Monitoring the concentrations of Cd, Cu, Pb, Ni, Cr, Zn, Mn and Fe in cultivated Haplic Luvisol soils using near-infrared reflectance spectroscopy and chemometrics.

This study illustrates the successful application of near-infrared reflectance spectroscopy extended with chemometric modeling to profile Cd, Cu, Pb, Ni, Cr, Zn, Mn, and Fe in cultivated and fertilized Haplic Luvisol soils. The partial least-squares regression (PLSR) models were built to predict the elements present in the soil samples at very low contents. A total of 234 soil samples were investigated, and their reflectance spectra were recorded in the spectral range of 1100-2500 nm. The optimal spectral preprocessing was selected among 56 different scenarios considering the root mean squared error of prediction (RMSEP). The partial robust M-regression method (PRM) was used to handle the outlying samples. The most promising models were obtained for estimating the amount of Cu (using PRM) and Pb (using the classic PLS), leading to RMSEP expressed as a percentage of the response range, equal to 9.63% and 11.5%, respectively. The respective coefficients of determination for validation samples were equal to 0.86 and 0.58, respectively. Assuming similar variability of model residuals for the model and test set samples, coefficients of determination for validation samples were 0.94 and 0.89, respectively. Moreover, the favorable PLS models were also built for Zn, Mn, and Fe with coefficients of determinations equal to 0.87, 0.87, and 0.79.

Detecting chemical markers to uncover counterfeit rebated excise duty diesel oil.

In this study, differences in the chemical compositions of rebated excise duty diesel oil samples that were caused by fuel laundering were investigated. Two possible laundering pathways were simulated using either reduction or adsorption agents in model samples that were spiked with Solvent Yellow 124 and Solvent Red 19. The samples were characterized by their chromatographic fingerprints, which were recorded using gas chromatography coupled with a nitrogen chemiluminescence detector. The collections of fingerprints were further analyzed by discriminant partial least squares and the models with the optimal complexities presented the correct discrimination rates in the range of 69.1%-99.6%, respectively. The most informative fingerprint sections that were associated with the investigated differences were identified using the variable importance in projection, selectivity ratio and uninformative variable elimination methods. The reduced multivariate discriminant models presented a relatively high performance with the correct classification rates in the range of 74.9%-99.8%, respectively. O-toluidine and 2,5-diaminotoluene were identified as potential markers of diesel oil counterfeiting by laundering through a reduction agent.

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data.

The aim of this work was to check whether a methodology based on the analysis of data that contain the entire phospholipid fatty acid, PLFA, compositions of water samples can be successfully used to interpret spatial and temporal changes in the microbial communities in water reservoirs. The proposed methodology consists of the construction of a modified weighted multivariate mixture model for the PLFA profiles of the water samples collected in a given monitoring campaign and the identification of latent PLFA components through a comparison with the known PLFA profiles of some cultivated or non-cultivated microbial communities. A 16S rDNA analysis of some of the selected water samples in the monitoring campaign was performed in order to verify the results of the PLFA analysis. The results showed that the proposed methodology can be useful for a dynamic and sensitive evaluation of changes in the microbial quality of water before and after flash flooding and can help in taking a decision regarding further risk assessment.

Practical approaches to principal component analysis for simultaneously dealing with missing and censored elements in chemical data.

Multivariate chemical data often contain elements that are missing completely at random and the so-called left-censored elements whose values are only known to be below a definite threshold value (reporting limit). In the last several years, attention has been paid to developing methods for dealing with data containing missing elements and those that can handle data with missing elements and outliers. However, processing data with both missing and left-censored elements is still an ongoing problem. The aim of this work was to investigate which method is most suitable for handling left-censored and missing completely at random elements that are present simultaneously in chemical data by using a comparison of the generalized nonlinear iterative partial least squares (NIPALS(1)) algorithm that has been recently proposed, methods that include uncertainty information like maximum likelihood principal component analysis, MLPCA(2), and replacement methods. The results of the Monte Carlo simulation study for artificial and real data sets showed that substitution with half of the reporting limit can be used when the percentage of left-censored elements per variable is up to 30-40%. The generalized NIPALS algorithm is generally recommended for a large percentage of left-censored elements per variable and particularly when a large number of variables are censored. The expectation-maximization approach applied to data with censored elements substituted with half of the reporting limits can be a strategy for dealing with missing and left-censored elements in data, but if the converge criterion is not fulfilled, then the generalized NIPALS algorithm can be applied.

High-dimensional nested analysis of variance to assess the effect of production season, quality grade and steam pasteurization on the phenolic composition of fermented rooibos herbal tea.

A nested analysis of variance combined with simultaneous component analysis, ASCA, was proposed to model high-dimensional chromatographic data. The data were obtained from an experiment designed to investigate the effect of production season, quality grade and post-production processing (steam pasteurization) on the phenolic content of the infusion of the popular herbal tea, rooibos, at 'cup-of-tea' strength. Specifically, a four-way analysis of variance where the experimental design involves nesting in two of the three crossed factors was considered. For the purpose of the study, batches of fermented rooibos plant material were sampled from each of four quality grades during three production seasons (2009, 2010 and 2011) and a sub-sample of each batch was steam-pasteurized. The phenolic content of each rooibos infusion was characterized by high performance liquid chromatography (HPLC)-diode array detection (DAD). In contrast to previous studies, the complete HPLC-DAD signals were used in the chemometric analysis in order to take into account the entire phenolic profile. All factors had a significant effect on the phenolic content of a 'cup-of-tea' strength rooibos infusion. In particular, infusions prepared from the grade A (highest quality) samples contained a higher content of almost all phenolic compounds than the lower quality plant material. The variations of the content of isoorientin and orientin in the different quality grade infusions over production seasons are larger than the variations in the content of aspalathin and quercetin-3-O-robinobioside. Ferulic acid can be used as an indicator of the quality of rooibos tea as its content generally decreases with increasing tea quality. Steam pasteurization decreased the content of the majority of phenolic compounds in a 'cup-of-tea' strength rooibos infusion.

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.

The goal of the present study is to assess the effects of anticancer treatment with cyclophosphamide and cytarabine during pregnancy on the mineralization of mandible bones in 7-, 14- and 28-day-old rats. Each bone sample was described by its X-ray fluorescence spectrum characterizing the mineral composition. The data collected are multivariate in nature and their structure is difficult to visualize and interpret directly. Therefore, methods like analysis of variance-principal component analysis (ANOVA-PCA) and ANOVA-simultaneous component analysis (ASCA), which are suitable for the analysis of highly correlated spectral data and are able to incorporate information about the underlined experimental design, are greatly valued. In this study, the ASCA methodology adapted for unbalanced data was used to investigate the impact of the anticancer drug treatment during pregnancy on the mineralization of the mandible bones of newborn rats and to examine any changes in the mineralization of the bones over time. The results showed that treatment with cyclophosphamide and cytarabine during pregnancy induces a decrease in the K and Zn levels in the mandible bones of newborns. This suppresses the development of mandible bones in rats in the early stages (up to 14 days) of formation. An interesting observation was that the levels of essential minerals like K, Mg, Na and Ca vary considerably in the different regions of the mandible bones.

Relating gas chromatographic profiles to sensory measurements describing the end products of the Maillard reaction.

Often in analytical practice, a set of samples is described by different types of measurements in the hope that a comprehensive characterisation of samples will provide a more complete picture and will help in determining the similarities among samples. The main focus is then on how to combine the information described by different measurement variables and how to analyse it simultaneously. In other words, the main goal is to find a common representation of samples that emphasises the individual and common properties of the different blocks of variables. Several methods can be adopted for the simultaneous analysis of multiblock data with a common object mode. These are: consensus principal component analysis (CPCA), SUM-PCA, multiple factor analysis (MFA) and structuration des tableaux à trois indices de la statistique (STATIS).In this article we present a comparison of the performances of these methods for data describing the chemistry and sensory profiles of the Maillard reaction products. The aroma compounds formed during the reaction of thermal heating between one or two selected amino acids and one or two reducing sugars have been analysed by head space gas chromatography and the intensity and nature of the odour of the resulting products has been evaluated according to selected descriptors by a panel of sensory experts.The results showed that using the information of the chromatographic and sensory data in conjunction enhanced the interpretability of the data. SUM-PCA and more specifically multiple factor analysis, MFA, allowed for a detailed study of the similarities of mixtures in terms of reaction products and sensory profiles.

Recognizing paracetamol formulations with the same synthesis pathway based on their trace-enriched chromatographic impurity profiles.

The development of a new drug substance is an expensive and time-consuming process. Therefore, the developers want to maximize the profit from the drug by patenting the concerned molecule as well as its synthesis pathway. In a later stage a faster or cheaper manufacturing process can be developed and patented. The aim of this study is to recognize paracetamol-containing drug formulations in relation to their synthesis pathways, in order to demonstrate the possibility to reveal fraudulently synthesized paracetamol. Since different synthesis pathways require different starting materials, solvents, reagents and catalysts and since they can produce different intermediates, it is expected that drug products originating from a different synthesis pathway will exhibit a different impurity profile. Therefore, in this study several paracetamol samples, synthesized in four different ways, are analyzed using trace-enrichment high-performance liquid chromatography (HPLC). The resulting chromatographic data were chemometrically treated in order to reveal clustering tendencies in the hope of distinguishing the different pathways. When performing principal component analysis (PCA) only 3 vaguely outlined clusters appeared. Projection pursuit (PP) was able to reveal 4 clusters and the samples with known synthesis pathway, except one, were classified in the different clusters. When hierarchical clustering and auto-associative multivariate regression trees (AAMRT) were applied, the samples of the four synthesis pathways could also be distinguished. AAMRT has an added value, since it can indicate the variables (peaks and thus also the impurities) that are responsible for the differences between the samples synthesized differently.

Classification of data with missing elements and outliers.

Missing elements and outliers can often occur in experimental data. The presence of outliers makes the evaluation of any least squares model parameters difficult, while the missing values influence the adequate identification of outliers. Therefore, approaches that can handle incomplete data containing outliers are highly valued. In this paper, we present the expectation-maximization robust soft independent modeling of class analogy approach (EM-S-SIMCA) based on the recently introduced spherical SIMCA method. Several important issues like the possibility of choosing the complexity of the model with the leverage correction procedure, the selection of training and test sets using methods of uniform design for incomplete data and prediction of new samples containing missing elements are discussed. The results of a comparison study showed that EM-S-SIMCA outperforms the classic expectation-maximization SIMCA method. The performance of the method was illustrated on simulated and real data sets and led to satisfactory results.

Isotopic ratios to detect infringements of patents or proprietary processes of pharmaceuticals: two case studies.

Because of the increasing problem of drug counterfeiting and the potential danger related as well as the economic losses involved, the pharmaceutical industry and the regulatory instances are interested in the development of anti-counterfeiting and patent protection methodologies. In this paper, the evaluation of measured isotopic ratios by means of explorative chemometric techniques was performed to distinguish groups in two data sets containing samples of acetyl salicylic acid and ibuprofen, respectively. The samples in the data sets originated from different countries and manufacturers. For both compounds a clear distinction of groups of samples could be obtained. These groups could be explained based on the origin of the samples, both geographically as well as based on the manufacturer. Hypotheses were formulated concerning the synthetic pathways of the molecules and they were linked to the groups obtained with the chemometric tools.

Start-to-end processing of two-dimensional gel electrophoretic images.

Gel electrophoresis serves as a basic analytical tool in the proteomic studies. However, processing of gel electrophoretic images is still the main bottleneck of data analysis, and there is an increasing need for the fully automated approaches. The proposed start-to-end strategy of analyzing the gel images consists of chemometric tools, which allow their effective preprocessing, automatic warping, and data modeling. The image preprocessing techniques: denoising in the wavelet domain and the penalized asymmetric least squares approach for the background estimation are proposed. Matching of images is based on fuzzy warping of features, extracted from the gel images. For the classification or calibration purpose, multivariate approaches such, as partial least squares (PLS) or kernel-PLS methods are used. Performance of the proposed strategy is demonstrated on the real set of the two-dimensional gel images.

Dealing with missing values and outliers in principal component analysis.

An efficient methodology for dealing with missing values and outlying observations simultaneously in principal component analysis (PCA) is proposed. The concept described in the paper consists of using a robust technique to obtain robust principal components combined with the expectation maximization approach to process data with missing elements. It is shown that the proposed strategy works well for highly contaminated data containing different amounts of missing elements. The authors come to this conclusion on the basis of the results obtained from a simulation study and from analysis of a real environmental data set.

Chemometric analysis of the water purification process data.

The aim of this work was to show usefulness of chemometric analysis in processing of the data describing production of drinking water in the Silesian region of Poland. Water samples have been collected within the period of 1 year and the quality of water was characterized by a number of physical, chemical and microbiological parameters. Principal component analysis (PCA) and STATIS (Structuration des Tableaux A Trois Indices de la Statistique) were employed to obtain the knowledge about the complete water treatment process. PCA makes it possible to uncover seasonal changes influencing the water treatment process. In particular, it was found out that the salt content, hardness and conductivity of water tend to obtain higher levels in winter rather than in summer, and the relatively lower acidity is also to be expected in winter. The sensory quality of water is considerably improved over the consecutive purification steps. Complementary information about the individual technological units of the process is gained with the STATIS approach. The obtained results show that the water produced by the two independent filtering branches of the water plant is of similar quality and the prescribed quality characteristics of drinking water are fulfilled.

Chemometric analysis of soil pollution data using the Tucker N-way method.

N-way methods, particularly the Tucker method, are often the methods of choice when analyzing data sets arranged in three- (or higher) way arrays, which is the case for most environmental data sets. In the future, applying N-way methods will become an increasingly popular way to uncover hidden information in complex data sets. The reason for this is that classical two-way approaches such as principal component analysis are not as good at revealing the complex relationships present in data sets. This study describes in detail the application of a chemometric N-way approach, namely the Tucker method, in order to evaluate the level of pollution in soil from a contaminated site. The analyzed soil data set was five-way in nature. The samples were collected at different depths (way 1) from two locations (way 2) and the levels of thirteen metals (way 3) were analyzed using a four-step-sequential extraction procedure (way 4), allowing detailed information to be obtained about the bioavailability and activity of the different binding forms of the metals. Furthermore, the measurements were performed under two conditions (way 5), inert and non-inert. The preferred Tucker model of definite complexity showed that there was no significant difference in measurements analyzed under inert or non-inert conditions. It also allowed two depth horizons, characterized by different accumulation pathways, to be distinguished, and it allowed the relationships between chemical elements and their biological activities and mobilities in the soil to be described in detail.

Chemometrical exploration of the wet precipitation chemistry from the Austrian Monitoring Network (1988-1999).

The present paper deals with the application of different chemometric methods to an environmental data set derived from the monitoring of wet precipitation in Austria (1988-1999). These methods are: principal component analysis (PCA); projection pursuit (PP); density-based spatial clustering of application with noise (DBSCAN); ordering points to identify the clustering structures (OPTICS); self-organizing maps (SOM), also called the Kohonen network; and the neural gas (NG) network. The aim of the study is to introduce some new approaches into environmetrics and to compare their usefulness with already existing techniques for the classification and interpretation of environmental data. The density-based approaches give information about the occurrence of natural clusters in the studied data set, which, however, do not occur in the case presented here; information about high-density zones (very similar samples) and extreme samples is also obtained. The partitioning techniques (clustering, but also neural gas and Kohonen networks) offer an opportunity to classify the objects of interest into several defined groups, the patterns of ionic concentration of which can be studied in detail. The visual aids, such as the color map and the Kohonen map, for each site are very helpful in understanding the relationships between samples and between samples and variables. All methods, and in particular projection pursuit, give information about samples with extreme characteristics.

Improving QSAR models for the biological activity of HIV Reverse Transcriptase inhibitors: Aspects of outlier detection and uninformative variable elimination.

The goal of this study is to derive a methodology for modeling the biological activity of non-nucleoside HIV Reverse Transcriptase (RT) inhibitors. The difficulties that were encountered during the modeling attempts are discussed, together with their origin and solutions. With the selected multivariate techniques: robust principal component analysis, partial least squares, robust partial least squares and uninformative variable elimination partial least squares, it is possible to explore and to model the contaminated data satisfactory. It is shown that these techniques are versatile and valuable tools in modeling and exploring biochemical data.

Environmetric modeling and interpretation of river water monitoring data.

This environmetric study deals with modeling and interpretation of river water monitoring data from the basin of the Saale river and its tributaries the Ilm and the Unstrut. For a period of one year of observation between September 1993 and August 1994 a data set from twelve campaigns at twenty-nine sampling sites from the Saale river and six campaigns from the river Ilm at seven sampling sites and from river Unstrut at ten sampling sites was collected. Twenty-seven chemical and physicochemical properties were measured to estimate the water quality. The application of cluster analysis, principal components analysis, and apportioning modeling on absolute principal components scores revealed important information about the ecological status of the region of interest:identification of two separate patterns of pollution (upper and lower stream of the rivers);identification of six latent factors responsible for the data structure with different content for the two identified pollution patterns; anddetermination of the contribution of each latent factor (source of emission) to the formation of the total concentration of the chemical burden of the river water. As a result more objective ecological policy and decision making is possible.