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Morais CLM, Lima KMG, Dickinson AW, Saba T, Bongers T, Singh MN, Martin FL, Bury D. Non-invasive diagnostic test for lung cancer using biospectroscopy and variable selection techniques in saliva samples. Analyst 2024. [PMID: 39105622 DOI: 10.1039/d4an00726c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Lung cancer is one of the most commonly occurring malignant tumours worldwide. Although some reference methods such as X-ray, computed tomography or bronchoscope are widely used for clinical diagnosis of lung cancer, there is still a need to develop new methods for early detection of lung cancer. Especially needed are approaches that might be non-invasive and fast with high analytical precision and statistically reliable. Herein, we developed a swab "dip" test in saliva whereby swabs were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy harnessed to principal component analysis-quadratic discriminant analysis (QDA) and variable selection techniques employing successive projections algorithm (SPA) and genetic algorithm (GA) for feature selection/extraction combined with QDA. A total of 1944 saliva samples (56 designated as lung-cancer positive and 1888 designed as controls) were obtained in a lung cancer-screening programme being undertaken in North-West England. GA-QDA models achieved, for the test set, sensitivity and specificity values of 100.0% and 99.1%, respectively. Three wavenumbers (1422 cm-1, 1546 cm-1 and 1578 cm-1) were identified using the GA-QDA model to distinguish between lung cancer and controls, including ring C-C stretching, CN adenine, Amide II [δ(NH), ν(CN)] and νs(COO-) (polysaccharides, pectin). These findings highlight the potential of using biospectroscopy associated with multivariate classification algorithms to discriminate between benign saliva samples and those with underlying lung cancer.
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Affiliation(s)
- Camilo L M Morais
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
- Center for Education, Science and Technology of the Inhamuns Region, State University of Ceará, Tauá 63660-000, Brazil
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
| | - Andrew W Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Maneesh N Singh
- Biocel UK Ltd, Hull HU10 6TS, UK
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
| | - Francis L Martin
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
- Biocel UK Ltd, Hull HU10 6TS, UK
| | - Danielle Bury
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
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Yan L, Su H, Liu J, Wen X, Luo H, Yin Y, Guo X. Rapid detection of lung cancer based on serum Raman spectroscopy and a support vector machine: a case-control study. BMC Cancer 2024; 24:791. [PMID: 38956551 PMCID: PMC11220989 DOI: 10.1186/s12885-024-12578-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/28/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Early screening and detection of lung cancer is essential for the diagnosis and prognosis of the disease. In this paper, we investigated the feasibility of serum Raman spectroscopy for rapid lung cancer screening. METHODS Raman spectra were collected from 45 patients with lung cancer, 45 with benign lung lesions, and 45 healthy volunteers. And then the support vector machine (SVM) algorithm was applied to build a diagnostic model for lung cancer. Furthermore, 15 independent individuals were sampled for external validation, including 5 lung cancer patients, 5 benign lung lesion patients, and 5 healthy controls. RESULTS The diagnostic sensitivity, specificity, and accuracy were 91.67%, 92.22%, 90.56% (lung cancer vs. healthy control), 92.22%,95.56%,93.33% (benign lung lesion vs. healthy) and 80.00%, 83.33%, 80.83% (lung cancer vs. benign lung lesion), repectively. In the independent validation cohort, our model showed that all the samples were classified correctly. CONCLUSION Therefore, this study demonstrates that the serum Raman spectroscopy analysis technique combined with the SVM algorithm has great potential for the noninvasive detection of lung cancer.
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Affiliation(s)
- Linfang Yan
- Guang'an People's Hospital, Guang'an, Sichuan Province, China
| | - Huiting Su
- Guang'an People's Hospital, Guang'an, Sichuan Province, China.
| | - Jiafei Liu
- Guang'an People's Hospital, Guang'an, Sichuan Province, China
| | - Xiaozheng Wen
- Guang'an People's Hospital, Guang'an, Sichuan Province, China
| | - Huaichao Luo
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Chengdu, China
| | - Yu Yin
- Sichuan Institute for Brain Science and Brain-Inspired Intelligence, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqiang Guo
- Guang'an People's Hospital, Guang'an, Sichuan Province, China
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Shi J, Li R, Wang Y, Zhang C, Lyu X, Wan Y, Yu Z. Detection of lung cancer through SERS analysis of serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124189. [PMID: 38569385 DOI: 10.1016/j.saa.2024.124189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
Early detection and postoperative assessment are crucial for improving overall survival among lung cancer patients. Here, we report a non-invasive technique that integrates Raman spectroscopy with machine learning for the detection of lung cancer. The study encompassed 88 postoperative lung cancer patients, 73 non-surgical lung cancer patients, and 68 healthy subjects. The primary aim was to explore variations in serum metabolism across these cohorts. Comparative analysis of average Raman spectra was conducted, while principal component analysis was employed for data visualization. Subsequently, the augmented dataset was used to train convolutional neural networks (CNN) and Resnet models, leading to the development of a diagnostic framework. The CNN model exhibited superior performance, as verified by the receiver operating characteristic curve. Notably, postoperative patients demonstrated an increased likelihood of recurrence, emphasizing the crucial need for continuous postoperative monitoring. In summary, the integration of Raman spectroscopy with CNN-based classification shows potential for early detection and postoperative assessment of lung cancer.
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Affiliation(s)
- Jiamin Shi
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China
| | - Rui Li
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China; State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yuchen Wang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China
| | - Chenlei Zhang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China
| | - Xiaohong Lyu
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, People's Republic of China
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Vestal, 13850 NY, USA
| | - Zhanwu Yu
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China.
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Wu Y, Liu J, Wang Y, Gibson S, Osadchy M, Fang Y. Reconstructing Randomly Masked Spectra Helps DNNs Identify Discriminant Wavenumbers. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2024; 46:3845-3861. [PMID: 38150338 DOI: 10.1109/tpami.2023.3347617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Nondestructive detection methods, based on vibrational spectroscopy, are vitally important in a wide range of applications including industrial chemistry, pharmacy and national defense. Recently, deep learning has been introduced into vibrational spectroscopy showing great potential. Different from images, text, etc. that offer large labeled data sets, vibrational spectroscopic data is very limited, which requires novel concepts beyond transfer and meta learning. To tackle this, we propose a task-enhanced augmentation network (TeaNet). The key component of TeaNet is a reconstruction module that inputs randomly masked spectra and outputs reconstructed samples that are similar to the original ones, but include additional variations learned from the domain. These augmented samples are used to train the classification model. The reconstruction and prediction parts are trained simultaneously, end-to-end with back-propagation. Results on both synthetic and real-world datasets verified the superiority of the proposed method. In the most difficult synthetic scenarios TeaNet outperformed CNN by 17%. We visualized and analysed the neuron responses of TeaNet and CNN, and found that TeaNet's ability to identify discriminant wavenumbers was excellent compared to CNN. Our approach is general and can be easily adapted to other domains, offering a solution to more accurate and interpretable few-shot learning.
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Hano H, Lawrie CH, Suarez B, Paredes Lario A, Elejoste Echeverría I, Gómez Mediavilla J, Crespo Cruz MI, Lopez E, Seifert A. Power of Light: Raman Spectroscopy and Machine Learning for the Detection of Lung Cancer. ACS OMEGA 2024; 9:14084-14091. [PMID: 38559992 PMCID: PMC10975667 DOI: 10.1021/acsomega.3c09537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide, emphasizing the urgent need for reliable and efficient diagnostic methods. Conventional approaches often involve invasive procedures and can be time-consuming and costly, thereby delaying the effective treatment. The current study explores the potential of Raman spectroscopy, as a promising noninvasive technique, by analyzing human blood plasma samples from lung cancer patients and healthy controls. In a benchmark study, 16 machine learning models were evaluated by employing four strategies: the combination of dimensionality reduction with classifiers; application of feature selection prior to classification; stand-alone classifiers; and a unified predictive model. The models showed different performances due to the inherent complexity of the data, achieving accuracies from 0.77 to 0.85 and areas under the curve for receiver operating characteristics from 0.85 to 0.94. Hybrid methods incorporating dimensionality reduction and feature selection algorithms present the highest figures of merit. Nevertheless, all machine learning models deliver creditable scores and demonstrate that Raman spectroscopy represents a powerful method for future in vitro diagnostics of lung cancer.
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Affiliation(s)
- Harun Hano
- CIC
nanoGUNE BRTA, 20018 San Sebastián, Spain
- Department
of Physics, University of the Basque Country
(UPV/EHU), 20018 San Sebastián, Spain
| | - Charles H. Lawrie
- IKERBASQUE—Basque
Foundation for Science, 48009 Bilbao, Spain
- Biogipuzkoa
Health Research Institute, 20014 San Sebastián, Spain
- Sino-Swiss
Institute of Advanced Technology (SSIAT), University of Shanghai, 201800 Shanghai, China
- Radcliffe
Department of Medicine, University of Oxford, OX3 9DU Oxford, U.K.
| | - Beatriz Suarez
- Faculty
of Nursing and Medicine, University of the
Basque Country (UPV/EHU), 20014 San Sebastián, Spain
- Biogipuzkoa
Health Research Institute, 20014 San Sebastián, Spain
| | - Alfredo Paredes Lario
- Servicio
de Oncología Médica, Hospital
Universitario Donostia, 20014 San Sebastián, Spain
| | | | | | | | - Eneko Lopez
- CIC
nanoGUNE BRTA, 20018 San Sebastián, Spain
- Department
of Physics, University of the Basque Country
(UPV/EHU), 20018 San Sebastián, Spain
| | - Andreas Seifert
- CIC
nanoGUNE BRTA, 20018 San Sebastián, Spain
- IKERBASQUE—Basque
Foundation for Science, 48009 Bilbao, Spain
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6
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Costa S, Fang Q, Farrell T, Dao E, Farquharson M. Time-resolved fluorescence and diffuse reflectance for lung squamous carcinoma margin detection. Lasers Surg Med 2024; 56:279-287. [PMID: 38357847 DOI: 10.1002/lsm.23761] [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: 09/11/2023] [Revised: 12/26/2023] [Accepted: 01/13/2024] [Indexed: 02/16/2024]
Abstract
OBJECTIVES A major challenge in non-small cell lung cancer surgery is the occurrence of positive tumor margins. This may lead to the need for additional surgeries and has been linked to poor patient prognosis. This study aims to develop an in vivo surgical tool that can differentiate cancerous from noncancerous lung tissue at the margin. METHODS A time-resolved fluorescence and diffuse reflectance bimodal device was used to measure the lifetime, spectra, and intensities of endogenous fluorophores as well as optical properties of lung tissue. The tumor and fibrotic tissue data, each containing 36 samples, was obtained from patients who underwent surgical removal of lung tissue after being diagnosed with squamous carcinoma but before any other treatment was administered. The normal lung tissue data were obtained from nine normal tissue samples. RESULTS The results show a statistically significant difference between cancerous and noncancerous tissue. The results also show a difference in metabolic related optical properties between fibrotic and normal lung tissue samples. CONCLUSIONS This work demonstrates the feasibility of a device that can differentiate cancerous and noncancerous lung tissue for patients diagnosed with squamous cell carcinoma.
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Affiliation(s)
- Sarah Costa
- Department of Physics, McMaster University, Ontario, Hamilton, Canada
| | - Qiyin Fang
- Department of Engineering Physics, Faculty of Engineering, McMaster University, Ontario, Hamilton, Canada
| | - Thomas Farrell
- Radiation Physics Program, Juravinski Cancer Centre, Ontario, Hamilton, Canada
| | - Erica Dao
- Department of Physics, McMaster University, Ontario, Hamilton, Canada
| | - Michael Farquharson
- Department of Interdisciplinary Science, McMaster University, Ontario, Hamilton, Canada
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Akdeniz M, Al-Shaebi Z, Altunbek M, Bayraktar C, Kayabolen A, Bagci-Onder T, Aydin O. Characterization and discrimination of spike protein in SARS-CoV-2 virus-like particles via surface-enhanced Raman spectroscopy. Biotechnol J 2024; 19:e2300191. [PMID: 37750467 DOI: 10.1002/biot.202300191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Non-infectious virus-like particles (VLPs) are excellent structures for development of many biomedical applications such as drug delivery systems, vaccine production platforms, and detection techniques for infectious diseases including SARS-CoV-2 VLPs. The characterization of biochemical and biophysical properties of purified VLPs is crucial for development of detection methods and therapeutics. The presence of spike (S) protein in their structure is especially important since S protein induces immunological response. In this study, development of a rapid, low-cost, and easy-to-use technique for both characterization and detection of S protein in the two VLPs, which are SARS-CoV-2 VLPs and HIV-based VLPs was achieved using surface-enhanced Raman spectroscopy (SERS). To analyze and classify datasets of SERS spectra obtained from the VLP groups, machine learning classification techniques including support vector machine (SVM), k-nearest neighbors (kNN), and random forest (RF) were utilized. Among them, the SVM classification algorithm demonstrated the best classification performance for SARS-CoV-2 VLPs and HIV-based VLPs groups with 87.5% and 92.5% accuracy, respectively. This study could be valuable for the rapid characterization of VLPs for the development of novel therapeutics or detection of structural proteins of viruses leading to a variety of infectious diseases.
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Affiliation(s)
- Munevver Akdeniz
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Zakarya Al-Shaebi
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Mine Altunbek
- Department of Chemical Engineering, University of Massachusetts, Lowell, Massachusetts, USA
| | - Canan Bayraktar
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Omer Aydin
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
- Clinical Engineering Research and Implementation Center (ERKAM), Erciyes University, Kayseri, Turkey
- Nanotechnology Research and Application Center (ERNAM), Erciyes University, Kayseri, Turkey
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Kopec M, Beton-Mysur K, Abramczyk H. Raman imaging and chemometric methods in human normal bronchial and cancer lung cells: Raman biomarkers of lipid reprogramming. Chem Phys Lipids 2023; 257:105339. [PMID: 37748746 DOI: 10.1016/j.chemphyslip.2023.105339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
This paper presents an approach to study biochemical changes in human normal bronchial cells (BEpiC) and human cancer lung cells (A549) by Raman spectroscopy and Raman imaging combined with chemometric methods. Based on Raman spectra and Raman imaging combined with chemometric methods we have proved that peaks at 845 cm-1, 2845 cm-1, 2936 cm-1, 1444 cm-1, 750 cm-1, 1126 cm-1, 1584 cm-1, can be treated as Raman biomarkers probing phosphorylation, lipid reprogramming, oxidative phosphorylation and changes in cholesterol and cytochrome in normal and cancer cells. Raman analysis of the bands at 845 cm-1, 2845 cm-1, 1444 cm-1, and 1126 cm-1 in human cancer lung cells and human normal bronchial cells demonstrate enhanced phosphorylation and triglycerides de novo synthesis, reduced levels of cholesterol and cytochrome c in cancer cells. The sensitivity is equal to 100% (nucleus), 87.5% (mitochondria), 100% (endoplasmic reticulum), 87.5% (lipid droplets), 87.5% (cytoplasm), 87.5% (cell membrane) for A549 cell line and 83.3% (nucleus), 100% (mitochondria), 83.3% (endoplasmic reticulum), 100% (lipid droplets), 100% (cytoplasm), 83.3% (cell membrane) for BEpiC. The values of specificity for cross-validation equal 93.4% (nucleus), 85.5% (mitochondria), 89.5% (endoplasmic reticulum), 90.8% (lipid droplets), 61.8% (cytoplasm), 94.7% (cell membrane) for A549 cell line and 88.5% (nucleus), 85.9% (mitochondria), 85.9% (endoplasmic reticulum), 97.4% (lipid droplets), 75.6% (cytoplasm), 92.3% (cell membrane) for BEpiC. We have confirmed that Raman spectroscopy methods combined with PLS-DA are useful tools to monitor changes in human cancer lung cells and human normal bronchial cells.
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Affiliation(s)
- Monika Kopec
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, Lodz 93-590, Poland.
| | - Karolina Beton-Mysur
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, Lodz 93-590, Poland
| | - Halina Abramczyk
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, Lodz 93-590, Poland
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Khristoforova Y, Bratchenko L, Bratchenko I. Raman-Based Techniques in Medical Applications for Diagnostic Tasks: A Review. Int J Mol Sci 2023; 24:15605. [PMID: 37958586 PMCID: PMC10647591 DOI: 10.3390/ijms242115605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Raman spectroscopy is a widely developing approach for noninvasive analysis that can provide information on chemical composition and molecular structure. High chemical specificity calls for developing different medical diagnostic applications based on Raman spectroscopy. This review focuses on the Raman-based techniques used in medical diagnostics and provides an overview of such techniques, possible areas of their application, and current limitations. We have reviewed recent studies proposing conventional Raman spectroscopy and surface-enhanced Raman spectroscopy for rapid measuring of specific biomarkers of such diseases as cardiovascular disease, cancer, neurogenerative disease, and coronavirus disease (COVID-19). As a result, we have discovered several most promising Raman-based applications to identify affected persons by detecting some significant spectral features. We have analyzed these approaches in terms of their potentially diagnostic power and highlighted the remaining challenges and limitations preventing their translation into clinical settings.
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Affiliation(s)
| | | | - Ivan Bratchenko
- Department of Laser and Biotechnical Systems, Samara National Research University, 34 Moskovskoye Shosse, Samara 443086, Russia; (Y.K.)
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Sharaha U, Hania D, Lapidot I, Salman A, Huleihel M. Early Detection of Pre-Cancerous and Cancerous Cells Using Raman Spectroscopy-Based Machine Learning. Cells 2023; 12:1909. [PMID: 37508572 PMCID: PMC10378363 DOI: 10.3390/cells12141909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Cancer is the most common and fatal disease around the globe, with an estimated 19 million newly diagnosed patients and approximately 10 million deaths annually. Patients with cancer struggle daily due to difficult treatments, pain, and financial and social difficulties. Detecting the disease in its early stages is critical in increasing the likelihood of recovery and reducing the financial burden on the patient and society. Currently used methods for the diagnosis of cancer are time-consuming, producing discomfort and anxiety for patients and significant medical waste. The main goal of this study is to evaluate the potential of Raman spectroscopy-based machine learning for the identification and characterization of precancerous and cancerous cells. As a representative model, normal mouse primary fibroblast cells (NFC) as healthy cells; a mouse fibroblast cell line (NIH/3T3), as precancerous cells; and fully malignant mouse fibroblasts (MBM-T) as cancerous cells were used. Raman spectra were measured from three different sites of each of the 457 investigated cells and analyzed by principal component analysis (PCA) and linear discriminant analysis (LDA). Our results showed that it was possible to distinguish between the normal and abnormal (precancerous and cancerous) cells with a success rate of 93.1%; this value was 93.7% when distinguishing between normal and precancerous cells and 80.2% between precancerous and cancerous cells. Moreover, there was no influence of the measurement site on the differentiation between the different examined biological systems.
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Affiliation(s)
- Uraib Sharaha
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biology, Science and Technology College, Hebron University, Hebron P760, Palestine
| | - Daniel Hania
- Department of Green Engineering, SCE-Shamoon College of Engineering, Beer-Sheva 84100, Israel
| | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
- Laboratoire Informatique d'Avignon (LIA), Avignon Université, 339 Chemin des Meinajaries, 84000 Avignon, France
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering, Beer-Sheva 84100, Israel
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Luo H, Zu R, Li L, Deng Y, He S, Yin X, Zhang K, He Q, Yin Y, Yin G, Yao D, Wang D. Serum laser Raman spectroscopy as a potential diagnostic tool to discriminate the benignancy or malignancy of pulmonary nodules. iScience 2023; 26:106693. [PMID: 37197326 PMCID: PMC10183669 DOI: 10.1016/j.isci.2023.106693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
It has been proved that Raman spectral intensities could be used to diagnose lung cancer patients. However, the application of Raman spectroscopy in identifying the patients with pulmonary nodules was barely studied. In this study, we revealed that Raman spectra of serum samples from healthy participants and patients with benign and malignant pulmonary nodules were significantly different. A support vector machine (SVM) model was developed for the classification of Raman spectra with wave points, according to ANOVA test results. It got a good performance with a median area under the curve (AUC) of 0.89, when the SVM model was applied in discriminating benign from malignant individuals. Compared with three common clinical models, the SVM model showed a better discriminative ability and added more net benefits to participants, which were also excellent in the small-size nodules. Thus, the Raman spectroscopy could be a less-invasive and low-costly liquid biopsy.
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Affiliation(s)
- Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Corresponding author
| | - Ruiling Zu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Lintao Li
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Xing Yin
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qiao He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Yin
- Sichuan Institute for Brain Science and Brain-Inspired Intelligence, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Gang Yin
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Dezhong Yao
- Sichuan Institute for Brain Science and Brain-Inspired Intelligence, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Corresponding author
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12
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Colniță A, Toma VA, Brezeștean IA, Tahir MA, Dina NE. A Review on Integrated ZnO-Based SERS Biosensors and Their Potential in Detecting Biomarkers of Neurodegenerative Diseases. BIOSENSORS 2023; 13:bios13050499. [PMID: 37232860 DOI: 10.3390/bios13050499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) applications in clinical diagnosis and spectral pathology are increasing due to the potential of the technique to bio-barcode incipient and differential diseases via real-time monitoring of biomarkers in fluids and in real-time via biomolecular fingerprinting. Additionally, the rapid advancements in micro/nanotechnology have a visible influence in all aspects of science and life. The miniaturization and enhanced properties of materials at the micro/nanoscale transcended the confines of the laboratory and are revolutionizing domains such as electronics, optics, medicine, and environmental science. The societal and technological impact of SERS biosensing by using semiconductor-based nanostructured smart substrates will be huge once minor technical pitfalls are solved. Herein, challenges in clinical routine testing are addressed in order to understand the context of how SERS can perform in real, in vivo sampling and bioassays for early neurodegenerative disease (ND) diagnosis. The main interest in translating SERS into clinical practice is reinforced by the practical advantages: portability of the designed setups, versatility in using nanomaterials of various matter and costs, readiness, and reliability. As we will present in this review, in the frame of technology readiness levels (TRL), the current maturity reached by semiconductor-based SERS biosensors, in particular that of zinc oxide (ZnO)-based hybrid SERS substrates, is situated at the development level TRL 6 (out of 9 levels). Three-dimensional, multilayered SERS substrates that provide additional plasmonic hot spots in the z-axis are of key importance in designing highly performant SERS biosensors for the detection of ND biomarkers.
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Affiliation(s)
- Alia Colniță
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Vlad-Alexandru Toma
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor, 400006 Cluj-Napoca, Romania
- Institute of Biological Research, Department of Biochemistry and Experimental Biology, 48 Republicii, Branch of NIRDBS Bucharest, 400015 Cluj-Napoca, Romania
| | - Ioana Andreea Brezeștean
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Muhammad Ali Tahir
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Nicoleta Elena Dina
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
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13
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Thomas G, Fitzgerald ST, Gautam R, Chen F, Haugen E, Rasiah PK, Adams WR, Mahadevan-Jansen A. Enhanced characterization of breast cancer phenotypes using Raman micro-spectroscopy on stainless steel substrate. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1188-1205. [PMID: 36799369 DOI: 10.1039/d2ay01764d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Biochemical insights into varying breast cancer (BC) phenotypes can provide a fundamental understanding of BC pathogenesis, while identifying novel therapeutic targets. Raman spectroscopy (RS) can gauge these biochemical differences with high specificity. For routine RS, cells are traditionally seeded onto calcium fluoride (CaF2) substrates that are costly and fragile, limiting its widespread adoption. Stainless steel has been interrogated previously as a less expensive alternative to CaF2 substrates, while reporting increased Raman signal intensity than the latter. We sought to further investigate and compare the Raman signal quality measured from stainless steel versus CaF2 substrates by characterizing different BC phenotypes with altered human epidermal growth factor receptor 2 (HER2) expression. Raman spectra were obtained on stainless steel and CaF2 substrates for HER2 negative cells - MDA-MB-231, MDA-MB-468 and HER2 overexpressing cells - AU565, SKBr3. Upon analyzing signal-to-noise ratios (SNR), stainless steel provided a stronger Raman signal, improving SNR by 119% at 1450 cm-1 and 122% at 2925 cm-1 on average compared to the CaF2 substrate. Utilizing only 22% of laser power on sample relative to the CaF2 substrate, stainless steel still yielded improved spectral characterization over CaF2, achieving 96.0% versus 89.8% accuracy in BC phenotype discrimination and equivalent 100.0% accuracy in HER2 status classification. Spectral analysis further highlighted increased lipogenesis and altered metabolism in HER2 overexpressing cells, which was subsequently visualized with coherent anti-Stokes Raman scattering microscopy. Our findings demonstrate that stainless steel substrates deliver improved Raman signal and enhanced spectral characterization, underscoring its potential as a cost-effective alternative to CaF2 for non-invasively monitoring cellular biochemical dynamics in translational cancer research.
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Affiliation(s)
- Giju Thomas
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Sean T Fitzgerald
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Rekha Gautam
- Tyndall National Institute, Cork, T12 R5CP, Ireland
| | - Fuyao Chen
- Yale School of Medicine, Yale University, New Haven 06510, CT, USA
| | - Ezekiel Haugen
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Pratheepa Kumari Rasiah
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Wilson R Adams
- Department of Pharmacology, Vanderbilt University, Nashville 37232, TN, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
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14
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Koster HJ, Guillen-Perez A, Gomez-Diaz JS, Navas-Moreno M, Birkeland AC, Carney RP. Fused Raman spectroscopic analysis of blood and saliva delivers high accuracy for head and neck cancer diagnostics. Sci Rep 2022; 12:18464. [PMID: 36323705 PMCID: PMC9630497 DOI: 10.1038/s41598-022-22197-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
As a rapid, label-free, non-destructive analytical measurement requiring little to no sample preparation, Raman spectroscopy shows great promise for liquid biopsy cancer detection and diagnosis. We carried out Raman analysis and mass spectrometry of plasma and saliva from more than 50 subjects in a cohort of head and neck cancer patients and benign controls (e.g., patients with benign oral masses). Unsupervised data models were built to assess diagnostic performance. Raman spectra collected from either biofluid provided moderate performance to discriminate cancer samples. However, by fusing together the Raman spectra of plasma and saliva for each patient, subsequent analytical models delivered an impressive sensitivity, specificity, and accuracy of 96.3%, 85.7%, and 91.7%, respectively. We further confirmed that the metabolites driving the differences in Raman spectra for our models are among the same ones that drive mass spectrometry models, unifying the two techniques and validating the underlying ability of Raman to assess metabolite composition. This study bolsters the relevance of Raman to provide additive value by probing the unique chemical compositions across biofluid sources. Ultimately, we show that a simple data augmentation routine of fusing plasma and saliva spectra provided significantly higher clinical value than either biofluid alone, pushing forward the potential of clinical translation of Raman spectroscopy for liquid biopsy cancer diagnostics.
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Affiliation(s)
- Hanna J. Koster
- grid.27860.3b0000 0004 1936 9684Biomedical Engineering, University of California, Davis, CA USA
| | - Antonio Guillen-Perez
- grid.27860.3b0000 0004 1936 9684Electrical and Computer Engineering, University of California, Davis, CA USA
| | - Juan Sebastian Gomez-Diaz
- grid.27860.3b0000 0004 1936 9684Electrical and Computer Engineering, University of California, Davis, CA USA
| | | | - Andrew C. Birkeland
- grid.27860.3b0000 0004 1936 9684Department of Otolaryngology, University of California, CA Davis, USA
| | - Randy P. Carney
- grid.27860.3b0000 0004 1936 9684Biomedical Engineering, University of California, Davis, CA USA
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15
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Lunter D, Klang V, Kocsis D, Varga-Medveczky Z, Berkó S, Erdő F. Novel aspects of Raman spectroscopy in skin research. Exp Dermatol 2022; 31:1311-1329. [PMID: 35837832 PMCID: PMC9545633 DOI: 10.1111/exd.14645] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 07/12/2022] [Indexed: 11/27/2022]
Abstract
The analytical technology of Raman spectroscopy has an almost 100‐year history. During this period, many modifications and developments happened in the method like discovery of laser, improvements in optical elements and sensitivity of spectrometer and also more advanced light detection systems. Many types of the innovative techniques appeared (e.g. Transmittance Raman spectroscopy, Coherent Raman Scattering microscopy, Surface‐Enhanced Raman scattering and Confocal Raman spectroscopy/microscopy). This review article gives a short description about these different Raman techniques and their possible applications. Then, a short statistical part is coming about the appearance of Raman spectroscopy in the scientific literature from the beginnings to these days. The third part of the paper shows the main application options of the technique (especially confocal Raman spectroscopy) in skin research, including skin composition analysis, drug penetration monitoring and analysis, diagnostic utilizations in dermatology and cosmeto‐scientific applications. At the end, the possible role of artificial intelligence in Raman data analysis and the regulatory aspect of these techniques in dermatology are briefly summarized. For the future of Raman Spectroscopy, increasing clinical relevance and in vivo applications can be predicted with spreading of non‐destructive methods and appearance with the most advanced instruments with rapid analysis time.
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Affiliation(s)
- Dominique Lunter
- University of Tübingen, Department of Pharmaceutical Technology, Institute of Pharmacy and Biochemistry, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Victoria Klang
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Technology and Biopharmaceutics, Faculty of Life Sciences, Vienna, Austria
| | - Dorottya Kocsis
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - Zsófia Varga-Medveczky
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - Szilvia Berkó
- University of Szeged, Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, Szeged, Hungary
| | - Franciska Erdő
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary.,University of Tours EA 6295 Nanomédicaments et Nanosondes, Tours, France
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16
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Dai Y, Li W, Wang L, Luo C, Huang Q, Pang L. Correlation and Difference Between Raman Spectral Characteristic and Feature Evaluation for Leukocytes and Tumor Cells. APPLIED SPECTROSCOPY 2021; 75:1516-1525. [PMID: 34643137 DOI: 10.1177/00037028211050663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tumor detection supported by Raman spectroscopy is becoming increasingly popular, yet the relevance of spectral variation and feature selection retains unclear. Here we determined the correlation and difference between spectral characteristic and feature evaluation for leukocytes and tumor cells. Some peaks were found to show noticeable spectral differences, and their intensity distributions were investigated, finding using log-normal distribution to describe Raman intensity pattern may be more appropriate. Further the importance of all Raman features was calculated, where some other peak features occupied the top status. By surveying the intensity variation and feature evaluation for those peaks, we concluded the peak with the highest importance does not correspond to the peak location with the most noticeable intensity difference in spectra. Moreover, the peak intensity ratio of I1517/I719 associated with protein to nucleic acid level presented the maximum separation, thus, it can be recognized as a special indicator to develop an alternative cancer detection. It is inspiring to introduce advanced statistical models into bio-spectroscopic fields but those intrinsic spectral variations rather than classification performance should be valued. Our explorations can provide possibilities to reveal the essences within tumor carcinogenesis based on Raman spectroscopy, further overwhelming the obstacles during the translation into clinical applications.
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Affiliation(s)
- Yixin Dai
- College of Physics, Sichuan University, Chengdu, China
| | - Wenxue Li
- College of Physics, Sichuan University, Chengdu, China
| | - Liu Wang
- Department of Laboratory Medicine, Army Medical University Daping Hospital, Chongqing, China
| | - Chuan Luo
- Department of Laboratory Medicine, Army Medical University Southwest Hospital, Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Army Medical University Daping Hospital, Chongqing, China
| | - Lin Pang
- College of Physics, Sichuan University, Chengdu, China
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17
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Leszczenko P, Borek-Dorosz A, Nowakowska AM, Adamczyk A, Kashyrskaya S, Jakubowska J, Ząbczyńska M, Pastorczak A, Ostrowska K, Baranska M, Marzec KM, Majzner K. Towards Raman-Based Screening of Acute Lymphoblastic Leukemia-Type B (B-ALL) Subtypes. Cancers (Basel) 2021; 13:cancers13215483. [PMID: 34771646 PMCID: PMC8582787 DOI: 10.3390/cancers13215483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy originating from abnormal lymphoid progenitor cells. Since ALL is genetically highly heterogenous, more sensitive and rapid methods for identifying the molecular subtype of ALL are still being searched, and Raman spectroscopy (RS) has a chance of becoming a valuable tool for this purpose. Herein, the RS was applied to analyze normal B cells and three subtypes of B-ALL, characterized by the presence of the product of gene fusion, i.e., BCR-ABL1, TEL-AML1, and TCF3-PBX1. The classification and discrimination of normal and neoplastic cells were carried out with the chemometric approach. Normal B cells were characterized mostly by bands assigned to nucleic acids and proteins, whereas three subtypes of ALL appeared to contain a higher lipid content. Spectral differences between particular ALL subtypes were modest. The results lead to the conclusion that RS has the potential as a diagnostic tool in clinical practice. Abstract Acute lymphoblastic leukemia (ALL) is the most common type of malignant neoplasms in the pediatric population. B-cell precursor ALLs (BCP-ALLs) are derived from the progenitors of B lymphocytes. Traditionally, risk factors stratifying therapy in ALL patients included age at diagnosis, initial leukocytosis, and the response to chemotherapy. Currently, treatment intensity is modified according to the presence of specific gene alterations in the leukemic genome. Raman imaging is a promising diagnostic tool, which enables the molecular characterization of cells and differentiation of subtypes of leukemia in clinical samples. This study aimed to characterize and distinguish cells isolated from the bone marrow of patients suffering from three subtypes of BCP-ALL, defined by gene rearrangements, i.e., BCR-ABL1 (Philadelphia-positive, t(9;22)), TEL-AML1 (t(12;21)) and TCF3-PBX1 (t(1;19)), using single-cell Raman imaging combined with multivariate statistical analysis. Spectra collected from clinical samples were compared with single-cell spectra of B-cells collected from healthy donors, constituting the control group. We demonstrated that Raman spectra of normal B cells strongly differ from spectra of their malignant counterparts, especially in the intensity of bands, which can be assigned to nucleic acids. We also showed that the identification of leukemia subtypes could be automated with the use of chemometric methods. Results prove the clinical suitability of Raman imaging for the identification of spectroscopic markers characterizing leukemia cells.
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Affiliation(s)
- Patrycja Leszczenko
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
| | - Aleksandra Borek-Dorosz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Anna Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
| | - Adriana Adamczyk
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
| | - Sviatlana Kashyrskaya
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
| | - Justyna Jakubowska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Sporna 36/50, 91-738 Lodz, Poland; (J.J.); (M.Z.); (A.P.); (K.O.)
| | - Marta Ząbczyńska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Sporna 36/50, 91-738 Lodz, Poland; (J.J.); (M.Z.); (A.P.); (K.O.)
| | - Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Sporna 36/50, 91-738 Lodz, Poland; (J.J.); (M.Z.); (A.P.); (K.O.)
| | - Kinga Ostrowska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Sporna 36/50, 91-738 Lodz, Poland; (J.J.); (M.Z.); (A.P.); (K.O.)
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Katarzyna Maria Marzec
- Lukasiewicz Research Network—Krakow Institute of Technology, Zakopiańska 73, 30-418 Krakow, Poland
- Correspondence: (K.M.M.); (K.M.)
| | - Katarzyna Majzner
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (P.L.); (A.B.-D.); (A.M.N.); (A.A.); (S.K.); (M.B.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Correspondence: (K.M.M.); (K.M.)
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18
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Kramer T, Annema JT. Advanced bronchoscopic techniques for the diagnosis and treatment of peripheral lung cancer. Lung Cancer 2021; 161:152-162. [PMID: 34600406 DOI: 10.1016/j.lungcan.2021.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 12/14/2022]
Abstract
Lung cancer is the leading cause of cancer related deaths worldwide. As a result of the increasing use of chest CT scans and lung cancer screening initiatives, there is a rapidly increasing need for lung lesion analysis and - in case of confirmed cancer - treatment. A desirable future concept is the one-stop outpatient bronchoscopic approach including navigation to the tumor, malignancy confirmation and immediate treatment. Several novel bronchoscopic diagnostic and treatment concepts are currently under evaluation contributing to this concept. As the majority of suspected malignant lung lesions develop in the periphery of the lungs, improved bronchoscopic navigation to the target lesion is of key importance. Fortunately, the field of interventional pulmonology is evolving rapidly and several advanced bronchoscopic navigation techniques are clinically available, allowing an increasingly accurate tissue diagnosis of peripheral lung lesions. Additionally, multiple bronchoscopic treatment modalities are currently under investigation. This review will provide a concise overview of advanced bronchoscopic techniques to diagnose and treat peripheral lung cancer by describing their working mechanisms, strengths and weaknesses, identifying knowledge gaps and indicating future developments. The desired one-step concept of bronchoscopic 'diagnose and treat' peripheral lung cancer is on the horizon.
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Affiliation(s)
- Tess Kramer
- Department of Respiratory Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jouke T Annema
- Department of Respiratory Medicine, Amsterdam UMC, Amsterdam, The Netherlands.
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19
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Guo Y, Hu C, Xia B, Zhou X, Luo S, Gan R, Duan P, Tan Y. Iodine excess induces hepatic, renal and pancreatic injury in female mice as determined by attenuated total reflection Fourier-transform infrared spectrometry. J Appl Toxicol 2021; 42:600-616. [PMID: 34585417 DOI: 10.1002/jat.4242] [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: 05/12/2021] [Revised: 08/23/2021] [Accepted: 09/05/2021] [Indexed: 11/08/2022]
Abstract
Limited knowledge of the long-term effects of excessive iodine (EI) intake on biomolecular signatures in the liver/pancreas/kidney prompted this study. Herein, following 6 months of exposure in mice to 300, 600, 1200 or 2400 μg/L iodine, the biochemical signature of alterations to the liver/pancreas/kidney was profiled using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with principal component analysis-linear discriminant analysis (PCA-LDA). Our research showed that serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN), serum creatinine (Scr), insulin, blood glucose levels and homeostasis model assessment for insulin resistance (HOMA-IR) index in the 1200 and 2400 μg/L iodine-treated groups were significantly increased compared with those in the control group. Moreover, histological analysis showed that the liver/kidney/pancreas tissues of mice exposed to EI treatment displayed substantial morphological abnormalities, such as a loss of hepatic architecture, glomerular cell vacuolation and pancreatic neutrophilic infiltration. Notably, EI treatment caused distinct biochemical signature segregation between EI-exposed versus the control liver/pancreas/kidney. The main biochemical alterations between EI-exposed and control groups were observed for protein phosphorylation, protein secondary structures and lipids. The ratios of amide I-to-amide II (1674 cm-1 /1570 cm-1 ), α-helix-to-β-sheet (1657 cm-1 /1635 cm-1 ), glycogen-to-phosphate (1030 cm-1 /1086 cm-1 ) and the peptide aggregation (1 630 cm-1 /1650 cm-1 ) level of EI-treated groups significantly differed from the control group. Our study demonstrated that EI induced hepatic, renal and pancreatic injury by disturbing the structure, metabolism and function of the cell membrane. This finding provides the new method and implication for human health assessment regarding long-term EI intake.
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Affiliation(s)
- Yang Guo
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China.,College of Pharmacy, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chunhui Hu
- Department of Clinical Laboratory, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Bintong Xia
- Department of Urology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xianwen Zhou
- Fourth Clinical College, Hubei University of Medicine, Shiyan, China
| | - Sihan Luo
- Fourth Clinical College, Hubei University of Medicine, Shiyan, China
| | - Ruijia Gan
- Fourth Clinical College, Hubei University of Medicine, Shiyan, China
| | - Peng Duan
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Yan Tan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China.,Department of Andrology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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20
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Baum ZJ, Yu X, Ayala PY, Zhao Y, Watkins SP, Zhou Q. Artificial Intelligence in Chemistry: Current Trends and Future Directions. J Chem Inf Model 2021; 61:3197-3212. [PMID: 34264069 DOI: 10.1021/acs.jcim.1c00619] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of artificial intelligence (AI) to chemistry has grown tremendously in recent years. In this Review, we studied the growth and distribution of AI-related chemistry publications in the last two decades using the CAS Content Collection. The volume of both journal and patent publications have increased dramatically, especially since 2015. Study of the distribution of publications over various chemistry research areas revealed that analytical chemistry and biochemistry are integrating AI to the greatest extent and with the highest growth rates. We also investigated trends in interdisciplinary research and identified frequently occurring combinations of research areas in publications. Furthermore, topic analyses were conducted for journal and patent publications to illustrate emerging associations of AI with certain chemistry research topics. Notable publications in various chemistry disciplines were then evaluated and presented to highlight emerging use cases. Finally, the occurrence of different classes of substances and their roles in AI-related chemistry research were quantified, further detailing the popularity of AI adoption in the life sciences and analytical chemistry. In summary, this Review offers a broad overview of how AI has progressed in various fields of chemistry and aims to provide an understanding of its future directions.
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Affiliation(s)
- Zachary J Baum
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
| | - Xiang Yu
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
| | - Philippe Y Ayala
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
| | - Yanan Zhao
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
| | - Steven P Watkins
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
| | - Qiongqiong Zhou
- Chemical Abstracts Service, 2540 Olentangy River Road, Columbus, Ohio 43210, United States
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21
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Yakimov BP, Venets AV, Schleusener J, Fadeev VV, Lademann J, Shirshin EA, Darvin ME. Blind source separation of molecular components of the human skin in vivo: non-negative matrix factorization of Raman microspectroscopy data. Analyst 2021; 146:3185-3196. [PMID: 33999054 DOI: 10.1039/d0an02480e] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Determination of the molecular composition of the skin is crucial for numerous tasks in medicine, pharmacology, dermatology and cosmetology. Confocal Raman microspectroscopy is a sensitive method for the evaluation of molecular depth profiles in the skin in vivo. Since the Raman spectra of most of the skin constituents significantly superimpose, a spectral decomposition by a set of predefined library components is usually performed to disentangle their contributions. However, the incorrect choice of the number and type of components or differences between the spectra of the basic components measured in vitro and in vivo can lead to incorrect results of the decomposition procedure. Here, we investigate an alternative data-driven approach based on a non-negative matrix factorization (NNMF) algorithm of depth-resolved Raman spectra of skin that does not require a priori information of spectral data for the analysis. Using the model and experimentally measured depth-resolved Raman spectra of the upper epidermis in vivo, we show that NNMF provides depth profiles of endogenous molecular components and exogenous agents penetrating through the upper epidermis for the spectra and concentration. Moreover, we demonstrate that this approach is capable of providing new information on the molecular profiles of the skin.
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Affiliation(s)
- B P Yakimov
- M.V. Lomonosov Moscow State University, Faculty of physics, 1-2 Leninskie Gory, Moscow, 119991, Russia.
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22
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Fernandes S, Williams G, Williams E, Ehrlich K, Stone J, Finlayson N, Bradley M, Thomson RR, Akram AR, Dhaliwal K. Solitary pulmonary nodule imaging approaches and the role of optical fibre-based technologies. Eur Respir J 2021; 57:2002537. [PMID: 33060152 PMCID: PMC8174723 DOI: 10.1183/13993003.02537-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
Solitary pulmonary nodules (SPNs) are a clinical challenge, given there is no single clinical sign or radiological feature that definitively identifies a benign from a malignant SPN. The early detection of lung cancer has a huge impact on survival outcome. Consequently, there is great interest in the prompt diagnosis, and treatment of malignant SPNs. Current diagnostic pathways involve endobronchial/transthoracic tissue biopsies or radiological surveillance, which can be associated with suboptimal diagnostic yield, healthcare costs and patient anxiety. Cutting-edge technologies are needed to disrupt and improve, existing care pathways. Optical fibre-based techniques, which can be delivered via the working channel of a bronchoscope or via transthoracic needle, may deliver advanced diagnostic capabilities in patients with SPNs. Optical endomicroscopy, an autofluorescence-based imaging technique, demonstrates abnormal alveolar structure in SPNs in vivo Alternative optical fingerprinting approaches, such as time-resolved fluorescence spectroscopy and fluorescence-lifetime imaging microscopy, have shown promise in discriminating lung cancer from surrounding healthy tissue. Whilst fibre-based Raman spectroscopy has enabled real-time characterisation of SPNs in vivo Fibre-based technologies have the potential to enable in situ characterisation and real-time microscopic imaging of SPNs, which could aid immediate treatment decisions in patients with SPNs. This review discusses advances in current imaging modalities for evaluating SPNs, including computed tomography (CT) and positron emission tomography-CT. It explores the emergence of optical fibre-based technologies, and discusses their potential role in patients with SPNs and suspected lung cancer.
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Affiliation(s)
- Susan Fernandes
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Gareth Williams
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Elvira Williams
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Katjana Ehrlich
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - James Stone
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
- Centre for Photonics and Photonic Materials, Dept of Physics, The University of Bath, Bath, UK
| | - Neil Finlayson
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
- Institute for Integrated Micro and Nano Systems, School of Engineering, The University of Edinburgh, Edinburgh, UK
| | - Mark Bradley
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
- EaStCHEM, School of Chemistry, The University of Edinburgh, Edinburgh, UK
| | - Robert R. Thomson
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
- Institute of Photonics and Quantum Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Ahsan R. Akram
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
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Electrochemical ultrasensitive detection of CYFRA21-1 using Ti 3C 2T x-MXene as enhancer and covalent organic frameworks as labels. Anal Bioanal Chem 2021; 413:2543-2551. [PMID: 33576855 DOI: 10.1007/s00216-021-03212-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 02/04/2023]
Abstract
The concentration level of cytokeratin fragment antigen 21-1 (CYFRA21-1) can be used as an important indicator for predicting non-small cell lung cancer (NSCLC). Here, a sandwich-type electrochemical immunosensor for ultrasensitive detection of CYFRA21-1 is developed. The sensor based on a combination of gold nanoparticle (AuNPs) decorated Ti3C2Tx-MXene (Au-Ti3C2Tx) as the substrate enhancer, and toluidine blue (TB) modified AuNPs doped covalent organic framework (COF) polymer as the signal tag (TB-Au-COF). The Au-Ti3C2Tx is used to capture numerous primary antibodies and accelerate the electron transfer rate of the substrate, while the TB-Au-COF can be applied to provide a large number of signal units TB and secondary antibodies. These features of composites endow the proposed immunosensor with high sensitivity and current response to CYFRA21-1. Under optimum conditions, the immunosensor offers a wide current response for CYFRA21-1 from 0.5-1.0 × 104 pg·mL-1 with a detection limit of 0.1 pg·mL-1. Furthermore, the biosensing platform can be applied for CYFRA21-1 detection to analyze real serum samples, providing an effective and useful avenue for the applicability of Au-Ti3C2Tx and TB-Au-COF composite materials in biosensing field.
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24
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Ren G, Liu Y, Ning J, Zhang Z. Hyperspectral imaging for discrimination of Keemun black tea quality categories: Multivariate calibration analysis and data fusion. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Guangxin Ren
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei 230036 China
| | - Ying Liu
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei 230036 China
| | - Jingming Ning
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei 230036 China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei 230036 China
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Ralbovsky NM, Lednev IK. Towards development of a novel universal medical diagnostic method: Raman spectroscopy and machine learning. Chem Soc Rev 2020; 49:7428-7453. [DOI: 10.1039/d0cs01019g] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review summarizes recent progress made using Raman spectroscopy and machine learning for potential universal medical diagnostic applications.
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Affiliation(s)
| | - Igor K. Lednev
- Department of Chemistry
- University at Albany
- SUNY
- Albany
- USA
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