Discrimination of biofilm samples using pattern recognition techniques

Biofilms are complex aggregates formed by microorganisms such as bacteria, fungi and algae, which grow at the interfaces between water and natural or artificial materials. They are actively involved in processes of sorption and desorption of metal ions in water and reflect the environmental conditions in the recent past. Therefore, biofilms can be used as bioindicators of water quality. The goal of this study was to determine whether the biofilms, developed in different aquatic systems, could be successfully discriminated using data on their elemental compositions. Biofilms were grown on natural or polycarbonate materials in flowing water, standing water and seawater bodies. Using an unsupervised technique such as principal component analysis (PCA) and several supervised methods like classification and regression trees (CART), discriminant partial least squares regression (DPLS) and uninformative variable elimination–DPLS (UVE-DPLS), we could confirm the uniqueness of sea biofilms and make a distinction between flowing water and standing water biofilms. The CART, DPLS and UVE-DPLS discriminant models were validated with an independent test set selected either by the Kennard and Stone method or the duplex algorithm. The best model was obtained from CART with 100% correct classification rate for the test set designed by the Kennard and Stone algorithm. With CART, one variable describing the Mg content in the biofilm water phase was found to be important for the discrimination of flowing water and standing water biofilms.     

Comparative study of artificial neural network and multivariate methods to classify Spanish DO rose wines

Classical multivariate analysis techniques such as factor analysis and stepwise linear discriminant analysis and artificial neural networks method (ANN) have been applied to the classification of Spanish denomination of origin (DO) rose wines according to their geographical origin. Seventy commercial rose wines from four different Spanish DO (Ribera del Duero, Rioja, Valdepeñas and La Mancha) and two successive vintages were studied. Nineteen different variables were measured in these wines. The stepwise linear discriminant analyses (SLDA) model selected 10 variables obtaining a global percentage of correct classification of 98.8% and of global prediction of 97.3%. The ANN model selected seven variables, five of which were also selected by the SLDA model, and it gave a 100% of correct classification for training and prediction. So, both models can be considered satisfactory and acceptable, being the selected variables useful to classify and differentiate these wines by their origin. Furthermore, the casual index analysis gave information that can be easily explained from an enological point of view.     

Chemometric classification of traditional Chinese medicines by their geographical origins using near-infrared reflectance spectra.

Some raw materials that have different places of production for the plant sources of the drugs Astragalus membranaceus and ginseng have been studied, based on their near-infrared reflectance spectra. The experimentally recorded spectra represent heavily ill-posed and highly correlative data sets. Three related methods, i.e. the Fisher linear discriminant analysis (FLDA), the ridge-type linear discriminant analysis (RLDA) and a newly proposed penalized ridge-type linear discriminant analysis (PRLDA), have been investigated. FLDA over-fits for the training objects of the two data sets to a high extent and is unstable for the predictive objects of the two data sets. RLDA shows obvious improvement in terms of over-fitting and unstability, but the stability for the predictive objects of the two data sets is too sensitive to their ridge-type penalized weights, tending to produce erroneous discrimination results. The proposed PRLDA can circumvent the two aforementioned problems with a large domain of penalized weights for correct discriminant analysis of the two data sets studied. The combination of the PRLDA method and near infrared reflectance spectroscopy can be adapted for the discrimination of the production places of plant sources of these drugs.     

Determination of rice type by 1H NMR spectroscopy in combination with different chemometric tools

A 400‐MHz ¹H nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis were used in the context of food surveillance to discriminate 46 authentic rice samples according to type. It was found that the optimal sample preparation consists of preparing aqueous rice extracts at pH 1.9. For the first time, the chemometric method independent component analysis (ICA) was applied to differentiate clusters of rice from the same type (Basmati, non‐Basmati long‐grain rice, and round‐grain rice) and, to a certain extent, their geographical origin. ICA was found to be superior to classical principal component analysis (PCA) regarding the verification of rice authenticity. The chemical shifts of the principal saccharides and acetic acid were found to be mostly responsible for the observed clustering. Among classification methods (linear discriminant analysis, factorial discriminant analysis, partial least squares discriminant analysis (PLS‐DA), soft independent modeling of class analogy, and ICA), PLS‐DA and ICA gave the best values of specificity (0.96 for both methods) and sensitivity (0.94 for PLS‐DA and 1.0 for ICA). Hence, NMR spectroscopy combined with chemometrics could be used as a screening method in the official control of rice samples. Copyright © 2013 John Wiley & Sons, Ltd.     

FTIR spectroscopy coupled with multivariate classification methods to identify different powdered infant formulas adulterated with melamine and cyanuric acid

Fourier transform infrared spectroscopy (FTIR) is a nondestructive, simple, rapid, and cheap measurement technique for analysis of many multicomponent chemical systems, e.g., detection of adulterants in food samples. In this respect, this study proposes combining FTIR spectroscopy with multivariate classification methods for classification and discrimination of different samples of infant formulas adulterated by melamine or/and cyanuric acid. Different parametric and non-parametric multivariate classification methods including the linear discriminant analysis (LDA), partial least squares-discriminant analysis (PLS-DA), soft independent modeling of class analogy (SIMCA), K-nearest neighbors (KNN), and classification and regression tree (CART) approaches were used to classify the recorded FTIR data. Assessing the performance of the multivariate methods according to their sensitivity, specificity and percent of correct prediction results demonstrated that coupling FTIR spectroscopy with multivariate classification can be applied as a rapid and powerful technique to the simultaneous detection of melamine and cyanuric acid in powdered infant formulas. This combinatorial method is efficient for adulterant concentrations as low as 0.0001 w/w%.     

Discrimination of Beers by Cyclic Voltammetry Using a Single Carbon Screen-printed Electrode

A fast, simple and costless methodology without sample pre-treatment is proposed for the discrimination of beers. It is based on cyclic voltammetry (CV) using commercial carbon screen-printed electrodes (SPCE) and includes a correction of the signals measured with different SPCE units. Data are submitted to partial least squares discriminant analysis (PLS−DA) and support vector machine discriminant analysis (SVM−DA), which allow a reasonable classification of the beers. Also, CV data from beers can be used to predict their alcoholic degree by partial least squares (PLS) and artificial neural networks (ANN). In general, non-linear methods provide better results than linear ones.     

基于近红外光谱分析技术的食品包装塑料的定性分析

该文基于近红外漫反射光谱分析技术对食品包装材料聚乙烯、聚丙烯进行定性判别试验研究,选取不同波段范围、采用不同光谱预处理方法,使用主成分分析法(Principal component analysis,PCA)结合SIMCA、贝叶斯判别、K-近邻3种模式识别方法建立定性预测模型,并根据正确识别率比较了各模型预测性能。结果表明：使用SIMCA方法、贝叶斯判别、K-近邻3种方法建立的定性校正模型均在1 050~1 550 nm波长范围内效果较好;采用矢量归一化、标准正态变量变换、中心化、滑动均值滤波、多项式平滑滤波、一阶微分6种光谱预处理方法和上述3种模式识别方法对塑料样品近红外光谱进行了数据处理,其中在1 050~1 550 nm范围内,主成分因子数为3,采用原始光谱建立的K-近邻定性校正模型较优,对样品校正集和预测集的正确识别率均为100%。可为食品包装材料聚乙烯、聚丙烯的快速鉴别研究提供参考。     

Supervised pattern recognition to discriminate the geographical origin of rice bran oils: a first study

Supervised pattern recognition appears to be a useful tool to authenticate foodstuffs according to their geographical or varietal origin, when a set of samples whose classification is known a priori are available. In this work, linear discriminant analysis and artificial neural networks trained by the back-propagation algorithm have been used to discriminate rice bran oils manufactured in three different countries (Italy, Thailand and Switzerland) according to their geographical origin. The variables to be included in the mathematical models have been chosen by means of Fisher F-ratio value among the chemical indices routinely determined on vegetable oils (particularly fatty acids, triglycerides and sterol composition). The prediction ability of all the classifiers was 100% as evaluated by cross-validation.     

Shrunken centroids regularized discriminant analysis as a promising strategy for metabolomics data exploration

Metabolomics datasets generated by modern analytical instruments tend to be increasingly complex. In this study, a recent method named shrunken centroids regularized discriminant analysis (SCRDA) has been introduced and applied in the exploration of metabolomics dataset. It is a supervised method for variable selection, discriminant analysis and biomarker screening. By regularizing the estimate of the within‐class covariance matrix, SCRDA can deal with the singularity issue of linear discriminant analysis. Then a shrinkage estimator is applied to perform variable selection. The method presented is illustrated through the simulated datasets and three complex metabolomics datasets. Commonly used orthogonal partial least squares discriminant analysis and two other similar statistical methods, penalized linear discriminant analysis and nearest shrunken centroids, are used for comparisons. The results illustrate that SCRDA has some desirable abilities in variable selection, classification and prediction. Moreover, the biomarkers identified by SCRDA are further demonstrated to be in accordance with the biochemical research. It has been proved that SCRDA can be applied as a promising strategy in metabolomics. Copyright © 2014 John Wiley & Sons, Ltd.     

Metal content in southern Spain wines and their classification according to origin and ageing

Young and aged wines from two viticole zones in the Andalusian province of Córdoba (southern Spain) were analysed for their content in Ca, Mg, Fe, Cu, Mn and Zn by flame atomic absorption spectrophotometry, and Na, K, Al and Sr by flame atomic emission spectrophotometry. Significant differences in mean content were found for Na, Mn, Mg, Fe and Zn between wines from Montilla–Moriles and Villaviciosa. Linear discriminant analysis using those variables gave 97.9% recognition ability and 95.7% prediction ability. Cluster and principal component analysis show some differences in wines according to geographical origin and to the ageing of wines. Significant differences between young and aged wines were found in the mean content for Mg, K, Sr, Zn and Mn, obtaining 93.62% recognition ability and prediction ability by using linear discriminant analysis and leave-one-out cross-validation test, respectively. Finally, linear discriminant analysis could also be able to classify the samples according to their provenance and to their ageing simultaneously, obtaining 93.6% of the wines correctly classified.     

疏水常数在RTLC中的新应用

本文用 Rekker 提出的疏水碎片常数(f)对逆向薄层色谱 R_M 值进行了多项式相关分析,发现f 能够更确切地描述逆向薄层色谱中有机分子间的疏水亲脂作用,比用 Hansch 常数时要好得多。     

Differentiation of Mint (Mentha haplocalyx Briq.) from different regions in China using gas and liquid chromatography

In this study, complex substances such as Mint (Mentha haplocalyx Briq.) samples from different growing regions in China were analyzed for phenolic compounds by high‐performance liquid chromatography with diode array detection and for the volatile aroma compounds by gas chromatography with mass spectrometry. Chemometrics methods, e.g. principal component analysis, back‐propagation artificial neural networks, and partial least squares discriminant analysis, were applied to resolve complex chromatographic profiles of Mint samples. A total of 49 aroma components and 23 phenolic compounds were identified in 79 Mint samples. Principal component analysis score plots from gas chromatography with mass spectrometry and high‐performance liquid chromatography with diode array detection data sets showed a clear distinction among Mint from three different regions in China. Classification results showed that satisfactory performance of prediction ability for back‐propagation artificial neural networks and partial least squares discriminant analysis. The major compounds that contributed to the discrimination were chlorogenic acid, unknown 3, kaempherol 7‐O‐rutinoside, salvianolic acid L, hesperidin, diosmetin, unknown 6 and pebrellin in Mint according to regression coefficients of the partial least squares discriminant analysis model. This study indicated that the proposed strategy could provide a simple and rapid technique to distinguish clearly complex profiles from samples such as Mint.     

Noninvasive Surface Detection of Papillary Thyroid Carcinoma by Fourier Transform Infrared Spectroscopy

Previously Fourier transform infrared(FTIR) spectroscopy has been applied to detecting thyroid cancer during operations and to discriminating cervical metastatic ones from non-metastatic lymph nodes. This study explored the possibility of establishing a sensitive, accurate and noninvasive screen or diagnosis by preoperative FTIR spectroscopy. 111 patients undergone a thyroid operation and 50 healthy volunteers were enrolled in the study. The FTIR spectra were obtained by two mid-infrared optical fibers with an attenuated total reflectance(ATR) probe closely contacting the subjects' skin on the thyroid nodules. The FTIR spectra obtained from normal thyroid, nodular goiter(NG) and papillary thyroid carcinoma(PTC) patients were compared. A Fisher's discriminant analysis was created based on these data. There were 41 PTC patients and 70 NG patients according to their histopathological examinations. A total of 23(of 39) parameters were statistically different among the three groups(P<0.05). The F₁₃₀₀ and F₁₀₈₀ parameters were significantly different between the three groups. In total, 9 out of 39 FTIR parameters were selected as independent factors by the Wilks' lambda stepwise discriminant analysis. The discrimination accuracy of papillary thyroid carcinoma in the three groups was 88.8%. Surface detection of PTC by FTIR spectroscopy is feasible. FTIR spectroscopy can be used for rapid and noninvasive PTC screen and auxiliary diagnosis.     

Classification of wines from five Spanish origin denominations by aromatic compound analysis

Wine is a complex matrix in which aroma compounds play an important role in the characterization of the flavor pattern of a given wine. Twelve volatile compounds were determined in 244 samples of Spanish red wines from different denominations of origin: Rioja, Navarra, Valdepe?as, La Mancha, and Cari?ena. The samples were analyzed by GC using headspace solid-phase microextraction. The concentration (mg/mL) intervals obtained were 3-methyl-butyl acetate (3.9 to 116), 3-methyl-1-butanol (93 to 724), ethyl hexanoate (0.8 to 39), 1-hexanol (0.3 to 6.7), ethyl octanoate (1.4 to 41), diethyl succinate (0.2 to 13), 2-phenyl ethyl acetate (0 to 5.3), hexanoic acid (0 to 8.3), geraniol (0 to 3.0), 2-phenylethanol (1.5 to 56), octanoic acid (0 to 20), and decanoic acid (0 to 3.3). Wines were classified by multivariate statistical methods: principal component analysis, and lineal discriminant analysis. A correct differentiation among wines according to their origin was obtained by lineal discriminant analysis.     

Characterisation of the comonomer composition and distribution of copolymers using chemometric techniques

Chemometric techniques have been applied to FTIR and DSC data to correlate polymer composition. Since structural differences in the polymers with only hydrocarbon structure, often cause subtle changes in spectra, the ability of chemometric techniques is required to discern these differences. FTIR spectra and thermal fractionation using DSC were measured for 28 types of polyethylenes (PE) varying in chain branching type, content and distribution. Unsupervised clustering methods such as principal component analysis (PCA) and supervised discriminant analysis were used to classify the PEs according to their structural class. The DSC data was the more successful in both classifying PEs according to their class. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development of diagnostic models for canine osteoarthritis based on serum and joint fluid mid‐infrared spectral data using five different discrimination and classification methods

Osteoarthritis (OA) is an insidious joint disease that gradually leads to cartilage loss and the morphological impairment of other joint tissues. Therefore, early diagnosis and timely therapeutic intervention are of importance. Although there are a few diagnostic techniques used in clinics, these methods have various drawbacks. Infrared spectroscopy has emerged as an important analytical technique with wide applications in a variety of areas including clinical diagnosis. Research has shown that the presence of OA is associated with biochemical changes that are presumed to be reflected in serum or joint fluid. Hence, OA may be detected provided that serum or joint fluid is measured by infrared spectroscopy and appropriate data analysis methods are used to extract the diagnostic information from the infrared spectra. In this work, 5 discrimination and classification methods ([1] principal component analysis coupled with linear discriminant analysis, [2] principal component analysis coupled with multiple logistic regression, [3] partial least squares discriminant analysis, [4] regularized linear discriminant analysis, and [5] support vector machine) were used to build OA diagnostic models based on mid‐infrared spectra of serum and joint fluid. Useful diagnostic models were developed, indicating that infrared spectroscopy coupled with multivariate data analysis methods is very promising as a simple and accurate approach for OA diagnosis. The results also showed that models built from the 5 methods were different, as were the models' predictive performances. Therefore, choice of appropriate data analysis methods in model development should be taken into account.     

Discrimination of Rhizoma Corydalis from two sources by near-infrared spectroscopy supported by the wavelet transform and least-squares support vector machine methods

Near-infrared spectroscopy (NIRS) was applied for direct and rapid collection of characteristic spectra from Rhizoma Corydalis, a common traditional Chinese medicine (TCM), with the aim of developing a method for the classification of such substances according to their geographical origin. The powdered form of the TCM was collected from two such different sources, and their NIR spectra were pretreated by the wavelet transform (WT) method. A training set of such Rhizoma Corydalis spectral objects was modeled with the use of the least-squares support vector machines (LS-SVM), radial basis function artificial neural networks (RBF-ANN), partial least-squares discriminant analysis (PLS-DA) and K-nearest neighbors (KNN) methods. All the four chemometrics models performed reasonably on the basis of spectral recognition and prediction criteria, and the LS-SVM method performed best with over 95% success on both criteria. Generally, there are no statistically significant differences in all these four methods. Thus, the NIR spectroscopic method supported by all the four chemometrics models, especially the LS-SVM, are recommended for application to classify TCM, Rhizoma Corydalis, samples according to their geographical origin.     

An alignment-free measure based on physicochemical properties of amino acids for protein sequence comparison

Sequence comparison is an important topic in bioinformatics. With the exponential increase of biological sequences, the traditional protein sequence comparison methods — the alignment methods become limited, so the alignment-free methods are widely proposed in the past two decades. In this paper, we considered not only the six typical physicochemical properties of amino acids, but also their frequency and positional distribution. A 51-dimensional vector was obtained to describe the protein sequence. We got a pairwise distance matrix by computing the standardized Euclidean distance, and discriminant analysis and phylogenetic analysis can be made. The results on the Influenza A virus and ND5 datasets indicate that our method is accurate and efficient for classifying proteins and inferring the phylogeny of species.     

Chemometrics in near-infrared spectroscopy

Spectroscopy methods of chemical analysis are excellent for the application of chemometric methods, because the measurements at many different wavelengths provide inherently multivariate data. The chemist generally requires three categories of information from specimens under investigation: quantitative data, qualitative data, and fundamental information on the properties of the material. Spectroscopy has long been used for all three purposes; the recent application of chemometric algorithms has assisted greatly in these endeavors. Although there is some overlap, three chemometric methods correspond to the three types of information: multiple regression, discriminant analysis, and principal components analysis. The basis of these chemometric methods and some of their strengths and limitations in application to near-infrared spectroscopy are discussed.     

Quality control and original discrimination of Ganoderma lucidum based on high-performance liquid chromatographic fingerprints and combined chemometrics methods

In this paper, the feasibility and advantages of employing high-performance liquid chromatographic (HPLC) fingerprints combined with chemometrics methods for quality control of the cultured fruiting bodies of Ganoderma lucidum were investigated and demonstrated for the first time. In order to compare the HPLC fingerprints chromatograms between G. lucidum from different origins, the similarities of all the 60 samples and relative peak areas of 19 characteristic compounds were firstly calculated respectively. Then different pattern recognition procedures, including hierarchical cluster analysis (HCA), principal component analysis (PCA), partial least squares-discrimination analysis (PLS-DA) and soft independent modeling of class analogy (SIMCA) were applied to classify the G. lucidum samples according to their cultivated origins. Consistent results were obtained to show that G. lucidum samples could be successfully grouped in accordance with the province of origin. Furthermore, four marker constituents were screened out to be the most discriminant variables, which could be applied to accurate discrimination and quality control of G. lucidum by quantitative analysis. Finally, the chemical properties of those samples were also investigated to find out the differences of quality between them. Ranked in decreasing order, the quality of the G. lucidum can be arranged as Jinzhai/Huangshan, Shandong followed by Zhejiang samples. Our results revealed that the developed method has potential perspective for the original discrimination and quality control of G. lucidum.