Fluorescence techniques are being considered for the detection and identification of bacterial spores. This thesis sets out to empirically characterize the detailed autofluorescence spectroscopic properties of spores and their target molecules. The multiwavelength fluorescence studies from a unique endogenous biomarker, dipicolinic acid (DPA) and its calcium salt (CaDPA) in bacterial spores are found to be useful for fluorescence characterization of spores. A systematic determination of the fluorescence profile of the major chemical components of Bacillus spores and the effect of UV irradiation on them has been performed in dry samples, wet paste and in aqueous solution. The thesis applies reliable tools for accurately describing complex nature of spectral profile from bacterial spores, and for interpreting and identifying their spectral properties. We show that multiwavelength fluorescence technique combined with Principal Component Analysis (PCA) clearly indicates identifiable grouping among dry and wet Bacillus spore species. Differences are also observed between dried, wet and redried spores, indicating the stark effect of hydration on fluorescence fingerprints. The study revealed that changes in fluorescence of spores due to hydration/drying were reversible and supports a recent model of a dynamic and dormant spore structure. The spectra were analysed with PCA, revealing several spectroscopically characteristic features enabling spore species separation. The identified spectral features could be attributed to specific spore chemical components by comparing the spore sample signals with spectra obtained from the target molecules. PCA indicated underlying spectral patterns strongly related to species and the derived components were correlated with the chemical composition of the spore samples. More importantly, we examined and compared the fluorescence of normal spores with a mutant of the same strain whose spores lack DPA. We discovered that the dramatic fluorescence enhancement of Bacillus spores can be caused by UV irradiation in the spectral region of this unique biomarker without any pre treatment. Differences between spectra of spores, spore strains and other biological samples are very marked and are due to the dominance of the dipicolinate features in the spore spectra. This could lead to a cheap, more sensitive, faster and reagentless bacterial spore detector.

Thesis (M.S.)--Rochester Institute of Technology, 2008. / Typescript. Includes bibliographical references (leaves 70-73).

Thesis (M.S.E.C.E.)--Baylor University, 2007. / Includes bibliographical references (p. 56-58).

Thesis (Ph.D.)--Rochester Institute of Technology, 2008. / Typescript. Includes bibliographical references (p. 175-179) and index.

Includes bibliographical references (p. 162-177).

Thesis (Ph. D.)--University of Florida, 2001. / Title from first page of PDF file. Document formatted into pages; contains xi, 124 p.; also contains graphics. Vita. Includes bibliographical references (p. 120-123).

Η ανάλυση σε κύριες συνιστώσες είναι μια τεχνική μείωσης του δείγματος. Χρησιμοποιείται όταν έχουμε ψηλά συσχετισμένες μεταβλητές. Μειώνει τον αριθμό των αρχικών μεταβλητών σε ένα μικρότερο αριθμό κύριων συνιστωσών που μετρούν τη μεγαλύτερη δυνατή διασπορά του δείγματος. Είναι μια διαδικασία που εφαρμόζεται για μεγάλα δείγματα. Η παραγοντική ανάλυση είναι μια τεχνική μείωσης των μεταβλητών του δείγματος η οποία αναγνωρίζει τον αριθμό των λανθάνουσων δομών και δημιουργεί μια δομή, ένα νέο σύνολο μεταβλητών, τους κοινούς παράγοντες που ερμηνεύουν το δείγμα. Προϋποθέτει μια δομή από μη παρατηρήσιμες μεταβλητές που δεν μπορούν να μετρηθούν άμεσα. Εκτιμά τους παράγοντες εκείνους που έχουν επίδραση και αντανακλούν τις αρχικές μεταβλητές. Επιτρέπει στον ερευνητή να περιγράψει αλλά ακόμη και να αναγνωρίσει τους παράγοντες εκείνους που παριστάνουν το δείγμα. Συμπεριλαμβάνει τους ειδικούς παράγοντες (ειδικά σφάλματα) που οφείλονται για την αναξιοπιστία των μετρήσεων. / Principal component analysis is a technique for reducing the sample, used when we have high correlated variables. It reduces the number of input variables into a smaller number of key components that measure the maximum sample variance. It is a process applied to large samples. Factor analysis is a technique to reduce the variables in the sample that identifies the number of latent structures and creates a structure, a new set of variables, called common factors explaining the sample. Implies a structure of non-observable variables that can not be measured directly. It considers the factors that affect and reflect the original variables. It allows the researcher to describe and even to identify the factors that represent the sample. Includes special factors (specific errors) due to unreliability of measurement.

Thesis (MSc (Mathematical Statistics))--University of Stellenbosch, 2008. / In this study several procedures for finding robust principal components (RPCs) for low and high dimensional data sets are investigated in parallel with robust principal component analysis (RPCA) biplots. These RPCA biplots will be used for the simultaneous visualisation of the observations and variables in the subspace spanned by the RPCs. Chapter 1 contains: a brief overview of the difficulties that are encountered when graphically investigating patterns and relationships in multidimensional data and why PCA can be used to circumvent these difficulties; the objectives of this study; a summary of the work done in order to meet these objectives; certain results in matrix algebra that are needed throughout this study. In Chapter 2 the derivation of the classic sample principal components (SPCs) is first discussed in detail since they are the „building blocks‟ of classic principal component analysis (CPCA) biplots. Secondly, the traditional CPCA biplot of Gabriel (1971) is reviewed. Thirdly, modifications to this biplot using the new philosophy of Gower & Hand (1996) are given attention. Reasons why this modified biplot has several advantages over the traditional biplot – some of which are aesthetical in nature – are given. Lastly, changes that can be made to the Gower & Hand (1996) PCA biplot to optimally visualise the correlations between the variables is discussed. Because the SPCs determine the position of the observations as well as the orientation of the arrows (traditional biplot) or axes (Gower and Hand biplot) in the PCA biplot subspace, it is useful to give estimates of the standard errors of the SPCs together with the biplot display as an indication of the stability of the biplot. A computer-intensive statistical technique called the Bootstrap is firstly discussed that is used to calculate the standard errors of the SPCs without making underlying distributional assumptions. Secondly, the influence of outliers on Bootstrap results is investigated. Lastly, a robust form of the Bootstrap is briefly discussed for calculating standard error estimates that remain stable with or without the presence of outliers in the sample. All the preceding topics are the subject matter of Chapter 3. In Chapter 4, reasons why a PC analysis should be made robust in the presence of outliers are firstly discussed. Secondly, different types of outliers are discussed. Thirdly, a method for identifying influential observations and a method for identifying outlying observations are investigated. Lastly, different methods for constructing robust estimates of location and dispersion for the observations receive attention. These robust estimates are used in numerical procedures that calculate RPCs. In Chapter 5, an overview of some of the procedures that are used to calculate RPCs for lower and higher dimensional data sets is firstly discussed. Secondly, two numerical procedures that can be used to calculate RPCs for lower dimensional data sets are discussed and compared in detail. Details and examples of robust versions of the Gower & Hand (1996) PCA biplot that can be constructed using these RPCs are also provided. In Chapter 6, five numerical procedures for calculating RPCs for higher dimensional data sets are discussed in detail. Once RPCs have been obtained by using these methods, they are used to construct robust versions of the PCA biplot of Gower & Hand (1996). Details and examples of these robust PCA biplots are also provided. An extensive software library has been developed so that the biplot methodology discussed in this study can be used in practice. The functions in this library are given in an appendix at the end of this study. This software library is used on data sets from various fields so that the merit of the theory developed in this study can be visually appraised.

Made available in DSpace on 2015-03-26T13:32:06Z (GMT). No. of bitstreams: 1 texto completo.pdf: 358534 bytes, checksum: 24e75168f2f6257c7ffe917ef5ade7c8 (MD5) Previous issue date: 2009-02-16 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Nowadays research often collect information on many variables from a great number of experimental units, hence produce and store large amount of data, which in turn requires methods that can handle such situations. Statistical methods such as the principal component analysis (PCA), that can reduce the dimensionality of the analysis without significant information loss, are of great interest. PCA can use either the covariance (S) or the correlation (R) matrix among variables, but the analysis may result in different Principal Components (PC) resulting from R or S. In order to indicate the best strategies for different scenarios, we conducted a simulation study to investigate the effects of variable scaling over the viability and quality of the results from PCA analysis used to cluster experimental units. In addition to this first simulation study, we also conducted a second one using animal science and economical variables from 255 dairy producers from three locations of Minas Gerais State. The goal was to verify the most appropriate data structure for cluster analysis, such that it best classifies the most economically viable producers. In both studies we used a transformation of variables based on its coefficient of variation, which resulted in a new covariance matrix named S*. Results showed that the use of matrix S favored economical variables with larger variances, while use of R matrix resulted as the most important variables the ones with larger correlations among them. Calculations of PC using matrix S* minimized these scaling problems when S and R matrices are used. Analysis using S is entirely affected by the variable scale while using R is not affected by the scale at all. We concluded that the S* matrix was the most appropriate for the present case study because it considered the most important economical variables to be the ones most related to the animal science variables. / Com o aumento substancial na quantidade de dados armazenados, surge a necessidade da utilização de métodos que permitam analisar simultaneamente várias variáveis medidas em cada elemento amostral, e ainda com a possibilidade de reduzir a dimensionalidade desse conjunto sem perda significativa de informação. Entre eles, pode-se citar o método dos componentes principais, cuja obtenção pode envolver a matriz de covariâncias (S) ou a de correlações (R) das variáveis de interesse. Como a utilização dessas matrizes pode fornecer diferentes componentes, objetivou-se investigar, por meio da simulação de dados, os efeitos das escalas das características sobre a qualidade e a viabilidade da classificação dos elementos amostrais, buscando assim, indicar estratégias de análise mais adequadas em diferentes casos. Além do estudo de simulação, foi realizado outro com variáveis zootécnicas e econômicas referentes a 255 produtores de leite de três regiões do estado de Minas Gerais, com o objetivo de verificar qual a melhor estrutura de dados em classificar de forma mais apropriada os produtores mais viáveis economicamente. Em ambos os estudos, foi efetuada uma transformação nos valores das variáveis baseada nos respectivos coeficientes de variação, cuja matriz de covariâncias foi denominada de S*. Observou-se que a utilização da matriz S privilegiou as variáveis econômicas de maiores variâncias, enquanto a matriz R considerou as variáveis mais correlacionadas entre si como as mais importantes. A obtenção dos CPs com base na matriz S* minimizou os problemas das escalas inerentes aos usos das matrizes S e R. A primeira, por considerá-la totalmente e, a segunda, por desconsiderá-la. Desta forma, considerou-se a matriz S* como a mais indicada no presente estudo de caso, uma vez que priorizou como mais importantes, as variáveis econômicas mais relacionadas às variáveis zootécnicas.

Geochemistry plays a vital role in our understanding mechanisms behind major geological systems such as the Earth's crust and its oceans (Albarède, F. 2003). More recently, geo-chemistry has played a vital role in the field of forensic investigation and in period dating. Forensic soil samples have been traditionally analysed via examinations of colour, texture and mineral content by physical or chemical methods. However, these methods leave any organic or water-soluble fractions unexamined. Tephrochronology (the dating of sedimentary sequences using volcanic ash layers) is an important tool for the dating and correlation of sedimentary sequences containing archives and proxies of past environmental change. Its importance in this area has increased since the increased free carbon in out atmosphere has made radio-carbon dating unreliable. Tephrochronology requires successful geo-chemical identification of the tephras, a method reliant on electron probe micro-analysis (EPMA) to analyse major element composition. However, it is often impossible to differentiate key tephra layers using EPMA alone. Raman spectroscopy is commonly used in chemistry, since vibrational information is specific to the chemical bonds and symmetry of molecules, and can provide a fingerprint by which these can be identified. Here, we demonstrate how Raman spectroscopy can be used for the successful discrimination of mineral species in tephra through the analysis of individual glass shards. We further demonstrate how, with the use of oxidative preparation methods, Raman spectroscopy can be used to successfully discriminate between soil types using mineralogy as well as the organic and water-soluble fractions of soils.