Thesis (PhD (Biochemistry))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Metabolic Control Analysis (MCA) provides a powerful quantitative framework for understanding and explaining the control and regulation within a cellular system. MCA allows the global control of a steady-state system to be quantified in terms of control coeficients, which we can express in terms of the local properties referred to as elasticity coeficients. MCA relates elasticities to control coeficients through a matrix inversion, thus allowing scientists to predict and quantify how the kinetics of the individual enzymes affect the systemic behaviour of cellular systems. Traditionally we solved this problem numerically, while we used algebraic and symbolic control analysis techniques less frequently. By using symbolic algebraic computation we present a general implementation of the symbolic matrix inversion of MCA, known as SymCA, which requires only the description of any allosteric modifier interactions and the stoichiometry of a cellular system. The algebraic expressions generated allow an in-depth analysis of the distribution of the control within a system and also of the parameters which exhibit the greatest effect on this control distribution. This also applies when the exact values for the elasticities or control coeficients are unknown. We have demonstrated that by quantifying the control patterns, referred to as `routes of regulation', inherent in all control coeficient expressions, we can gain insight into how perturbations are propagated through a cellular system and which regulatory pathways are favoured under changing conditions. / AFRIKAANSE OPSOMMING: Metaboliese Kontrole-Analise (MKA) bied 'n kragtige kwantitatiewe raamwerk om die beheer en regulering binne sellulere sisteme te verstaan en te verduidelik. 'n Sleutelaspek van MKA is dat die globale beheer van 'n sisteem met 'n bestendige toestand gekwantifiseer kan word in terme van kontrole-koefisente en dat hierdie koefisente uitgedruk kan word in terme van die sisteem se lokale eienskappe, genaamd elastisiteitskoefisente. Deur van matriksinversie gebruik te maak kan MKA die verband tussen elastisiteitskoefisente en kontrole-koefisente aflei wat mens in staat stel om te sien hoe die kinetika van die individuele ensiemreaksies die sisteemgedrag op sellulere vlak beinvloed. Die probleem word tradisioneel hoofsaaklik op numeriese wyse bereken terwyl die gebruik van algebraiese en simboliese kontrole-analise minder gereeld gebruik word. In hierdie proefskrif verskaf ons, deur van simboliese algebraiese metodes gebruik te maak, 'n generiese implementasie van die simboliese matriksinversie van MKA, genaamd SymCA, wat slegs 'n beskrywing van 'n sellulere sisteem se allosetriese interaksies en die stoichiometrie benodig. Die algebraiese uitdrukkings sodanig gegenereer stel mens in staat om 'n in-diepte analise te doen om vas te stel waar die beheer binne 'n sisteem le, asook watter parameters die grootste effek op die kontrole-verspreiding het. Dit geld selfs in die geval waar die presiese waardes van die elastisiteitskoefisente of kontrole-koefisente onbekend is. Hierdie proefskrif demonstreer hoe die kwantifisering van kontrole-patrone, ook gesien as 'roetes van regulering', wat inherent is aan kontrole-koefisent vergelykings, mens in staat stel om te sien hoe perturbasies in 'n sellulere sisteem voortplant en watter regulatoriese paaie bevoordeel word onder veranderde kondisies.

Interstitial lung diseases are a heterogeneous group of disorders that vary widely in etiology, clinic-radiologic presentation, histopathologic features, and clinical course. MDCT is the modality of choice for determining the extent of diffuse interstitial lung disease and predicting the clinical outcomes as the scoring of fibrosis correlates well with the mortality rate. Different visual scoring systems for evaluating ILDs’ extent on HRCT have been developed over the past 20 years. Several visual scoring methods have been used to characterize and quantify the disease, correlate with common clinical parameters, prognosticate patients, assess disease progression and evaluate response to treatment. Up to date, visual scoring remains the method of choice for assessing disease extent in clinical practice. However, these methods show variable reproducibility in literature and therefore, a more accurate classification system is necessary for objective and reproducible assessment of disease extent. This has lead to considerable research efforts in advanced computer-based ILD extent quantification systems in the last 10 years. In this Thesis we compare four different available methods for the assessment of interstitial lung disease, for total, ground glass and reticular extent. A radiologist in training evaluated disease extent using a semi-quantitative visual scoring method (a), a visual pixel-based method (b) and semi-automated histogram thresholding technique (c). An automated CAD algorithm (d) was also utilized. All methods were applied to the same data sample of patients with collagen vascular diseases and lung involvement. The sample performance is reported on axial slice basis in terms of mean, standard deviation and range. Furthermore, methods have been compared pairwise by means of Bland-Altman analysis, utilized in order to assess by inspection the degree of agreement for varying disease extent. Additionally, the Intraclass Correlation Coefficient index has been calculated for all pairs compared. Statistical analysis showed almost perfect agreement between our visual pixel based method and the automated system concerning total and reticular disease extent, while the CAD algorithm and thresholding technique have demonstrated substantial agreement. None of the pairwise comparisons exhibited a high degree of agreement concerning ground glass extent estimation. Inter-observer comparison manifested significantly higher degree of agreement for the visual pixel based technique as compared to semi-quantitative visual scoring method. CAD algorithms provide a fast and reproducible disease extent and in our study present a high agreement with visual pixel based method, which is accounted for the more precise, albeit time wasting method. Resultantly, these automated systems could replace semi-quantitative visual scoring methods, not radiologists, in terms of accuracy, reproducibility and more precise clinical decision. / Οι διάμεσες πνευμονοπάθειες αποτελούν μια ετερογενή κατηγορία διαταραχών με ποικίλη αιτιολογία, κλινική, ιστολογική και ακτινολογική εικόνα. Η MDCT αποτελεί τη μέθοδο εκλογής για την εκτίμηση της έκτασης της νόσου και επομένως για την κλινική πορεία των ασθενών, εφόσον η έκταση της ίνωσης εμφανίζει υψηλή συσχέτιση με το δείκτη θνητότητας. Τα τελευταία 20 χρόνια έχουν αναπτυχθεί πολλά διαφορετικά συστήματα και μέθοδοι, που βασίζονται στην οπτική παρατήρηση και αποσκοπούν στον χαρακτηρισμό και την ποσοτικοποίηση της έκτασης της διάμεσης νόσου, καθώς και στο συσχετισμό της με κλινικές παραμέτρους, όπως η πρόγνωση και η ανταπόκριση στη θεραπεία. Οι ημιποσοτικές μέθοδοι, που βασίζονται στην οπτική παρατήρηση παραμένουν έως και σήμερα μέθοδοι εκλογής για την αξιολόγηση και ποσοτικοποίηση της έκτασης της νόσου. Εντούτοις, χαρακτηρίζονται σύμφωνα με τα βιβλιογραφικά δεδομένα από χαμηλούς δείκτες επαναληψιμότητας. Ως εκ τούτου, η αναζήτηση περισσότερο αντικειμενικών και επαναλήψιμων μεθόδων για την εκτίμηση της διάμεσης πνευμονοπάθειας είναι επιτακτική ανάγκη. Ως αποτέλεσμα, τα τελευταία 10 χρόνια η ερευνητική προσπάθεια έχει προσανατολιστεί σε αυτοματοποιημένες μεθόδους για την ποσοτικοποίηση της διάμεσης νόσου. Στην παρούσα διπλωματική συγκρίθηκαν τέσσερεις διαφορετικές μέθοδοι, διαθέσιμες για την ποσοτικοποίηση των αλλοιώσεων του πνευμονικού ιστού. Η έκταση της νόσου αξιολογήθηκε από έναν ειδικευόμενο ακτινολόγο με ημιποσοτική μέθοδο με οπτική παρατήρηση (α), με ποσοτική μέθοδο χειρονακτικού σχεδιασμού και τμηματοποίησης των προσβεβλημένων περιοχών (β) και με μια ημι-αυτόματη μέθοδο κατωφλίωσης ιστογράμματος (γ). Για τον ίδιο σκοπό χρησιμοποιήθηκε ένας αλγόριθμος υποβοήθησης διάγνωσης (CAD) (δ). Όλες οι μέθοδοι εφαρμόστηκαν στο ίδιο δείγμα δεδομένων από ασθενείς με νοσήματα του συνδετικού ιστού και πνευμονική προσβολή. Τα ημιποσοτικά αποτελέσματα, καθώς και αυτά της χειρωνακτικής τμηματοποίησης συγκρίθηκαν με τα αντίστοιχα δύο έμπειρων ακτινολόγων in consensus και μελετήθηκε η συμφωνία τους. Οι αποδόσεις των μεθόδων που χρησιμοποιήθηκαν στην εκτίμηση τόσο της συνολικής έκτασης της νόσου, όσο και των επιμέρους προτύπων συγκρίθηκαν ανά ζεύγη με ανάλυση κατά Bland-Altman και με υπολογισμό του δείκτη ICC (Intraclass Correlation Coefficient). Η στατιστική ανάλυση των αποτελεσμάτων έδειξε σημαντική συσχέτιση μεταξύ του CAD και του χειρωνακτικού σχεδιασμού για τη συνολική έκταση και το reticular πρότυπο, ενώ χαμηλότερη είναι η συμφωνία μεταξύ του CAD και της μεθόδου κατωφλίωσης ιστογράμματος. Δεν παρατηρήθηκε υψηλός δείκτης συμφωνίας σε κανένα ζεύγος συσχέτισης όσο αφορά την εκτίμηση του προτύπου θαμβής υάλου. Η συμφωνία των ακτινολόγων είναι υψηλότερη για την οπτική μέθοδο αξιολόγησης με χειρονακτική τμηματοποίηση σε σχέση με την ημιποσοτική μέθοδο με οπτική παρατήρηση. Οι αλγόριθμοι υποβοήθησης διάγνωσης παρέχουν γρήγορη και επαναλήψιμη εκτίμηση της έκτασης της διάμεσης νόσου και στη δικιά μας μελέτη παρουσιάζουν υψηλού βαθμού συσχέτιση με την ποσοτική μέθοδο, η οποία θεωρείται η πιο ακριβής, εντούτοις χρονοβόρα μέθοδος. Συμπερασματικά, τα αυτόματα αυτά συστήματα θα μπορούσαν να αντικαταστήσουν τις υποκειμενικές ημιποσοτικές μεθόδους στην ποσοτικοποίηση των διάμεσων αλλοιώσεων του πνεύμονα.

This Thesis addresses issues that lie at the intersection of two broad philosophical projects: inferentialism and contextualism. It discusses and defends an account of the logical concepts based on the following two ideas: 1) that the logical concepts are constituted by our canonical inferential usages of them; 2) that to grasp, or possess, a logical concept is to undertake an inferential commitment to the canonical consequences of the concept when deploying it in a linguistic practice. The account focuses on the concept of universal quantification, with respect to which it also defends the view that linguistic context contributes to an interpretation of instances of the concept by determining the scope of our commitments to the canonical consequences of the quantifier. The model that I offer for the concept of universal quantification relies on, and develops, three main ideas: 1) our understanding of the concept’s inferential role is one according to which the concept expresses full inferential generality; 2) what I refer to as the ‘domain model’ (the view that the universal quantifier always ranges over a domain of quantification, and that the specification of such a domain contributes to determine the proposition expressed by sentences in which the quantifier figures) is subject to a series of crucial difficulties, and should be abandoned; 3) we should regard the undertaking of an inferential commitment to the canonical consequences of the universal quantifier as a stable and objective presupposition of a universally quantified sentence expressing a determinate proposition in context. In the last chapter of the Thesis I sketch a proposal about how contextual quantifier restrictions should be understood, and articulate the main challenges that a commitment-theoretic story about the context-sensitivity of the universal quantifier faces.

Pour l'évaluation de la fonction rénale, l'Imagerie par Résonance Magnétique (IRM) dynamique à rehaussement de contraste est une alternative intéressante à la scintigraphie. Les résultats obtenus doivent cependant être évalués à grande échelle avant son utilisation en pratique clinique. L'exploitation des séquences acquises demande un recalage de la série d'images et la segmentation des structures internes du rein. Notre objectif est de fournir un outil fiable et simple à utiliser pour automatiser en partie ces deux opérations. Des méthodes statistiques de recalage utilisant l'information mutuelle sont testées sur des données réelles. La segmentation du cortex, de la médullaire et des cavités est réalisée en classant les voxels rénaux selon leurs courbes temps-intensité. Une stratégie de classification en deux étapes est proposée. Des classificateurs sont d'abord construits grâce à la coupe rénale principale en utilisant deux algorithmes de quantification vectorielle (K-moyennes et Growing Neural Gas). Ils sont validés sur données simulées, puis réelles, en évaluant des critères de similarité entre une segmentation manuelle de référence et des segmentations fonctionnelles ou une seconde segmentation manuelle. Les voxels des autres coupes sont ensuite triés avec le classificateur optimum pour la coupe principale. La théorie de la généralisation permet de borner l'erreur de classification faite lors de cette extension. La méthode proposée procure les avantages suivants par rapport à une segmentation manuelle : gain de temps important, intervention de l'opérateur limitée et aisée, bonne robustesse due à l'utilisation de toute la séquence et bonne reproductibilité.

La mesure de la perte du volume cérébral est un marqueur IRM de la neurodégénérescence dans la sclérose en plaques. Les techniques actuelles permettent de quantifier soit directement la perte de volume cérébral entre deux examens, soit de la mesurer indirectement à partir du volume cérébral de chaque examen. La fiabilité de ces techniques reste difficile à évaluer en l'absence de gold standard. Ce travail a consisté premièrement, en une étude de reproductibilité réalisée chez 9 patients à partir d'acquisitions semestrielles (3 IRM), sur deux machines différentes et post-traitées par sept algorithmes : BBSI, FreeSurfer, Intégration Jacobienne, KNBSI, un algorithme Segmentation / Classification, SIENA et SIENAX. Deuxièmement, un suivi longitudinal et prospectif a été effectué chez 90 patients SEP. L'étude des variabilités inter-techniques et inter-sites a montré que les techniques de mesures indirectes (Segmentation/Classification, FreeSurfer) et SIENAX fournissaient des pourcentages d'atrophie hétérogènes. A l'inverse, les techniques de mesures directes telles que BBSI, KNBSI, Intégration Jacobienne et à un moindre degré SIENA obtenaient des résultats reproductibles. Toutefois BBSI, KNBSI et l'Intégration Jacobienne obtenaient des pourcentages faibles, suggérant une possible sous-estimation de l'atrophie. L'évaluation de la perte du volume cérébral par Intégration Jacobienne a montré sur 2½ ans de suivi, une atrophie de 1,21% pour les 90 patients et de 1,55%, 1,51%, 0,84%, 1,21% respectivement pour les patients CIS, RR, SP et PP. A l'avenir l'évaluation de la perte de volume cérébral impose des défis d'ordre technique afin d'améliorer la fiabilité des algorithmes actuels.

Le but de cette thèse est d'étudier quelques aspects algébriques du problème de quantification par déformation. On considère d'une part la formalité dans le cas des algèbres libres et de l'algèbre de Lie so(3), et on s'intéresse d'autre part à la quantification par déformation pour des structures Hom-algébriques. Suivant le résultat de formalité de Kontsevich en 1997 pour les algèbres symétriques, on étudie dans la première partie de cette thèse les algèbres libres, qui sont un cas particulier d'algèbres enveloppantes, et on montre qu'il n'y a pas formalité en général, sauf dans les cas triviaux. On montre aussi qu'il n'y a pas formalité pour l'algèbre de Lie so(3). Les techniques utilisées sont de type homologiques. On calcule la cohomologie de ces algèbres et on procède à la construction du L-infini-quasi-isomorphisme entre l'algèbre de Lie différentielle graduée des cochaînes de Hochschild munie du crochet de Gerstenhaber et l'algèbre de la cohomologie munie du crochet de Schouten. Dans la seconde partie de ce travail, on utilise un principe de déformation par twist pour les structures Hom-algébriques, pour construire de nouvelles structures de même type, ou encore pour déformer une structure classique en une Hom-structure correspondante à l'aide d'un morphisme d'algèbres. En particulier, on applique ce procédé aux structures de Poisson et aux star-produits de Moyal-Weyl. Par ailleurs, on établit une correspondance entre les algèbres enveloppantes d'algèbres Hom-Lie possédant une structure Hom-coPoisson et les bigèbres Hom-Lie.

Breast cancer (BC) is one of the leading causes of cancer-related deaths in Canadian women. Aggressive BCs (e.g. triple-negative subtype; TN) present a clinical challenge as defined biomarkers, particularly those indicative of unique cancer-associated signaling pathways, are needed to improve prognostication and prediction of therapeutic response. Overexpression of Src and its substrates, Ezrin and Tks5, have been associated with poor prognosis in many cancers. We have previously shown that Ezrin regulates proteolytic-independent invasion, while others have shown that Tks5 is associated with proteolytic-dependent invasion. Thus, expression of Ezrin versus Tks5 in BC cases may represent different invasion modalities. Additionally, immunofluorescence (IF)-based technologies may provide a more quantitative and objective approach for analysis of biomarker expression and subcellular compartmentalization compared to immunohistochemistry (IHC). In this study, I hypothesize that expression and subcellular localization of Src, Ezrin and Tks5, have improved prognostic significance in BCs, compared to current clinico-pathological parameters. To assess this, I optimized an IF-based automated quantification analysis (AQUA) system to measure subcellular expression in a 63-patient BC cohort and tested associations with clinico-pathological data. This thesis presents that: 1) Expression of Src and Ezrin increased, but that of Tks5 decreased in breast tumours compared to normal breast. 2) Src and Ezrin localized to the apical regions of normal breast epithelia but shifted to the cytoplasm in breast tumours. Tks5 exhibited a granular basal expression in normal breast epithelia, and is weakly expressed in tumour cellular compartments. 3) In our 63-patient cohort, Src and Ezrin had significant correlations with multiple clinico-pathological parameters, including TN status and lymphovascular invasion. 4) Clinico-pathological associations with IF-based AQUA scoring are directly comparable to conventional manual IHC scoring. Our study supports the role of Src and Ezrin as potential prognostic biomarkers for BC. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2013-07-09 12:51:09.527

Excipients are used in pharmaceutical formulations as fillers and drug carriers. Their successful function is inextricably linked to their physicochemical properties and, in turn, these properties are directly related to their structure. This thesis is concerned with the structural and spectroscopic characterisation of a selection of excipients by powder and single crystal X-ray diffraction, Raman and IR spectroscopy and MASNMR and an investigation of their stability as a function of temperature, humidity and particle size. As well as being a well-known excipient used in the pharmaceutical industry, lactose is also a common food additive. The diverse usage of lactose has led to a wealth of contradictory information relating to both structure and properties of this material. The first part of experimental work in this thesis identifies the four real lactose polymorphs; the naturally occurring a-lactose monohydrate; the anhydrous stable form of a-lactose; the hygroscopic unstable form of a-lactose; and the anomeric equivalent, p-lactose using powder X-ray diffraction. The work shows that anhydrous lactose formed by solvent dehydration often termed aM is simply the anhydrous stable form of a-lactose formed via a different route. Simple methods for discerning between the polymorphs using standard laboratory equipment are suggested. IlC MASNMR data were collected on all four forms of lactose for the first time and illustrate key differences between the four structures. Single crystal data were successfully collected on the a-lactose monohydrate and refinement carried at low temperature to determine the hydrogen bonded arrangement for the first time. Rietveld refmement of the hygroscopic unstable form of a-lactose using in-situ temperature resolved X-ray diffraction has shown that the hygroscopic form can be produced as a single phase. Refinement of Plactose using the Rietveld method has shown that powder diffraction data were comparable with single crystal data, with respect to structure refinement but attempts at both crystallisation and refinement of the stable anhydrous a-lactose polymorph were unsuccessful due to the complexity of the structure. Powder X-ray diffraction analysis was shown to be an effective tool in the quantification of mixed phase lactose samples with respect to both mixed phase stable anhydrous a-lactose and a-lactose monohydrate; and mixed p-Iactose and a-lactose monohydrate samples. The accuracy of the technique was determined to be at least 5%. Quantification was carried out using relative intensities of a well resolved unique reflection for each phase within the system. Dehydration techniques applied to lactose were applied to other hydrated pharmaceutical sugars; trehalose dihydrate and raffmose pentabydrate. Solid state techniques; powder X-ray diffraction, Raman and IR spectroscopy; showed that discrimination of other sugar hydrates became more complex with increasing levels of hydration.

Cardiovascular magnetic resonance imaging (MRI) is a well established technique in clinical cardiology. Different MRI sequences are routinely used to assess cardiac anatomy, function, viability and other parameters that aid diagnosing cardiac disease. Conversely, cardiac magnetic resonance spectroscopy (MRS), the only available method for a non-invasive study of human cardiac metabolism, has not evolved into a clinical tool yet. The combination of both techniques holds great potential to gain insight into the causality of cardiomyopathy diseases or other medical conditions with high cardiovascular risk profile, like diabetes or obesity and improve the clinical management of cardiac diseases. Nowadays, high field clinical MR systems have the great potential of improving the low spatial and temporal resolution and reproducibility of MRS. The aim of this thesis was to develop and implement a cardiac 1H-MRS method at 3 T that can be applied in clinical routine for the assessment of creatine and lipid levels in the human myocardium. The methodological developments to advance cardiac MRS are presented first. A robust 1H-MRS method comprising an optimized single-voxel technique, phased-array coil combination routine, optimized water suppression, breath-hold averaging and post-processing methods were developed. First, reproducibility and feasibility of the method were validated in vivo by acquiring 1H-MRS of the liver in almost one hundred healthy subjects. Subsequently, myocardial lipids levels were obtained in healthy volunteers by single breath-hold 1H-MRS triggered to mid-diastole, showing good reproducibility in an acquisition time less than 12 s. The good spectral resolution achieved using this method was demonstrated by the ability to differentiate for the first time two pools of myocardial lipids in spectra from the septum of patients with suspected myocardial lipid excess. Finally, creatine levels for healthy volunteers were investigated using multiple breath-hold acquisitions. Thus, this study shows the practicality and feasibility to incorporate this rapid cardiac 1H-MRS method into clinical studies of the human myocardium.

This paper looks at economic factors and water rights quantification on 95 Native American reservations economies in the western United States (U.S.). The study looks at the issues in two parts: (1) the characteristics of reservations quantifying their water rights compared to those who do not and (2) the effects of water rights quantification on reservation economic characteristics. Data was compiled from the U.S. Census Bureau, USDA, water specialists, court decrees, news articles, and scholarly papers. Results found that tribes who operate casinos and have higher revenues from agricultural goods are more likely to have quantified their water rights. Tribes with quantified water rights also had increased income levels. This study can help tribes design policies to create sustainable water management policies and economies on tribal reservations.