151
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Le Corvec M, Boussard-Plédel C, Charpentier F, Fatih N, Le Dare B, Massart F, Rojas F, Tariel H, Loréal O, Bureau B, Boustie J, Sire O, LohézicLe Dévéhat F. Chemotaxonomic discrimination of lichen species using an infrared chalcogenide fibre optic sensor: a useful tool for on-field biosourcing. RSC Adv 2016. [DOI: 10.1039/c6ra17140k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spectral analysis of lichen extracts obtained by MIR-FEWS permits to discriminate species and the identification of their major compounds. MIR-FEWS is a rapid, efficient and convenient tool for metabolic profiling.
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152
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Lin LH, Lo YL, Liao CC, Lin JX. Optical detection of glucose concentration in samples with scattering particles. APPLIED OPTICS 2015; 54:10425-10431. [PMID: 26836866 DOI: 10.1364/ao.54.010425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An optical-based method is proposed for measuring the glucose concentration of samples containing scattering particles. In the proposed approach, a Stokes-Mueller reflection-based polarimetry technique is used to solve the Mueller matrices of a turbid glucose sample with circular birefringence and depolarization properties given six incident lights with different polarization states. Using an error function defined as the difference between the simulated output Stokes vectors and the experimental ones, a genetic algorithm is used to inversely derive the optical rotation and depolarization parameters of the experimental sample corresponding to the glucose concentration and scattering depolarization effect, respectively. The validity of the proposed method is demonstrated using glucose samples containing 0.02 ml and 0.04 ml lipofundin, respectively.
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153
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Albert JD, Monbet V, Jolivet-Gougeon A, Fatih N, Le Corvec M, Seck M, Charpentier F, Coiffier G, Boussard-Pledel C, Bureau B, Guggenbuhl P, Loréal O. A novel method for a fast diagnosis of septic arthritis using mid infrared and deported spectroscopy. Joint Bone Spine 2015; 83:318-23. [PMID: 26677999 DOI: 10.1016/j.jbspin.2015.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/28/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To assess the ability of mid infrared deported spectroscopy to discriminate synovial fluids samples of septic arthritis patients from other causes of joint effusion. METHODS Synovial fluids obtained from patients with clinically suspected arthritis were collected, analysed and classified according to standard diagnostic procedures as septic or non-septic. A spectroscopic analysis on synovial fluid samples was then performed using a coiled optical fiber made with chalcogenide glass. After a factorial analysis of the normalized spectra and the computation of a Fisher test used to select the most relevant components, a logistic regression model was fitted, allowing to attribute a score between 0 - non-septic -, and 1 - septic. RESULTS In a first phase, we analysed the synovial fluids from 122 different synovial fluids including 6 septic arthritis among arthritis of various origins. Septic synovial fluids were identified with a sensitivity of 95.8% and a specificity of 93.9% and an AUROC of 0.977. The analysis of an independent set of samples (n=42, including two septic arthritis) gave similar values. CONCLUSIONS Our data strongly supports the interest of mid infrared deported spectroscopy, which could be used potentially at point of care, for a rapid and easy diagnosis of septic arthritis. Now, the precision of the diagnosis must be evaluated through a multicentric study on a larger panel of patients.
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Affiliation(s)
- Jean-David Albert
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France.
| | - Valérie Monbet
- University of Rennes 1, 35043 Rennes, France; UMR-CNRS 6625, IRMAR Mathematics Research Institute of Rennes, 35033 Rennes, France; INRIA/ASPI, 35033 Rennes, France
| | - Anne Jolivet-Gougeon
- Pole of Biology, EA 1254 Microbiologie, CHU of Rennes, University of Rennes 1, 35033 Rennes, France
| | - Nadia Fatih
- Diafir™, avenue Chardonnet, Parc Lorans, 26J, 35700 Rennes, France
| | - Maëna Le Corvec
- Diafir™, avenue Chardonnet, Parc Lorans, 26J, 35700 Rennes, France; Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), University of Bretagne-Sud, CER Yves-Coppens, BP 573, 56017 Vannes cedex, France
| | - Malik Seck
- University of Rennes 1, 35043 Rennes, France
| | | | - Guillaume Coiffier
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France
| | | | - Bruno Bureau
- ISCR UMR-CNRS 6226, Verres et Céramiques, Université de Rennes 1, 35042 Rennes, France
| | - Pascal Guggenbuhl
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France; University of Rennes 1, 35043 Rennes, France
| | - Olivier Loréal
- INSERM UMR 991, 35033 Rennes, France; University of Rennes 1, 35043 Rennes, France
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154
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Gautam R, Vanga S, Ariese F, Umapathy S. Review of multidimensional data processing approaches for Raman and infrared spectroscopy. EPJ TECHNIQUES AND INSTRUMENTATION 2015; 2:8. [PMID: 0 DOI: 10.1140/epjti/s40485-015-0018-6] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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155
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Mitchell A, Ashton L, Yang XB, Goodacre R, Tomlinson MJ, Smith A, Kirkham J. Aseptic Raman spectroscopy can detect changes associated with the culture of human dental pulp stromal cells in osteoinductive culture. Analyst 2015; 140:7347-54. [PMID: 26374253 PMCID: PMC4621535 DOI: 10.1039/c5an01595b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/10/2015] [Indexed: 12/16/2022]
Abstract
There is an unmet need for the non-invasive characterisation of stem cells to facilitate the translation of cell-based therapies. Raman spectroscopy has proven utility in stem cell characterisation but as yet no method has been reported capable of taking repeated Raman measurements of living cells aseptically over time. The aim of this study was to determine if Raman spectroscopy could be used to monitor changes in a well characterised cell population (human dental pulp stromal cells (DPSCs)) by taking repeated Raman measurements from the same cell populations in osteoinductive culture over time and under aseptic conditions. DPSCs were isolated from extracted premolar teeth from 3 consenting donors. Following in vitro expansion, DPSCs were maintained for 28 days in osteo-inductive medium. Raman spectra were acquired from the cells at days 0, 3, 7, 10, 14 and 28. Principal component analysis (PCA) was carried out to assess if there was any temporal spectral variation. At day 28, osteoinduction was confirmed using alizarin red staining and qRT-PCR for alkaline phosphatase and osteocalcin. Alizarin red staining was positive in all samples at day 28 and significant increases in alkaline phosphatase (p < 0.001) and osteocalcin (p < 0.05) gene expression were also observed compared with day 0. PCA of the Raman data demonstrated trends in PC1 from days 0-10, influenced by protein associated features and PC2 from days 10-28, influenced by DNA/RNA associated features. We conclude that spectroscopy can be used to monitor changes in Raman signature with time associated with the osteoinduction of DPSCs using repeated measurements via an aseptic methodology.
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Affiliation(s)
- Adam Mitchell
- University of Leeds , Department of Oral Biology , Leeds School of Dentistry , Leeds , UK .
| | - Lorna Ashton
- Department of Chemistry , Faraday Building , Lancaster University , Lancaster , UK
| | - Xuebin B. Yang
- University of Leeds , Department of Oral Biology , Leeds School of Dentistry , Leeds , UK .
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology , University of Manchester , Manchester , UK
| | - Matthew J. Tomlinson
- University of Leeds , Department of Oral Biology , Leeds School of Dentistry , Leeds , UK .
| | | | - Jennifer Kirkham
- University of Leeds , Department of Oral Biology , Leeds School of Dentistry , Leeds , UK .
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156
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Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi DK, Ellis DI, Linton D, Goodacre R. Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst 2015; 141:111-22. [PMID: 26523729 DOI: 10.1039/c5an01945a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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157
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Wu H, Read E, White M, Chavez B, Brorson K, Agarabi C, Khan M. Real time monitoring of bioreactor mAb IgG3 cell culture process dynamics via Fourier transform infrared spectroscopy: Implications for enabling cell culture process analytical technology. Front Chem Sci Eng 2015. [DOI: 10.1007/s11705-015-1533-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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158
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Pérez-Guaita D, Kuligowski J, Garrigues S, Quintás G, Wood BR. Assessment of the statistical significance of classifications in infrared spectroscopy based diagnostic models. Analyst 2015; 140:2422-7. [PMID: 25382314 DOI: 10.1039/c4an01783h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fourier transform infrared (IR) spectroscopy in combination with multivariate data analysis is a versatile tool that can be applied to disease diagnosis. However, a rigorous validation of the obtained models is necessary in order to obtain robust results. This work evaluates the advantages of the use of permutation testing for determining the statistical significance of the misclassification errors obtained from IR based diagnostic models through cross validation (CV). The model performance, estimated by CV, is compared to a distribution of CV-performance values obtained using randomly permuted class labels. The distribution of 'random CV-values' is considered as a null distribution and used to establish the significance of the model estimators obtained using real class labels. ATR-FTIR spectra of serum samples were classified using random forest (RF) classifiers according to two criteria, the tag number (a randomly assigned pseudo class membership) and the level of urea (real class). CV errors obtained were compared to the null distribution of CV errors from a permutation test and an independent validation set. The procedure was evaluated testing typical conditions leading to overoptimistic estimations provided by the CV like e.g. the size of subsamples used during CV, variable selection and the use of replicates. Results show that for the tag number (pseudo class), CV indicated classification errors between 23 and 33% depending on the subsample size employed. Those values were even lower when variable selection or replicates were used. However, permutation testing indicated that those CV errors were non-significant. In contrast, for sample classification according to their levels of urea, all cross validation errors were found to be significant. Although the proposed method is computationally intensive, it provides a simple way of calculating an empirical p-value of the CV-estimator, thus establishing the statistical significance and providing a feasibility indicator especially useful for studies where the number of samples is limited.
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Affiliation(s)
- David Pérez-Guaita
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, 3800 VIC, Australia.
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159
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Kim S, Shin BK, Lim DK, Yang TJ, Lim J, Park JH, Kwon SW. Expeditious discrimination of four species of the Panax genus using direct infusion-MS/MS combined with multivariate statistical analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:329-36. [PMID: 26350425 DOI: 10.1016/j.jchromb.2015.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/12/2015] [Accepted: 08/23/2015] [Indexed: 01/08/2023]
Abstract
A practical approach based on direct infusion-MS/MS (DI-MS/MS) was demonstrated for metabolomic classification of four species in the Panax genus. The species Panax ginseng, Panax notoginseng, Panax quinquefolius and Panax vietnamensis were analyzed to develop an efficient tool for authenticating ginseng. Four target ions (m/z 783.5, 945.5, 1107.5 and 1149.2) were selected from LC-MS screening results for DI-MS/MS analysis. The target ions served as classifiers of the four species. As a targeted analysis, DI-MS/MS provided the structural identities of the target ions, clear spectral data and high sensitivity in a shorter time than routine LC-MS analysis. Principal component analysis and partial least squares-discriminant analysis of the DI-MS/MS fingerprinting revealed distinct grouping of the data. The results were validated by cross-validation and a permutation test to examine the utility of the statistical models. The spectral intensities of each species were compared with one another using box plots, which allowed straightforward authentication of the Panax species. The proposed method showed improved efficiency over other current methods for discrimination of large quantities of plant material. Additionally, to the best of our knowledge, this is the first study in which DI-MS/MS has been used to classify plant samples.
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Affiliation(s)
- Shinae Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Byong-Kyu Shin
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong Kyu Lim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Hill Park
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sung Won Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea.
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160
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Le Roux K, Prinsloo LC, Meyer D. Fourier Transform Infrared spectroscopy discloses different types of cell death in flow cytometrically sorted cells. Toxicol In Vitro 2015; 29:1932-40. [PMID: 26254093 DOI: 10.1016/j.tiv.2015.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 07/22/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022]
Abstract
Fourier Transform Infrared (FTIR) spectroscopy is a label free methodology showing promise in characterizing different types of cell death. Cervical adenocarcinoma (HeLa) and African monkey kidney (Vero) cells were treated with a necrosis inducer (methanol), novel apoptotic inducers (diphenylphosphino gold (I) complexes) and positive control, auranofin. Following treatment, cells stained with annexin-V and propidium iodide were sorted using a Fluorescence Activated Cell Sorter (FACS Aria) to obtain populations consisting of either viable, necrotic or apoptotic cells. Transmission Electron Microscopy confirmed successful sorting of all three populations. Four bands were identified which could discriminate between viable and necrotic cells namely 989 cm(-1), 2852 cm(-1), 2875 cm(-1) and 2923 cm(-1). In HeLa cells viable and induced apoptosis could be distinguished by 1294 cm(-1), while four bands were different in Vero cells namely; 1626 cm(-1), 1741 cm(-1), 2852 cm(-1) 2923 cm(-1). Principal Component Analysis showed separation between the different types of cell death and the loadings plots indicated an increase in an additional band at 1623 cm(-1) in dead cells. FTIR spectroscopy can be developed into an invaluable tool for the assessment of specific types of chemically induced cell death with notably different molecular signatures depending on whether the cells are cancerous and mechanism of cell death.
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Affiliation(s)
- K Le Roux
- Department of Biochemistry, University of Pretoria, Hatfield, Gauteng 0002, South Africa
| | - L C Prinsloo
- Department of Physics, University of Pretoria, Hatfield, Gauteng 0002, South Africa
| | - D Meyer
- Department of Biochemistry, University of Pretoria, Hatfield, Gauteng 0002, South Africa; Department of Biochemistry, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa (Current address).
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161
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Zhao F, Li M, Tsien JZ. Technology platforms for remote monitoring of vital signs in the new era of telemedicine. Expert Rev Med Devices 2015; 12:411-29. [PMID: 26037691 DOI: 10.1586/17434440.2015.1050957] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Driven by healthcare cost and home healthcare need, the development of remote monitoring technologies is poised to improve and revolutionize healthcare delivery and accessibility. This paper reviews the recent progress in the field of remote monitoring technologies that may have the potential to become the basic platforms for telemedicine. In particular, key techniques and devices for monitoring cardiorespiratory activity, blood pressure and blood glucose concentration are summarized and discussed. In addition, the US FDA approved remote vital signs monitoring devices currently available on the market are presented.
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Affiliation(s)
- Fang Zhao
- Medical College of Georgia, Georgia Regents University, Brain and Behavior Discovery Institute and Department of Neurology, Augusta, GA 30912, USA
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162
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Caetano Júnior PC, Strixino JF, Raniero L. Analysis of saliva by Fourier transform infrared spectroscopy for diagnosis of physiological stress in athletes. ACTA ACUST UNITED AC 2015. [DOI: 10.1590/2446-4740.0664] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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163
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Gromski PS, Muhamadali H, Ellis DI, Xu Y, Correa E, Turner ML, Goodacre R. A tutorial review: Metabolomics and partial least squares-discriminant analysis – a marriage of convenience or a shotgun wedding. Anal Chim Acta 2015; 879:10-23. [DOI: 10.1016/j.aca.2015.02.012] [Citation(s) in RCA: 509] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 01/14/2023]
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164
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Bellver J, De los Santos MJ, Alamá P, Castelló D, Privitera L, Galliano D, Labarta E, Vidal C, Pellicer A, Domínguez F. Day-3 embryo metabolomics in the spent culture media is altered in obese women undergoing in vitro fertilization. Fertil Steril 2015; 103:1407-15.e1. [DOI: 10.1016/j.fertnstert.2015.03.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/26/2015] [Accepted: 03/16/2015] [Indexed: 01/25/2023]
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165
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Tiwari S, Reddy VB, Bhargava R, Raman J. Computational chemical imaging for cardiovascular pathology: chemical microscopic imaging accurately determines cardiac transplant rejection. PLoS One 2015; 10:e0125183. [PMID: 25932912 PMCID: PMC4416885 DOI: 10.1371/journal.pone.0125183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 02/06/2023] Open
Abstract
Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures.
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Affiliation(s)
- Saumya Tiwari
- Department of Bioengineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, Illinois, 61801, United States of America
| | - Vijaya B. Reddy
- Department of Pathology, Rush University Medical Center, 1725 West Harrison St, Chicago, Illinois, 60612, United States of America
| | - Rohit Bhargava
- Department of Bioengineering, Chemistry, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology and University of Illinois Cancer Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Jaishankar Raman
- Cardiac Surgery, Advanced Heart Failure Transplantation & Mechanical Circulatory Support, Rush University Medical Center, 1725 West Harrison St, Chicago, Illinois, 60612, United States of America
- * E-mail:
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166
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Harris M, Cilwa K, Elster EA, Potter BK, Forsberg JA, Crane NJ. Pilot study for detection of early changes in tissue associated with heterotopic ossification: moving toward clinical use of Raman spectroscopy. Connect Tissue Res 2015; 56:144-52. [PMID: 25738521 DOI: 10.3109/03008207.2015.1013190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Over 60% of combat-wounded patients develop heterotopic ossification (HO). Nearly 33% of them require surgical excision for symptomatic lesions, a procedure that is both fraught with complications and can delay or regress functional rehabilitation. Relative medical contraindications limit widespread use of conventional means of primary prophylaxis, such as nonspecific nonsteroidal anti-inflammatory medications and radiotherapy. Better methods for risk stratification are needed to both mitigate the risk of current means of primary prophylaxis as well as to evaluate novel preventive strategies currently in development. We asked whether Raman spectral changes, measured ex vivo, could be associated with histologic evidence of the earliest signs of HO formation and substance P (SP) expression in tissue biopsies from the wounds of combat casualties. In this pilot study, we compared normal muscle tissue, injured muscle tissue, very early HO lesions (< 16 d post-injury), early HO lesions (> 16 d post-injury) and mature HO lesions. The Raman spectra of these tissues demonstrate clear differences in the Amide I and III spectral regions of HO lesions compared to normal tissue, denoted by changes in the Amide I band center (p < 0.01) and the 1340/1270 cm(-1) (p < 0.05) band area and band height ratios. SP expression in the HO lesions appears to peak between 16 and 30 d post-injury, as determined by SP immunohistochemistry of corresponding tissue sections, potentially indicating optimal timing for administration of therapeutics. Raman spectroscopy may therefore prove a useful, non-invasive and early diagnostic modality to detect HO formation before it becomes evident either clinically or radiographically.
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Affiliation(s)
- Mitchell Harris
- Department of Surgery, Uniformed Services University of Health Science , Bethesda, MD , USA
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167
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le Roux K, Prinsloo LC, Meyer D. Cellular injury evidenced by impedance technology and infrared microspectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 138:321-330. [PMID: 25506649 DOI: 10.1016/j.saa.2014.11.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Abstract
Fourier Transform Infrared (FTIR) spectroscopy is finding increasing biological application, for example in the analysis of diseased tissues and cells, cell cycle studies and investigating the mechanisms of action of anticancer drugs. Cancer treatment studies routinely define the types of cell-drug responses as either total cell destruction by the drug (all cells die), moderate damage (cell deterioration where some cells survive) or reversible cell cycle arrest (cytostasis). In this study the loss of viability and related chemical stress experienced by cells treated with the medicinal plant, Plectranthus ciliatus, was investigated using real time cell electronic sensing (RT-CES) technology and FTIR microspectroscopy. The use of plants as medicines is well established and ethnobotany has proven that crude extracts can serve as treatments against various ailments. The aim of this study was to determine whether FTIR microspectroscopy would successfully distinguish between different types of cellular injury induced by a potentially anticancerous plant extract. Cervical adenocarcinoma (HeLa) cells were treated with a crude extract of Pciliatus and cells monitored using RT-CES to characterize the type of cellular responses induced. Cell populations were then investigated using FTIR microspectroscopy and statistically analysed using One-way Analysis of Variance (ANOVA) and Principal Component Analysis (PCA). The plant extract and a cancer drug control (actinomycin D) induced concentration dependent cellular responses ranging from nontoxic, cytostatic or cytotoxic. Thirteen spectral peaks (915cm(-)(1), 933cm(-)(1), 989cm(-)(1), 1192cm(-)(1), 1369cm(-)(1), 1437cm(-)(1), 1450cm(-)(1), 1546cm(-)(1), 1634cm(-)(1), 1679cm(-)(1) 1772cm(-)(1), 2874cm(-)(1) and 2962cm(-)(1)) associated with cytotoxicity were significantly (p value<0.05, one way ANOVA, Tukey test, Bonferroni) altered, while two of the bands were also indicative of early stress related responses. In PCA, poor separation between nontoxic and cytostatic responses was evident while clear separation was linked to cytotoxicity. RT-CES detected morphological changes as indicators of cell injury and could distinguish between viable, cytostatic and cytotoxic responses. FTIR microspectroscopy confirmed that cytostatic cells were viable and could still recover while also describing early cellular stress related responses on a molecular level.
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Affiliation(s)
- K le Roux
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa
| | - L C Prinsloo
- Department of Physics, University of Pretoria, Pretoria 0002, South Africa
| | - D Meyer
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa.
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168
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Kwak JT, Kajdacsy-Balla A, Macias V, Walsh M, Sinha S, Bhargava R. Improving prediction of prostate cancer recurrence using chemical imaging. Sci Rep 2015; 5:8758. [PMID: 25737022 PMCID: PMC4348620 DOI: 10.1038/srep08758] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/03/2015] [Indexed: 01/02/2023] Open
Abstract
Precise Outcome prediction is crucial to providing optimal cancer care across the spectrum of solid cancers. Clinically-useful tools to predict risk of adverse events (metastases, recurrence), however, remain deficient. Here, we report an approach to predict the risk of prostate cancer recurrence, at the time of initial diagnosis, using a combination of emerging chemical imaging, a diagnostic protocol that focuses simultaneously on the tumor and its microenvironment, and data analysis of frequent patterns in molecular expression. Fourier transform infrared (FT-IR) spectroscopic imaging was employed to record the structure and molecular content from tumors prostatectomy. We analyzed data from a patient cohort that is mid-grade dominant – which is the largest cohort of patients in the modern era and in whom prognostic methods are largely ineffective. Our approach outperforms the two widely used tools, Kattan nomogram and CAPRA-S score in a head-to-head comparison for predicting risk of recurrence. Importantly, the approach provides a histologic basis to the prediction that identifies chemical and morphologic features in the tumor microenvironment that is independent of conventional clinical information, opening the door to similar advances in other solid tumors.
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Affiliation(s)
- Jin Tae Kwak
- 1] Center for Interventional Oncology, National Institutes of Health, Bethesda, MD 20892, USA [2] Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA [3] Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - André Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Virgilia Macias
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Michael Walsh
- 1] Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA [2] Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rohit Bhargava
- 1] Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA [2] Department of Bioengineering, Mechanical Science and Engineering, Electrical and Computer Engineering, Chemical and Biomolecular Engineering and University of Illinois Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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169
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Mayerich D, Walsh MJ, Kadjacsy-Balla A, Ray PS, Hewitt SM, Bhargava R. Stain-less staining for computed histopathology. TECHNOLOGY 2015; 3:27-31. [PMID: 26029735 PMCID: PMC4445956 DOI: 10.1142/s2339547815200010] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dyes such as hematoxylin and eosin (H&E) and immunohistochemical stains have been increasingly used to visualize tissue composition in research and clinical practice. We present an alternative approach to obtain the same information using stain-free chemical imaging. Relying on Fourier transform infrared (FT-IR) spectroscopic imaging and computation, stainless computed histopathology can enable a rapid, digital, quantitative and non-perturbing visualization of morphology and multiple molecular epitopes simultaneously in a variety of research and clinical pathology applications.
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Affiliation(s)
- David Mayerich
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michael J Walsh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 and Carle Foundation Hospital, Urbana, IL 61801, USA
| | - Andre Kadjacsy-Balla
- Department of Pathology and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Partha S Ray
- Carle Cancer Center, Carle Foundation Hospital, Urbana, IL and Department of Surgery, and University of Illinois Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 and Carle Foundation Hospital, Urbana, IL 61801, USA. ; Departments of Mechanical Science and Engineering, Electrical and Computer Engineering, Chemical and Biomolecular Engineering and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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170
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Portable Infrared Spectrometer to Characterize and Differentiate Between Organic and Conventional Bovine Butter. J AM OIL CHEM SOC 2015. [DOI: 10.1007/s11746-015-2591-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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171
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Bunaciu AA, Hoang VD, Aboul-Enein HY. Applications of FT-IR Spectrophotometry in Cancer Diagnostics. Crit Rev Anal Chem 2015; 45:156-65. [DOI: 10.1080/10408347.2014.904733] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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172
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Havlik I, Scheper T, Reardon KF. Monitoring of Microalgal Processes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 153:89-142. [PMID: 26289537 DOI: 10.1007/10_2015_328] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Process monitoring, which can be defined as the measurement of process variables with the smallest possible delay, is combined with process models to form the basis for successful process control. Minimizing the measurement delay leads inevitably to employing online, in situ sensors where possible, preferably using noninvasive measurement methods with stable, low-cost sensors. Microalgal processes have similarities to traditional bioprocesses but also have unique monitoring requirements. In general, variables to be monitored in microalgal processes can be categorized as physical, chemical, and biological, and they are measured in gaseous, liquid, and solid (biological) phases. Physical and chemical process variables can be usually monitored online using standard industrial sensors. The monitoring of biological process variables, however, relies mostly on sensors developed and validated using laboratory-scale systems or uses offline methods because of difficulties in developing suitable online sensors. Here, we review current technologies for online, in situ monitoring of all types of process parameters of microalgal cultivations, with a focus on monitoring of biological parameters. We discuss newly introduced methods for measuring biological parameters that could be possibly adapted for routine online use, should be preferably noninvasive, and are based on approaches that have been proven in other bioprocesses. New sensor types for measuring physicochemical parameters using optical methods or ion-specific field effect transistor (ISFET) sensors are also discussed. Reviewed methods with online implementation or online potential include measurement of irradiance, biomass concentration by optical density and image analysis, cell count, chlorophyll fluorescence, growth rate, lipid concentration by infrared spectrophotometry, dielectric scattering, and nuclear magnetic resonance. Future perspectives are discussed, especially in the field of image analysis using in situ microscopy, infrared spectrophotometry, and software sensor systems.
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Affiliation(s)
- Ivo Havlik
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstrasse 5, 30167, Hannover, Germany.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstrasse 5, 30167, Hannover, Germany
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173
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Li J, Ying GG, Jones KC, Martin FL. Real-world carbon nanoparticle exposures induce brain and gonadal alterations in zebrafish (Danio rerio) as determined by biospectroscopy techniques. Analyst 2015; 140:2687-2695. [DOI: 10.1039/c4an02227k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Differential tissue-specific effects of nanoparticles: biospectroscopy as a toxicity-sensing tool.
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Affiliation(s)
- Junyi Li
- Centre for Biophotonics
- Lancaster Environment Centre
- Lancaster University
- Lancaster LA1 4YQ
- UK
| | - Guang-Guo Ying
- State Key Laboratory of Organic Geochemistry
- Guangzhou Institute of Geochemistry
- Chinese Academy of Sciences
- Guangzhou 510640
- China
| | - Kevin C. Jones
- Centre for Biophotonics
- Lancaster Environment Centre
- Lancaster University
- Lancaster LA1 4YQ
- UK
| | - Francis L. Martin
- Centre for Biophotonics
- Lancaster Environment Centre
- Lancaster University
- Lancaster LA1 4YQ
- UK
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174
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González-Domínguez R, García-Barrera T, Gómez-Ariza JL. Metabolite profiling for the identification of altered metabolic pathways in Alzheimer's disease. J Pharm Biomed Anal 2014; 107:75-81. [PMID: 25575172 DOI: 10.1016/j.jpba.2014.10.010] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 10/08/2014] [Accepted: 10/10/2014] [Indexed: 01/05/2023]
Abstract
Gas chromatography coupled to mass spectrometry is the most frequent tool for metabolomic profiling of low molecular weight metabolites. Its suitability in health survey is beyond doubt, given that primary metabolites involved in central pathways of metabolism are usually altered in diseases. The objective of this work is to investigate metabolic differences in serum between Alzheimer's disease patients and healthy controls in order to elucidate pathological mechanisms underlying to disease. Alterations in levels of 23 metabolites were detected, including increased lactic acid, α-ketoglutarate, isocitric acid, glucose, oleic acid, adenosine and cholesterol, as well as decreased urea, valine, aspartic acid, pyroglutamate, glutamine, phenylalanine, asparagine, ornithine, pipecolic acid, histidine, tyrosine, palmitic and uric acid, tryptophan, stearic acid and cystine. Metabolic pathway analysis revealed the involvement of multiple affected pathways, such as energy deficiencies, oxidative stress, hyperammonemia, and others. Moreover, it is noteworthy that some of these compounds have not been previously described in AD research, such as α-ketoglutarate, isocitrate pipecolic acid, pyroglutamate and adenosine, confirming the potential of this metabolomic approach in the search of novel potential markers for early detection of Alzheimer's disease.
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Affiliation(s)
- Raúl González-Domínguez
- Department of Chemistry and CC.MM, Faculty of Experimental Science, University of Huelva, Campus de El Carmen, 21007 Huelva, Spain; Campus of Excellence International ceiA3, University of Huelva, Spain; Research Center of Health and Environment (CYSMA), University of Huelva, Campus de El Carmen, 21007 Huelva, Spain.
| | - Tamara García-Barrera
- Department of Chemistry and CC.MM, Faculty of Experimental Science, University of Huelva, Campus de El Carmen, 21007 Huelva, Spain; Campus of Excellence International ceiA3, University of Huelva, Spain; Research Center of Health and Environment (CYSMA), University of Huelva, Campus de El Carmen, 21007 Huelva, Spain.
| | - José Luis Gómez-Ariza
- Department of Chemistry and CC.MM, Faculty of Experimental Science, University of Huelva, Campus de El Carmen, 21007 Huelva, Spain; Campus of Excellence International ceiA3, University of Huelva, Spain; Research Center of Health and Environment (CYSMA), University of Huelva, Campus de El Carmen, 21007 Huelva, Spain.
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175
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McAughtrie S, Faulds K, Graham D. Surface enhanced Raman spectroscopy (SERS): Potential applications for disease detection and treatment. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2014. [DOI: 10.1016/j.jphotochemrev.2014.09.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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176
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Choi S, Moon SW, Shin JH, Park HK, Jin KH. Label-Free Biochemical Analytic Method for the Early Detection of Adenoviral Conjunctivitis Using Human Tear Biofluids. Anal Chem 2014; 86:11093-9. [DOI: 10.1021/ac5025478] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Samjin Choi
- Department
of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 130-701, Korea
- Healthcare
Industry Research Institute, Kyung Hee University, Seoul 130-701, Korea
- Department
of Medical Engineering, College of Medicine, Kyung Hee University, Seoul 130-701, Korea
| | - Sung Woon Moon
- Department
of Ophthalmology, Kyung Hee University, Seoul 130-701, Korea
| | - Jae-Ho Shin
- Department
of Ophthalmology, Kyung Hee University, Seoul 130-701, Korea
| | - Hun-Kuk Park
- Department
of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 130-701, Korea
- Healthcare
Industry Research Institute, Kyung Hee University, Seoul 130-701, Korea
- Department
of Medical Engineering, College of Medicine, Kyung Hee University, Seoul 130-701, Korea
| | - Kyung-Hyun Jin
- Department
of Ophthalmology, Kyung Hee University, Seoul 130-701, Korea
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177
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Kuligowski J, Pérez-Guaita D, Escobar J, Lliso I, de la Guardia M, Lendl B, Vento M, Quintás G. Infrared biospectroscopy for a fast qualitative evaluation of sample preparation in metabolomics. Talanta 2014; 127:181-90. [DOI: 10.1016/j.talanta.2014.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 10/25/2022]
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178
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Kafle D, Krähmer A, Naumann A, Wurst S. Genetic Variation of the Host Plant Species Matters for Interactions with Above- and Belowground Herbivores. INSECTS 2014; 5:651-67. [PMID: 26462832 PMCID: PMC4592585 DOI: 10.3390/insects5030651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/22/2014] [Accepted: 08/08/2014] [Indexed: 11/20/2022]
Abstract
Plants are challenged by both above- and belowground herbivores which may indirectly interact with each other via herbivore-induced changes in plant traits; however, little is known about how genetic variation of the host plant shapes such interactions. We used two genotypes (M4 and E9) of Solanum dulcamara (Solanaceae) with or without previous experience of aboveground herbivory by Spodoptera exigua (Noctuidae) to quantify its effects on subsequent root herbivory by Agriotes spp. (Elateridae). In the genotype M4, due to the aboveground herbivory, shoot and root biomass was significantly decreased, roots had a lower C/N ratio and contained significantly higher levels of proteins, while the genotype E9 was not affected. However, aboveground herbivory had no effects on weight gain or mortality of the belowground herbivores. Root herbivory by Agriotes increased the nitrogen concentration in the roots of M4 plants leading to a higher weight gain of conspecific larvae. Also, in feeding bioassays, Agriotes larvae tended to prefer roots of M4 over E9, irrespective of the aboveground herbivore treatment. Fourier-Transform Infrared Spectroscopy (FT-IR) documented differences in metabolic profiles of the two plant genotypes and of the roots of M4 plants after aboveground herbivory. Together, these results demonstrate that previous aboveground herbivory can have genotype-specific effects on quantitative and qualitative root traits. This may have consequences for belowground interactions, although generalist root herbivores might not be affected when the root biomass offered is still sufficient for growth and survival.
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Affiliation(s)
- Dinesh Kafle
- Collaborative Research Center (CRC) 973, Institute of Biology, Functional Biodiversity, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin 14195, Germany.
| | - Andrea Krähmer
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Str. 19, Berlin 14195, Germany.
| | - Annette Naumann
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Str. 19, Berlin 14195, Germany.
| | - Susanne Wurst
- Collaborative Research Center (CRC) 973, Institute of Biology, Functional Biodiversity, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin 14195, Germany.
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179
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Silva TS, da Costa AMR, Conceição LEC, Dias JP, Rodrigues PML, Richard N. Metabolic fingerprinting of gilthead seabream (Sparus aurata) liver to track interactions between dietary factors and seasonal temperature variations. PeerJ 2014; 2:e527. [PMID: 25210655 PMCID: PMC4157298 DOI: 10.7717/peerj.527] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 07/29/2014] [Indexed: 01/04/2023] Open
Abstract
Farmed gilthead seabream is sometimes affected by a metabolic syndrome, known as the "winter disease", which has a significant economic impact in the Mediterranean region. It is caused, among other factors, by the thermal variations that occur during colder months and there are signs that an improved nutritional status can mitigate the effects of this thermal stress. For this reason, a trial was undertaken where we assessed the effect of two different diets on gilthead seabream physiology and nutritional state, through metabolic fingerprinting of hepatic tissue. For this trial, four groups of 25 adult gilthead seabream were reared for 8 months, being fed either with a control diet (CTRL, low-cost commercial formulation) or with a diet called "Winter Feed" (WF, high-cost improved formulation). Fish were sampled at two time-points (at the end of winter and at the end of spring), with liver tissue being taken for FT-IR spectroscopy. Results have shown that seasonal temperature variations constitute a metabolic challenge for gilthead seabream, with hepatic carbohydrate stores being consumed over the course of the inter-sampling period. Regarding the WF diet, results point towards a positive effect in terms of performance and improved nutritional status. This diet seems to have a mitigating effect on the deleterious impact of thermal shifts, confirming the hypothesis that nutritional factors can affect the capacity of gilthead seabream to cope with seasonal thermal variations and possibly contribute to prevent the onset of "winter disease".
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Affiliation(s)
- Tomé S Silva
- SPAROS Lda. , Olhão , Portugal ; CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas , Faro , Portugal
| | - Ana M R da Costa
- CIQA, Algarve Chemistry Research Centre, University of Algarve, Campus de Gambelas , Faro , Portugal ; Department of Chemistry and Pharmacy, University of Algarve, Campus de Gambelas , Faro , Portugal
| | | | | | - Pedro M L Rodrigues
- CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas , Faro , Portugal ; Department of Chemistry and Pharmacy, University of Algarve, Campus de Gambelas , Faro , Portugal
| | - Nadège Richard
- CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas , Faro , Portugal
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180
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Qamar W, Ahamad SR, Ali R, Khan MR, Al-Ghadeer AR. Metabolomic analysis of lung epithelial secretions in rats: an investigation of bronchoalveolar lavage fluid by GC-MS and FT-IR. Exp Lung Res 2014; 40:460-6. [PMID: 25153043 DOI: 10.3109/01902148.2014.947008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Rat bronchoalveolar lavage fluid (BALF) metabolome can be used to obtain valuable, precise, and accurate information about underlying lung conditions in an experiment. The present study focuses on the evaluation of the lung epithelium metabolome in a rat model using techniques including bronchoalveolar lavage, gas chromatography-mass spectroscopy (GC-MS), and Fourier transform infrared spectroscopy (FT-IR). MATERIALS AND METHODS Untargeted metabolites in BALF were extracted in ethyl acetate and derivatized by standard methods for the analysis by GC-MS. FT-IR spectra of ethyl acetate extract of BALF were obtained and read for the characteristic fingerprint of rats under investigation. Analyses were done in individual animals to obtain consistent data. BALF cells were counted by flow cytometry to monitor any inflammatory condition in rats. RESULTS FT-IR analysis finds two peaks which are characteristically different from the extract medium, which is ethyl acetate. FT-IR peaks correspond to that of amino acids and carbohydrates, including β-D-glucose, α-D-glucose, and β-D-galactose. GC-MS evaluation of the BALF finds several products of the metabolism or its participants. Main compounds in the BALF detected by GC-MS include succinate, fumarate, glycine, alanine, 2-methyl-3-oxovaleric acid, dodecanoic acid, tetradecanoic acid, hexadecanoic acid, octanoic acid, trans-9-octadecanoic acid, octadecanoic acid, and Prostaglandin F1α. CONCLUSION Several research reports reveal metabolomic parameters in murine model lung tissue or BALF, but they rarely reported a complete metabolomics model profile, particularly in rats. The present data of GC-MS and FT-IR suggest that the set up can be exploited to study metabolomic alterations in several lung conditions including acute lung toxicity, inflammation, asthma, bronchitis, fibrosis, and emphysema.
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Affiliation(s)
- Wajhul Qamar
- Central Laboratory, Research Center, College of pharmacy, King Saud University, Riyadh, Saudi Arabia
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181
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Abstract
We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear "one beam" geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments.
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182
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Salman A, Shufan E, Zeiri L, Huleihel M. Characterization and detection of Vero cells infected with Herpes Simplex Virus type 1 using Raman spectroscopy and advanced statistical methods. Methods 2014; 68:364-70. [DOI: 10.1016/j.ymeth.2014.02.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/04/2014] [Accepted: 02/15/2014] [Indexed: 01/19/2023] Open
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183
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State of the art Raman techniques for biological applications. Methods 2014; 68:338-47. [DOI: 10.1016/j.ymeth.2014.02.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022] Open
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184
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Fullwood LM, Griffiths D, Ashton K, Dawson T, Lea RW, Davis C, Bonnier F, Byrne HJ, Baker MJ. Effect of substrate choice and tissue type on tissue preparation for spectral histopathology by Raman microspectroscopy. Analyst 2014; 139:446-54. [PMID: 24308030 DOI: 10.1039/c3an01832f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Raman spectroscopy is a non-destructive, non-invasive, rapid and economical technique which has the potential to be an excellent method for the diagnosis of cancer and understanding disease progression through retrospective studies of archived tissue samples. Historically, biobanks are generally comprised of formalin fixed paraffin preserved tissue and as a result these specimens are often used in spectroscopic research. Tissue in this state has to be dewaxed prior to Raman analysis to reduce paraffin contributions in the spectra. However, although the procedures are derived from histopathological clinical practice, the efficacy of the dewaxing procedures that are currently employed is questionable. Ineffective removal of paraffin results in corruption of the spectra and previous experiments have shown that the efficacy can depend on the dewaxing medium and processing time. The aim of this study was to investigate the influence of commonly used spectroscopic substrates (CaF2, Spectrosil quartz and low-E slides) and the influence of different histological tissue types (normal, cancerous and metastatic) on tissue preparation and to assess their use for spectral histopathology. Results show that CaF2 followed by Spectrosil contribute the least to the spectral background. However, both substrates retain paraffin after dewaxing. Low-E substrates, which exhibit the most intense spectral background, do not retain wax and resulting spectra are not affected by paraffin peaks. We also show a disparity in paraffin retention depending upon the histological identity of the tissue with abnormal tissue retaining more paraffin than normal.
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Affiliation(s)
- Leanne M Fullwood
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, PR1 2HE, UK.
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185
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Potential of metabolomics in preclinical and clinical drug development. Pharmacol Rep 2014; 66:956-63. [PMID: 25443721 DOI: 10.1016/j.pharep.2014.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/03/2014] [Accepted: 06/10/2014] [Indexed: 12/29/2022]
Abstract
Metabolomics is an upcoming technology system which involves detailed experimental analysis of metabolic profiles. Due to its diverse applications in preclinical and clinical research, it became an useful tool for the drug discovery and drug development process. This review covers the brief outline about the instrumentation and interpretation of metabolic profiles. The applications of metabolomics have a considerable scope in the pharmaceutical industry, almost at each step from drug discovery to clinical development. These include finding drug target, potential safety and efficacy biomarkers and mechanisms of drug action, the validation of preclinical experimental models against human disease profiles, and the discovery of clinical safety and efficacy biomarkers. As we all know, nowadays the drug discovery and development process is a very expensive, and risky business. Failures at any stage of drug discovery and development process cost millions of dollars to the companies. Some of these failures or the associated risks could be prevented or minimized if there were better ways of drug screening, drug toxicity profiling and monitoring adverse drug reactions. Metabolomics potentially offers an effective route to address all the issues associated with the drug discovery and development.
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186
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Sitole L, Steffens F, Krüger TPJ, Meyer D. Mid-ATR-FTIR spectroscopic profiling of HIV/AIDS sera for novel systems diagnostics in global health. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:513-23. [PMID: 24937213 DOI: 10.1089/omi.2013.0157] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Global health, whether in developed or developing countries, is in need of robust systems diagnostics for major diseases, such as HIV/AIDS, impacting the world populations. Fourier transform Infrared (FTIR) spectroscopy of serum is a quick and reagent-free methodology with which to analyze metabolic alterations such as those caused by disease or treatment. In this study, Attenuated Total Reflectance Fourier-Transform (ATR-FTIR) Spectroscopy was investigated as a means of distinguishing HIV-infected treatment-experienced (HIV(pos) ART(pos), n=39) and HIV-infected-treatment-naïve (HIV(pos) ART(neg), n=16) subjects from uninfected control subjects (n=30). Multivariate pattern recognition techniques, including partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA), successfully distinguished sample classes, while univariate approaches identified significant differences (p<0.05) after Benjamini-Hochberg corrections. OPLS-DA discriminated between all groups with sensitivity, specificity, and accuracy of >90%. Compared to uninfected controls, HIV(pos) ART(pos) and HIV(pos) ART(neg) subjects displayed significant differences in spectral regions linked to lipids/fatty acids (3010 cm(-1)), carbohydrates (1299 cm(-1); 1498 cm(-1)), glucose (1035 cm(-1)), and proteins (1600 cm(-1); 1652 cm(-1)). These are all molecules shown by conventional biochemical analysis to be affected by HIV/ART interference. The biofluid metabolomics approach applied here successfully differentiated global metabolic profiles of HIV-infected patients and uninfected controls and detected potential biomarkers for development into indicators of host response to treatment and/or disease progression. Our findings therefore contribute to ongoing efforts for capacity-building in global health for robust omics science and systems diagnostics towards major diseases impacting population health.
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Affiliation(s)
- Lungile Sitole
- 1 Department of Biochemistry, University of Pretoria , Pretoria, South Africa
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187
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Mussap M, Noto A, Fanos V, Van Den Anker JN. Emerging biomarkers and metabolomics for assessing toxic nephropathy and acute kidney injury (AKI) in neonatology. BIOMED RESEARCH INTERNATIONAL 2014; 2014:602526. [PMID: 25013791 PMCID: PMC4071811 DOI: 10.1155/2014/602526] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/25/2014] [Indexed: 01/07/2023]
Abstract
Identification of novel drug-induced toxic nephropathy and acute kidney injury (AKI) biomarkers has been designated as a top priority by the American Society of Nephrology. Increasing knowledge in the science of biology and medicine is leading to the discovery of still more new biomarkers and of their roles in molecular pathways triggered by physiological and pathological conditions. Concomitantly, the development of the so-called "omics" allows the progressive clinical utilization of a multitude of information, from those related to the human genome (genomics) and proteome (proteomics), including the emerging epigenomics, to those related to metabolites (metabolomics). In preterm newborns, one of the most important factors causing the pathogenesis and the progression of AKI is the interaction between the individual genetic code, the environment, the gestational age, and the disease. By analyzing a small urine sample, metabolomics allows to identify instantly any change in phenotype, including changes due to genetic modifications. The role of liquid chromatography-mass spectrometry (LC-MS), proton nuclear magnetic resonance (1H NMR), and other emerging technologies is strategic, contributing basically to the sudden development of new biochemical and molecular tests. Urine neutrophil gelatinase-associated lipocalin (uNGAL) and kidney injury molecule-1 (KIM-1) are closely correlated with the severity of kidney injury, representing noninvasive sensitive surrogate biomarkers for diagnosing, monitoring, and quantifying kidney damage. To become routine tests, uNGAL and KIM-1 should be carefully tested in multicenter clinical trials and should be measured in biological fluids by robust, standardized analytical methods.
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Affiliation(s)
- M. Mussap
- Department of Laboratory Medicine, IRCCS San Martino-IST, University Hospital, National Institute for Cancer Research, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - A. Noto
- Department of Pediatrics and Clinical Medicine, Section of Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Mista and University of Cagliari, 09042 Cagliari, Italy
| | - V. Fanos
- Department of Pediatrics and Clinical Medicine, Section of Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Mista and University of Cagliari, 09042 Cagliari, Italy
| | - J. N. Van Den Anker
- Division of Pediatric Clinical Pharmacology, Children's National Medical Center, Washington, DC 20010, USA
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188
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Metabolomic prediction of pregnancy viability in superovulated cattle embryos and recipients with fourier transform infrared spectroscopy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:608579. [PMID: 24834432 PMCID: PMC4009133 DOI: 10.1155/2014/608579] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/30/2014] [Indexed: 12/31/2022]
Abstract
We analyzed embryo culture medium (CM) and recipient blood plasma using Fourier transform infrared spectroscopy (FTIR) metabolomics to identify spectral models predictive of pregnancy outcome. Embryos collected on Day 6 from superovulated cows in 2 countries were individually cultured in synthetic oviduct fluid medium with BSA for 24 h before embryo transfer. Spent CM, blank controls, and plasma samples (Day 0 and Day 7) were evaluated using FTIR. The spectra obtained were analyzed. The discrimination capability of the classifiers was assessed for accuracy, sensitivity (pregnancy), specificity (nonpregnancy), and area under the ROC curve (AUC). Endpoints considered were Day 60 pregnancy and birth. High AUC was obtained for Day 60 pregnancy in CM within individual laboratories (France AUC = 0.751 ± 0.039, Spain AUC = 0.718 ± 0.024), while cumulative data decreased the AUC (AUC = 0.604 ± 0.029). Predictions for CM at birth were lower than Day 60 pregnancy. Predictions with plasma at birth improved cumulative over individual results (Day 0: France AUC = 0.690 ± 0.044; Spain AUC < 0.55; cumulative AUC = 0.747 ± 0.032). Plasma generally predicted pregnancy and birth better than CM. These first results show that FTIR metabolomics could allow the identification of embryos and recipients with improved pregnancy viability, which may contribute to increasing the efficiency of selection schemes based on ET.
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189
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190
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Ollesch J, Heinze M, Heise HM, Behrens T, Brüning T, Gerwert K. It's in your blood: spectral biomarker candidates for urinary bladder cancer from automated FTIR spectroscopy. JOURNAL OF BIOPHOTONICS 2014; 7:210-221. [PMID: 24395618 DOI: 10.1002/jbio.201300163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/18/2013] [Accepted: 11/29/2013] [Indexed: 06/03/2023]
Abstract
Blood samples of urinary bladder cancer (UBC) patients and patients with urinary tract infection were analysed with advanced automated high throughput Fourier transform infrared (HT-FTIR)-spectroscopy. Thin dried film samples were robotically prepared on multi-well titer plates (MTP) for absorbance measurements in transmission mode. Within the absorbance, 1st and 2nd derivative spectra of serum and two plasma preparations, discriminative patterns were identified and validated using bioinformatic tools. The optimal spectral resolution for data acquisition was determined. An accurate discrimination of the patient groups was achieved with three different independent spectral variable sets. The HT-FTIR blood test may support future clinical diagnostics.
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Affiliation(s)
- Julian Ollesch
- Ruhr-Universität Bochum, Department of Biophysics ND04, Universitätsstraße 150, 44780 Bochum, Germany
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191
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Abstract
Calcinosis cutis (CC) is a type of calcinosis wherein insoluble compounds or salts deposited on the skin. Clinical diagnosis of CC is usually achieved through time consuming histopathological or immunohistochemical procedures, but it can only be empirically identified by experienced practitioners. The use of advanced vibrational spectroscopy has been recently shown to have great potential as a diagnostic technique for various diseased tissues because it analyses the chemical composition of diseased tissue rather than its anatomy and predicts disease progression. This review article includes a summary of the application of Fourier transform infrared (FT-IR) and Raman spectroscopic or microspectroscopic analysis for the rapid diagnosis and identification of the chemical composition of skin calcified deposits in patients with various CC symptoms. Both advanced techniques not only can detect the types of insoluble salts such as calcium phosphate, calcium carbonate, and monosodium urate, and β-carotene in the calcified deposits of human skin tissue but also can directly differentiate the carbonate substitution in the apatite structure of the skin calcified deposits. In particular, the combination of both vibrational techniques may provide complementary information to simultaneously assess the intact components of the calcified deposits. In the future, both FT-IR and Raman vibrational microspectroscopic techniques will become available tools to support the standard test techniques currently used in some clinical diagnoses. Molecular spectroscopy technique is rapidly changing disease diagnosis and management.
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192
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Suzuki M, Nishiumi S, Matsubara A, Azuma T, Yoshida M. Metabolome analysis for discovering biomarkers of gastroenterological cancer. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:59-69. [PMID: 24636738 DOI: 10.1016/j.jchromb.2014.02.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/28/2014] [Accepted: 02/22/2014] [Indexed: 12/18/2022]
Abstract
Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis.
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Affiliation(s)
- Makoto Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsuki Matsubara
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Azuma
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Kobe, Japan; Division of Metabolomics Research, Department of Internal Medicine related, Kobe University Graduate School of Medicine, Kobe, Japan.
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193
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Abstract
Preimplantation embryo metabolism demonstrates distinctive characteristics associated with the developmental potential of embryos. On this basis, metabolite content of culture media was hypothesized to reflect the implantation potential of individual embryos. This hypothesis was tested in consecutive studies reporting a significant association between culture media metabolites and embryo development or clinical pregnancy. The need for a noninvasive, reliable, and rapid embryo assessment strategy promoted metabolomics studies in vitro fertilization (IVF) in an effort to increase success rates of single embryo transfers. With the advance of analytical techniques and bioinformatics, commercial instruments were developed to predict embryo viability using spectroscopic analysis of surplus culture media. However, despite the initial promising results from proof-of-principal studies, recent randomized controlled trials using commercial instruments failed to show a consistent benefit in improving pregnancy rates when metabolomics is used as an adjunct to morphology. At present, the application of metabolomics technology in clinical IVF laboratory requires the elimination of factors underlying inconsistent findings, when possible, and development of reliable predictive models accounting for all possible sources of bias throughout the embryo selection process.
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Affiliation(s)
- Asli Uyar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
| | - Emre Seli
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
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194
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Bassan P, Mellor J, Shapiro J, Williams KJ, Lisanti MP, Gardner P. Transmission FT-IR chemical imaging on glass substrates: applications in infrared spectral histopathology. Anal Chem 2014; 86:1648-53. [PMID: 24410403 DOI: 10.1021/ac403412n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform-infrared (FT-IR) chemical imaging in transmission mode has traditionally been performed on expensive mid-IR transparent windows such as barium/calcium fluoride, which are more fragile than glass, making preparation in the histopathology laboratories more cumbersome. A solution is presented here by using cheap glass substrates for the FT-IR chemical imaging, which has a high-wavenumber transmission window allowing measurement of the C-H, N-H, and O-H stretches occurring at ca. 2500-3800 cm(-1). The "fingerprint" region of the IR spectrum occurring below 1800 cm(-1) is not obtainable; however, we demonstrate that a wealth of information is contained in the high wavenumber range using 71 patients on a breast tissue microarray (TMA) as a model for investigation. Importantly, we demonstrate that the tissue can be classified into four basic tissue cell types and that using just the epithelial cells, reasonable discrimination of normal and malignant tissue can be found.
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Affiliation(s)
- Paul Bassan
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
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195
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Bromer JG, Sakkas D, Seli E. Metabolomic profiling of embryo culture media to predict IVF outcome. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/17474108.3.4.441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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196
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Deepinder F, Chowdary HT, Agarwal A. Role of metabolomic analysis of biomarkers in the management of male infertility. Expert Rev Mol Diagn 2014; 7:351-8. [PMID: 17620044 DOI: 10.1586/14737159.7.4.351] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Metabolomics is the systematic study of metabolites as small-molecule biomarkers that represent the functional phenotype in a cell, tissue or organism. Detection of crucial disturbances in the concentration of metabolites by metabolomic profiling of key biomarkers can be beneficial in the management of various medical conditions, including male-factor infertility. Recent studies have demonstrated the potential role of this rapid, noninvasive analysis in the investigation of infertile men. Differences in the concentration of oxidative stress biomarkers (-CH, -NH, -OH and ROH) have been found to be uniquely associated with semen plasma of healthy men compared with patients with idiopathic infertility, varicocele and vasectomy reversal. Furthermore, NMR spectra have shown significant differences in citrate, lactate, glycerylphosphorylcholine and glycerylphosphorylethanolamine among semen samples of men with spermatogenesis failure, obstructive azoospermia, oligoasthenoteratozoospermia and healthy donors. Evidence has also shown the value of (31)P-magnetic resonance spectroscopy in differentiating patients with testicular failure and ductal obstruction by utilizing phosphomonoester and beta-adenosine triphosphate as biomarkers. In addition, metabolomics has shown promise in assisted reproductive techniques. Recent studies involving spectroscopic measurements of follicular fluid and embryo culture media have revealed an association between biomarkers of oxidative stress and pregnancy outcome of oocytes and embryos.
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Affiliation(s)
- Fnu Deepinder
- Glickman Urological & Kidney Institute, Reproductive Research Center, Department of Obstetrics-Gynecology, Cleveland Clinic, Cleveland, OH 44195, USA.
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197
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Nallala J, Piot O, Diebold MD, Gobinet C, Bouché O, Manfait M, Sockalingum GD. Infrared and Raman imaging for characterizing complex biological materials: a comparative morpho-spectroscopic study of colon tissue. APPLIED SPECTROSCOPY 2014; 68:57-68. [PMID: 24405955 DOI: 10.1366/13-07170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Complementary diagnostic methods to conventional histopathology are currently being investigated for developing rapid and objective molecular-level understanding of various disorders, especially cancers. Spectral histopathology using vibrational spectroscopic imaging has been put in the frontline as potentially promising in this regard as it provides a "spectral fingerprint" of the biochemical composition of cells and tissues. In order to ascertain the feasible conditions of vibrational spectroscopic methods for tissue-imaging analysis, vibrational multimodal imaging (infrared transmission, infrared-attenuated total reflection, and Raman imaging) of the same colon tissue has been implemented. The spectral images acquired were subjected to multivariate clustering analysis in order to identify on a molecular level the constituent histological organization of the colon tissue such as the epithelium, connective tissue, etc., by comparing the cluster images with the histological reference images. Based on this study, a comparative analysis of important factors involved in the vibrational multimodal imaging approaches such as image resolution, time constraints, their advantages and limitations, and their applicability to biological tissues has been carried out. Out of the three different vibrational imaging modalities tested, infrared-attenuated total reflection mode of imaging appears to provide a good compromise between the tissue histology and the time constraints in achieving similar image contrast to that of Raman imaging at an approximately 33-fold faster measurement time. The present study demonstrates the advantages, the limitations of the important parameters involved in vibrational multimodal imaging approaches, and their potential application toward imaging of biological tissues.
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Affiliation(s)
- Jayakrupakar Nallala
- MÉDIAN Biophotonique et Technologies pour la Santé , Université de Reims Champagne-Ardenne, FRE CNRS 3481 MEDyC, UFR de Pharmacie, SFR Cap Santé , 51 rue Cognacq-Jay, 51096 Reims cedex, France
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198
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Mukherjee R, Ray CD, Ray S, Dasgupta S, Chaudhury K. Altered metabolic profile in early and late onset preeclampsia: An FTIR spectroscopic study. Pregnancy Hypertens 2014; 4:70-80. [DOI: 10.1016/j.preghy.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 09/02/2013] [Accepted: 11/07/2013] [Indexed: 12/24/2022]
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199
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Abstract
Faced with an increasing demand to select one embryo to transfer back to patients, a number of techniques are being developed to assist in discriminating differences within the cohort of a patient's embryos. A new and emerging technology which allows us to measure the profile of different metabolites in embryo culture media and formulate a viability score correlated to implantation potential is metabolomics.
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Affiliation(s)
- D Sakkas
- Boston IVF, 130 2nd Avenue, Waltham, MA, 02451, USA,
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200
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Phinney KW, Ballihaut G, Bedner M, Benford BS, Camara JE, Christopher SJ, Davis WC, Dodder NG, Eppe G, Lang BE, Long SE, Lowenthal MS, McGaw EA, Murphy KE, Nelson BC, Prendergast JL, Reiner JL, Rimmer CA, Sander LC, Schantz MM, Sharpless KE, Sniegoski LT, Tai SSC, Thomas JB, Vetter TW, Welch MJ, Wise SA, Wood LJ, Guthrie WF, Hagwood CR, Leigh SD, Yen JH, Zhang NF, Chaudhary-Webb M, Chen H, Fazili Z, LaVoie DJ, McCoy LF, Momin SS, Paladugula N, Pendergrast EC, Pfeiffer CM, Powers CD, Rabinowitz D, Rybak ME, Schleicher RL, Toombs BMH, Xu M, Zhang M, Castle AL. Development of a Standard Reference Material for metabolomics research. Anal Chem 2013; 85:11732-8. [PMID: 24187941 PMCID: PMC4823010 DOI: 10.1021/ac402689t] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The National Institute of Standards and Technology (NIST), in collaboration with the National Institutes of Health (NIH), has developed a Standard Reference Material (SRM) to support technology development in metabolomics research. SRM 1950 Metabolites in Human Plasma is intended to have metabolite concentrations that are representative of those found in adult human plasma. The plasma used in the preparation of SRM 1950 was collected from both male and female donors, and donor ethnicity targets were selected based upon the ethnic makeup of the U.S. population. Metabolomics research is diverse in terms of both instrumentation and scientific goals. This SRM was designed to apply broadly to the field, not toward specific applications. Therefore, concentrations of approximately 100 analytes, including amino acids, fatty acids, trace elements, vitamins, hormones, selenoproteins, clinical markers, and perfluorinated compounds (PFCs), were determined. Value assignment measurements were performed by NIST and the Centers for Disease Control and Prevention (CDC). SRM 1950 is the first reference material developed specifically for metabolomics research.
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Affiliation(s)
- Karen W. Phinney
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Guillaume Ballihaut
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Mary Bedner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Brandi S. Benford
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Johanna E. Camara
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Steven J. Christopher
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - W. Clay Davis
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Nathan G. Dodder
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Gauthier Eppe
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Brian E. Lang
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Stephen E. Long
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Mark S. Lowenthal
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Elizabeth A. McGaw
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Karen E. Murphy
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Bryant C. Nelson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jocelyn L. Prendergast
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jessica L. Reiner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Catherine A. Rimmer
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Lane C. Sander
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Michele M. Schantz
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Katherine E. Sharpless
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Lorna T. Sniegoski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Susan S.-C. Tai
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jeanice B. Thomas
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Thomas W. Vetter
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Michael J. Welch
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Stephen A. Wise
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Laura J. Wood
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - William F. Guthrie
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Charles R. Hagwood
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Stefan D. Leigh
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - James H. Yen
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Nien-Fan Zhang
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Madhu Chaudhary-Webb
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Huiping Chen
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Zia Fazili
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Donna J. LaVoie
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Leslie F. McCoy
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Shahzad S. Momin
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Neelima Paladugula
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Elizabeth C. Pendergrast
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Christine M. Pfeiffer
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Carissa D. Powers
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Daniel Rabinowitz
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Michael E. Rybak
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Rosemary L. Schleicher
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Bridgette M. H. Toombs
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Mary Xu
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Mindy Zhang
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Arthur L. Castle
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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