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[pt] Devido à diminuição do número de descobertas de novas reservas de óleo e gás nas últimas décadas, as companhias de petróleo têm demonstrado um interesse cada vez maior em melhorar a eficiência dos processos de recuperação de óleo. Geralmente, após as fases de recuperação primário e secundário, uma grande quantidade de óleo permanece dentro do reservatório, pois a extração se torna não rentável. Assim, cresce o número de estudos voltados para a recuperação avançada de petróleo, com o objetivo de obter uma melhor fração de recuperação. O foco deste trabalho é estudar os fundamentos do deslocamento de óleo em meios porosos usando um microscópio confocal de varredura a laser, que possibilita visualizações 3D com boa resolução. A análise foi no deslocamento de óleo resultante da injeção de uma suspensão de capsulas de goma gelana em água após a injeção de água. Estas capsulas, movendo com a água, bloqueiam alguns dos caminhos preferenciais e forçam a água a deslocar uma parte do óleo preso. O resultado alcançado foi uma coleção de imagens 3D de meios porosos artificiais, nas quais foi possível distinguir a distribuição das fases (microcápsulas, fase aquosa e oleosa) dentro dos meios porosos, antes e após a injeção das microcápsulas. Essas imagens mostraram que as microcápsulas de goma gelana bloqueiam os caminhos preferenciais da água e que, após o bloqueio, alguns gânglios de óleo foram deslocados de suas posições originais. Esta tese aplica técnicas modernas de microscopia para examinar o conceito por trás da recuperação avançada de óleo usando microcápsulas. / [en] Thanks to decay of new discoveries of oil and gas reserves in the past decades, oil companies have a growing interest in the increase of oil recovery efficiency. Commonly, after primary and secondary recovery phases, a largeamount of oil remains inside the reservoir, as it becomes unprofitable to continue the extraction. Thus, the number of studies focused on enhanced oil recovery is growing, aiming to obtain a better recovery fraction. The focus of this work is to study the fundamentals of oil displacement in porous media using a confocal laser scanning microscope, which enables 3D visualization with a good resolution. The analysis was on oil displacement that results from the use of a suspension of gellan gum microcapsules in water injected after water injection. These microcapsules, moving along with the water, blocked some of the preferential paths and forced the water to displaces parcels of the trapped oil. The result achieved was a collection of 3D images from artificial porous media, in which it was possible to distinguish the distribution of phases (microcapsules, oil, and aqueous phases) inside the porous media, before and after the microcapsules injection. These images showed that indeed the gellan gum microcapsules blocked preferential water paths and that, after the blockage, some oil ganglia were displaced from their original positions. This thesis applies modern techniques of microscopy to investigate the concept behind enhanced oil recovery using microcapsules.

The purpose of this study was to observe penetration profiles of lysozyme on a variety of contact lens materials by confocal microscopy, to analyze influential factors that are involved in these penetration curves and to suggest possible mechanisms related to the in-eye clinical performance of these materials. An FITC-lysozyme conjugate was synthesized in-house by amine reaction. Contact lenses were incubated in a lysozyme solution with a final concentration of 1.9 mg/mL for various periods before undergoing microscopic analysis. Optimal parameters for confocal scanning were successfully obtained to acquire desired fluorescence signals on various contact lenses. Measurement units were converted into absolute amounts of lysozyme using lysozyme data from ^(125)I gamma counting studies. A rhodamine labeled dextran solution was applied to distingush the surface of the contact lenses under examination. The data from these studies were then used to calculate the theoretical numbers of layers of adsorbed lysozyme on the lens surface. The results show that there were distinct differences in lysozyme penetration in the twelve hydrogel materials examined. A pure pHEMA lens, with a water content of 38%, deposited lysozyme primarily on the lens surface after 24 hours, with full penetration occurring after 4-weeks of incubation. Three types of non-ionic contact lens materials with water contents > 50% exibited rapid penetration within the lens bulk after 24-hours incubation, with increased deposition within the matrix after 4 weeks. Two ionic, high water content polymers (Acuvue 2 and Focus Monthly) exhibited markedly different penetration profiles, particularly after 24 hours, with very rapid and total penetration in Acuvue 2, as compared with partial penetration in Focus Monthly. Modern silicone hydrogel contact lenses can be nominally divided into first generation, plasma-modified materials and second generation materials which incorporate an internal wetting agent such as polyvinyl pyrrolidone (PVP). These materials exhibited different lysozyme deposition profiles. Lysozyme fully penetrated PureVision after 24 hours, whereas no lysozyme penetration occurred on lenses manufactured from Focus Night & Day or O_2Optix, even after 4 weeks. Lenses manufactured from Acuvue Advance and Acuvue OASYS, two second generation silicone hydrogel lenses, also displayed their own characteristic deposition profile. Acuvue Advance always exhibited a partial penetration of lysozyme within the matrix, even after 4 weeks of doping. Interestingly, Acuvue OASYS showed a similar profile to Focus Night & Day and O_2Optix, with predominantly surface deposition occurring. To confirm possible surface adsorption of lysozyme on surface-coated Focus Night & Day and O_2Optix, a rigid polymethylmethacrylate (PMMA) contact lens was used as a model of surface adsorption. A mounting medium containing rhodamine labeled dextran was scanned to distinguish the lens surface, as it was assumed that no surface penetration of the very high molecular weight dextran would occur. Using this model, it was confirmed that surface adsorption of lysozyme occurred on these plasmacoated lens materials, which is similar to that seen with PMMA. In a further experiment, it was seen that lysozyme sorption on Acuvue OASYS exhibits a penetration profile which is different to that seen in Focus Night & Day and O_2Optix, with lysozyme just penetrating the lens surface. The results from the studies described above demonstrated that in 24 hours lysozyme sorption did not achieve a complete monolayer. However, after 4 weeks multi-layer adsorption occurred, with the more hydrophilic materials depositing the most lysozyme. The quantitative measurement of lysozyme penetration on and into contact lens materials by confocal microscopy combined with ^(125)I labelling offers a valuable tool to discover the potential mechanisms of interactions between protein and polymer materials. This study reveals some important information that may be beneficial to contact lens development and will prove to be valuable in other more broad areas of biomedical research in which polymers and biological fluids come into contact. / Thesis / Master of Applied Science (MASc)

The heart, as a vital organ, must pump continuously to deliver oxygenated blood to the tissues of the body. The physical stress of pumping is supported by the extracellular matrix (ECM), a dynamic protein scaffold inside and around the heart. While a regulated ECM is required to maintain heart function, aberrant or excessive ECM remodelling, called fibrosis, is associated with disease states and is a hallmark of cardiovascular disease. One major trigger of cardiovascular disease is obesity, and fibrotic remodelling is known to occur in this context. In order to study the impact of increased body size on heart function and the molecular and biophysical characteristics of the ECM, a larval overgrowth model for obesity in the genetic model Drosophila melanogaster has been developed and characterised. This model produces giant larvae twice as heavy as their wildtype counterparts, and allows a unique opportunity to study changes in the cardiac ECM in a simple genetic model. Results demonstrate a remarkable ability of the ECM to accommodate this increase in size. The muscles of the heart are particularly robust, and there are no obvious observable defects to the matrix. Preliminary results suggest Collagen fibres are thicker and more disperse. When observing heart functionality, the cross-sectional area of the heart lumen is increased significantly in giant larvae, both at diastole and systole. However, giant larvae display defects in contraction of the heart tube, characterised by an inability to contract fully at systole. This results in a less than proportional increase in stroke volume, and an increase in heart rate. Heart function of giant larvae is clearly affected by the increase in body size. To quantify the impact to the biophysical structure of the ECM, an atomic force microscopy protocol is being developed. / Thesis / Master of Science (MSc) / A known side effect of cardiovascular disease is fibrosis of the heart, a form of pathological extracellular matrix (ECM) remodelling. Fibrosis causes the stiffening of heart muscle, leading to impaired cardiac function. One of the main risk factors for the development of cardiovascular disease is obesity, and fibrosis is known to occur in this context. I have characterised changes in the morphology and physiology of the heart in a Drosophila model for obesity. The resulting cardiac hypertrophy reveals significant plasticity in the heart ECM, while heart contraction and output is compromised.

Yes / Diabetic Peripheral Neuropathy (DPN) is one of the most common types of diabetes that can affect the cornea. An accurate analysis of the nerve structures can assist the early diagnosis of this disease. This paper proposes a robust, fast and fully automatic nerve segmentation and morphometric parameter quantification system for corneal confocal microscope images. The segmentation part consists of three main steps. First, a preprocessing step is applied to enhance the visibility of the nerves and remove noise using anisotropic diffusion filtering, specifically a Coherence filter followed by Gaussian filtering. Second, morphological operations are applied to remove unwanted objects in the input image such as epithelial cells and small nerve segments. Finally, an edge detection step is applied to detect all the nerves in the input image. In this step, an efficient algorithm for connecting discontinuous nerves is proposed. In the morphometric parameters quantification part, a number of features are extracted, including thickness, tortuosity and length of nerve, which may be used for the early diagnosis of diabetic polyneuropathy and when planning Laser-Assisted in situ Keratomileusis (LASIK) or Photorefractive keratectomy (PRK). The performance of the proposed segmentation system is evaluated against manually traced ground-truth images based on a database consisting of 498 corneal sub-basal nerve images (238 are normal and 260 are abnormal). In addition, the robustness and efficiency of the proposed system in extracting morphometric features with clinical utility was evaluated in 919 images taken from healthy subjects and diabetic patients with and without neuropathy. We demonstrate rapid (13 seconds/image), robust and effective automated corneal nerve quantification. The proposed system will be deployed as a useful clinical tool to support the expertise of ophthalmologists and save the clinician time in a busy clinical setting.

Yes / There is an evolution in the demands of modern ophthalmology from descriptive findings to assessment of cellular level changes by using in vivo confocal microscopy. Confocal microscopy, by producing grey-scale images, enables a microstructural insight into the in vivo cornea in both health and disease, including epithelial changes, stromal degenerative or dystrophic diseases, endothelial pathologies, and corneal deposits and infections. Ophthalmologists use acquired confocal corneal images to identify health and disease states and then to diagnose which type of disease is affecting the cornea. This paper presents the main features of the healthy confocal corneal layers, and reviews the most common corneal diseases. It identifies the visual signature of each disease in the affected layer and extracts the main features of this disease in terms of intensity, certain regular shapes with both their size and diffusion, and some specific region of interest. These features will lead towards the development of a complete automatic corneal diagnostic system which predicts abnormalities in the confocal corneal data sets.

The organization of metabolism is an essential feature of cellular biochemistry. Metabolism does not occur as a linear assembly of freely diffusing enzymes, but as a complex web in which multiple interactions are possible. Because of the crowded environment of the cell, there must be structured and ordered mechanisms that control metabolic pathways. The following work will examine two metabolic pathways, one that is ubiquitous among living organisms and another that is entirely unique to plants, and examine the organization of each in an attempt to further define mechanisms that are fundamental features of metabolic control. One study offers some of the first characterizations of genes involved in [Fe-S] cluster assembly in Arabidopsis. The other explores the mechanisms that control localization of an enzyme that is part of the well-characterized flavonoid biosynthetic pathway. These two distinct pathways serve as unique models for genetic and biochemical studies that contribute to our overall understanding of plant metabolism. / Ph. D.

Yes / Background and Objective Corneal endothelial cell abnormalities may be associated with a number of corneal and systemic diseases. Damage to the endothelial cells can significantly affect corneal transparency by altering hydration of the corneal stroma, which can lead to irreversible endothelial cell pathology requiring corneal transplantation. To date, quantitative analysis of endothelial cell abnormalities has been manually performed by ophthalmologists using time consuming and highly subjective semi-automatic tools, which require an operator interaction. We developed and applied a fully-automated and real-time system, termed the Corneal Endothelium Analysis System (CEAS) for the segmentation and computation of endothelial cells in images of the human cornea obtained by in vivo corneal confocal microscopy. Methods First, a Fast Fourier Transform (FFT) Band-pass filter is applied to reduce noise and enhance the image quality to make the cells more visible. Secondly, endothelial cell boundaries are detected using watershed transformations and Voronoi tessellations to accurately quantify the morphological parameters of the human corneal endothelial cells. The performance of the automated segmentation system was tested against manually traced ground-truth images based on a database consisting of 40 corneal confocal endothelial cell images in terms of segmentation accuracy and obtained clinical features. In addition, the robustness and efficiency of the proposed CEAS system were compared with manually obtained cell densities using a separate database of 40 images from controls (n = 11), obese subjects (n = 16) and patients with diabetes (n = 13). Results The Pearson correlation coefficient between automated and manual endothelial cell densities is 0.9 (p < 0.0001) and a Bland–Altman plot shows that 95% of the data are between the 2SD agreement lines. Conclusions We demonstrate the effectiveness and robustness of the CEAS system, and the possibility of utilizing it in a real world clinical setting to enable rapid diagnosis and for patient follow-up, with an execution time of only 6 seconds per image.