Unmixing and deconvolution methods of objects in images : applications in astronomical high-contrast imaging

L'imagerie à haut-contraste d'environnements circumstellaires joue un rôle clé dans notre compréhension de la formation et de l'évolution des exoplanètes. Des instruments tels que SPHERE sont dédiés à l'imagerie de tels environnements grâce à une optique adaptative extrême ainsi qu'une puissante coronographie. Cependant, des aberrations dans le chemin optique produisent de fortes perturbations dans les données. Combinées aux effets de flous et aux bruits venant de l'instrument, ces «fuites stellaires» limitent fortement l'étude de ces environnements. Durant ma thèse, j'ai développé différentes méthodes pour surmonter le problème consistant à retrouver les objets d'intérêts à partir de données perturbées. À l'aide de simulations réalistes et de données brutes de l'instrument SPHERE/IRDIS, je discute dans ce manuscrit de la modélisation des données en termes de statistiques et en termes des différentes composantes qui les forment. En utilisant le maximum a posteriori, pour estimer les paramètres d'intérêt, j'ai concentré mon travail sur trois applications en imagerie astronomique. Abordant le flou inévitable des instruments optiques, j'ai d'abord travaillé sur le problème de la déconvolution aveugle. En posant le problème comme l'estimation à la fois de l'objet et des effets instrumentaux, j'ai discuté de l'ambiguïté d'échelle du modèle bilinéaire formé par ces deux composantes. En effet, en mettant à l'échelle une composante par un facteur et l'autre par le facteur inverse, on obtient le même modèle. J'ai proposé une stratégie, appelé Amors, pour estimer les deux composantes en utilisant cette ambiguïté d'échelle. L'algorithme utilise la mise à l'échelle optimale au sens du maximum a posteriori pour réduire le nombre d'hyper-paramètres lors de l'estimation des paramètres d'un modèle bilinéaire. Notant que des problèmes tels que la déconvolution aveugle dépendent fortement du point de départ, j'ai également considéré l'initialisation de l'algorithme. L'inclusion de la mise à l'échelle optimale dans le processus d'estimation améliore la vitesse de convergence quel que soit le facteur d'échelle de l'initialisation. J'ai également concentré mes travaux sur le mode de spectroscopie longue fente (LSS) de SPHERE/IRDIS. Pour extraire le spectre d'un compagnon des données LSS, j'ai développé l'algorithme Exospeco. Il utilise un modèle combiné de la contribution du compagnon et des fuites stellaires. En parallèle, j'ai développé une méthode de calibration flexible qui prend en compte les distorsions dues à l'optique de l'instrument (effets de cisaillement). J'ai démontré l'importance de cette étape en confrontant l'algorithme à des données réelles. Grâce à son estimation alternée des deux composantes, et en utilisant une seule image de données LSS, Exospeco réduit efficacement le biais d'auto-soustraction qui affecte les méthodes de l'état-de-l'art. Les résultats obtenus par la méthode sur des compagnons injectés dans des données réelles montrent une récupération fidèle de la SED pour des compagnons 10^4 fois plus faibles que leur étoile hôte à des séparations angulaires jusqu'à 0.4''. Dans la dernière partie de mon travail, j'ai discuté de l'impact du modèle statistique de ces fuites stellaires lors de l'imagerie d'objets étendus tels que les disques protoplanétaires autour de jeunes étoiles. Notant que les structures présentes dans les données d'imagerie différentielle angulaire (ADI) sont spatialement corrélées, je discute plusieurs approximations de la matrice de covariance de la composante bruit. Cette composante des données tient compte des fluctuations des fuites stellaires, du bruit de photons, ainsi que d'autres sources d'incertitudes. J'ai validé sur un jeu de données ADI réel l'approximation Asap qui construit une approximation parcimonieuse de l'inverse de la matrice de covariance. Enfin, j'ai développé une stratégie non supervisée qui sélectionne automatiquement le niveau de parcimonie de cette approximation.High-contrast imaging of circumstellar environments plays a key role in understanding the formation and evolution of exoplanets. Instruments such as SPHERE have been dedicated to imaging such environments thanks to the coupling of extreme adaptive optics and powerful coronagraphy. However, aberrations in the light path result in strong artifacts in the acquired data. These "stellar leakages", combined with blurring effects and noises from the instrument limit greatly the study of such environments. During my PhD thesis, I developed several methods to overcome the challenging problem of disentangling objects of interest from perturbed data. Using realistic simulations and raw data from the SPHERE/IRDIS instrument, I discuss the modeling of the data in terms of statistics and in terms of the different components that form them. Using the maximum a posteriori, to estimate the parameters of interest, I focused my work on three applications in astronomical imaging. Addressing the unavoidable blurring of optical instruments, I first worked on the blind deconvolution problem. Stating the problem as the estimation of both the object and the instrumental effects, I discussed the scaling ambiguity of the bi-linear model formed by these two components. Indeed scaling one component by a factor and the other by the inverse factor yields the same model. I proposed a strategy to estimate both components using this scaling ambiguity. Called Amors, the algorithm uses the optimal scaling in the sense of the maximum a posteriori to reduce the number of hyper-parameters when estimating parameters of a bi-linear model. Noting that problems such as blind deconvolution depend greatly on the starting point, I also considered the starting point of the algorithm. Including the optimal scaling in the estimation process improves the convergence speed whatever the scaling of the initialization. I also focused my work on the SPHERE/IRDIS long-slit spectroscopy (LSS) mode. To extract a companion spectrum from LSS data, I developed the Exospeco algorithm. It uses a combined model of the contribution of the companion and the stellar leakages. Jointly with Exospeco, I developed a flexible calibration method that takes into account any distortions due to the optics of the instrument (e.g. shear effects). I demonstrated the importance of this step by confronting the algorithm to real LSS data. Thanks to its alternating estimation of the two components, and using only a single frame of LSS data, Exospeco reduces effectively the self-subtraction bias that affects state-of-the-art methods. The results on injected companions in real data obtained by the method show a faithful recovery of the companion SED for companions 10^4 fainter than their host star at angular separations until 0.4''. Building upon the Amors algorithm, Exospeco is easy to use by limiting the number of tuning parameters. In the last part of my work, I discussed the impact of the statistical model of these stellar leakages when imaging extended objects such as protoplanetary disks around young stars. Noting that the structures present in angular differential imaging (ADI) data are spatially correlated, I discuss several approximations of the covariance matrix of the noise component. This component of the data accounts for fluctuations of the stellar leakages, photon noise, as well as other sources of uncertainties. I validated on a real ADI dataset the Asap approximation which builds a sparse approximation of the inverse of the covariance matrix. Finally, I developed an unsupervised strategy that selects automatically the level of sparsity of this approximation

AIDS Vaccination Studies Using an Ex Vivo Feline Immunodeficiency Virus Model: Reevaluation of Neutralizing Antibody Levels Elicited by a Protective and a Nonprotective Vaccine after Removal of Antisubstrate Cell Antibodies

In the feline immunodeficiency virus system, immunization with a fixed-infected-cell vaccine conferred protection against virulent homologous challenge but the immune effectors involved remained elusive. In particular, few or no neutralizing antibodies were detected in sera from vaccinated cats. Here we show that, when preadsorbed with selected feline cells, the same sera revealed clearly evident virus-neutralizing activity. Because high titers of neutralizing antibody in cell-adsorbed sera from 23 cats immunized with fixed-infected-cell or whole-inactivated-virus vaccines correlated with protection, it is likely that they were more important for protection than formerly realized. In vitro, the fixed-cell vaccine efficiently removed neutralizing antibody from immune sera while the whole-inactivated-virus vaccine was much less effective

Sulfur Derivatives of the Natural Polyarsenical Arsenicin A: Biologically Active, Organometallic Arsenic–Sulfur Cages Related to the Minerals Realgar and Uzonite

(±)-Arsenicin A (AsA), (±)-<b>1</b>, the first natural polyarsenical to be isolated, has the adamantane-type structure of the mineral arsenolite (As₄O₆), in which three of the oxygen atoms have been replaced by methylene groups to give an organometallic, arsenic–oxygen cage of <i>C</i>₂ symmetry. Heating of a benzene solution of AsA with aqueous sodium sulfide produces, by reductive desulfurization of the intermediate sulfur analog (±)-<b>2</b>, the monosulfide cage (±)-<b>4</b>, which contains two As–As bonds and which has a <i>C</i>₂-chiral cage structure related to the mineral realgar (α-As₄S₄). At room temperature the reaction affords a chiral disulfide derivative that exists as a pair of separable diastereomers, (±)-<b>3a</b> and (±)-<b>3b</b>, each of which contains a single As–As bond and is structurally related to the mineral uzonite (As₄S₅). The crystal structures of the monosulfide (±)-<b>4</b> and the diastereomeric disulfides (±)-<b>3a</b> and (±)-<b>3b</b> have been determined. As for AsA, the sulfur derivatives exhibit strong UV absorptions and can be resolved on a Chiralpak IA column. The monosulfur cage (±)-<b>4</b> is considerably more potent and more selective than AsA and the current “arsenical gold standard”, arsenic­(III) oxide as Trisenox, against the acute promelocytic leukemia cells (NB4) and certain solid cancer cell lines

Vitamin D Represses Retinoic Acid-Dependent Transactivation of the Retinoic Acid Receptor-β2 Promoter: The AF-2 Domain of the Vitamin D Receptor Is Required for Transrepression*

10 pages, 8 figures.Retinoic acid (RA)-dependent activation of the RA receptor ß2 (RARß2) gene in embryonal carcinoma cells is mediated by binding of retinoid receptor heterodimers (RAR/RXR) to a RA response element (RARE) located closely to the TATA box. We have analyzed the effect of vitamin D on the response of the RARß2 promoter to RA in pituitary GH4C1 cells that coexpress receptors for retinoids and vitamin D. Incubation with vitamin D markedly reduced the response to RA caused by transcriptional interference of the vitamin D receptor (VDR) on the RARE. This DNA element binds VDR/RXR heterodimers with high affinity, and these inactive heterodimers can displace active RAR/RXR from the RARE. Overexpression of RXR in GH4C1 cells, as well as incubation with BMS649 (a RXR-specific ligand), increased the inhibitory effect of vitamin D, suggesting that the VDR/RXR heterodimer is the repressive species and that titration of RXR is not responsible for this inhibition. Although DNA binding could be required for full potency of the inhibitory activity of VDR, it is not absolutely required because a truncated receptor (VDR {Delta}1–111), lacking the DNA binding domain, also displays repressor activity. Furthermore, the ability to mediate transrepression by vitamin D was strongly decreased when a mutant VDR in which the last 12 C-terminal aminoacids have been deleted (VDR {Delta}AF-2) was used. Because this region contains the domain responsible for ligand-dependent recruitment of coactivators, titration of common coactivators for VDR and RAR could be involved in the inhibitory effect of vitamin D. In agreement with this hypothesis, overexpression of E1A, which can act as a RARß2 promoter-specific coactivator, significantly reversed repression by vitamin D.This work was supported by Grants PM94–0094 and PM97–0135 from the Direccion General de Enseñanza Superior e Investigación Científica.Peer reviewe

Human Foamy Virus Capsid Formation Requires an Interaction Domain in the N Terminus of Gag

Retroviral Gag expression is sufficient for capsid assembly, which occurs through interaction between distinct Gag domains. Human foamy virus (HFV) capsids assemble within the cytoplasm, although their budding, which mainly occurs in the endoplasmic reticulum, requires the presence of homologous Env. Yet little is known about the molecular basis of HFV Gag precursor assembly. Using fusions between HFV Gag and a nuclear reporter protein, we have identified a strong interaction domain in the N terminus of HFV Gag which is predicted to contain a conserved coiled-coil motif. Deletion within this region in an HFV provirus abolishes viral production through inhibition of capsid assembly