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Yang W, Li F, Zhao Y, Lu X, Yang S, Zhu P. Quantitative analysis of heavy metals in soil by X-ray fluorescence with PCA-ANOVA and support vector regression. Anal Methods 2022; 14:3944-3952. [PMID: 36222117 DOI: 10.1039/d2ay00593j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Heavy metal concentration is an important index for evaluating soil pollution. It is of great significance to measure the trace element content accurately for green agriculture development. In order to detect the trace element content accurately, a new prediction framework including pre-processing, signal extraction, feature selection and decision-making was proposed. The energy dispersive X-ray fluorescence (ED-XRF) spectra of 57 national standard soil samples were investigated based on the proposed methods. Firstly, an innovative background deduction method called iterative adaptive window empirical wavelet transform (IAWEWT) was introduced to extract effective counts of characteristic peaks, and the proposed approach was validated by the coefficient of determination (R2) of the instrumental calibration curve compared with two other conventional methods. Secondly, principal component analysis (PCA) was combined with the analysis of variance (ANOVA) for variable selection optimization of the ED-XRF spectrum. After PCA feature extraction and ANOVA variable selection treatment, the optimum number of principal components for V, Cr, Cu, Zn, Mo, Cd and Pb were determined to be 7, 15, 4, 4, 4, 5 and 12 respectively. Furthermore, the support vector regression (SVR) model was adopted for heavy metal estimation. The evaluation indices included R2 and root mean square error (RMSE). It was demonstrated that the predictive capabilities of seven heavy metal elements were improved substantially for elemental analysis by the proposed PCA-ANOVA-SVR model, with excellent results for V, Cr, Cu, Zn, Mo, Cd and Pb estimates, and the R2 values were 0.993, 0.996, 0.999, 0.999, 0.997, 0.998 and 0.998 respectively. Therefore, the new framework proposed in this paper can effectively eliminate redundant features and determine the concentration of trace elements in soil. It provides an effective alternative for the quantitative analysis of X-ray fluorescence spectrometry.
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Affiliation(s)
- Wanqi Yang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
| | - Fusheng Li
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
| | - Yanchun Zhao
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
| | - Xin Lu
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
| | - Siyuan Yang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
| | - Pengfei Zhu
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P. R. China.
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, P. R. China
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Herrera JG, Ramos MP, de Lima Albuquerque BN, de Oliveira Farias de Aguiar JCR, Agra Neto AC, Guedes Paiva PM, do Amaral Ferraz Navarro DM, Pinto L. Multivariate evaluation of process parameters to obtain essential oil of Piper corcovadensis using supercritical fluid extraction. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Tormena CD, Pauli ED, Marcheafave GG, Scheel GL, Rakocevic M, Bruns RE, Scarminio IS. FT-IR biomarkers of sexual dimorphism in yerba-mate plants: Seasonal and light accessibility effects. Microchem J 2020; 158:105329. [DOI: 10.1016/j.microc.2020.105329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Bertinetto C, Engel J, Jansen J. ANOVA simultaneous component analysis: A tutorial review. Anal Chim Acta X 2020; 6:100061. [PMID: 33392497 PMCID: PMC7772684 DOI: 10.1016/j.acax.2020.100061] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/27/2022] Open
Abstract
When analyzing experimental chemical data, it is often necessary to incorporate the structure of the study design into the chemometric/statistical models to effectively address the research questions of interest. ANOVA-Simultaneous Component Analysis (ASCA) is one of the most prominent methods to include such information in the quantitative analysis of multivariate data, especially when the number of variables is large. This tutorial review intends to explain in a simple way how ASCA works, how it is operated and how to correctly interpret ASCA results, with approachable mathematical and visual descriptions. Two examples are given: the first, a simulated chemical reaction, serves to illustrate the ASCA steps and the second, from a real chemical ecology data set, the interpretation of results. An overview of methods closely related to ASCA is also provided, pointing out their differences and scope, to give a wide-ranging picture of the available options to build multivariate models that take experimental design into account. ASCA is a multivariate method for analysis of multi-factor data. An overview of the (mathematical) principles of ASCA is presented. Key aspects for practical application of ASCA are discussed. Detailed explanation of ASCA output in terms of score and loading plots is given. Literature review of other multivariate techniques for analysis of multi-factor data.
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Affiliation(s)
- Carlo Bertinetto
- Department of Analytical Chemistry, Institute of Molecular Materials, Radboud University, the Netherlands
| | - Jasper Engel
- Biometris, Wageningen UR, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Jeroen Jansen
- Department of Analytical Chemistry, Institute of Molecular Materials, Radboud University, the Netherlands
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Ryckewaert M, Gorretta N, Henriot F, Marini F, Roger JM. Reduction of repeatability error for analysis of variance-Simultaneous Component Analysis (REP-ASCA): Application to NIR spectroscopy on coffee sample. Anal Chim Acta 2020; 1101:23-31. [PMID: 32029115 DOI: 10.1016/j.aca.2019.12.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 11/22/2022]
Abstract
A method to reduce repeatability error in multivariate data for Analysis of variance-Simultaneous Component Analysis (REP-ASCA) has been developed. This method proposes to adapt the acquisition protocol by adding a set containing repeated measures for describing repeatability error. Then, an orthogonal projection is performed in the row-space to reduce the repeatability error of the original dataset. Finally, ASCA is performed on the orthogonalized dataset. This method was evaluated on NIR spectral data of coffee beans. This study shows that the repeatability error due to physical variations between measurements can alter results of the analysis of variance. These effects are predominant in factors analysis and can be seen on spectra as constant or non-constant baselines. By reducing repeatability error with REP-ASCA, baselines are removed and factor analysis provides more information about chemical content of the factors of interest.
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Shen G, Wang S, Dong J, Feng J, Xu J, Xia F, Wang X, Ye J. Metabolic Effect of Dietary Taurine Supplementation on Grouper ( Epinephelus coioides): A 1H-NMR-Based Metabolomics Study. Molecules 2019; 24:E2253. [PMID: 31212947 DOI: 10.3390/molecules24122253] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 02/07/2023] Open
Abstract
Taurine is an indispensable amino acid for many fish species and taurine supplementation is needed when plant-based diets are used as the primary protein source for these species. However, there is limited information available to understand the physiological or metabolic effects of taurine on fish. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomic analysis was conducted to identify the metabolic profile change in the fish intestine with the aim to assess the effect of dietary taurine supplementation on the physiological and metabolomic variation of fish, and reveal the possible mechanism of taurine's metabolic effect. Grouper (Epinephelus coioides) were divided into four groups and fed diets containing 0.0%, 0.5%, 1.0%, and 1.5% taurine supplementation for 84 days. After extraction using aqueous and organic solvents, 25 significant taurine-induced metabolic changes were identified. These metabolic changes in grouper intestine were characterized by differences in carbohydrate, amino acid, lipid and nucleotide. The results reflected both the physiological state and growth of the fish, and indicated that taurine supplementation significantly affects the metabolome of fish, improves energy utilization and amino acid uptake, promotes protein, lipid and purine synthesis, and accelerates fish growth.
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Shen G, Huang Y, Dong J, Wang X, Cheng KK, Feng J, Xu J, Ye J. Metabolic Effect of Dietary Taurine Supplementation on Nile Tilapia (Oreochromis nilotictus) Evaluated by NMR-Based Metabolomics. J Agric Food Chem 2018; 66:368-377. [PMID: 29215281 DOI: 10.1021/acs.jafc.7b03182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Taurine is indispensable in aquatic diets that are based solely on plant protein, and it promotes growth of many fish species. However, the physiological and metabolome effects of taurine on fish have not been well described. In this study, 1H NMR-based metabolomics approaches were applied to investigate the metabolite variations in Nile tilapia (Oreochromis nilotictus) muscle in order to visualize the metabolic trajectory and reveal the possible mechanisms of metabolic effects of dietary taurine supplementation on tilapia growth. After extraction using aqueous and organic solvents, 19 taurine-induced metabolic changes were evaluated in our study. The metabolic changes were characterized by differences in carbohydrate, amino acid, lipid, and nucleotide contents. The results indicate that taurine supplementation could significantly regulate the physiological state of fish and promote growth and development. These results provide a basis for understanding the mechanism of dietary taurine supplementation in fish feeding. 1H NMR spectroscopy, coupled with multivariate pattern recognition technologies, is an efficient and useful tool to map the fish metabolome and identify metabolic responses to different dietary nutrients in aquaculture.
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Affiliation(s)
- Guiping Shen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University , Xiamen 361005, China
| | - Ying Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University , Xiamen 361005, China
| | - Jiyang Dong
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University , Xiamen 361005, China
| | - Xuexi Wang
- Fisheries College, Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Jimei University , Xiamen 361021, China
| | - Kian-Kai Cheng
- Department of Bioprocess and Polymer Engineering, Innovation Centre in Agritechnology, University Teknologi Malaysia , Johor Bahru, Johor 81310, Malaysia
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University , Xiamen 361005, China
| | - Jingjing Xu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University , Xiamen 361005, China
| | - Jidan Ye
- Fisheries College, Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Jimei University , Xiamen 361021, China
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Xu J, Cheng KK, Yang Z, Wang C, Shen G, Wang Y, Liu Q, Dong J. (1) H NMR Metabolic Profiling of Biofluids from Rats with Gastric Mucosal Lesion and Electroacupuncture Treatment. Evid Based Complement Alternat Med 2015; 2015:801691. [PMID: 26170882 DOI: 10.1155/2015/801691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/03/2015] [Indexed: 12/21/2022]
Abstract
Gastric mucosal lesion (GML) is a common gastrointestinal disorder with multiple pathogenic mechanisms in clinical practice. In traditional Chinese medicine (TCM), electroacupuncture (EA) treatment has been proven as an effective therapy for GML, although the underlying healing mechanism is not yet clear. Here, we used proton nuclear magnetic resonance- (1H NMR-) based metabolomic method to investigate the metabolic perturbation induced by GML and the therapeutic effect of EA treatment on stomach meridian (SM) acupoints. Clear metabolic differences were observed between GML and control groups, and related metabolic pathways were discussed by means of online metabolic network analysis toolbox. By comparing the endogenous metabolites from GML and GML-SM groups, the disturbed pathways were partly recovered towards healthy state via EA treated on SM acupoints. Further comparison of the metabolic variations induced by EA stimulated on SM and the control gallbladder meridian (GM) acupoints showed a quite similar metabolite composition except for increased phenylacetylglycine, 3,4-dihydroxymandelate, and meta-hydroxyphenylacetate and decreased N-methylnicotinamide in urine from rats with EA treated on SM acupoints. The current study showed the potential application of metabolomics in providing further insight into the molecular mechanism of acupuncture.
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Abstract
In this work, the Jacobsen catalyst is decomposed under different truncation schemes, allowing the establishment of structure–property relationships for several Mn(salen) complexes.
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Affiliation(s)
- Filipe Teixeira
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciê ncias
- Universidade do Porto
- 4169-007 Porto, Portugal
| | - Ricardo A. Mosquera
- Departamento de Química Física
- Facultade de Química
- Universidade de Vigo
- 36310 Vigo, Spain
| | - André Melo
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciê ncias
- Universidade do Porto
- 4169-007 Porto, Portugal
| | - Cristina Freire
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciê ncias
- Universidade do Porto
- 4169-007 Porto, Portugal
| | - M. Natália D. S. Cordeiro
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciê ncias
- Universidade do Porto
- 4169-007 Porto, Portugal
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Momo RA, Povey JF, Smales CM, O'Malley CJ, Montague GA, Martin EB. MALDI-ToF mass spectrometry coupled with multivariate pattern recognition analysis for the rapid biomarker profiling of Escherichia coli in different growth phases. Anal Bioanal Chem 2013; 405:8251-65. [PMID: 23942565 DOI: 10.1007/s00216-013-7245-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/06/2013] [Accepted: 07/10/2013] [Indexed: 11/26/2022]
Abstract
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS) has been exploited extensively in the field of microbiology for the characterisation of bacterial species, the detection of biomarkers for early disease diagnosis and bacterial identification. Here, the multivariate data analysis technique of partial least squares-discriminant analysis (PLS-DA) was applied to 'intact cell' MALDI-ToF MS data obtained from Escherichia coli cell samples to determine if such an approach could be used to distinguish between, and characterise, different growth phases. PLS-DA is a technique that has the potential to extract systematic variation from large and noisy data sets by identifying a lower-dimensional subspace that contains latent information. The application of PLS-DA to the MALDI-ToF data obtained from cells at different stages of growth resulted in the successful classification of the samples according to the growth phase of the bacteria cultures. A further outcome of the analysis was that it was possible to identify the mass-to-charge (m/z) ratio peaks or ion signals that contributed to the classification of the samples. The Swiss-Prot/TrEMBL database and primary literature were then used to provisionally assign a small number of these m/z ion signals to proteins, and these tentative assignments revealed that the major contributors from the exponential phase were ribosomal proteins. Additional assignments were possible for the stationary phase and the decline phase cultures where the proteins identified were consistent with previously observed biological interpretation. In summary, the results show that MALDI-ToF MS, PLS-DA and a protein database search can be used in combination to discriminate between 'intact cell' E. coli cell samples in different growth phases and thus could potentially be used as a tool in process development in the bioprocessing industry to enhance cell growth and cell engineering strategies.
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Affiliation(s)
- Remi A Momo
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK,
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Cheong MW, Chong ZS, Liu SQ, Zhou W, Curran P, Bin Yu. Characterisation of calamansi (Citrus microcarpa). Part I: Volatiles, aromatic profiles and phenolic acids in the peel. Food Chem 2012; 134:686-95. [DOI: 10.1016/j.foodchem.2012.02.162] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/02/2012] [Accepted: 02/16/2012] [Indexed: 11/29/2022]
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12
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Scollary GR, Pásti G, Kállay M, Blackman J, Clark AC. Astringency response of red wines: Potential role of molecular assembly. Trends Food Sci Technol 2012. [DOI: 10.1016/j.tifs.2012.05.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zerzucha P, Boguszewska D, Zagdańska B, Walczak B. Non-parametric multivariate analysis of variance in the proteomic response of potato to drought stress. Anal Chim Acta 2012; 719:1-7. [PMID: 22340524 DOI: 10.1016/j.aca.2011.12.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 12/17/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
Abstract
Spot detection is a mandatory step in all available software packages dedicated to the analysis of 2D gel images. As the majority of spots do not represent individual proteins, spot detection can obscure the results of data analysis significantly. This problem can be overcome by a pixel-level analysis of 2D images. Differences between the spot and the pixel-level approaches are demonstrated by variance analysis for real data sets (part of a larger research project initiated to investigate the molecular mechanism of the response of the potato to drought stress). As the method of choice for the analysis of data variation, the non-parametric MANOVA was chosen. NP-MANOVA is recommended as a flexible and very fast tool for the evaluation of the statistical significance of the factor(s) studied.
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Affiliation(s)
- Piotr Zerzucha
- Institute of Chemistry, The University of Silesia, Szkolna Street 9, 40-006 Katowice, Poland
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Affiliation(s)
- Shankar Subramaniam
- Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- San Diego Supercomputer Center, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Departments of Chemistry and Biochemistry, and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Manish Sud
- San Diego Supercomputer Center, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Robert W. Byrnes
- San Diego Supercomputer Center, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Dawn Cotter
- San Diego Supercomputer Center, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Ashok Reddy Dinasarapu
- Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Mano Ram Maurya
- Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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Stanimirova I, Michalik K, Drzazga Z, Trzeciak H, Wentzell P, Walczak B. Interpretation of analysis of variance models using principal component analysis to assess the effect of a maternal anticancer treatment on the mineralization of rat bones. Anal Chim Acta 2011; 689:1-7. [DOI: 10.1016/j.aca.2011.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 12/26/2010] [Accepted: 01/10/2011] [Indexed: 11/24/2022]
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