<div>Fluorescence microscopy has emerged as a powerful tool for studying cell biology because it enables the acquisition of 3D image volumes deeper into tissue and the imaging of complex subcellular structures. Fluorescence microscopy images are frequently distorted by motion resulting from animal respiration and heartbeat which complicates the quantitative analysis of biological structures needed to characterize the structure and constituency of tissue volumes. This thesis describes a two pronged approach to quantitative analysis consisting of non-rigid registration and deep convolutional neural network segmentation. The proposed image registration method is capable of correcting motion artifacts in three dimensional fluorescence microscopy images collected over time. In particular, our method uses 3D B-Spline based nonrigid registration using a coarse-to-fine strategy to register stacks of images collected at different time intervals and 4D rigid registration to register 3D volumes over time. The results show that the proposed method has the ability of correcting global motion artifacts of sample tissues in four dimensional space, thereby revealing the motility of individual cells in the tissue.</div><div><br></div><div>We describe in thesis nuclei segmentation methods using deep convolutional neural networks, data augmentation to generate training images of different shapes and contrasts, a refinement process combining segmentation results of horizontal, frontal, and sagittal planes in a volume, and a watershed technique to enumerate the nuclei. Our results indicate that compared to 3D ground truth data, our method can successfully segment and count 3D nuclei. Furthermore, a microscopy image synthesis method based on spatially constrained cycle-consistent adversarial networks is used to efficiently generate training data. A 3D modified U-Net network is trained with a combination of Dice loss and binary cross entropy metrics to achieve accurate nuclei segmentation. A multi-task U-Net is utilized to resolve overlapping nuclei. This method was found to achieve high accuracy object-based and voxel-based evaluations.</div>

The role of Serrivomer beanii in bathypelagic food webs is poorly known, but abundance and biomass estimates from the 2004 G.O. Sars MAR-ECO Expedition suggest it to have a high level of importance. MAR-ECO, a Census of Marine Life field project, has allowed us to increase our knowledge of S. beanii through spatial analysis, including the congeneric species Serrivomer lanceolatoides, and trophic analysis. Serrivomer beanii abundance and biomass exhibited a decreasing trend along the northern Mid-Atlantic Ridge from north to south. In terms of size, S. beanii was found to increase as distance from the ridge decreased, suggesting a topographic aggregation strategy. The diet of S. beanii consisted of crustaceans, cephalopods, and teleosts. The trophic results of this study reveal a likely "alternative" trophic pathway in the deep mid-North Atlantic, and perhaps other, bathypelagic ecosystems: higher trophic-level predators are supported by micronektonic invertebrates as primary prey. / by Megan E. Geidner. / Thesis (M.S.)--Florida Atlantic University, 2008. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2008. Mode of access: World Wide Web.

Deep learning has in recent years come to dominate the previously separate fields of research in machine learning, computer vision, natural language understanding and speech recognition. Despite breakthroughs in training deep networks, there remains a lack of understanding of both the optimization and structure of deep networks. The approach advocated by many researchers in the field has been to train monolithic networks with excess complexity, and strong regularization --- an approach that leaves much to desire in efficiency. Instead we propose that carefully designing networks in consideration of our prior knowledge of the task and learned representation can improve the memory and compute efficiency of state-of-the art networks, and even improve generalization --- what we propose to denote as structural priors. We present two such novel structural priors for convolutional neural networks, and evaluate them in state-of-the-art image classification CNN architectures. The first of these methods proposes to exploit our knowledge of the low-rank nature of most filters learned for natural images by structuring a deep network to learn a collection of mostly small, low-rank, filters. The second addresses the filter/channel extents of convolutional filters, by learning filters with limited channel extents. The size of these channel-wise basis filters increases with the depth of the model, giving a novel sparse connection structure that resembles a tree root. Both methods are found to improve the generalization of these architectures while also decreasing the size and increasing the efficiency of their training and test-time computation. Finally, we present work towards conditional computation in deep neural networks, moving towards a method of automatically learning structural priors in deep networks. We propose a new discriminative learning model, conditional networks, that jointly exploit the accurate representation learning capabilities of deep neural networks with the efficient conditional computation of decision trees. Conditional networks yield smaller models, and offer test-time flexibility in the trade-off of computation vs. accuracy.

Submitted by Angela Maria de Oliveira (amolivei@uepg.br) on 2019-02-28T17:58:29Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Renan Rosa.pdf: 4067327 bytes, checksum: eb0bd9e84fbd89a24b4a397c9655fa62 (MD5) / Made available in DSpace on 2019-02-28T17:58:29Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Renan Rosa.pdf: 4067327 bytes, checksum: eb0bd9e84fbd89a24b4a397c9655fa62 (MD5) Previous issue date: 2018-11-19 / As pragas em lavouras causam prejuízos econômicos na agricultura, reduzindo a produção e consequentemente os lucros. O manejo de pragas é essencial, para reduzir estes prejuízos, e consiste na identificação e posterior controle desse tipo de ameaça. O controle é fundamentalmente dependente da identificação, pois é a partir dela que o manejo é feito. A identificação é feita visualmente, baseando-se nas características da praga. Essas características são inerentes e diferem de espécie para espécie. Devido à dificuldade da identificação, esse processo é realizado principalmente por profissionais especializados na área, o que acarreta na concentração do conhecimento. Esta dissertação apresenta uma metodologia para classificação de pragas por meio de técnicas de computação, onde um sistema computacional do tipo clienteservidor foi criado a fim de prover a classificação de pragas por meio de serviço, que é realizado pelo uso de rede neural convolucional baseada na arquitetura Inception V3. As pragas Anticarsia Gemmatalis, Helicoverpa armigera e Spodoptera Cosmioides, foram escolhidas para classificação por serem bastante comuns no estado do Paraná. A rede neural convolucional obteve índice de acerto de 92,5%. / Pests on crops cause economic damage to agriculture, reducing production and consequently profits. Pest management is essential to reduce these losses, and consists in the identification and subsequent control of this type of threat. Control is fundamentally dependent on identification, because management is done from it. The identification is made visually, based on the characteristics of the pest. These characteristics are inherent and differ from species to species. Due to the difficulty of identification, this process is carried out mainly by professionals specialized in the area, which entails the concentration of knowledge. This dissertation presents a methodology for pest classification by means of computational techniques, in which a client-server computational system was created in order to provide pest classification by means of a service, which is performed by the use of convolutional neural network based in the Inception V3 architecture. The pests Anticarsia Gemmatalis, Helicoverpa armigera and Spodoptera Cosmioides, were chosen for classification because they are quite common in the state of Paraná. The convolutional neural network obtained a success rate of 92.5%.

Cette thèse a pour but de caractériser le fonctionnement de supercondensateurs asymétriques composés de dioxyde de manganèse de structure birnessite et de carbone activé dans différents électrolytes. Les électrolytes aqueux neutres à base de sels inorganiques montrent les meilleures performances électrochimiques. La nature et la structure des cations et des anions du sel semblent impacter les performances électrochimiques et la stabilité de la structure du matériau d’oxyde de manganèse. Lors de cyclage en milieu aqueux avec de large de fenêtre de tension de fonctionnement appliquée, un mécanisme de dégradation du dispositif a été avancé tenant compte de la nature des anions ou des cations des sels utilisés. Quelques voies de modification du matériau MnO2, afin d’améliorer ces performances électrochimiques, ont été étudiés. Des électrolytes non aqueux originaux ont été également caractérisés et plus particulièrement, les solvants « Deep Eutectic » à base de N-méthylacétamide et de sels de Lithium. Ces derniers semblent prometteurs comme électrolytes pour des applications en température sur carbone activé ou matériaux d’insertion tels que le ferrophosphate de lithium. Cependant ils semblent non adaptés aux oxydes de manganèse, mais donnent de bons résultats en cyclage avec le carbone activé. / The aim of this thesis was to investigate the performances of asymmetric supercapacitors based on manganese dioxide (birnessite) and activated carbon electrode materials using various electrolytes. From this work, it appears that neutral aqueous electrolytes containing inorganic salts have the best electrochemical performances. Furthermore, the nature and the structure of both ions (cations and anions) in solution seem to impact strongly the electrochemical performances of the supercapacitors, as well as, the MnO2’s structure stability and affinity. In the case of aqueous-based electrolyte, a device degradation mechanism has been proposed as a function of salt ions structure and nature to further understand the supercapacitor’s life-cycling when a large potential window is applied. Some novel synthesis ways and/or modifications were investigated to further improve the electrochemical properties of MnO2 material. Additionaly, original non-aqueous electrolytes has been also formulated and then characterized, particularly the ‘Deep Eutectic’ Solvents, based on the N-methylacetamide mixed with a lithium salt. However, these electrolytes don’t have a good affinity with manganese oxide-based materials. Interestingly, these Deep Eutectic Solvents show good cycling results with activated carbon. In fact, these electrolytes seem to be promising for high temperature energy storage applications, especially using activated carbon or insertion electrode material like the lithium ferrophosphate.

Les travaux de recherche de cette thèse consistent à mettre en place des solutions performantes et légères permettant de répondre aux problèmes de sécurisation de produits sensibles. Motivé par une collaboration avec différents acteurs au sein du projet Nuc-Track,le développement d'un système de sécurité biométrique, possiblement multimodal, mènera à une étude sur différentes caractéristiques biométriques telles que le visage, les empreintes digitales et le réseau vasculaire. Cette thèse sera axée sur une adéquation algorithme et architecture, dans le but de minimiser la taille de stockage des modèles d'apprentissages tout en garantissant des performances optimales. Cela permettra leur stockage sur un support personnel, respectant ainsi les normes de vie privée. / Research of this thesis consists in setting up efficient and light solutions to answer the problems of securing sensitive products. Motivated by a collaboration with various stakeholders within the Nuc-Track project, the development of a biometric security system, possibly multimodal, will lead to a study on various biometric features such as the face, fingerprints and the vascular network. This thesis will focus on an algorithm and architecture matching, with the aim of minimizing the storage size of the learning models while guaranteeing optimal performances. This will allow it to be stored on a personal support, thus respecting privacy standards.

The Northern Carnarvon Basin is the richest petroleum province in Australia. About 50 gas/condensate and oil fields, associated mainly with Jurassic source rocks, have been discovered in the sub-basins and on the Rankin Platform since 1964. The basin is located at the southern end of the North West Shelf of Australia. It can be mainly subdivided into the Exmouth, Barrow, Dampier and Beagle Sub-basins, the Rankin Platform and Exmouth Plateau. The sub-basins are rift-related grabens and half-grabens developed during the Jurassic to the earliest Cretaceous and contain over 10 kilometres of Mesozoic and Cainozoic sedimentary rocks, among which are several thousand meters of Jurassic rocks. The formations of the Jurassic and the lower part of the Barrow Group of Early Cretaceous age in the sub-basins of the Northern Carnarvon Basin were found to be overpressured with excess pressures of 5-29 MPa at depths of 2900-3600 m indicated by repeat formation tests (RFTs) and drill stem tests (DSTs). The characteristics of organic matter, thermal history and thermal maturity, pressure seal and overpressure evolution in the sub-basins are crucial to a proper understanding of the nature and dynamic processes of hydrocarbon generation and migration in the basin. Based on organic geochemical data, the important source rocks in the basin are Jurassic organic-rich fine-grained rocks including the Murat Siltstone, the rift-related Athol Formation and Dingo Claystone. The Mungaroo Formation of the Middle-Upper Triassic contains gas-generating source rocks. These formations recognised to be organic rich based on 1256 values of the total organic carbon content (TOC, %) from 17 wells. Average TOC values (calculated from samples with TOC < 15 %) are about 2.19 % in the Mungaroo Formation, about 2.09 % in the Murat Siltstone and about 1.74 % in the Athol Formation and Dingo Claystone. / Data from kerogen element analysis, Rock-Eval pyrolysis, visual kerogen composition and some biomarkers have been used to evaluate the kerogen type in the basin. It appears that type III kerogen is the dominant organic-matter type in the Triassic and Jurassic source rocks, while the Dingo Claystone may contain some oil-prone organic matter. The vitrinite reflectance (Ro) data in some wells of the Northern Carnarvon Basin are anomalously low. As a major thermal maturity indicator, the anomalously low Ro data seriously hinder the assessment of thermal maturity in the basin. This study differs from other studies in that it has paid more attention to Rock-Eval Tmax data. Therefore, problems affecting Tmax data in evaluating thermal maturity were investigated. A case study of contaminated Rock-Eval data in Bambra-2 and thermal modelling using Tmax data in 16 wells from different tectonic subdivisions were carried out. The major problems for using Tmax data were found to be contamination by drilling-mud additives, natural bitumen and suppression due to hydrogen index (HI) > 150 in some wells. Although the data reveal uncertainties and there is about ±3-10 % error for thermal modelling by using the proposed relationship of Ro and Tmax, the "reliable" Tmax data are found to be important, and useful to assess thermal maturity and reduce the influence of unexpectedly low Ro data. / This study analyzed the characteristics of deep overpressured zones and top pressure seals, in detail, in 7 wells based on the observed fluid pressure data and petrophysical data. The deep overpressured system (depth greater than 2650-3000 m) in the Jurassic formations and the lower part of the Barrow Group is shown by the measured fluid pressure data including RFTs, DSTs and mud weights. The highly overpressured Jurassic fine-grained rocks also exhibit well-log responses of high sonic transit times and low formation resistivities. The deep overpressured zone, however, may not necessarily be caused by anomalously high porosities due to undercompaction. The porosities in the deep overpressured Jurassic rocks may be significantly less than the well-log derived porosities, which may indicate that the sonic-log and resistivity-log also directly respond to the overpressuring in the deep overpressured fine-grained rocks of the sub-basins. Based on the profiles of fluid pressure and well-log data in 5 wells of the Barrow Sub-basin, a top pressure seal was interpreted to be consistent with the transitional pressure zone in the Barrow Sub-basin. This top pressure seal was observed to consist of a rock layer of 60-80 % claystone and siltstone. The depths of the rock layer range from 2650 m to 3300 m with thicknesses of 300-500 m and temperatures of 110-135 °C. Based on the well-log data, measured porosity and sandstone diagenesis, the rock layer seems to be well compacted and cemented with a porosity range of about 2-5 % and calculated permeabilities of about 10-19 to 10-22 M2. / This study performed thermal history and maturity modelling in 14 wells using the BasinMod 1D software. It was found that the thermal maturity data in 4 wells are consistent with the maturity curves predicted by the rifting heat flow history associated with the tectonic regime of this basin. The maximum heat flows during the rift event of the Jurassic and earliest Cretaceous possibly ranged from 60-70 mW/m2 along the sub-basins and 70-80 mW/m2 on the southern and central Exmouth Plateau. This study also carried out two case studies of thermal maturity and thermal modelling within the deep overpressured system in the Barrow and Bambra wells of the Barrow Sub-basin. These case studies were aimed at understanding whether overpressure has a determinable influence on thermal maturation in this region. It was found that there is no evidence for overpressure-related retardation of thermal maturity in the deep overpressured system, based on the measured maturity, biomarker maturity parameters and 1D thermal modelling. Therefore, based on the data analysed, overpressure is an insignificant factor in thermal maturity and h hydrocarbon generation in this basin. / Three seismic lines in the Exmouth, Barrow and Dampier Sub-basins were selected and converted to depth cross-sections, and then 2D geological models were created for overpressure evolution modelling. A major object of these 2D geological models was to define the critical faults. A top pressure seal was also detected based on the 2D model of the Barrow Sub-basin. Two-dimensional overpressure modelling was performed using the BasinMod 2D software. The mathematical 2D model takes into consideration compaction, fluid thermal expansion, pressure produced by hydrocarbon generation and quartz cementation. The sealed overpressured conditions can be modelled with fault sealing, bottom pressure seal (permeabilities of 10-23 to 10-25 M2 ) and top pressure seal (permeabilities of 10-19 to 10-22 m2). The modelling supports the development of a top pressure seal with quartz cementation. The 2D modelling suggests the rapid sedimentation rates can cause compaction disequilibrium in the fine-grained rocks, which may be a mechanism for overpressure generation during the Jurassic to the Early Cretaceous. The data suggest that the present-day deep overpressure is not associated with the porosity anomaly due to compaction disequilibrium and that compaction may be much less important than recurrent pressure charges because most of the porosity in the Jurassic source rocks has been lost through compaction and deposition rates have been very slow since the beginning of the Cainozoic. / Three simple 1D models were developed and applied to estimate how rapidly the overpressure dissipates. The results suggest that the present day overpressure would be almost dissipated after 2 million years with a pressure seal with an average permeability of 10-22 M2 (10-7 md). On the basis of numerous accumulations of oil and gas to be expelled from the overpressured Jurassic source rocks in the basin and the pressure seal modelling, it seems that the top pressure seal with permeabilities of 10-19 to 10-22 M2 (10-4 to 10-7 md) is not enough to retain the deep overpressure for tens of millions of years without pressure recharging. Only if the permeabilities were 10-23 m2 (10-8 md) or less, would a long-lived overpressured system be preserved. This study suggests that hydrocarbon generation, especially gas generation and thermal expansion, within sealed conditions of low-permeability is a likely major cause for maintaining the deep overpressure over the past tens of millions of years. Keywords: Thermal history; Deep overpressure; Type III kerogen; Rock-Eval Tmax; Thermal maturity; Palaeoheatflow modelling; Pressure seal; 2D deep overpressure modelling; Pressure behaviour modelling; Overpressure generation; Northern Carnarvon Basin.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

The strength of the Atlantic meridional overturning circulation (AMOC) is believed to be associated with changes in surface buoyancy in the subpolar North Atlantic, which naturally leads to a notion that the AMOC has been weakening under global warming. Yet, a variety source of observations and its assimilation into ocean circulation models have not supported such an AMOC decline so far. In this study, an aspect that has not been paid attention, regarding the maintenance of the AMOC strength, is explored: storm activity in the subpolar North Atlantic (NA). An analysis using reanalysis data shows that the wintertime turbulent heat flux variability in the LS deep convection region is largely controlled by a small number of extreme heat flux event days, suggesting a pivotal role of winter storms in prompting LS deep-water formation. A set of forced ocean-ice model simulations, in which synoptic winter storm activity associated with these event days is either suppressed or doubled over the subpolar NA, confirms the above analysis as the altered storm activity results in a substantial change in LS convection and the AMOC strength. These experiments also show an upward AMOC trend during the late twentieth century, the degree of which is to some extent related to the intensity of storm activity in the LS. The upward AMOC trend found in the first part of the dissertation opposes to a downward AMOC trend in the twentieth century coupled model simulations employing the identical ocean component. An analysis suggests that contrast to the ocean-ice model, storm activity in the LS convection region and associated heat flux decreases during the late twentieth century. Although there is also a buoyancy increase over the LS, the wintertime heat flux decrease appears to be a more dominant factor for a decrease in convection in the LS, as an increasing freshwater input from Arctic/Subarctic Ocean bypasses the interior LS along the western boundary current. Therefore, the downward AMOC trend in the coupled model can be linked ultimately to the decreasing storm activity over the LS. This study therefore suggests that storm activity over the major convection regions needs to be paid further attention in assessing AMOC variations, including long-term trend in response to a warming scenario, in future studies.

L’objet de ce travail de thèse porte sur la synthèse originale en milieu fluide supercritique (FSC) de précurseurs « bulk » de catalyseurs d’hydrodésulfuration (HDS) à haute surface spécifique (SBET), destinés à l’HDS de composés soufrés réfractaires tels que le 4,6 diméthyldibenzothiophène (4,6¬ DMDBT). Ce projet a été réalisé en collaboration entre l'Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB-CNRS) et l'Instituto de Tecnología Química de Valencia (ITQ-CSIC) dans le cadre du réseau européen d’excellence Functional Advanced Materials and Engineering of Hybrids and Ceramics (FAMEnoe). Les études à l’ICMCB se sont portées sur l’optimisation des paramètres de synthèse en milieu FSC de NixCo1-xMoO4 (0 ≤ x ≤ 1) (précurseurs métalliques, solvant, température, pression). Des poudres de précurseurs « bulk » majoritairement composées de la phase hydratée (NiMoO4.0,75H2O) - phase la plus active en HDS - de composition contrôlée et pouvant atteindre près de 200 m2.g-1 ont été obtenues et caractérisées.Les propriétés catalytiques de ces précurseurs « bulk » après sulfuration ont ensuite été testées à l’ITQ sur la réaction de Deep-HDS d’un mélange modèle et d’une fraction pétrolière réelle. L’étude souligne plus particulièrement leurs meilleures capacités d’hydrogénation et de catalyse de l’HDS du 4,6 DMDBT que le catalyseur commercial utilisé comme référence dans ces travaux. / This work deals with an original synthesis using supercritical fluids (SCF) of “bulk” catalyst precursors of hydrodesulfurization (HDS) with high specific surface area (SBET) and dedicated to the HDS of refractive sulfur compounds such as 4,6 dimethyldibenzothiophene (4,6-DMDBT). This work was performed in collaboration between the Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB-CNRS) and the Instituto de Tecnología Química de Valencia (ITQ-CSIC) within the Functional Advanced Materials and Engineering of Hybrids and Ceramics network of excellence (FAMEnoe).Studies performed at the ICMCB consisted in optimizing the parameters of the synthesis in SCF of NixCo1-xMoO4 (0 ≤ x ≤ 1) (metallic precursors, solvent, temperature, pressure). Powders of “bulk” precursors mainly consisting of the hydrated phase (NiMoO4.0,75H2O) - the most active phase in HDS - with controlled composition and SBET up to 200 m2.g-1 were obtained and characterized.The catalytic properties of those “bulk” precursors after sulfidation were then tested at the ITQ for the reaction of Deep-HDS of a model feedstock and a real feedstock. The experiments highlighted their better hydrogenation capacity and efficiency in catalyzing the HDS of 4,6 DMDBT than the commercial catalyst used as a reference in this work.