Approximation de la distribution a posteriori d'un modèle Gamma-Poisson hiérarchique à effets mixtes

La méthode que nous présentons pour modéliser des données dites de "comptage" ou données de Poisson est basée sur la procédure nommée Modélisation multi-niveau et interactive de la régression de Poisson (PRIMM) développée par Christiansen et Morris (1997). Dans la méthode PRIMM, la régression de Poisson ne comprend que des effets fixes tandis que notre modèle intègre en plus des effets aléatoires. De même que Christiansen et Morris (1997), le modèle étudié consiste à faire de l'inférence basée sur des approximations analytiques des distributions a posteriori des paramètres, évitant ainsi d'utiliser des méthodes computationnelles comme les méthodes de Monte Carlo par chaînes de Markov (MCMC). Les approximations sont basées sur la méthode de Laplace et la théorie asymptotique liée à l'approximation normale pour les lois a posteriori. L'estimation des paramètres de la régression de Poisson est faite par la maximisation de leur densité a posteriori via l'algorithme de Newton-Raphson. Cette étude détermine également les deux premiers moments a posteriori des paramètres de la loi de Poisson dont la distribution a posteriori de chacun d'eux est approximativement une loi gamma. Des applications sur deux exemples de données ont permis de vérifier que ce modèle peut être considéré dans une certaine mesure comme une généralisation de la méthode PRIMM. En effet, le modèle s'applique aussi bien aux données de Poisson non stratifiées qu'aux données stratifiées; et dans ce dernier cas, il comporte non seulement des effets fixes mais aussi des effets aléatoires liés aux strates. Enfin, le modèle est appliqué aux données relatives à plusieurs types d'effets indésirables observés chez les participants d'un essai clinique impliquant un vaccin quadrivalent contre la rougeole, les oreillons, la rub\'eole et la varicelle. La régression de Poisson comprend l'effet fixe correspondant à la variable traitement/contrôle, ainsi que des effets aléatoires liés aux systèmes biologiques du corps humain auxquels sont attribués les effets indésirables considérés.

Space and time characterization of laser-induced plasmas for applications in chemical analysis and thin film deposition

Après des décennies de développement, l'ablation laser est devenue une technique importante pour un grand nombre d'applications telles que le dépôt de couches minces, la synthèse de nanoparticules, le micro-usinage, l’analyse chimique, etc. Des études expérimentales ainsi que théoriques ont été menées pour comprendre les mécanismes physiques fondamentaux mis en jeu pendant l'ablation et pour déterminer l’effet de la longueur d'onde, de la durée d'impulsion, de la nature de gaz ambiant et du matériau de la cible. La présente thèse décrit et examine l'importance relative des mécanismes physiques qui influencent les caractéristiques des plasmas d’aluminium induits par laser. Le cadre général de cette recherche forme une étude approfondie de l'interaction entre la dynamique de la plume-plasma et l’atmosphère gazeuse dans laquelle elle se développe. Ceci a été réalisé par imagerie résolue temporellement et spatialement de la plume du plasma en termes d'intensité spectrale, de densité électronique et de température d'excitation dans différentes atmosphères de gaz inertes tel que l’Ar et l’He et réactifs tel que le N2 et ce à des pressions s’étendant de 10‾7 Torr (vide) jusqu’à 760 Torr (pression atmosphérique). Nos résultats montrent que l'intensité d'émission de plasma dépend généralement de la nature de gaz et qu’elle est fortement affectée par sa pression. En outre, pour un délai temporel donné par rapport à l'impulsion laser, la densité électronique ainsi que la température augmentent avec la pression de gaz, ce qui peut être attribué au confinement inertiel du plasma. De plus, on observe que la densité électronique est maximale à proximité de la surface de la cible où le laser est focalisé et qu’elle diminue en s’éloignant (axialement et radialement) de cette position. Malgré la variation axiale importante de la température le long du plasma, on trouve que sa variation radiale est négligeable. La densité électronique et la température ont été trouvées maximales lorsque le gaz est de l’argon et minimales pour l’hélium, tandis que les valeurs sont intermédiaires dans le cas de l’azote. Ceci tient surtout aux propriétés physiques et chimiques du gaz telles que la masse des espèces, leur énergie d'excitation et d'ionisation, la conductivité thermique et la réactivité chimique. L'expansion de la plume du plasma a été étudiée par imagerie résolue spatio-temporellement. Les résultats montrent que la nature de gaz n’affecte pas la dynamique de la plume pour des pressions inférieures à 20 Torr et pour un délai temporel inférieur à 200 ns. Cependant, pour des pressions supérieures à 20 Torr, l'effet de la nature du gaz devient important et la plume la plus courte est obtenue lorsque la masse des espèces du gaz est élevée et lorsque sa conductivité thermique est relativement faible. Ces résultats sont confirmés par la mesure de temps de vol de l’ion Al+ émettant à 281,6 nm. D’autre part, on trouve que la vitesse de propagation des ions d’aluminium est bien définie juste après l’ablation et près de la surface de la cible. Toutefois, pour un délai temporel important, les ions, en traversant la plume, se thermalisent grâce aux collisions avec les espèces du plasma et du gaz.

Can salvage logging affect seed dispersal by birds into burned forests?

The recovery of vegetation in Mediterranean ecosystems after wildfire is mostly a result of direct regeneration, since the same species existing before the fire regenerate on-site by seeding or resprouting. However, the possibility of plant colonization by dispersal of seeds from unburned areas remains poorly studied. We addressed the role of the frugivorous, bird-dependent seed dispersal (seed rain) of fleshy-fruited plants in a burned and managed forest in the second winter after a fire, before on-site fruit production had begun. We also assessed the effect on seed rain of different microhabitats resulting from salvage logging (erosion barriers, standing snags, open areas), as well as the microhabitats of unlogged patches and an unburned control forest, taking account of the importance of perches as seed rain sites. We found considerable seed rain by birds in the burned area. Seeds, mostly from Olive trees Olea europaea and Evergreen pistaches Pistacia lentiscus, belonged to plants fruiting only in surrounding unburned areas. Seed rain was heterogeneous, and depended on microhabitat, with the highest seed density in the unburned control forest but closely followed by the wood piles of erosion barriers. In contrast, very low densities were found under perches of standing snags. Furthermore, frugivorous bird richness seemed to be higher in the erosion barriers than elsewhere. Our results highlight the importance of this specific post-fire management in bird-dependent seed rain and also may suggest a consequent heterogeneous distribution of fleshy-fruited plants in burned and managed areas. However, there needs to be more study of the establishment success of dispersed seeds before an accurate assessment can be made of the role of bird-mediated seed dispersal in post-fire regeneration

Gaussian anamorphosis in the analysis step of the EnKF: a joint state-variable/observation approach

The analysis step of the (ensemble) Kalman filter is optimal when (1) the distribution of the background is Gaussian, (2) state variables and observations are related via a linear operator, and (3) the observational error is of additive nature and has Gaussian distribution. When these conditions are largely violated, a pre-processing step known as Gaussian anamorphosis (GA) can be applied. The objective of this procedure is to obtain state variables and observations that better fulfil the Gaussianity conditions in some sense. In this work we analyse GA from a joint perspective, paying attention to the effects of transformations in the joint state variable/observation space. First, we study transformations for state variables and observations that are independent from each other. Then, we introduce a targeted joint transformation with the objective to obtain joint Gaussianity in the transformed space. We focus primarily in the univariate case, and briefly comment on the multivariate one. A key point of this paper is that, when (1)-(3) are violated, using the analysis step of the EnKF will not recover the exact posterior density in spite of any transformations one may perform. These transformations, however, provide approximations of different quality to the Bayesian solution of the problem. Using an example in which the Bayesian posterior can be analytically computed, we assess the quality of the analysis distributions generated after applying the EnKF analysis step in conjunction with different GA options. The value of the targeted joint transformation is particularly clear for the case when the prior is Gaussian, the marginal density for the observations is close to Gaussian, and the likelihood is a Gaussian mixture.

An Ensemble Smoother with Error Estimates

A smoother introduced earlier by van Leeuwen and Evensen is applied to a problem in which real obser vations are used in an area with strongly nonlinear dynamics. The derivation is new , but it resembles an earlier derivation by van Leeuwen and Evensen. Again a Bayesian view is taken in which the prior probability density of the model and the probability density of the obser vations are combined to for m a posterior density . The mean and the covariance of this density give the variance-minimizing model evolution and its errors. The assumption is made that the prior probability density is a Gaussian, leading to a linear update equation. Critical evaluation shows when the assumption is justified. This also sheds light on why Kalman filters, in which the same ap- proximation is made, work for nonlinear models. By reference to the derivation, the impact of model and obser vational biases on the equations is discussed, and it is shown that Bayes’ s for mulation can still be used. A practical advantage of the ensemble smoother is that no adjoint equations have to be integrated and that error estimates are easily obtained. The present application shows that for process studies a smoother will give superior results compared to a filter , not only owing to the smooth transitions at obser vation points, but also because the origin of features can be followed back in time. Also its preference over a strong-constraint method is highlighted. Further more, it is argued that the proposed smoother is more efficient than gradient descent methods or than the representer method when error estimates are taken into account

Draft Proposed Public Transportation Routes for Waterville, ME

Currently, there is a public bus transportation route in Waterville, Maine. However, this system could be improved. Our goal was to use GIS to find optimal public transportation routes throughout the city based on given points of interest and high population density areas. Three different groups of points of interest were created in the North, West, and South sections of Waterville. Using the Network Analyst tool, which calculates optimal routes, using existing street data, based on the input of stops, barriers, and impedance, we ran an analysis of what we thought would be the routes that best served the greatest number of people. Two different sets of routes were found: one with length as the impedance (the shortest length between the selected stops was favored), and one with population density as the impedance (the roads with the highest population density were favored). Finally, the times of the resulting routes (given a constant speed limit of 25 mph) were calculated and evaluated.

Dielectric properties of thermosetting material nanocomposites

The dieletric relaxation properties of thermosetting material nanocomposites based on spherosilicate nanoplatforms were studied from room temperature to 170 degrees C, varying the frequency from 10 to 1000 KHz. Permittivity (epsilon'), dielectric loss (epsilon ''), and activation energy (E-a) were calculated. The results of dielectric relaxation were confirmed by those of the final properties. The dielectric loss amplitude decreases with increasing ODPG content until about 70-73 wt % and slightly increases at higher ODPG content. This means that the increasing of the ODPG content in the composite samples decreases the number of pendants groups and/or increases crosslink densitv, causing decreased motion of organic tethers, and subsequently decreasing of the dipolar mobility. The results of apparent activation energy, fracture toughness and tensile modulus mechanical properties show the same profile with respect to ODPG content, in the sense that they exhibit maxima around 70 wt % ODPG. For the ODPG/MDA composites, this formulation of 70 wt % ODPG containing excess of amine is not composition where the highest crosslinked density is reached. This implies that the best mechanical properties and E-a are provided by some degree of chain flexibility. (c) 2007 Wiley Periodicals, Inc.

Custos e rentabilidade da produção de juvenis de tilápia-do-nilo em tanques-rede utilizando-se diferentes densidades de estocagem

Neste trabalho foi realizada a análise econômica da produção de juvenis de tilápia-do-nilo em tanques-rede utilizando-se diferentes densidades de estocagem. O experimento foi desenvolvido em área aquícola, em delineamento de blocos casualizados, com quatro densidades de estocagem (100, 200, 300 e 400 peixes m-3), avaliadas com seis repetições, em dois períodos de criação: de março a abril de 2005 (52 dias - peso inicial de 43,08 ± 2,98 g e peso final de 262,14 ± 47,86 g) e de março a abril de 2006 (58 dias - peso inicial de 43,16 ± 5,34 g e peso final 314,24 ± 73,30 g). Foram avaliadas as seguintes variáveis econômicas: custo da ração mais custo do juvenil dividido pela biomassa, em R$ kg-1; porcentagem do custo da ração por quilo de peixe produzido sobre o preço de venda; porcentagem do custo do juvenil por quilo de peixe produzido sobre o preço de venda e; porcentagem dos custos da ração mais do juvenil por quilo de peixe produzido sobre o preço de venda. da menor densidade de estocagem (100) para a maior (400), ocorreu diminuição no ganho de peso diário e elevação do índice de conversão alimentar aparente, mas essa redução não comprometeu a taxa de sobrevivência. Entretanto, o ganho de biomassa aumentou com o adensamento de peixes. As maiores receitas líquidas foram obtidas nas densidades de estocagem de 100 e 200 peixes m-3. Os preços não remuneraram os custos operacionais (efetivo e total) em maiores densidades (300 e 400 peixes m-3). Os melhores resultados para a produção de juvenis de tilápia-do-nilo foram obtidos com densidades de até 200 peixes m-3.

Flutuação populacional e distribuição vertical de Brevicoryne brassicae (L.) (Hemiptera: Aphididae) em couve

O conhecimento da dinâmica populacional e da distribuição vertical de insetos pragas em plantas hospedeiras é fundamental para o desenvolvimento de programas de manejo integrado de pragas. No presente trabalho efetuou-se um levantamento populacional de formas ápteras do pulgão Brevicoryne brassicae (L.), visando determinar a época de maior densidade populacional e a distribuição vertical em plantas de couve, (Brassica oleracea L. var. acephala DC.), cultivadas em Jaboticabal, SP. O estudo foi realizado durante as safras de brássicas de 1998 e 1999, efetuando-se correção da acidez do solo por meio de aplicação de calcário apenas no campo utilizado em 1998. A amostragem dos pulgões foi feita visualmente em folhas classificadas em três categorias: apical, mediana e basal. Nas duas safras estudadas, a infestação de B. brassicae na couve atingiu a maior densidade populacional em setembro, diminuindo rapidamente a seguir. Nos dois campos não se observou a mesma distribuição de B. brassicae em folhas apicais, medianas e basais. Os fatores que podem ter contribuído para as diferenças observadas no padrão de distribuição do pulgão devem estar relacionados com a precipitação pluvial e o calcário magnesiano.

Dinâmica populacional de Triozoida limbata, Costalimaita ferruginea e inimigos naturais em pomar orgânico e convencional de goiaba

We investigated the population dynamics of Triozoida limbata (Hemiptera: Triozidae) and Costalimaita ferruginea (Coleoptera: Chrysomelidae) and its correlation with the population of natural enemies in organic and conventional orchard of guava. The experiments were performed in two distinct orchards of guava in the 2010/2011 harvest. For monitoring pests and natural enemies, we installed five yellow sticky traps in each orchard. To obtain the correlation between population densities of pests with natural enemies, we used Pearson linear correlation analysis (SAS). The population density of T. limbata remained low, and reaches the top in October in organic orchard of guava. The main pest in conventional orchard of guava was T. limbata and population reaches the top several times. The damage caused by T. limbata in new leaves of guava was more pronounced in conventional orchard. There was a low population density of C. ferruginea in both orchards; however we observed that the population reaches the top in November in organic orchard. The species C. ferruginea caused higher damage in young leaves of guava tree in organic orchard. The highest population density of natural enemies was observed in organic orchard, which presented positive correlation between T. limbata and the coccinellid predator Scymnus spp.

Microbial alterations of the soil influenced by induced compaction

A compactação é um dos fatores mais agravantes para a qualidade do solo, porém o seu efeito na comunidade e atividade enzimática microbiana não tem sido suficientemente estudado. Seis níveis de compactação foram obtidos pela passagem de tratores com diferentes pesos em um Latossolo Vermelho, e a densidade final foi medida. Amostras de solo foram coletadas nas profundidades de 0-10 e 10-20 cm, após a colheita do milho. O efeito da compactação foi evidente em todos os parâmetros estudados, mas nem sempre foi significativo. A contagem das bactérias totais reduziu significativamente em 22-30 %, e a das nitrificantes, em 38-41 %, no solo com maior densidade em relação ao controle. Contudo, a população de fungos aumentou de 55 a 86 %, e a das bactérias desnitrificantes, de 49 a 53 %. A atividade da desidrogenase diminuiu de 20 a 34 %; a da urease, de 44 a 46 %; e a da fosfatase, de 26 a 28 %. O conteúdo de matéria orgânica e o pH do solo diminuíram na camada 0-0,10 em relação à de 0,10-0,20 m e influíram possivelmente na redução das contagens microbianas exceto das bactérias desnitrificantes, e na atividade das enzimas, menos a da urease. Esses resultados indicam que a compactação do solo teve influência na comunidade de microrganismos aeróbios e na sua atividade. Esse efeito pode alterar a ciclagem de nutrientes e diminuir a produção da planta.

Detection of bovine Herpesvirus type 5 in formalin-fixed, paraffin-embedded bovine brain by PCR: a useful adjunct to conventional tissue-based diagnostic test of bovine encephalitis

The aim of this study was to evaluate the application of PCR technique for the detection of BoHV-5 in routinely formalin-fixed, paraffin-embedded brain tissues in 20 naturally infected calves affected by fatal meningoencephalitis. Brains were divided into two halves, one kept fresh for virus isolation and PCR assay, targeting the glycoprotein C gene from BoHV-5 genome. The other half brain, corresponding to posterior cortex region, was submitted to formalin fixation and embedded into paraffin blocks for microscopic evaluation and total DNA isolation. Most of the slides showed severe multifocal non-supurative encephalitis with neuronal degeneration, neurophagia, and no acidophilic intranuclear inclusions could be found in neurons and glial. The 20 fresh samples were confirmed, by virus isolation and PCR assay, as having the BoHV-5 virus and, respective glicoprotein C sequence, while 15 of 20 formalin-fixed, paraffin-embedded samples were considered positive for the same analysis. The results revealed the first description of PCR efficiency, applied to formalin-fixed, paraffin-embedded brain collected from naturally infected calves, improving the detection of BoHV-5 from archival samples in South America. (c) 2007 Published by Elsevier B.V.

Origin of sensory and autonomic innervation of the rat temporomandibular joint: A retrograde axonal tracing study with the fluorescent dye fast blue

Previous studies that have used retrograde axonal tracers (horseradish peroxidase alone or conjugated with wheat germ agglutinin) have shown that the temporomandibular joint (TMJ) is supplied with nerve fibers originating mainly from the trigeminal ganglion, in addition to other sensory and sympathetic ganglia. The existence of nerve fibers in the TMJ originating from the trigeminal mesencephalic nucleus is unclear, and the possible innervation by parasympathetic nerve fibers has not been determined. In the present work, the retrograde axonal tracer, fast blue, was used to elucidate these questions and re-evaluated the literature data. The tracer was deposited in the supradiscal articular space of the rat TMJ, and an extensive morphometric analysis was performed of the labeled perikaryal profiles located in sensory and autonomic ganglia. This methodology permitted us to observe labeled small perikaryal profiles in the trigeminal ganglion, clustered mainly in the posterior-lateral region of the dorsal, medial and ventral thirds of horizontal sections, with some located in the anterior-lateral region of the ventral third. Sensory perikarya were also labeled in the dorsal root ganglia from C2 to C5. No labeled perikaryal profiles were found in the trigeminal mesencephalic nucleus. on the other hand, autonomic labeled perikaryal profiles were distributed in the sympathetic superior cervical and stellate ganglia, and parasympathetic otic ganglion. Our results confirmed those of previous studies and also demonstrated that: (i) there is a distribution pattern of labeled perikaryal profiles in the trigeminal ganglion; (ii) some perikaryal profiles located in the otic ganglion were labeled; and (iii) the trigeminal mesencephalic nucleus did not show any retrogradely labeled perikaryal profiles.

Activation of the serotonergic 5-HT1A receptor in the paraventricular nucleus of the hypothalamus inhibits water intake and increases urinary excretion in water-deprived rats

The paraventricular nucleus (PVN) may be considered as a dynamic mosaic of chemically-specified subgroups of neurons. 5-HT1A is one of the prime receptors identified and there is expressed throughout all magnocellular regions of the PVN. Several reports have demonstrated that a subpopulation of the magnocellular neurons expressing 5-HT1A receptors are oxytocin (OT) neurons and activation of 5-HT1A receptors in the PVN increases the plasma OT. Increasing evidence shows that OT inhibits water intake and increases urinary excretion in rats. The aim of this study was to investigate the role of serotonergic 5-HT1A receptors in the lateral-medial posterior magnocellular region of the PVN in the water intake and diuresis induced by 24 h of water deprivation. Cannulae were implanted in the PVN of rats. 5-HT injections in the PVN reduced water intake and increased urinary excretion. 8-OH-DPAT (a 5-HT1A agonist) injections blocked the water intake and increased urinary output in all the periods of the observation. pMPPF (a 5-HT1A antagonist) injected bilaterally before the 8-OH-DPAT blocked its inhibitory effect on water intake and its diuretic effect. We suggest that antidipsogenic and diuretic responses seem to be mediated via 5-HT1A receptors of the lateral-medial posterior magnocellular region of the PVN in water-deprived rats. (C) 2008 Elsevier B.V. All rights reserved.

The role of habitat heterogeneity for the functional response of the spider Nesticodes rufipes (Araneae : Theridiidae) to houseflies

We investigated whether or not different degrees of refuge for prey influence the characteristic of functional response exhibited by the spider Nesticodes rufipes on Musca domestica, comparing the inherent ability of N. rufipes to kill individual houseflies in such environments at two distinct time intervals. To investigate these questions, two artificial habitats were elaborated in the laboratory. For 168 h of predator-prey interaction, logistic regression analyses revealed a type 11 functional response, and a significant decrease in prey capture in the highest prey density was observed when habitat complexity was increased. Data from habitat 1 (less complex) presented a greater coefficient of determination than those from habitat 2 (more complex), indicating a higher variation of predation of the latter. For a 24 h period of predator-prey interaction, spiders killed significantly fewer prey in habitat 2 than in habitat 1. Although prey capture did not enable data to fit properly in the random predator equation in this case, predation data from habitat 2 presented a higher variation than data from habitat 1, corroborating results from 168 h of interaction. The high variability observed on data from habitat 2 (more complex habitat) is an interesting result because it reinforces the importance of refuge in promoting spatial heterogeneity, which can affect the extent of predator-prey interactions.