Dissertations / Theses on the topic 'Shape morphology analyses'

L'analyse de la morphologie axonale est un problème important en neuroscience. Diverses études ont montré que les caractéristiques morphologiques de ces structures donnent des informations sur son fonctionnement et permettent la caractérisation d'états pathologiques. En conséquence, il est important de développer des méthodes pour étudier leurs formes et quantifier leurs différences structurelles.Dans cette thèse on propose une méthode pour la comparaison des arbres axonaux qui inclue des informations topologiques et géométriques. La méthode est fondée sur la théorie des formes élastiques. Avec cette approche, nous pouvons exhiber le chemin géodésique entre deux formes et la forme moyenne d'un ensemble d'échantillons. En outre, nous proposons un schéma de classification à partir de cette métrique que nous comparons à l'état de l'art. Finalement, nous proposons un modèle stochastique pour la simulation de la croissance axonale défini par une chaîne de Markov. Il considère 2 processus principaux qui modélisent l'élongation et forme de l'axone et la génération des branches. Le processus de croissance dépend de différentes variables, dont un champ externe d'attraction généré par certaines molécules dans l'environnement. Les deux techniques proposées ont été validées sur une base d'images de microscopie confocale de neurones chez la Drosophile. Des neurones normaux et modifiés génétiquement ont été considérés. Les résultats montrent que la méthode de comparaison proposée fournit de meilleurs résultats que les méthodes décrites dans la littérature. De plus, les paramètres du modèle donnent des informations sur le processus de croissance de chaque population d'axones
The morphological analysis of axonal trees is an important problem in neuroscience. It has been shown that the morphological characteristics of thesestructures provide information on their functioning and allows the characterization of pathological states. Therefore, it is of great importance to develop methods to analyze their shape and to quantify differences between structures. In this thesis we propose a method for the comparison of axonal trees that takes into account both topological and geometrical information. Using this method, which is based on the Elastic Shape Analysis Framework, we can compute the geodesic path between two axons and the mean shape of a population of trees. In addition, we derive a classfication scheme based on this metric and compare it with state of the art approaches. Finally, we propose a 2D discrete stochastic model for the simulation of axonal biogenesis. The model is defined by a third order Markov Chain and considers two main processes: the growth process that models the elongation and shape of the neurites and the bifurcation process that models the generation of branches. The growth process depends, among other variables, on an external attraction field. Both techniques were validated on a database of real fluorescent confocal microscopy images of neurons within Drosophila fly brains. Both normal neurons and neurons in which certain genes were inactivated have been considered. Results show that the proposed comparison method obtains better results that other methods found in the literature, and that the model parameter values provide information about the growth properties of the populations

Oral Biology
M.S.
Three-dimensional analysis of mandibular growth provides the potential for pedodontists, orthodontists and surgeons to prescribe treatment that works in harmony with the individual growth of the patient. Despite efforts by 3D pioneers, the visualization of growth and development remains reminiscent of the landmark-based cephalometric analyses used in two-dimensional studies. The objective of this study was to identify 3D topographical changes of the mandible during growth and development of adolescent orthodontic patients. Nine pairs of pre- and post-orthodontic cone-beam computed tomography (CBCT) scans were used to generate mandibular surfaces. Surfaces were superimposed on trabecular bone in the anterior mandible using a mutual information algorithm, and topographical changes were visualized and quantified. The intra- and inter-rater intraclass correlation coefficients for surface generation (0.94 and 0.93, respectively) and superimposition (0.96 and 0.82, respectively) demonstrate the reliability of the techniques. The findings of this study support the theories of bone remodeling reported in histological, implant-based, and landmark studies of mandibular growth.
Temple University--Theses

The analysis of microstructural shapes is an underutilized tool in the field of materials science. Typical observations of morphology are qualitative, rather than quantitative, which prevents the identification of relationships between shape and the mechanical properties of a material. Recent advances in the fields of computer vision and high-dimensional analysis have made computer-based shape characterization feasible on a variety of materials. In this work, the relationship between microstructural shapes, and the properties and function of the material as a whole, is explored using moment invariants as global shape descriptors. A diifferent relationship is examined in each of three material systems: how the three-dimensional shapes of cells in the cotyledons of the plant Arabidopsis Thaliana can be used to identify cell function; the two-dimensional shapes of additive manufacturing feedstock powder and the ability to distinguish between images of powders from different samples; and the two-dimensional shapes of ' precipitates and their influence on the creep resistance of single crystal nickel-base superalloys. In the case of Arabidopsis Thaliana cotyledon cells, three-dimensional Zernike and Cartesian moment invariants were used to quantify morphology, and combined with size and orientation information. These feature sets were then analyzed using unsupervised and supervised machine learning methods. Moderate success was found using unsupervised methods, indicating that natural delineations in the data correlate to cell roles to some degree. Using supervised methods, a success rate of 90% was possible, indicating that these features can be used to identify cell function. The ability of two-dimensional Cartesian moment invariants to distinguish meaningful features in particles of additive manufacturing feedstock was tested by using these features to classify images of feedstock. Ultimately, simple histogram matching methods were unsuccessful, likely because they rely on the most common particles to draw conclusions. A bag-of-words method was used, which uses high-dimensional visualization and clustering techniques to classify individual particles by common features. Histograms of particle clusters are then used to represent each image. This method was far more successful, and a correct classification rate of up to 90% was found, and comparable rates were discovered using invariants which describe the shapes only broadly. This indicates that moment invariants are an effective measure of the morphologies of these types of particles, and can be used to classify powder shapes, which control many properties which are relevant to the additive manufacturing process. In the case of the superalloys, it has been shown that the shape distribution of ' precipitates can be tracked using second order moment invariants. In addition, several loworder moment invariants are shown to correlate to creep resistance in four alloys examined, which supports the idea that the shape of precipitates plays role in determining creep resistance in these alloys.

Le but de notre étude était de valider un indicateur de la qualité de l’environnement, parmi trois approches : des mesures morphologiques de juvéniles de poissons ; la quantification de l’asymétrie fluctuante de leurs otolithes ; l’analyse de la forme de leurs otolithes. Les résultats in aquaria sur Dicentrarchus labrax ont montré une absence d’effet de mono contaminations par des polluants classiques comme le phosphore ou le zinc, à des concentrations correspondant à celles in situ en zones fortement anthropisées. Des concentrations plus élevées de zinc ont toutefois induit une modification de la forme des otolithes en plus d’un effet négatif sur la taille et le poids. Par nos prélèvement in situ sur trois ans d’Oblada melanura, nous avons mis en évidence de manière reproductible que, comparativement à des sites préservés et des arrivées de petits cours d’eau, des ports de plaisance de taille moyenne ont un effet négatif sur la longueur standard des juvéniles et induisent une modification de la forme de leurs otolithes. De l’ensemble de nos résultats nous pouvons déduire que tailles et poids sont facilement mesurables mais présentent des variabilités dans leurs réponses. La mesure de l’asymétrie des otolithes de juvéniles ne semble pas adaptée à une utilisation en bioindication. Au contraire, l’analyse de formes des sagittae de juvéniles paraît adaptée pour suivre des modifications de l’environnement pour des poissons de deux familles différentes, Moronidés et Sparidés. Cette analyse semble un outil prometteur en bioindication, applicable pour les gestionnaires de l’environnement
The aim of our study was to validate the most suitable environmental indicator among three approaches: morphological measurements of fish juveniles; quantification of the fluctuating asymmetry of their otoliths; analysis of their otolith shape. In aquaria, results for Dicentrarchus labrax have shown that mono-contamination by classical pollutants, such as phosphorus or zinc, has no effect for concentrations corresponding to those measured in highly anthropized environments. Nevertheless, higher zinc concentrations induce otolith shape alterations in addition to their negative impact on fish size and weight. On the basis of our three-year in situ Oblada melanura samplings, we have demonstrated that, in a replicable manner, compared to preserved areas and small waterway mouths, mid-size recreational harbours negatively impact juvenile standard length and also alter otolith shape. By comparison with in aquaria results, these alterations are consistent with a synergy of disturbance sources which taken independently do not have any impact. Taking into account all our results, we deduce that size and weight are easy to measure but show response variability. Measurement of fish juvenile otoliths' fluctuating asymmetry does not seem to be suitable for use in bioindication. Conversely, fish juvenile sagittae shape analysis is well-suited to surveys of environmental modifications, for fishes from two different families, Moronidae and Sparidae. This analysis seems to be a promising tool for bioindication, with a practical application for environmental managers

It is known that fission yeast Schizosaccharomyces pombe maintains its nuclear envelope during mitosis and it undergoes an interesting shape change during cell division - from a spherical via an ellipsoidal and a peanut-like to a dumb-bell shape. However, the biomechanical system behind this amazing transformation is still not understood. What we know is, that the shape must change due to forces acting on the membrane surrounding the nucleus and the microtubule based mitotic spindle is thought to play a key role. To estimate the locations and directions of the forces, the shape of the nucleus was recorded by confocal light microscopy. But such data is often inhomogeneously labeled with gaps in the boundary, making classical segmentation impractical. In order to accurately determine the shape we developed a global parametric shape description method, based on a Fourier coordinate expansion. The method implicitly assumes a closed and smooth surface. We will calculate the geometrical properties of the 2-dimensional shape and extend it to 3-dimensional properties, assuming rotational symmetry. Using a mechanical model for the lipid bilayer and the so called Helfrich-Canham free energy we want to calculate the minimum energy shape while respecting system-specific constraints to the surface and the enclosed volume. Comparing it with the observed shape leads to the forces. This provides the needed research tools to study forces based on images.

It is known that fission yeast Schizosaccharomyces pombe maintains its nuclear envelope during mitosis and it undergoes an interesting shape change during cell division - from a spherical via an ellipsoidal and a peanut-like to a dumb-bell shape. However, the biomechanical system behind this amazing transformation is still not understood. What we know is, that the shape must change due to forces acting on the membrane surrounding the nucleus and the microtubule based mitotic spindle is thought to play a key role. To estimate the locations and directions of the forces, the shape of the nucleus was recorded by confocal light microscopy. But such data is often inhomogeneously labeled with gaps in the boundary, making classical segmentation impractical. In order to accurately determine the shape we developed a global parametric shape description method, based on a Fourier coordinate expansion. The method implicitly assumes a closed and smooth surface. We will calculate the geometrical properties of the 2-dimensional shape and extend it to 3-dimensional properties, assuming rotational symmetry. Using a mechanical model for the lipid bilayer and the so called Helfrich-Canham free energy we want to calculate the minimum energy shape while respecting system-specific constraints to the surface and the enclosed volume. Comparing it with the observed shape leads to the forces. This provides the needed research tools to study forces based on images.

Osteoarthritis (OA) is the most common form of human joint disease causing significant pain and disability. Current treatment for hip OA is limited to pain management and joint replacement for end-stage disease. The development of methods for early diagnosis and new treatment options are urgently needed to minimise the impact of the disease. Studies of hip OA have shown that hip joint morphology correlates with susceptibility to hip OA and disease progression. Bone shape analyses play an important role in disease diagnosis, pre-operative planning, and treatment analysis as well as in epidemiological studies aimed at identifying risk factors for hip OA. Statistical Shape Models (SSMs) are being increasingly applied to imaging-based bone shape analyses as they provide a means of quantitatively describing the global shape of the bone. This is in contrast to conventional clinical and research practice where the analysis of bone shape is reduced to a series of measurements of lengths and angles. This thesis describes the development of a novel fully automatic software system that segments the proximal femur from anteroposterior (AP) pelvic radiographs by densely placing 65 points along its contour. These annotations can then be used for the detailed morphometric analysis of proximal femur shape. The performance of the system was evaluated on a large dataset of 839 radiographs of mixed quality. Achieving a mean point-to-curve error of less than 0.9mm for 99% of all 839 AP pelvic radiographs, this is the most accurate and robust automatic method for segmenting the proximal femur in two-dimensional radiographs yet published. The system was also applied to a number of morphometric analyses of the proximal femur, showing that SSM-based radiographic proximal femur shape significantly differs between males and females, and is highly symmetric between the left and right hip joint of an individual. In addition, the research described in this thesis demonstrates how the point annotations resulting from the system can be used for univariate and multivariate genetic association analyses, identifying three novel genetic variants that contribute to radiographic proximal femur shape while also showing an association with hip OA.The developed system will facilitate complex morphometric and genetic analyses of shape variation of the proximal femur across large datasets, paving the way for the development of new options to diagnose, treat and prevent hip OA.

With the technological development in biologically orientated industries more and more natural products in powdered form are being handled and processed. Three differently comminuted liquorice rhizome products were classified into 23 narrow size fractions to investigate the particle and bulk characteristics of the material, and to study the influence of particle shape on powder flowability. The morphology of the fibrous particulate was investigated by using a Quantimet 720 Image Analyser. The perimeter (P), projected area (A), breadth (B), length (L), horizontal and vertical projected lengths (P V and Pi) and the horizontal and vertical Feret diameters (FV FH) were measured from which four dimensionless shape factors were evaluated, [P2/47rA, PHxPV/A, L/B, FV/FH]. The surface texture of the particles was measured by fractal analysis. The influence of particle shape and size on the mean flow rate, coefficient of flow variation and flow uniformity were measured using a specially designed inclined tube flowmeter. The failure properties of powdered liquorice when sheared under known normal compressive stresses were measured and from a series of yield loci the unconfined yield strength, major consolidation stress and effective angle of internal friction were obtained. The effects of particle shape and size on the angle of internal friction, wall friction, bulk and packed densities were. investigated and the experimental correlations expressed in terms of mathematical equations. These relationships, together with the failure function plots, indicate that comminuted liquorice powder behaves as a "simple" powder.

The thesis investigates development, improvement and evaluation of methods for quantitative characterization of objects from their digital images and similarity measurements between digital images. Methods for quantitative characterization of objects from their digital images are increasingly used in applications in which error can have crtical consequences, but the traditional methods for shape quantification are of low precision and accuracy. In the thesis is shown that the coverage of a pixel by a shape can be used to highly improve the accuracy and precision of using digital images to estimate the maximal distance between objects furthest points measured in a given direction. It is highly desirable that a distance measure between digital images can be related to a certain shape property and morphological operations are used when defining a distance for this purpose. Still, the distances defined in this manner turns out to be insufficiently sensitive to relevant data representing shape properties in images. We show that the idea of adaptive mathematical morphology can be used successfully to overcome problems related to sensitivity of distances defined via morphological operations when comparing objects from their digital image representations.
У тези су размотрени развој, побољшање и евалуација метода за квантитативну карактеризацију објеката приказаних дигиталним сликама, као и мере растојања између дигиталних слика. Методе за квантитативну карактеризацију објеката представљених дигиталним сликама се  све више користе у применама у којима грешка може имати критичне последице, а традиционалне методе за  квантитативну карактеризацију су мале прецизности и тачности. У тези се показује да се коришћењем информације о покривеност пиксела обликом може значајно побољшати прецизност и тачност оцене растојања између две најудаљеније тачке облика мерено у датом правцу. Веома је пожељно да мера растојања између дигиталних слика може да се веже за одређену особину облика и морфолошке операције се користе приликом дефинисања растојања у ту сврху. Ипак, растојања дефинисана на овај начин показују се недовољно осетљива на релевантне податке дигиталних слика који представљају особине облика. У тези се показује да идеја адаптивне математичке морфологије може успешно да се користи да би се превазишао поменути  проблем осетљивости растојања дефинисаних користећи морфолошке операције.
U tezi su razmotreni razvoj, poboljšanje i evaluacija metoda za kvantitativnu karakterizaciju objekata prikazanih digitalnim slikama, kao i mere rastojanja između digitalnih slika. Metode za kvantitativnu karakterizaciju objekata predstavljenih digitalnim slikama se  sve više koriste u primenama u kojima greška može imati kritične posledice, a tradicionalne metode za  kvantitativnu karakterizaciju su male preciznosti i tačnosti. U tezi se pokazuje da se korišćenjem informacije o pokrivenost piksela oblikom može značajno poboljšati preciznost i tačnost ocene rastojanja između dve najudaljenije tačke oblika mereno u datom pravcu. Veoma je poželjno da mera rastojanja između digitalnih slika može da se veže za određenu osobinu oblika i morfološke operacije se koriste prilikom definisanja rastojanja u tu svrhu. Ipak, rastojanja definisana na ovaj način pokazuju se nedovoljno osetljiva na relevantne podatke digitalnih slika koji predstavljaju osobine oblika. U tezi se pokazuje da ideja adaptivne matematičke morfologije može uspešno da se koristi da bi se prevazišao pomenuti  problem osetljivosti rastojanja definisanih koristeći morfološke operacije.

This thesis is dedicated to the production of aluminum casting alloys. It maps the course of changes in the morphology of eutectic and its influence on mechanical properties during the long-term meltdown. In particular, the use of image analysis methods contributes to describing these processes. The presented results show that the eutectic shape does not change even during the meltdown for 110 minutes. There is only a roughing and an increase in grain size. There was also no influence on the mechanical properties that fit the practical application of the alloy examined

L’évaluation et la gestion des populations de poissons se basent sur l'utilisation d’unités de gestion appelées « stocks halieutiques ». Pour discriminer ces stocks, la forme des otolithes, pièces calcifiées de l’oreille interne des poissons, peut être utilisée. Dans ce contexte, cette thèse s'est consacrée premièrement à l’étude de la variabilité spatio-temporelle de la forme des otolithes chez 3 espèces de poissons présentant des caractéristiques écologiques (taille, vitesse de nage, comportement dans la colonne d’eau, etc.) et des environnements biogéographiques différents. Les résultats montrent qu’il existe un gradient structurel décroissant de taille des stocks allant des espèces de grands pélagiques aux espèces démersales. Ceci est lié au fait que certaines espèces démersales comme la bogue (Boops boops) sont contraintes par la présence de barrières géographiques et de fronts hydrologiques ce qui n’est pas le cas chez les espèces pélagiques analysées (merlan bleu, Micromesistius poutassou ; Espadon, Xiphias gladius). Dans un deuxième temps, nous avons testé les effets de facteurs confondants potentiels (e.g. l’asymétrie bilatérale directionnelle, AD) sur le pouvoir discriminant de la forme des otolithes. Ainsi, nous avons montré qu'il existe chez la bogue une AD, induite par un processus de latéralisation et qui varie en amplitude et en direction selon la zone géographique étudiée. Chez la bogue, cette AD impacte les résultats d’identification des stocks par la forme qui changent en fonction de l'otolithe, droit ou gauche, utilisé. Si la forme de l’otolithe est utilisée pour discriminer les stocks halieutiques, c’est parce qu’elle reflète en particulier les conditions environnementales qu’a subi le poisson au cours de sa vie. Ainsi, dans la troisième partie de la thèse, nous avons analysé, en conditions contrôlées, les effets de la température et du taux d'acides gras polyinsaturés omega-3 (n-3 AGPI) contenus dans l’alimentation sur la morphogenèse des otolithes de bars (Dicentrachus labrax). Après la naissance, deux étapes peuvent être distinguées dans l’ontogenèse de la forme de l’otolithe avec en premier lieu un allongement qui traduit une croissance moins rapide de l’axe dorso-ventral par rapport à l’axe antéro-postérieur. Il s'en suit des modifications plus localisées avec en particulier une complexification de la zone comprise entre le rostre et l’anti-rostre a priori essentiellement liée au facteur thermique. A l’inverse, le taux de n-3 AGPI ne semble pas influencer la morphogenèse de l’otolithe. L’utilisation des degrés-jours de croissance (GDD) a permis de montrer que l’effet de la température est bien d’accélérer la morphogenèse, mais aussi de changer sa trajectoire: à valeur de GDD fixe, pour 2 températures données, les formes diffèrent. L’ensemble des résultats acquis lors de cette thèse valident l’utilisation de la forme des otolithes pour discriminer les stocks de poissons, mais souligne également le besoin de connaître précisément les sources de la variabilité morphologique des otolithes intra-stock pour pouvoir déterminer plus précisément les limites des stocks halieutiques
The assessment and management of fish populations is based on the use of management units called fish stocks. The shape of otoliths, calcified structures of the fish's inner ear, can be used to discriminate these stocks. First, this thesis focuses on the study of the spatio-temporal variability of the otolith’s shape for three fish species with different ecological characteristics (size, swimming speed, behaviour in the water column, etc.) and biogeographical environments. The results showed that there is a decreasing structural gradient across stock sizes from large pelagic species to more localised demersal species. This is linked to the fact that some demersal species such as the bogue (Boops boops) are constrained by the presence of geographical barriers and hydrological fronts, which is not the case for the analysed pelagic species (blue whiting, Micromesistius poutassou; swordfish, Xiphias gladius). Secondly, we tested the effects of potential confounding factors (e. g. bilateral directional asymmetry, DA) on the discriminating power of an otolith’s shape. We have shown that there is a DA for bogue, induced by the lateralisation process, which varies in amplitude and direction according to the geographical area. In the bogue, this DA impacts stock identification by otolith shape, which changes according to which otolith is used (i.e. right or left). Otolith shape is useful to discriminate among fish stocks because it reflects the specific environmental conditions that fish have experienced during their lifetime. Finally, in the third part of the thesis, we analyzed, under controlled conditions, the effects of temperature and the diet content of omega-3 polyunsaturated fatty acids (n-3 PUFAs) on otolith morphogenesis for seabass (Dicentrachus labrax). After emergence, two phases can be distinguished in the ontogenesis of otolith shape with an initial elongation that reflects slower growth of the dorso-ventral axis compared to the antero-posterior axis. This leads to more localized modifications, in particular, in a more complex area between the rostrum and the anti-rostrum, which is clearly linked to the thermal regime. Conversely, the percentage of n-3 PUFAs does not appear to influence otolith morphogenesis. The use of growing degree days (GDD) has shown that the effect of temperature is to accelerate morphogenesis, but also to change its trajectory: at a fixed GDD value, for two given temperatures, the shapes differ. All the results obtained in this thesis validate the use of the otolith shape to discriminate fish stocks, but also emphasize the need to know the precise sources of morphological variability of intra-stock otoliths in order to determine more precisely the limits of fish stocks

L'etude des formations sableuses aux embouchures des oueds tensift, ksob et souss de l'atlas-atlantique (maroc) permet de mettre en evidence les processus de leur mise en place, ainsi que l'origine de leur materiel. Les oueds apportent jusqu'a l'ocean des elements terrigenes (quartz, feldspaths et mineraux lourds). Ces elements sont remanies et melanges aux depots marins. Le stock sedimentaire est redistribue par les actions marines, et principalement une forte derive littorale nord-sud. Ainsi, dans le systeme du tensift, le materiel dunaire evolue sous l'influence des alizes et des vents d'ouest, mais l'activite de ces derniers se revele plus efficace. Dans le systeme de ksob, le materiel dunaire evolue sous l'action principale des alizes. Dans le systeme du souss, la dynamique eolienne se fait sous l'action conjuguee des alizes et des vents d'ouest. Ces evolutions sedimentaires se traduisent par une amelioration du tri, une diminution progressive du grain moyen et des teneurs en carbonates et mineraux lourds, ainsi que par une eolisation croissante des grains quartz.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1990.
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The functional properties of nanoparticles highly depend on the surface morphology of the particles, so precise measurements of a particle's morphology enable reliable characterizing of the nanoparticle's properties. Obtaining the measurements requires image analysis of electron microscopic pictures of nanoparticles. Today's labor-intensive image analysis of electron micrographs of nanoparticles is a significant bottleneck for efficient material characterization. The objective of this dissertation is to develop automated morphology analysis methods. Morphology analysis is comprised of three tasks: separate individual particles from an agglomerate of overlapping nano-objects (image segmentation); infer the particle's missing contours (shape inference); and ultimately, classify the particles by shape based on their complete contours (shape classification). Two approaches are proposed in this dissertation: the divide-and-conquer approach and the convex shape analysis approach. The divide-and-conquer approach solves each task separately, taking less than one minute to complete the required analysis, even for the largest-sized micrograph. However, its separating capability of particle overlaps is limited, meaning that it is able to split only touching particles. The convex shape analysis approach solves shape inference and classification simultaneously for better accuracy, but it requires more computation time, ten minutes for the biggest-sized electron micrograph. However, with a little sacrifice of time efficiency, the second approach achieves far superior separation than the divide-and-conquer approach, and it handles the chain-linked structure of particle overlaps well. The capabilities of the two proposed methods cannot be substituted by generic image processing and bio-imaging methods. This is due to the unique features that the electron microscopic pictures of nanoparticles have, including special particle overlap structures, and large number of particles to be processed. The application of the proposed methods to real electron microscopic pictures showed that the two proposed methods were more capable of extracting the morphology information than the state-of-the-art methods. When nanoparticles do not have many overlaps, the divide-and-conquer approach performed adequately. When nanoparticles have many overlaps, forming chain-linked clusters, the convex shape analysis approach performed much better than the state-of-the-art alternatives in bio-imaging. The author believes that the capabilities of the proposed methods expedite the morphology characterization process of nanoparticles. The author further conjectures that the technical generality of the proposed methods could even be a competent alternative to the current methods analyzing general overlapping convex-shaped objects other than nanoparticles.

Naïvement perçu, le processus d’évolution est une succession d’événements de duplication et de mutations graduelles dans le génome qui mènent à des changements dans les fonctions et les interactions du protéome. La famille des hydrolases de guanosine triphosphate (GTPases) similaire à Ras constitue un bon modèle de travail afin de comprendre ce phénomène fondamental, car cette famille de protéines contient un nombre limité d’éléments qui diffèrent en fonctionnalité et en interactions. Globalement, nous désirons comprendre comment les mutations singulières au niveau des GTPases affectent la morphologie des cellules ainsi que leur degré d’impact sur les populations asynchrones. Mon travail de maîtrise vise à classifier de manière significative différents phénotypes de la levure Saccaromyces cerevisiae via l’analyse de plusieurs critères morphologiques de souches exprimant des GTPases mutées et natives. Notre approche à base de microscopie et d’analyses bioinformatique des images DIC (microscopie d’interférence différentielle de contraste) permet de distinguer les phénotypes propres aux cellules natives et aux mutants. L’emploi de cette méthode a permis une détection automatisée et une caractérisation des phénotypes mutants associés à la sur-expression de GTPases constitutivement actives. Les mutants de GTPases constitutivement actifs Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V ont été analysés avec succès. En effet, l’implémentation de différents algorithmes de partitionnement, permet d’analyser des données qui combinent les mesures morphologiques de population native et mutantes. Nos résultats démontrent que l’algorithme Fuzzy C-Means performe un partitionnement efficace des cellules natives ou mutantes, où les différents types de cellules sont classifiés en fonction de plusieurs facteurs de formes cellulaires obtenus à partir des images DIC. Cette analyse démontre que les mutations Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V induisent respectivement des phénotypes amorphe, allongé, rond et large qui sont représentés par des vecteurs de facteurs de forme distincts. Ces distinctions sont observées avec différentes proportions (morphologie mutante / morphologie native) dans les populations de mutants. Le développement de nouvelles méthodes automatisées d’analyse morphologique des cellules natives et mutantes s’avère extrêmement utile pour l’étude de la famille des GTPases ainsi que des résidus spécifiques qui dictent leurs fonctions et réseau d’interaction. Nous pouvons maintenant envisager de produire des mutants de GTPases qui inversent leur fonction en ciblant des résidus divergents. La substitution fonctionnelle est ensuite détectée au niveau morphologique grâce à notre nouvelle stratégie quantitative. Ce type d’analyse peut également être transposé à d’autres familles de protéines et contribuer de manière significative au domaine de la biologie évolutive.
Evolution is a gradual process that gives rise to changes in the form of mutations that are reflected at the protein level. We propose that evolution of new pathways occurs by switching binding partners, hence creating new functions. The different functions encountered in a given family of related proteins have emerged from a common ancestor that has been duplicated and mutated to become implicated in new interactions and to gain new functions. In this study, we will use native and constitutive active mutant variants of the Ras-like family of small GTPases as working model, to explore such gene duplications, followed by neo / sub-functionalization. The reason for choosing this family resides in the fact that it is a defined set of proteins with well known functions that are mediated through multiple protein-protein interactions. The aim of this master is to perform a classification of budding yeast phenotypes using different approaches in order to statistically determine at which level of the population these constitutively active mutations are capable to affect cell morphology. Working with a subset of the Ras-like small GTPases family, we recently developed an approach to catalogue and classify these proteins based on multiple physical and chemical criteria. Using microscopic and bioinformatics methods, we characterized phenotypes associated with over-expression of the native small GTPases of the budding yeast Saccharomyces cerevisiae, showing that an established classification is not very clear. We are interested to investigate how point mutations in small GTPases can affect the cell morphology and their level of impact on asynchronous population. We want to establish a method to determine and quantify mutant and wild type-like phenotypes on these populations using Differential interference contrast microscopy (DIC) images only. As for the first aim of this study, we hypothesize that clustering algorithms can partition mutant cells from wild type cells based on cell shape factor measurements. To prove this hypothesis, we proposed to implement different clustering algorithms to analyze datasets which combines measurements from wild type and respective mutant populations. We created constitutively active forms of these small GTPases and used Cdc42, Rho5, Ras1 and Rsr1 to validate our results. We observed that Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L and Rsr1 G12V mutations induced characteristic amorphous, clumped/elongated, rounded and discrete large phenotypes respectively. This classification allowed us to define a phenotypical classification related to functions. Phenotype classification of the small GTPases has been confirmed using shape factor formulas accompanied with bioinformatics approaches. These approaches which involved different clustering methods allowed an automated quantitative characterization of the phenotypes of up to 7293 mutant cells. Sequence alignment of Cdc42 and Rho5 showed 46.1% identity as well as 62.6% for Ras1 and Rsr1 allowing the identification of diverged residues potentially involved in specific functions and protein-protein interactions. Directed mutagenesis and substitution of these sites from one gene to another have been performed in some positions to test for specificity and involvement in morphology changes. In parallel, interactions observed for native and constitutively active mutants Cdc42 and Rho5 will be assayed with protein-fragment complementation assay (PCA). This will enable us to determine whether a high correlation exists between functions switches and binding partner’s switches. We propose to expand this approach to the whole Ras-like small GTPases family and monitor protein-protein interactions and functions at a network scale. This research will confirm whether enrichment or depletion of residues in specific sites induces a switch of function due to switching binding partners. Understanding the mechanism underlying such correlation is important to gain insight in the biological mechanisms underlying the Ras-like small GTPases and other proteins evolution. Such knowledge is of fundamental importance in biomedical and pharmaceutical fields, since Ras-like small GTPases represent important targets for therapeutic interventions and for the evolutionary biology field.

Changes occur to the mandible with dental loss and senescence. However, the influence that these changes have on sex and ancestry estimations remains unclear. The purpose of this study was to investigate the influence of dental loss and senescence on changes in mandibular morphology. The outcome has implications for both forensic anthropology and restorative dentistry. The study sample consisted of 717 mandibles consisting of both male and female South Africans of African (SAA) and European ancestry (SAE). To minimise the effects of variation in dentition amongst sex-ancestry groups, the sample included individuals with a spectrum of tooth loss patterns, namely efficient and inefficient occlusions as well as no occlusions. Dentition was considered efficient when the remaining teeth in occlusion were evenly distributed between the sides. Linear measurements as well as geometric morphometric shape analyses were performed. Shape analyses of the complete mandible were performed on models from digitised landmarks by using a MicroScribe G2. Detailed shape analyses of the ramus and chin area as well as measurements of the cortical thickness at specific sites were executed on images generated by cone beam computed tomography (CBCT). A comprehensive assessment of changes in shape, size and cortical thickness of the mandible with age and dental loss were made. Shape and size differences of the mandible were evaluated for discriminant abilities between sex and ancestry groups. Although most dimensions decreased with tooth loss, the greatest impact was noted in the loss of alveolar bone. The mandibular angle increased minimally in size when a few teeth were lost, but recovered to some extent with further tooth loss. The cortical thicknesses at the mental foramen lingually as well as in the midline in females, were relatively spared with tooth loss. Male individuals of SAA were often the most resilient to tooth loss. In general external linear dimensions were maintained with age despite tooth loss. Conversely, measurements of cortical bone thickness decreased slightly, but could have been influenced by dental loss. The shape of the chin and gonial area was more affected by aging in SAE. The sex and ancestry discriminant ability of the linear dimensions when considered collectively approximated 90%, in general improving further when tooth loss was taken into account. All linear measurements were smaller in females and in general tooth loss accentuated sex differences. SAA exhibited greater dimensions, apart from maximum ramus height, bigonial breadth and cortical thickness at the gonion. The mental tubercles were more prominent than the pogonion in SAE (square chin) and vice versa in individuals of SAA (pointed chin). The gonial area in individuals of African ancestry was broad and more convex and the gonial eversion more prominent with a more upright ramus. Discriminant qualities of the gonial shape for sex in individuals of African ancestry reached 90% within dentition groups. Ramus flexure and chin shape were not found to be useful in sex estimation. In conclusion, this research elucidated the effects of tooth loss and senescence on the morphology of the mandible for the forensic anthropological setting.
Thesis (PhD)--University of Pretoria, 2015.
tm2015
Anatomy
PhD
Unrestricted

Particulate matter emission is one of the major air pollution problems of coal fired power plants. Fine particulates constitute a smaller fraction by weight of the total suspended particle matter in a typical particulate emission, but they are considered potentially hazardous to health because of the high probability of deposition in deeper parts of the respiratory tract. Electrostatic precipitators (ESP) are the most widely used devices that are capable of controlling particulate emission effectively from power plants and other process industries. Although the dust collection efficiency of the industrial precipitator is reported as about 99.5%, an anticipation of future stricter environmental protection agency (EPA) regulations have led the local power station seeking new technologies to achieve the new requirements at minimum cost and thus control their fine particulate emissions to a much greater degree than ever before.

This study aims to identify the options for controlling fine particle emission through improvement of the ESP performance efficiency. An ESP system consists of flow field, electrostatic field and particle dynamics. The performance of an ESP is significantly affected by its complex flow distribution arising as a result of its complex internal geometry, hence the aerodynamic characteristics of the flow inside an ESP always need considerable attention to improve the efficiency of an ESP. Therefore, a laboratory scale ESP model, geometrically similar to an industrial ESP, was designed and fabricated at the Thermodynamics Laboratory of CQUniversity, Australia to examine the flow behaviour inside the ESP. Particle size and shape morphology analyses were conducted to reveal the properties of the fly ash particles which were used for developing numerical models of the ESP.

Numerical simulations were carried out using Computational Fluid Dynamics (CFD) code FLUENT and comparisons were made with the experimental results. The ESP was modelled in two steps. Firstly, a novel 3D fluid (air) flow was modelled considering the detailed geometrical configuration inside the ESP. A novel boundary condition was applied at the inlet boundary of this model to overcome all previous assumptions on uniform velocity at the inlet boundary. Numerically predicted velocity profiles inside the ESP model are compared with the measured data obtained from the laboratory experiment. The model with a novel boundary condition predicted the flow distribution more accurately. In the second step, as the complete ESP system consists of an electric field and a particle phase in addition to the fluid flow field, a two dimensional ESP model was developed. The electrostatic force was applied to the flow equations using User Defined Functions (UDF). A discrete phase model was incorporated with this two dimensional model to study the effect of particle size, electric field and flue gas flow on the collection efficiency of particles inside the ESP. The simulated results revealed that the collection efficiency cannot be improved by the increased electric force only unless the flow velocity is optimized.

The CFD model was successfully applied to a prototype ESP at the power plant and used to recommend options for improving the efficiency of the ESP. The aerodynamic behaviour of the flow was improved by geometrical modifications in the existing 3D numerical model. In particular, the simulation was performed to improve and optimize the flow in order to achieve uniform flow and to increase particle collection inside the ESP. The particles injected in the improved flow condition were collected with higher efficiency after increasing the electrostatic force inside the 2D model. The approach adopted in this study to optimize flow and electrostatic field properties is a novel approach for improving the performance of an electrostatic precipitator.

Thesis (Ph.D.)--University of Alberta, 2009.
Title from PDF file main screen (viewed on Apr. 1, 2010). A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy, Department of Electrical and Computer Engineering, University of Alberta. Includes bibliographical references.