X-ray computed tomography (CT) holds a critical role in current medical practice for the evaluation of patients, particularly in the emergency department and intensive care units. Expensive high resolution stationary scanners are available in radiology departments of most hospitals. In many situations however, a small, inexpensive, portable CT unit would be of significant value. Several mobile or miniature CT scanners are available, but none of these systems have the range, flexibility or overall physical characteristics of a truly portable device. The main challenge is the design of a geometry that optimally trades image quality for system size. The goal of this work has been to develop analysis tools to help simulate and evaluate novel system geometries. To test the tools we have developed, three geometries have been considered in the thesis, namely, parallel projections, clam-shell and parallel plate geometries. The parallel projections geometry is commonly used in reconstruction of images by filtered back projection technique. A clam-shell structure consists of two semi-cylindrical braces that fold together over the patient's body and connect at the top. A parallel plate structure uses two fixed flat or curved plates on either side of the patient's body and image from fixed sources/detectors that are gated on and off so as to step the X-ray field through the body. The parallel plate geometry has been found to be the least reliable of the three geometries investigated, with the parallel projections geometry being the most reliable. For the targeted application, the clam-shell geometry seems to be the solution with more chances to succeed in the short term. We implemented the Van Cittert iterative technique for the reconstruction of images from projections. The thesis discusses a number of variations on the algorithm, such as the use of the Conjugate Gradient Method, several choices for the initial guess, and the incorporation of a priori information to handle the reconstruction of images with metal inserts.

Composante importante de l’écosystème marin benthique, les bivalves exploités sont surtout situés dans la zone littorale dont les caractéristiques spatiales et temporelles engendrent des fluctuations populationnelles naturelles et contribuent à de fortes variations de biomasse et de structure démographique s’ajoutant aux effets d’activités anthropiques. La compréhension des interactions entre l’espèce, son environnement et son exploitation est cruciale. Leur formalisation, y compris pour la gestion, passe par le développement de modèles mathématiques qui visent à décrire le fonctionnement du système, expliquer des phénomènes observés en termes de cause à effet ou prédire l’effets de nouvelles causes. Espèce introduite en France dans les années 1980, la palourde japonaise (Venerupis philippinarum) constitue une ressource économique importante pour des zones littorales. Pour le bassin d’Arcachon, les pêcheurs à pied professionnels capturent quelques 600 tonnes par an. Outre la réglementation européenne qui fixe une taille minimale de capture, des mesures de gestion complémentaires sont établies par les structures professionnelles locales de la pêche dans un cadre de cogestion impliquant ces structures, scientifiques et administration.Ce travail de thèse s’inscrit dans ce contexte en intégrant les traits d’histoire de vie de la population dans le modèle de simulation utilisé à des fins de gestion. A l’échelle locale, l’analyse de forme conventionnelle basée sur des mesures métriques et pondérales établit des relations d’allométrie entre des paires de descripteurs avec un changement significatif de morphologie à partir d’une longueur de 16-20 mm. La variabilité phénotypique intra-site s’articule en trois patrons morphologiques. Dans le bassin d’Arcachon, le caractère globuleux, décrit pour la première fois ici, est associé à de faibles densités et à de fortes proportions d’individus affectés par la maladie du muscle marron, maladie émergente sur le bassin. A l’échelle de la façade atlantique française, trois ratios morphométriques (indices d’élongation, de densité de la valve et de poids de la valve sur sa longueur) discriminent les populations des sites nord (Banc du Guer, golfe du Morbihan) de celles des sites sud (Bellevue, bassin d’Arcachon). Une corrélation significative entre ces ratios et les conditions trophiques approchées par la concentration en chlorophylle a ainsi qu’un lien entre l’indice de densité de la valve et le pourcentage de températures comprises entre 12 et 20°C sont démontrés. La complexité des facteurs intervenant sur la morphologie intra et inter-sites laisse supposer l’intervention d’autres facteurs comme la nature du substrat, ce qui est conforté par des premières analyses de contours. Les travaux ont confirmé l’importance de la température sur les variables d’état du stock notamment lors de la période de reproduction. Pour ces mêmes variables, un rôle majeur des ressources trophiques a aussi été démontré avec des réponses différant selon les stades. Une partie de ces résultats a contribué à des modifications dans le modèle de simulation. Elles ont surtout concerné l’intégration de l’effet des ressources trophiques sur le recrutement, la révision de la production de juvéniles et des taux de croissance par classe de taille, la précision de données de captures et l’ajout d’un effet prix sur les stratégies de pêche. En parallèle à la validation du modèle, l’analyse de sensibilité a mis en évidence la sensibilité du modèle aux paramètres environnementaux et aux variables relatives aux stades les plus jeunes. Dans un contexte de cogestion, l’outil a été utilisé pour réaliser des projections sur le devenir de la population selon différents scénarios de gestion. Les différences de tendances d’évolution de la biomasse en réponse à ces dispositifs d’action ont servi aux gestionnaires pour la définition des mesures de gestion actuellement en vigueur. Au final, le modèle renforce la démarche participative engagée. / Significant component of the marine benthic ecosystem, exploited bivalves are mainly located inside the coastal area, which temporal and spatial features generate natural population fluctuations and contribute to considerable biomass and demographic structure changes added to anthropogenic activities’ effects (fishing, pollution,…). Understanding of the relationships between the species, its environment and its exploitation is crucial and their formalization, including for management purposes, requires development of mathematical models that aim at describing the functioning of the system, to explain the observed phenomenon in terms of cause and effect or predict effects of new causes. Originating from venerid culture trials carried out in France in the 80s, Manila clam (Venerupis philippinarum) is an important economic resource for coastal areas. Inside the Arcachon Bay, professional fishermen catch about 600 tonnes annually. Whereas the minimum legal harvest size is set by European legislation, complementary management measures are established by regional and departmental professional organizations in the framework of a co-management approach involving professional, scientists and administration. This doctoral thesis is part of this objective of co-management by integrating life history traits of the population in a simulation model used for management purposes. At local scale, conventional shape analysis methods using metric weights and measures establish allometric relationships between pairs of descriptors with a significant morphological change detected from a length of ca. 16-20 mm. Intra-site phenotypic variability is structured in three morphological patterns. Occurrence of globular character inside the Arcachon Bay, described here for the first time, is associated to low densities and to high proportions of individuals affected by brown muscle disease, an emerging disease in the Bay. At the scale of the French Atlantic coast, three morphological ratios (elongation, valve density and weight related to length indices) discriminate populations from northern (Banc du Guer and Morbihan Gulf) and southern sites (Bellevue and Arcachon Bay). Significant relationships between those ratios and trophic conditions expressed by chlorophyll a concentrations, as well as a link between weight surface ratios and percentage of seawater temperature ranging from 12 to 20°C are demonstrated. Complexity of factors involved in intrasite and intersite morphology suggests intervention of other factors such as sediment characteristics, which is supported by a first outlines analysis. This work confirmed the importance of seawater temperature on stock state variables particularly during the reproduction period. For those same variables, a major role of trophic conditions has also been demonstrated with answers depending on development stages. Part of this result contributed to modifications within the simulation model dedicated to this population. The modifications mainly concerned integration of trophic resources effect on recruitment level, juveniles’ production and growth rates per length class revision, accuracy of catches by professional fishermen and addition of a price effect on the fishing strategies. In conjonction with the model validation, the sensitivity analysis undertaken highlighted the sensitivity of the model to environmental parameters and to variables related to the younger stages. In a co-management context, this tool was used to perform projections on the future of the population according to various management scenarios. The differences in the patterns of biomass evolution in response to those action schemes were used by the stakeholders to identify management measures currently in force. In the end the model reinforces the engaged participatory process.

Hard clams, Mercenaria mercenaria, are slow-moving organisms that are heavily preyed upon by both blue crabs and knobbed whelks in coastal Georgia. Hard clams are unable to escape from these predators, and when found, are commonly injured and/or consumed. Thus, their best survival strategy is to avoid their predators. In this study, we compared changes in clam behavior when exposed to blue crab and knobbed whelk predators. Clams reduced their feeding time when exposed to crabs and whelks, exudates from these predators, and to injured conspecifics. In a field experiment, we compared clam survival when caged predators where near clam beds vs. controls with empty cages. Clam survival was significantly higher when caged crabs or whelks were near, suggesting that clams detected these predators, reduced their feeding time, and were less apparent to ambient consumers. In lab behavioral assays, clams were less responsive to blue crabs in turbulent flows, and in the field, turbulence reduced the distance clams reacted to blue crabs. Previous studies have shown that blue crabs turbulence also diminishes blue crab foraging efficiency, and we conducted a field experiment to determine how turbulence affected clam-crab interactions. Our results suggest that predation intensity is greatest at intermediate turbulence levels, and lowest in flows with low and high turbulence levels. We attribute this pattern of predation intensity to differential effects of turbulence on the sensory abilities of crabs and clams. That is, in low turbulent flows, clams have a sensory advantage over crabs, and initiate avoidance behaviors before they are detected. However, as turbulence increases, clam perception diminishes faster than crabs, switching the sensory advantage to crabs, and making clams more vulnerable to consumers. In highly turbulent flows, crab perception declines at a rate faster than clams, and the sensory advantage returns to clams.

À partir des ovocytes de la palourde Spisula solidissima, un ADNc codant un récepteur nommé Spi-OAR a été cloné et séquencé. Une analyse de la séquence en acides aminés a indiqué que ce nouveau récepteur possède une forte similarité avec les récepteurs β-adrénergiques et les récepteurs à octopamine. En effet, il est étroitement lié à la classe des récepteurs à octopamine « β-adrénergique-like » couplés à une protéine Gs. L’ADNc de Spi-OAR a été introduit dans un vecteur d'expression (pCEP4) et un épitope reconnaissable par un anticorps commercial a été ajouté au segment N-terminal. Cette construction a été transfectée dans des cellules hôtes (HEK 293) et des études d’immunofluorescence ont montré une expression efficace du récepteur au niveau membranaire. Également, des mesures d'AMPc pour les cellules exprimant Spi-OAR ont révélé une augmentation de ce messager secondaire lors de l'ajout de l'octopamine, et dans une moindre mesure, la tyramine, tandis que la dopamine, la sérotonine et l'histamine n’ont engendré aucun effet. Une légère activité constitutive de ce récepteur dans les cellules hôtes a été observée. De plus, une analyse RT-PCR avec des oligonucléotides spécifiques a révélé l'ARNm de Spi-OAR non seulement dans les ovocytes, mais aussi dans les gonades, le cœur, les muscles adducteurs, les branchies et les ganglions suggérant que ce récepteur soit exprimé de façon ubiquitaire dans divers tissus et dans différents stades embryonnaires chez la palourde. En outre, des études avec des ovocytes isolés n'ont montré aucun effet de l’octopamine sur la réactivation méiotique. Des études éventuelles pourront finalement confirmer le rôle fonctionnel de Spi-OAR. / A cDNA encoding for an octopamine receptor named Spi-OAR was cloned and sequenced from the surf clam Spisula solidissima oocytes. An analysis of its predicted amino acid sequence showed a high degree of similarity with β-adrenergic and octopamine receptors. This receptor qualifies as a novel receptor closely related to the proposed class of insect octopamine « β-adrenergic–like » receptors coupled to Gs protein. This cDNA was introduced into an expression vector (pCEP4), with an added N-terminal FLAG tag sequence, and transfected in host cells (HEK 293). Immunofluorescence studies showed expression of the receptor with a proper localization to the plasma membrane. Measurements of cAMP in transfected cells revealed that addition of octopamine, and to a lower extent, tyramine induced a rise in cAMP while dopamine, serotonine and histamine had no effect. Overexpression of Spi-OAR in mammalian cells induced slight constitutive increase of cAMP. An RT-PCR analysis with specific oligonucleotides revealed the presence of the receptor mRNA not only in oocytes but also in whole gonads, heart, adductor muscle, gills and ganglia suggesting that this receptor is likely ubiquitously expressed. Expression of Spi-OAR was also detected at different embryonic stages. Despite the demonstrated expression of Spi-OAR in oocytes, octopamine had no effect on meiotic reinitiation. Further studies will examine the function of Spi-OAR.

Made available in DSpace on 2015-04-22T19:34:51Z (GMT). No. of bitstreams: 1 tese final capitulo 2 a 6.pdf: 676743 bytes, checksum: 94bb8fab0aa966e3c47acb177fd19ae7 (MD5) Previous issue date: 2012-12-14 / FAPEAM - Fundação de Amparo à Pesquisa do Estado do Amazonas / In Brazil, the species Carapa guianensis Aublet. and Carapa procera DC are known as andiroba. In the Amazon region, andiroba oil is considered medicinal and used primarily as an anti-inflammatory. The fruits of these species were collected and separated (seeds, peels seeds and pericarp) and separately extracted with different solvents in order of increasing polarity. From the seeds of the species C. guianensis were isolated the mixture of the limonoids 6α-acetoxygedunin and 7-deacetoxy-7-oxogedunin, and the mixture of the limonoids 7-deacetylgedunin and 6α-acetoxy-7-deacetylgedunin (first time isolated in the fruits of andiroba), and also those same limonoids were isolated separately. The hexane extract of the pericarp of the same species were isolated limonoids methyl angolensate and 6-hydroxy-methyl angolensate (first time described in the species). For comparison purposes, a method in HPLC/DAD was developed for quantification of the limonoids isolated in samples of extracts from different parts of the fruit of the two species. Two commercial samples of andiroba oil produced in the traditional way were also analyzed. The results of analyzes of the extracts obtained in the samples of both species showed the accumulation of almost all the limonoids in the seeds oil, and the limonoid 7-deacetylgedunin can be used as a chemical marker for the differentiation between species. The analysis of samples of commercial andiroba oil produced in the traditional way for method developed in HPLC / DAD showed differences in concentrations of limonoids analyzed. The extracts of the two species were assayed for larvicidal activity against Aedes aegypti, in which the precipitate from the oil of C. guianensis was the most interesting with an LC50= 36.9 ± 1.0 mg/mL. In the inhibition assay of the enzyme acetylcholinesterase showed inhibition of almost all limonoids and extracts tested, except the limonoid 7-deacetoxy-7-oxogedunin. These results are first time described in the literature for andiroba and are quite promising. / No Brasil, as espécies Carapa guianensis Aublet. e Carapa procera D.C. são conhecidas como andiroba. Na região Amazônica, o óleo de andiroba é considerado medicinal e utilizado principalmente como anti-inflamatório. Os frutos dessas espécies foram coletados e separados (amêndoas, cascas das amêndoas e pericarpos) e extraídos separadamente com solventes em ordem crescente de polaridade. Das amêndoas da espécie C. guianensis foram isolados a mistura dos limonoides 6α-acetoxigedunia e 7-desacetoxi-7-oxogedunia, e a mistura dos limonoides 7-desacetilgedunina e 6α-acetoxi-7-desacetilgedunina (isolado pela primeira vez nos frutos de andiroba), além desses mesmos limonoides em separado. Do extrato hexânico do pericarpo da mesma espécie foram isolados os limonoides angolensato de metila e 6-hidroxi-angolensato de metila (inédito na espécie). Para fins de comparação, um método foi desenvolvido em CLAE/DAD para quantificar os limonoides isolados nas amostras de extratos obtidos das diferentes partes dos frutos das duas espécies. Duas amostras comerciais de óleo de andiroba produzidos de forma tradicional também foram analisadas. O resultado das análises nas amostras dos extratos obtidos das duas espécies indica o acúmulo de quase todos os limonoides isolados no óleo das amêndoas e que o limonoide 7-desacetilgedunina pode ser utilizado como marcador químico para a diferenciação entre as espécies. A análise das amostras dos óleos de andiroba tradicionais comercializados pelo método desenvolvido em CLAE/DAD mostrou diferenças em termos de concentrações dos limonoides analisados. Os extratos das duas espécies foram testados para a atividade larvicida contra Aedes aegypti, nos quais o precipitado obtido do óleo da C. guianensis foi o mais interessante apresentando uma CL50 de 36,9 ± 1,0 μg/mL. No ensaio de inibição da enzima acetilcolinesterase foi observada inibição para quase todas as amostras dos extratos testados, bem como dos limonoides isolados, exceto o limonoide 7-desacetoxi-7-oxogedunina. Esses resultados são apresentados pela primeira vez para a andiroba e são bastante promissores.

Malgré leur rôle fonctionnel au sein des écosystèmes coralliens, les populations de bénitiers (Tridacninae) sont en déclin à travers le monde en raison de leur surexploitation. En Nouvelle-Calédonie, 1 à 9 tonnes sont prélevées par an. Dans ce contexte, cette thèse a pour principaux objectifs de fournir des indications quant aux connectivités démographiques et évolutives des populations de deux espèces de bénitiers en Nouvelle-Calédonie, Tridacna maxima et Hippopus hippopus afin d'estimer les échelles spatiales de dispersion larvaire, comprendre leur dynamique et proposer des mesures de conservation adaptées. La connectivité des populations a été estimée via l'analyse de marqueurs génétiques microsatellites spécifiquement développés pour ces deux espèces. L'échantillonnage a permis l'identification de deux nouvelles espèces en Nouvelle-Calédonie. A l'échelle d'un récif et de quelques kilomètres, les tests de parenté montrent des taux d'auto-recrutement variables, jusqu'à 8% pour T. maxima dans le lagon sud-ouest et 29% pour H. hippopus dans le lagon nord-est. Les échelles spatiales de dispersion larvaire varient selon les espèces, jusqu'à au moins 35km pour H. hippopus. A l'échelle du territoire, les populations de bénitiers sont peu structurées, indiquant une connectivité évolutive certaine. Néanmoins, des différences significatives ont été observées entre la Grande Terre et Chesterfield, les Iles Loyautés et les atolls d'Entrecasteaux pour H. hippopus et entre la côte ouest et les Îles Loyautés pour T. maxima. Ces résultats fournissent d'importants éléments de réponse relatifs aux échelles spatiales de dispersion des bénitiers en Nouvelle-Calédonie. / Despite their functional role in coral reef ecosystems, giant clams (Tridacninae) are in decline worldwide due to their overexploitation. In New Caledonia, 1 to 9 tons are harvested per year. In this context, the main objectives of this thesis are to provide information about the demographic and evolutionary population’s connectivity for two species of giant clams in New Caledonia, Tridacna maxima and Hippopus hippopus, in order to estimate the spatial scales of larval dispersal, understand their population dynamics and propose appropriate conservation measures. The connectivity of populations was estimated by analyzing microsatellite genetic markers specifically developed for these two species. Sampling allowed the identification of two new species in New Caledonia. At reef scale and up to a few kilometers, parentage analysis showed that giant clam populations have varying self-recruitment rates, up to 8% for T. maxima in southwest lagoon and 29% for H. hippopus in northeastern lagoon. The spatial scales of larval dispersal varied for the two species, up to at least 35km for H. hippopus. At the scale of the territory, giant clam populations showed a weak genetic structure, highlighting evolutionary connectivity among sampled sites. However, significant differences were observed between the Mainland and Chesterfield, Loyalty Islands and Entrecasteaux for H. hippopus and between the west coast and the Loyalty Islands for T. maxima. These results provide important answers related to the spatial scales of larval dispersal in giant clams in New Caledonia.

No description available.

No description available.

El objetivo de esta tesis es avanzar en el conocimiento de la dinámica ecológica de la almeja fina nativa de Europa, Ruditapes decussatus, y la almeja japonesa introducida, Ruditapes philippinarum. Se estudian aspectos relevantes de la dinámica ecológica que requerían ser investigados, tales como la expansión de almeja japonesa, la interacción competitiva, la dispersión larvaria y reclutamiento o la estimación de la talla mínima de captura. A la vez se explora la idoneidad de una metodología de muestreo para la evaluación continua de estas poblaciones en estuarios de gran extensión. Para el desarrollo de estos estudios se realizaron muestreos y experimentos de las especies objetivo en el ámbito de estudio y se llevaron a cabo los análisis de laboratorio asociados a los mismos. Además, se desarrollaron y se aplicaron modelos ecológicos predictivos. Los resultados de la tesis proveen información y herramientas para apoyar los modelos de gestión del marisqueo de las especies estudiadas tanto, en general, para los estuarios donde están presentes y son explotadas como, en particular, para la Bahía de Santander. / The objective of the thesis is to advance in the understanding of ecological dynamics of the European native grooved carpet shell clam Ruditapes decussatus and the introduced Manila clam Ruditapes philippinarum. Ecologically relevant aspects requiring investigation, such as the expansion of the Manila clam, competitive interaction, larval dispersal and recruitment or suitable specific catch size have been investigated. Moreover, the suitability of a sampling methodology for the assessment of these clam populations in large estuaries have been evaluated. For this purpose, field surveys, laboratory procedures and field experiments have been conducted, together with the development and application of ecological predictive models. The results of this thesis provide information and tools to support the studied species fishery management models both in general, for the estuaries where these species dwell and exploited and, in particular, for the Bay of Santander.

The reason for this story was to investigate a narrative that is important to the identity of North America’s Pacific Northwest Coast – a narrative that revolves around wild salmon, a narrative that always seemed too simple to me, a narrative that gives salmon a mythical status, and yet what does the average person know about this fish other than it floods grocery stores in fall and tastes good. How do we know this fish that supposedly defines the natural world of this place? I began my research as a science writer, inspired by John Steinbeck’s The Log from the Sea of Cortez, in which he writes that the best way to achieve reality is by combining narrative with scientific data. So I went looking for a different story from the one most people read about in popular media, a story that’s overwhelmingly about conflict: I searched for a narrative that combines the science of what we know about salmon and a story of the scientists who study the fish, either directly or indirectly. I tried to follow Steinbeck’s example and include the narrative journeys we take in understanding the world around us, the journeys that rarely make it into scientific journals. I went on about eight field trips with biology, ecology, and archaeology lab teams from the University of British Columbia and Simon Fraser University in Vancouver, with the Department of Fisheries and Oceans onboard the Canadian Coast Guard Ship the W.E. Ricker, and an archaeological crew from the Laich-Kwil-Tach Treaty Society in Campbell River, B.C. At the same time, I was reading a number of things, including a 1938 dissertation by anthropologist Homer Barnett from the University of Oregon titled The Nature and Function of the Potlatch, a 2011 book by economist Ronald Trosper at the University of Arizona, Resilience, Reciprocity and Ecological Economics, and works by psychologist Douglas Medin at Northwestern University and anthropologist Scott Atran at the University of Michigan, written over the past two decades, particular paying attention to their writings on taxonomy and folkbiology. My conclusions surprised me, a little. / Graduate / 0329 / 0324 / 0391