli Hfr K-12, and E. coli HF4714. Raman spectra from 600 to 2000 cm(-1) were analyzed with two multivariate chemometric techniques, principal component-discriminant function analysis and partial least squares-discriminant analysis, to determine optimal parameters for the discrimination of pathogenic E. coli from the non-pathogenic strains. Spectral preprocessing techniques such as smoothing with windows of various sizes and differentiation were investigated. The sensitivity and specificity of both techniques was in excess of 95%, determined by external testing of the chemometric models. This study suggests that spontaneous Raman spectroscopy with visible wavelength excitation is potentially useful for the rapid identification and classification of clinically-relevant bacteria at the strain level.
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Affiliation(s)
- Khozima Hamasha
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
- Now with Department of Basic Science, Al-Huson University College, Al-Balqa Applied University, Irbid, Jordan
| | - Qassem I. Mohaidat
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
- Now with Department of Physics, Yarmouk University, Irbid, Jordan
| | - Russell A. Putnam
- Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ryan C. Woodman
- Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Sunil Palchaudhuri
- Department of Immunology and Microbiology, Wayne State University, Detroit, Michigan 48201, USA
| | - Steven J. Rehse
- Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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24
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He XN, Allen J, Black PN, Baldacchini T, Huang X, Huang H, Jiang L, Lu YF. Coherent anti-Stokes Raman scattering and spontaneous Raman spectroscopy and microscopy of microalgae with nitrogen depletion. Biomed Opt Express 2012; 3:2896-906. [PMID: 23162727 PMCID: PMC3493223 DOI: 10.1364/boe.3.002896] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/13/2012] [Accepted: 10/15/2012] [Indexed: 05/04/2023]
Abstract
Microalgae are extensively researched as potential feedstocks for biofuel production. Energy-rich compounds in microalgae, such as lipids, require efficient characterization techniques to investigate the metabolic pathways and the environmental factors influencing their accumulation. The model green alga Coccomyxa accumulates significant amounts of triacylglycerols (TAGs) under nitrogen depletion (N-depletion). To monitor the growth of TAGs (lipid) in microalgal cells, a study of microalgal cells (Coccomyxa sp. C169) using both spontaneous Raman and coherent anti-Stokes Raman scattering (CARS) spectroscopy and microscopy were carried out. Spontaneous Raman spectroscopy was conducted to analyze the components in the algal cells, while CARS was carried out to monitor the distribution of lipid droplets in the cells. Raman signals of carotenoid are greater in control microalgae compared to N-depleted cells. Raman signals of lipid droplets appear after N-depletion and its distribution can be clearly observed in the CARS microscopy. Both spontaneous Raman spectroscopy and CARS microscopy were found to be suitable analysis tools for microalgae.
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Affiliation(s)
- X. N. He
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - J. Allen
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, USA
| | - P. N. Black
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, USA
| | - T. Baldacchini
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
- Technology and Applications Center, Newport Corporation, Irvine, CA 92606, USA
| | - X. Huang
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - H. Huang
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - L. Jiang
- Department of Mechanical and Automation Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Y. F. Lu
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
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25
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Saha A, Barman I, Dingari NC, McGee S, Volynskaya Z, Galindo LH, Liu W, Plecha D, Klein N, Dasari RR, Fitzmaurice M. Raman spectroscopy: a real-time tool for identifying microcalcifications during stereotactic breast core needle biopsies. Biomed Opt Express 2011; 2:2792-803. [PMID: 22025985 PMCID: PMC3191446 DOI: 10.1364/boe.2.002792] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 05/05/2023]
Abstract
Microcalcifications are an early mammographic sign of breast cancer and a target for stereotactic breast needle biopsy. We present here a Raman spectroscopic tool for detecting microcalcifications in breast tissue based on their chemical composition. We collected ex vivo Raman spectra from 159 tissue sites in fresh stereotactic breast needle biopsies from 33 patients, including 54 normal sites, 75 lesions with microcalcifications and 30 lesions without microcalcifications. Application of our Raman technique resulted in a positive predictive value of 97% for detecting microcalcifications. This study shows that Raman spectroscopy has the potential to detect microcalcifications during stereotactic breast core biopsies and provide real-time feedback to radiologists, thus reducing non-diagnostic and false negative biopsies.
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Affiliation(s)
- A. Saha
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - I. Barman
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - N. C. Dingari
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - S. McGee
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Current Address, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Z. Volynskaya
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
- Current Address, Aperio Technologies, Inc., 1360 Park Center Dr., Vista, CA 92081, USA
| | - L. H. Galindo
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - W. Liu
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA
| | - D. Plecha
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA
| | - N. Klein
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA
| | - R. R. Dasari
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - M. Fitzmaurice
- Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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26
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Kumamoto Y, Taguchi A, Smith NI, Kawata S. Deep UV resonant Raman spectroscopy for photodamage characterization in cells. Biomed Opt Express 2011; 2:927-36. [PMID: 21483614 PMCID: PMC3072131 DOI: 10.1364/boe.2.000927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/18/2011] [Accepted: 03/09/2011] [Indexed: 05/22/2023]
Abstract
We employed deep UV (DUV) Raman spectroscopy for characterization of molecular photodamage in cells. 244 nm light excitation Raman spectra were measured for HeLa cells exposed to the excitation light for different durations. In the spectra obtained with the shortest exposure duration (0.25 sec at 16 µW/µm(2) irradiation), characteristic resonant Raman bands of adenine and guanine at 1483 cm(-1) and tryptophan and tyrosine at 1618 cm(-1) were clearly visible. With increasing exposure duration (up to 12.5 sec), these biomolecular Raman bands diminished, while a photoproduct Raman band at 1611 cm(-1) grew. By exponential function fitting analyses, intensities of these characteristic three bands were correlated with sample exposure duration at different intensities of excitation light. We then suggest practical excitation conditions effective for DUV Raman observation of cells without photodamage-related spectral distortion.
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Affiliation(s)
- Yasuaki Kumamoto
- Department of Applied Physics, Graduate School of Engineering, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Nanophotonics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
| | - Atsushi Taguchi
- Nanophotonics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
| | - Nicholas Isaac Smith
- Biophotonics Laboratory, Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Kawata
- Department of Applied Physics, Graduate School of Engineering, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Nanophotonics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
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