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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 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 / A confocal microscope provides a sequence of images, at incremental depths, of the various corneal layers and structures. From these, medical practioners can extract clinical information on the state of health of the patient's cornea. In this work we are addressing problems associated with capturing and processing these images including blurring, non-uniform illumination and noise, as well as the displacement of images laterally and in the anterior posterior direction caused by subject movement. The latter may cause some of the captured images to be out of sequence in terms of depth. In this paper we introduce automated algorithms for classification, reordering, registration and segmentation to solve these problems. The successful implementation of these algorithms could open the door for another interesting development, which is the 3D modelling of these sequences.

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.

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.