Active deformation fields: dense deformation field estimation for atlas-based segmentation using the active contour framework.

This paper presents a new and original variational framework for atlas-based segmentation. The proposed framework integrates both the active contour framework, and the dense deformation fields of optical flow framework. This framework is quite general and encompasses many of the state-of-the-art atlas-based segmentation methods. It also allows to perform the registration of atlas and target images based on only selected structures of interest. The versatility and potentiality of the proposed framework are demonstrated by presenting three diverse applications: In the first application, we show how the proposed framework can be used to simulate the growth of inconsistent structures like a tumor in an atlas. In the second application, we estimate the position of nonvisible brain structures based on the surrounding structures and validate the results by comparing with other methods. In the final application, we present the segmentation of lymph nodes in the Head and Neck CT images, and demonstrate how multiple registration forces can be used in this framework in an hierarchical manner.

Caspase-1 autoproteolysis is differentially required for NLRP1b and NLRP3 inflammasome function.

Inflammasomes are caspase-1-activating multiprotein complexes. The mouse nucleotide-binding domain and leucine rich repeat pyrin containing 1b (NLRP1b) inflammasome was identified as the sensor of Bacillus anthracis lethal toxin (LT) in mouse macrophages from sensitive strains such as BALB/c. Upon exposure to LT, the NLRP1b inflammasome activates caspase-1 to produce mature IL-1β and induce pyroptosis. Both processes are believed to depend on autoproteolysed caspase-1. In contrast to human NLRP1, mouse NLRP1b lacks an N-terminal pyrin domain (PYD), indicating that the assembly of the NLRP1b inflammasome does not require the adaptor apoptosis-associated speck-like protein containing a CARD (ASC). LT-induced NLRP1b inflammasome activation was shown to be impaired upon inhibition of potassium efflux, which is known to play a major role in NLRP3 inflammasome formation and ASC dimerization. We investigated whether NLRP3 and/or ASC were required for caspase-1 activation upon LT stimulation in the BALB/c background. The NLRP1b inflammasome activation was assessed in both macrophages and dendritic cells lacking either ASC or NLRP3. Upon LT treatment, the absence of NLRP3 did not alter the NLRP1b inflammasome activity. Surprisingly, the absence of ASC resulted in IL-1β cleavage and pyroptosis, despite the absence of caspase-1 autoprocessing activity. By reconstituting caspase-1/caspase-11(-/-) cells with a noncleavable or catalytically inactive mutant version of caspase-1, we directly demonstrated that noncleavable caspase-1 is fully active in response to the NLRP1b activator LT, whereas it is nonfunctional in response to the NLRP3 activator nigericin. Taken together, these results establish variable requirements for caspase-1 cleavage depending on the pathogen and the responding NLR.

Comportamento do NDVI obtido por sensor ótico ativo em cereais

O objetivo deste trabalho foi avaliar, com um sensor ótico ativo, o comportamento do índice de vegetação por diferença normalizada (NDVI - "normalized difference vegetation index"), nas culturas de trigo, triticale, cevada e milho. Cinco experimentos foram conduzidos no Paraná e São Paulo, com variação de classes de solo, doses e fontes de N, e variedades de trigo. As seguintes variáveis foram avaliadas: NDVI, teor de N foliar, matéria seca e produtividade das culturas. Análises de regressões foram realizadas entre as doses de N aplicadas e NDVI, teor de N foliar, matéria seca e produtividade. Análises de correlação entre as variáveis foram realizadas. O trigo, triticale e cevada apresentaram resposta às aplicações de doses crescentes de N, pelo aumento nas leituras do NDVI, no teor de N foliar e na produtividade. Medido pelo sensor ótico ativo utilizado, o NDVI apresenta alto potencial para manejo do N nas culturas do trigo, triticale e cevada, e baixo potencial para a cultura do milho. Há interferência das variedades de trigo nas leituras do sensor ótico ativo.

Post-switching beta synchronization reveals concomitant sensory reafferences and active inhibition processes

It is known that post-movement beta synchronization (PMBS) is involved both in active inhibition and in sensory reafferences processes. The aim of this study was examine the temporal and spatial dynamics of the PMBS involved during multi-limb coordination task. We investigated post-switching beta synchronization (assigned PMBS) using time-frequency and source estimations analyzes. Participants (n = 17) initiated an auditory-paced bimanual tapping. After a 1500 ms preparatory period, an imperative stimulus required to either selectively stop the left while maintaining the right unimanual tapping (Switch condition: SWIT) or to continue the bimanual tapping (Continue condition: CONT). PMBS significantly increased in SWIT compared to CONT with maximal difference within right central region in broad-band 14âeuro"30 Hz and within left central region in restricted-band 22âeuro"26 Hz. Source estimations localized these effects within right pre-frontal cortex and left parietal cortex, respectively. A negative correlation showed that participants with a low percentage of errors in SWIT had a large PMBS amplitude within right parietal and frontal cortices. This study shows for the first time simultaneous PMBS with distinct functions in different brain regions and frequency ranges. The left parietal PMBS restricted to 22âeuro"26 Hz could reflect the sensory reafferences of the right hand tapping disrupted by the switching. In contrast, the right pre-frontal PMBS in a broad-band 14âeuro"30 Hz is likely reflecting the active inhibition of the left hand stopped. Finally, correlations between behavioral performance and the magnitude of the PMBS suggest that beta oscillations can be viewed as a marker of successful active inhibition.

GacS sensor domains pertinent to the regulation of exoproduct formation and to the biocontrol potential of Pseudomonas fluorescens CHA0.

In the root-colonizing biocontrol strain CHA0 of Pseudomonas fluorescens, cell density-dependent synthesis of extracellular, plant-beneficial secondary metabolites and enzymes is positively regulated by the GacS/GacA two-component system. Mutational analysis of the GacS sensor kinase using improved single-copy vectors showed that inactivation of each of the three conserved phosphate acceptor sites caused an exoproduct null phenotype (GacS-), whereas deletion of the periplasmic loop domain had no significant effect on the expression of exoproduct genes. Strain CHA0 is known to synthesize a solvent-extractable extracellular signal that advances and enhances the expression of exoproduct genes during the transition from exponential to stationary growth phase when maximal exoproduct formation occurs. Mutational inactivation of either GacS or its cognate response regulator GacA abolished the strain's response to added signal. Deletion of the linker domain of the GacS sensor kinase caused signal-independent, strongly elevated expression of exoproduct genes at low cell densities. In contrast to the wild-type strain CHA0, the gacS linker mutant and a gacS null mutant were unable to protect tomato plants from crown and root rot caused by Fusarium oxysporum f. sp. radicis-lycopersici in a soil-less microcosm, indicating that, at least in this plant-pathogen system, there is no advantage in using a signal-independent biocontrol strain.

Discriminação da cobertura vegetal do Cerrado matogrossense por meio de imagens MODIS

O objetivo do presente trabalho foi avaliar o potencial de uso do modelo linear de mistura espectral (MLME), aplicado em imagens "Moderate Resolution Imaging Spectroradiometer" (MODIS), para discriminar as classes de cobertura vegetal natural e antropogênica do Cerrado matogrossense. O monitoramento do bioma Cerrado está se tornando muito importante devido à sua forte antropização, principalmente nas últimas quatro décadas. Nesse contexto, o sensor MODIS apresenta-se como opção devido à sua alta resolução temporal. Entretanto, considerando sua moderada resolução espacial, é indicada a decomposição de sua resposta espectral. O MLME apresenta-se como uma técnica viável, pois permite estimar o percentual dos componentes do pixel. Os dados utilizados nos perfis temporais das classes corresponderam às seguintes imagens fração do MLME: vegetação, solo e sombra. A discriminação das classes naturais e antropogênicas foi avaliada por meio do cálculo da distância Mahalanobis e apresentada por meio de dendrogramas. As imagens fração permitem análises de séries temporais na caracterização espacial e temporal das classes. As imagens fração solo e sombra, na estação seca, apresentam melhores resultados na discriminação das classes selecionadas. Para discriminação de classes com composições florísticas semelhantes, são indicadas as imagensfraçãoda estação chuvosa.

Avaliação de fluxos de calor e evapotranspiração pelo modelo SEBAL com uso de dados do sensor ASTER

O objetivo deste trabalho foi avaliar a eficiência da aplicação do modelo SEBAL em estimar os fluxos de energia em superfície e a evapotranspiração diária, numa extensa área de cultivo de arroz irrigado, no município de Paraíso do Sul, RS, tendo como parâmetros dados do sensor ASTER. As variáveis estudadas constituem importantes parâmetros do tempo e do clima em estudos agrometeorológicos e de racionalização no uso da água. As metodologias convencionais de estimativa desses parâmetros são pontuais e geralmente apresentam incertezas, que aumentam quando o interesse é o comportamento espacial desses parâmetros. Aplicou-se o algoritmo "Surface Energy Balance Algorithm for Land" (SEBAL), em uma imagem do sensor "Advanced Spaceborne Thermal Emission and Reflection Radiometer" (ASTER). As estimativas obtidas foram comparadas com medições em campo, realizadas por uma estação micrometeorológica localizada no interior da área de estudo. As estimativas mais precisas foram as de fluxo de calor sensível e de evapotranspiração diária, e a estimativa que apresentou maior erro foi a do fluxo de calor no solo. A metodologia empregada foi capaz de reproduzir os fluxos de energia em superfície de maneira satisfatória para estudos agrometeorológicos e de rendimento de culturas.

Lack of Mycobacterium tuberculosis-specific interleukin-17A-producing CD4(+) T cells in active disease.

Protective immunity to Mycobacterium tuberculosis (Mtb) is commonly ascribed to a Th1 profile; however, the involvement of Th17 cells remains to be clarified. Here, we characterized Mtb-specific CD4(+) T cells in blood and bronchoalveolar lavages (BALs) from untreated subjects with either active tuberculosis disease (TB) or latent Mtb infection (LTBI), considered as prototypic models of uncontrolled or controlled infection, respectively. The production of IL-17A, IFN-γ, TNF-α, and IL-2 by Mtb-specific CD4(+) T cells was assessed both directly ex vivo and following in vitro antigen-specific T-cell expansion. Unlike for extracellular bacteria, Mtb-specific CD4(+) T-cell responses lacked immediate ex vivo IL-17A effector function in both LTBI and TB individuals. Furthermore, Mtb-specific Th17 cells were absent in BALs, while extracellular bacteria-specific Th17 cells were identified in gut biopsies of healthy individuals. Interestingly, only Mtb-specific CD4(+) T cells from 50% of LTBI but not from TB subjects acquired the ability to produce IL-17A following Mtb-specific T-cell expansion. Finally, IL-17A acquisition by Mtb-specific CD4(+) T cells correlated with the coexpression of CXCR3 and CCR6, currently associated to Th1 or Th17 profiles, respectively. Our data demonstrate that Mtb-specific Th17 cells are selectively undetectable in peripheral blood and BALs from TB patients.

Characterization of GLUT8 and GLUT9, two novel glucose transporter isoforms

Summary Prevalence of type 2 diabetes is increasing worldwide at alarming rates, probably secondarily to that of obesity. As type 2 diabetes is characterized by blood hyperglycemia, controlling glucose entry into tissues from the bloodstream is key to maintain glycemia within acceptable ranges. In this context, several glucose transporter isoforms have been cloned recently and some of them have appeared to play important regulatory roles. Better characterizing two of them (GLUT8 and GLUT9) was the purpose of my work. The first part of my work was focused on GLUT8, which is mainly expressed in the brain and is able to transport glucose with high affinity. GLUT8 is retained intracellularly at basal state depending on an N-terminal dileucine motif, thus implying that cell surface expression may be induced by extracellular triggers. In this regard, I was interested in better defining GLUT8 subcellular localization at basal state and in finding signals promoting its translocation, using an adenoviral vector expressing a myc epitope-tagged version of the transporter, thus allowing expression and detection of cell-surface GLUT8 in primary hippocampal neurons and PC 12 cells. This tool enabled me to found out that GLUT8 resides in a unique compartment different from lysosomes, endoplasmic reticulum, endosomes and the Golgi. In addition, absence of GLUT8 translocation following pharmacological activation of several signalling pathways suggests that GLUT8 does not ever translocate to the cell surface, but would rather fulfill its role in its unique intracellular compartment. The second part of my work was focused on GLUT9, which -contrarily to GLUT8 - is unable to transport glucose, but retains the ability to bind glucose-derived cross-linker molecules, thereby suggesting that it may be a glucose sensor rather than a true glucose transporter. The aim of the project was thus to define if GLUT9 triggers intracellular signals when activated. Therefore, adenoviral vectors expressing GLUTS were used to infect both ßpancreatic and liver-derived cell lines, as GLUTS is endogenously expressed in the liver. Comparison of gene expression between cells infected with the GLUTS-expressing adenovirus and cells infected with a GFP-expressing control adenovirus ended up in the identification of the transcription factor HNF4α as being upregulated in aGLUT9-dependent manner. Résumé La prévalence du diabète de type 2 augmente de façon alarmante dans le monde entier, probablement secondairement à celle de l'obésité. Le diabète de type 2 étant caractérisé par une glycémie sanguine élevée, l'entrée du glucose dans les tissus depuis la circulation sanguine constitue un point de contrôle important pour maintenir la glycémie à des valeurs acceptables. Dans ce contexte, plusieurs isoformes de transporteurs au glucose ont été clonées récemment et certaines d'entre elles sont apparues comme jouant d'importants rôles régulateurs. Mieux caractériser deux d'entre elles (GLUT8 et GLUT9) était le but de mon travail. La première partie de mon travail a été centrée sur GLUT8, qui est exprimé principalement dans le cerveau et qui peut transporter le glucose avec une haute affinité. GLUT8 est retenu intracellulairement à l'état basal de façon dépendante d'un motif dileucine N-terminal, ce qui implique que son expression à la surface cellulaire pourrait être induite par des stimuli extracellulaires. Dans cette optique, je me suis intéressé à mieux définir la localisation subcellulaire de GLUT8 à l'état basal et à trouver des signaux activant sa translocation, en utilisant comme outil un vecteur adénoviral exprimant une version marquée (tag myc) du transporteur, me permettant ainsi d'exprimer et de détecter GLUT8 à la surface cellulaire dans des neurones hippocampiques primaires et des cellules PC12. Cet outil m'a permis de montrer que GLUT8 réside dans un compartiment unique différent des lysosomes, du réticulum endoplasmique, des endosomes, ainsi que du Golgi. De plus, l'absence de translocation de GLUT8 à la suite de l'activation pharmacologique de plusieurs voies de signalisation suggère que GLUT8 ne transloque jamais à la membrane plasmique, mais jouerait plutôt un rôle au sein même de son compartiment intracellulaire unique. La seconde partie de mon travail a été centrée sur GLUT9, lequel -contrairement à GLUT8 -est incapable de transporter le glucose, mais conserve la capacité de se lier à des molécules dérivées du glucose, suggérant que ce pourrait être un senseur de glucose plutôt qu'un vrai transporteur. Le but du projet a donc été de définir si GLUT9 active des signaux intracellulaires quand il est lui-même activé. Pour ce faire, des vecteurs adénoviraux exprimant GLUT9 ont été utilisés pour infecter des lignées cellulaires dérivées de cellules ßpancréatiques et d'hépatocytes, GLUT9 étant exprimé de façon endogène dans le foie. La comparaison de l'expression des gènes entre des cellules infectées avec l'adénovirus exprimant GLUT9 et un adénovirus contrôle exprimant la GFP a permis d'identifier le facteur de transcription HNF4α comme étant régulé de façon GLUT9-dépendante. Résumé tout public Il existe deux types bien distincts de diabète. Le diabète de type 1 constitue environ 10 des cas de diabète et se déclare généralement à l'enfance. Il est caractérisé par une incapacité du pancréas à sécréter une hormone, l'insuline, qui régule la concentration sanguine du glucose (glycémie). Il en résulte une hyperglycémie sévère qui, si le patient n'est pas traité à l'insuline, conduit à de graves dommages à divers organes, ce qui peut mener à la cécité, à la perte des membres inférieurs, ainsi qu'à l'insuffisance rénale. Le diabète de type 2 se déclare plus tard dans la vie. Il n'est pas causé par une déficience en insuline, mais plutôt par une incapacité de l'insuline à agir sur ses tissus cibles. Le nombre de cas de diabète de type 2 augmente de façon dramatique, probablement à la suite de l'augmentation des cas d'obésité, le surpoids chronique étant le principal facteur de risque de diabète. Chez l'individu sain, le glucose sanguin est transporté dans différents organes (foie, muscles, tissu adipeux,...) où il est utilisé comme source d'énergie. Chez le patient diabétique, le captage de glucose est altéré, expliquant ainsi l'hyperglycémie. Il est ainsi crucial d'étudier les mécanismes permettant ce captage. Ainsi, des protéines permettant l'entrée de glucose dans la cellule depuis le milieu extracellulaire ont été découvertes depuis une vingtaine d'années. La plupart d'entre elles appartiennent à une sous-famille de protéines nommée GLUT (pour "GLUcose Transporters") dont cinq membres ont été caractérisés et nommés selon l'ordre de leur découverte (GLUT1-5). Néanmoins, la suppression de ces protéines chez la souris par des techniques moléculaires n'affecte pas totalement le captage de glucose, suggérant ainsi que des transporteurs de glucose encore inconnus pourraient exister. De telles protéines ont été isolées ces dernières années et nommées selon l'ordre de leur découverte (GLUT6-14). Durant mon travail de thèse, je me suis intéressé à deux d'entre elles, GLUT8 et GLUT9, qui ont été découvertes précédemment dans le laboratoire. GLUT8 est exprimé principalement dans le cerveau. La protéine n'est pas exprimée à la surface de la cellule, mais est retenue à l'intérieur. Des mécanismes complexes doivent donc exister pour déplacer le transporteur à la surface cellulaire, afin qu'il puisse permettre l'entrée du glucose dans la cellule. Mon travail a consisté d'une part à définir où se trouve le transporteur à l'intérieur de la cellule, et d'autre part à comprendre les mécanismes capables de déplacer GLUT8 vers la surface cellulaire, en utilisant des neurones exprimant une version marquée du transporteur, permettant ainsi sa détection par des méthodes biochimiques. Cela m'a permis de montrer que GLUT8 est localisé dans une partie de la cellule encore non décrite à ce jour et qu'il n'est jamais déplacé à la surface cellulaire, ce qui suggère que le transporteur doit jouer un rôle à l'intérieur de la cellule et non à sa surface. GLUT9 est exprimé dans le foie et dans les reins. Il ressemble beaucoup à GLUT8, mais ne transporte pas le glucose, ce qui suggère que ce pourrait être un récepteur au glucose plutôt qu'un transporteur à proprement parler. Le but de mon travail a été de tester cette hypothèse, en comparant des cellules du foie exprimant GLUT9 avec d'autres n'exprimant pas la protéine. Par des méthodes d'analyses moléculaires, j'ai pu montrer que la présence de GLUT9 dans les cellules du foie augmente l'expression de HNF4α, une protéine connue pour réguler la sécrétion d'insuline dans le pancréas ainsi que la production de glucose dans le foie. Des expériences complémentaires seront nécessaires afin de mieux comprendre par quels mécanismes GLUT9 influence l'expression de HNF4α dans le foie, ainsi que de définir l'importance de GLUT9 dans la régulation de la glycémie chez l'animal entier.

Active strain and activation models in cardiac electromechanics

We present a model for mechanical activation of the cardiac tissue depending on the evolution of the transmembrane electrical potential and certain gating/ionic variables that are available in most of electrophysiological descriptions of the cardiac membrane. The basic idea consists in adding to the chosen ionic model one ordinary differential equation for the kinetics of the mechanical activation function. A relevant example illustrates the desired properties of the proposed model, such as delayed muscle contraction and correct magnitude of the muscle fibers' shortening.

Validação de modelo para predição do potencial produtivo de trigo com sensor óptico ativo

O objetivo deste trabalho foi validar um modelo baseado no índice de vegetação por diferença normalizada (NDVI), para a predição da variabilidade espacial da biomassa acumulada na parte aérea e da produtividade de grãos de trigo. Foram realizadas leituras georreferenciadas de NDVI e biomassa, no final do afilhamento, e produtividade. O modelo proposto permitiu relacionar classes de variabilidade espacial do NDVI e da biomassa, com 81% de correspondência entre elas. Entretanto, a relação entre as classes de variabilidade espacial da produtividade e do NDVI foi menor, com 48% de correspondência.

Detection and characterization of hydraulically active fractures in a carbonate aquifer: Results from self-potential, temperature and fluid conductivity logging along a 260-m-deep borehole in the Combioula hydrothermal system in the southwestern Swiss Alps

A geophysical and geochemical study has been conducted in a fractured carbonate aquifer located at Combioula in the southwestern Swiss Alps with the objective to detect and characterize hydraulically active fractures along a 260-m-deep borehole. Hydrochemical analyses, borehole diameter, temperature and fluid electrical conductivity logging data were integrated in order to relate electrokinetic self-potential signals to groundwater flow inside the fracture network. The results show a generally good, albeit locally variable correlation of variations of the self-potential signals with variations in temperature, fluid electrical conductivity and borehole diameter. Together with the hydrochemical evidence, which was found to be critical for the interpretation of the self-potential data, these measurements not only made it possible to detect the hydraulically active fractures but also to characterize them as zones of fluid gain or fluid loss. The results complement the available information from the corresponding litholog and illustrate the potential of electrokinetic self-potential signals in conjunction with temperature, fluid electrical conductivity and hydrochemical analyses for the characterization of fractured aquifers, and thus may offer a perspective for an effective quantitative characterization of this increasingly important class of aquifers and geothermal reservoirs.