Domain Adaptation in remote sensing: increasing the portability of land-cover classifiers

Among the types of remote sensing acquisitions, optical images are certainly one of the most widely relied upon data sources for Earth observation. They provide detailed measurements of the electromagnetic radiation reflected or emitted by each pixel in the scene. Through a process termed supervised land-cover classification, this allows to automatically yet accurately distinguish objects at the surface of our planet. In this respect, when producing a land-cover map of the surveyed area, the availability of training examples representative of each thematic class is crucial for the success of the classification procedure. However, in real applications, due to several constraints on the sample collection process, labeled pixels are usually scarce. When analyzing an image for which those key samples are unavailable, a viable solution consists in resorting to the ground truth data of other previously acquired images. This option is attractive but several factors such as atmospheric, ground and acquisition conditions can cause radiometric differences between the images, hindering therefore the transfer of knowledge from one image to another. The goal of this Thesis is to supply remote sensing image analysts with suitable processing techniques to ensure a robust portability of the classification models across different images. The ultimate purpose is to map the land-cover classes over large spatial and temporal extents with minimal ground information. To overcome, or simply quantify, the observed shifts in the statistical distribution of the spectra of the materials, we study four approaches issued from the field of machine learning. First, we propose a strategy to intelligently sample the image of interest to collect the labels only in correspondence of the most useful pixels. This iterative routine is based on a constant evaluation of the pertinence to the new image of the initial training data actually belonging to a different image. Second, an approach to reduce the radiometric differences among the images by projecting the respective pixels in a common new data space is presented. We analyze a kernel-based feature extraction framework suited for such problems, showing that, after this relative normalization, the cross-image generalization abilities of a classifier are highly increased. Third, we test a new data-driven measure of distance between probability distributions to assess the distortions caused by differences in the acquisition geometry affecting series of multi-angle images. Also, we gauge the portability of classification models through the sequences. In both exercises, the efficacy of classic physically- and statistically-based normalization methods is discussed. Finally, we explore a new family of approaches based on sparse representations of the samples to reciprocally convert the data space of two images. The projection function bridging the images allows a synthesis of new pixels with more similar characteristics ultimately facilitating the land-cover mapping across images.

Coupled synthesis and translocation restrains polyphosphate to acidocalcisome-like vacuoles and prevents its toxicity.

Eukaryotes contain inorganic polyphosphate (polyP) and acidocalcisomes, which sequester polyP and store amino acids and divalent cations. Why polyP is sequestered in dedicated organelles is not known. We show that polyP produced in the cytosol of yeast becomes toxic. Reconstitution of polyP translocation with purified vacuoles, the acidocalcisomes of yeast, shows that cytosolic polyP cannot be imported, whereas polyP produced by the vacuolar transporter chaperone (VTC) complex, an endogenous vacuolar polyP polymerase, is efficiently imported and does not interfere with growth. PolyP synthesis and import require an electrochemical gradient, probably as a driving force for polyP translocation. VTC exposes its catalytic domain to the cytosol and carries nine vacuolar transmembrane domains. Mutations in the VTC transmembrane regions, which are likely to constitute the translocation channel, block not only polyP translocation but also synthesis. Given that they are far from the cytosolic catalytic domain of VTC, this suggests that the VTC complex obligatorily couples synthesis of polyP to its import in order to avoid toxic intermediates in the cytosol. Sequestration of otherwise toxic polyP might be one reason for the existence of acidocalcisomes in eukaryotes.

Voir le monde comme une image : le schème de l'image mimétique dans la philosophie de Platon (Cratyle, Sophiste, Timée)

Résumé de la thèse Le travail de thèse «VOIR LE MONDE COMME UNE IMAGE. Le schème de l'image mimétique dans la philosophie de Platon (Cratyle, Sophiste, Timée) » d'Alexandre NEVSKY étudie la conception philosophique de l'image chez Platon. En posant la question : qu'est-ce que l'image pour Platon? l'étude se propose, dans un premier temps, d'analyser la manière précise dont l'idée de l'image fonctionne dans l'articulation logique de l'enquête platonicienne, en se basant avant tout sur trois dialogues majeurs où cette idée est explicitement thématisée par Platon lui-même, à savoir le Cratyle, le Sophiste et le Timée. Par une analyse détaillée de ces textes, Alexandre Nevsky essaie de démontrer que l'idée de l'image fonctionne comme un schème euristique dont la logique interne détermine les moments clés dans le déroulement de chaque dialogue examiné, et constitue ainsi une véritable méthode d'investigation philosophique pour Platon. En suivant cette stratégie platonicienne, l'auteur nous montre quel rôle le schème de l'image joue selon Platon d'abord dans la constitution du langage (le Cratyle), puis, dans celle du discours (le Sophiste) et, enfin, dans celle du monde (le Timée). Une telle approche lui permet de revoir l'interprétation traditionnelle de certains passages clés, célèbres pour leurs difficultés, en mettant en évidence la façon dont la nouvelle perspective platonicienne, introduite grâce au schème de l'image, permet de formuler une solution philosophique originale du problème initial. On y trouve ainsi rediscutés, pour ne citer que quelques exemples, la théorie curieuse de l'imitation phonétique et le problème de la justesse propre du nom-image, la définition philosophique de la notion d'image et la distinction platonicienne entre limage-ressemblance et l'image-apparence, la logique paradoxale de l'introduction d'un troisième genre dans la structure ontologique de l'être et la question du sens exact à donner au «discours vraisemblable » de Platon sur la naissance de l'univers. Dans un deuxième temps, cette étude tente de dégager, derrière la méthode heuristique basée sur le schème de l'image, une véritable conception de l'image mimétique chez Platon. L'une des idées principales de la thèse est ici de montrer que cette conception présente une solution philosophique de Platon au problème de l'apparence archaïque. Car, face à la question sophistique : comment une chose - que ce soit le discours ou le monde - peut-elle être une apparence, quelque chose qui n'existe pas? Platon apporte une réponse tout à fait originale elle le peut en tant qu'image. Or, l'image n'est pas une simple apparence illusoire, elle est le reflet d'une autre réalité, indépendante et véritable, que l'on doit supposer, selon Platon, même quand sa nature exacte nous échappe encore. La conception platonicienne de l'image apparaît ainsi comme un pendant indispensable de la théorie des Formes intelligibles et aussi comme son étape préalable au niveau de laquelle l'âme du philosophe, dans son ascension vers la vérité, se retrouve dans un espace intermédiaire, déjà au-delà des illusions du monde phénoménal, mais encore en-deçà des engagements métaphysiques de la théorie des Formes.

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal.

Quorum sensing, a cell-to-cell communication system based on small signal molecules, is employed by the human pathogen Pseudomonas aeruginosa to regulate virulence and biofilm development. Moreover, regulation by small trans-encoded RNAs has become a focal issue in studies of virulence gene expression of bacterial pathogens. In this study, we have identified the small RNA PhrS as an activator of PqsR synthesis, one of the key quorum-sensing regulators in P. aeruginosa. Genetic studies revealed a novel mode of regulation by a sRNA, whereby PhrS uses a base-pairing mechanism to activate a short upstream open reading frame to which the pqsR gene is translationally coupled. Expression of phrS requires the oxygen-responsive regulator ANR. Thus, PhrS is the first bacterial sRNA that provides a regulatory link between oxygen availability and quorum sensing, which may impact on oxygen-limited growth in P. aeruginosa biofilms.

Metabolic engineering of plants for the synthesis of polyhydroxyalkanoates

Synthesis of polyhydroxyalkanoates (PHAs) in crop is viewed as an attractive approach for the production of this family of biodegradable plastics in large quantities and at low costs. Synthesisof PHAs containing various monomers has so far been demonstrated in the cytosol, plastids, and peroxisomes of plants. Several biochemical pathways have been modifies to achieve this, including the isoprenois pathway, the fatty acid biosynthetic pathway, and the fatty acid

The squeeze cell hypothesis for the activation of jasmonate synthesis in response to wounding

Jasmonates are lipid mediators that control defence gene expression in response to wounding and other environmental stresses. These small molecules can accumulate at distances up to several cm from sites of damage and this is likely to involve cell-to-cell jasmonate transport. Also, and independently of jasmonate synthesis, transport and perception, different long-distance wound signals that stimulate distal jasmonate synthesis are propagated at apparent speeds of several cmmin(-1) to tissues distal to wounds in a mechanism that involves clade 3 GLUTAMATE RECEPTOR-LIKE (GLR) genes. A search for jasmonate synthesis enzymes that might decode these signals revealed LOX6, a lipoxygenase that is necessary for much of the rapid accumulation of jasmonic acid at sites distal to wounds. Intriguingly, the LOX6 promoter is expressed in a distinct niche of cells that are adjacent to mature xylem vessels, a location that would make these contact cells sensitive to the release of xylem water column tension upon wounding. We propose a model in which rapid axial changes in xylem hydrostatic pressure caused by wounding travel through the vasculature and lead to slower, radially dispersed pressure changes that act in a clade 3 GLR-dependent mechanism to promote distal jasmonate synthesis.

Advanced Kernel Methods For Remote Sensing Image Classification

Résumé Suite aux recentes avancées technologiques, les archives d'images digitales ont connu une croissance qualitative et quantitative sans précédent. Malgré les énormes possibilités qu'elles offrent, ces avancées posent de nouvelles questions quant au traitement des masses de données saisies. Cette question est à la base de cette Thèse: les problèmes de traitement d'information digitale à très haute résolution spatiale et/ou spectrale y sont considérés en recourant à des approches d'apprentissage statistique, les méthodes à noyau. Cette Thèse étudie des problèmes de classification d'images, c'est à dire de catégorisation de pixels en un nombre réduit de classes refletant les propriétés spectrales et contextuelles des objets qu'elles représentent. L'accent est mis sur l'efficience des algorithmes, ainsi que sur leur simplicité, de manière à augmenter leur potentiel d'implementation pour les utilisateurs. De plus, le défi de cette Thèse est de rester proche des problèmes concrets des utilisateurs d'images satellite sans pour autant perdre de vue l'intéret des méthodes proposées pour le milieu du machine learning dont elles sont issues. En ce sens, ce travail joue la carte de la transdisciplinarité en maintenant un lien fort entre les deux sciences dans tous les développements proposés. Quatre modèles sont proposés: le premier répond au problème de la haute dimensionalité et de la redondance des données par un modèle optimisant les performances en classification en s'adaptant aux particularités de l'image. Ceci est rendu possible par un système de ranking des variables (les bandes) qui est optimisé en même temps que le modèle de base: ce faisant, seules les variables importantes pour résoudre le problème sont utilisées par le classifieur. Le manque d'information étiquétée et l'incertitude quant à sa pertinence pour le problème sont à la source des deux modèles suivants, basés respectivement sur l'apprentissage actif et les méthodes semi-supervisées: le premier permet d'améliorer la qualité d'un ensemble d'entraînement par interaction directe entre l'utilisateur et la machine, alors que le deuxième utilise les pixels non étiquetés pour améliorer la description des données disponibles et la robustesse du modèle. Enfin, le dernier modèle proposé considère la question plus théorique de la structure entre les outputs: l'intègration de cette source d'information, jusqu'à présent jamais considérée en télédétection, ouvre des nouveaux défis de recherche. Advanced kernel methods for remote sensing image classification Devis Tuia Institut de Géomatique et d'Analyse du Risque September 2009 Abstract The technical developments in recent years have brought the quantity and quality of digital information to an unprecedented level, as enormous archives of satellite images are available to the users. However, even if these advances open more and more possibilities in the use of digital imagery, they also rise several problems of storage and treatment. The latter is considered in this Thesis: the processing of very high spatial and spectral resolution images is treated with approaches based on data-driven algorithms relying on kernel methods. In particular, the problem of image classification, i.e. the categorization of the image's pixels into a reduced number of classes reflecting spectral and contextual properties, is studied through the different models presented. The accent is put on algorithmic efficiency and the simplicity of the approaches proposed, to avoid too complex models that would not be used by users. The major challenge of the Thesis is to remain close to concrete remote sensing problems, without losing the methodological interest from the machine learning viewpoint: in this sense, this work aims at building a bridge between the machine learning and remote sensing communities and all the models proposed have been developed keeping in mind the need for such a synergy. Four models are proposed: first, an adaptive model learning the relevant image features has been proposed to solve the problem of high dimensionality and collinearity of the image features. This model provides automatically an accurate classifier and a ranking of the relevance of the single features. The scarcity and unreliability of labeled. information were the common root of the second and third models proposed: when confronted to such problems, the user can either construct the labeled set iteratively by direct interaction with the machine or use the unlabeled data to increase robustness and quality of the description of data. Both solutions have been explored resulting into two methodological contributions, based respectively on active learning and semisupervised learning. Finally, the more theoretical issue of structured outputs has been considered in the last model, which, by integrating outputs similarity into a model, opens new challenges and opportunities for remote sensing image processing.

Synthesis of chemically functionalized superparamagnetic nanoparticles as delivery vectors for chemotherapeutic drugs.

Superparamagnetic iron oxide nanoparticles (SPIONs) are in clinical use for disease detection by MRI. A major advancement would be to link therapeutic drugs to SPIONs in order to achieve targeted drug delivery combined with detection. In the present work, we studied the possibility of developing a versatile synthesis protocol to hierarchically construct drug-functionalized-SPIONs as potential anti-cancer agents. Our model biocompatible SPIONs consisted of an iron oxide core (9-10 nm diameter) coated with polyvinylalcohols (PVA/aminoPVA), which can be internalized by cancer cells, depending on the positive charges at their surface. To develop drug-functionalized-aminoPVA-SPIONs as vectors for drug delivery, we first designed and synthesized bifunctional linkers of varied length and chemical composition to which the anti-cancer drugs 5-fluorouridine or doxorubicin were attached as biologically labile esters or peptides, respectively. These functionalized linkers were in turn coupled to aminoPVA by amide linkages before preparing the drug-functionalized-SPIONs that were characterized and evaluated as anti-cancer agents using human melanoma cells in culture. The 5-fluorouridine-SPIONs with an optimized ester linker were taken up by cells and proved to be efficient anti-tumor agents. While the doxorubicin-SPIONs linked with a Gly-Phe-Leu-Gly tetrapeptide were cleaved by lysosomal enzymes, they exhibited poor uptake by human melanoma cells in culture.

Glutamine synthesis rate in the hyperammonaemic rat brain using simultaneous localized in vivo H-1 and N-15 MRS

Objectives: Glutamine synthetase is a critical step in the glutamate-glutamine cycle, the major mechanism of glutamate neurotransmission and is implicated in the mechanism of ammonia toxicity. 15N MRS is an alternative approach to 13C MRS in studying glutamate- glutamine metabolism. 15N MRS studies allow to measure an apparent glutamine synthesis rate (Vsyn) which reflects a combination of the glutamate- glutamine cycle activity (Vnt) and net glutamine accumulation. The net glutamine synthesis (Vsyn-Vnt) can be directly measured from 1H NMR. Therefore, the aim of this study was to perform in vivo localized 1H MRS interleaved with 15N MRS to directly measure the net glutamine synthesis rate and the apparent glutamine synthesis rate under 15N labeled ammonia infusion in the rat brain, respectively. Methods: 1H and 15N MRS data were acquired interleaved on a 9.4T system (Varian/Magnex Scientific) using 5 rats. 15NH4Cl solution was infused continuously into the femoral vein for up to 10 h (4.5 mmol/h/kg).1 The plasma ammonia concentration was increased to 0.95±0.08 mmol/L (Analox GM7 analyzer). 1H spectra were acquired and quantified as described previously.2 15N unlocalized and localized spectra were acquired using the sequence;3 and quantified using AMARES and an external reference method.4 The metabolic model used to analyze the total Gln and 5-15N labeled Gln time courses is shown on Figure 1A. Results: Glutamine concentration increased from 2.5±0.3 to 15±3.3 mmol/kg whereas the total glutamate concentrations remained unchanged (Figure 1B). The linear fit of the time-evolution of the total Gln from the 1H spectra gave the net synthesis flux (Vsyn-Vnt), which was 0.021± 0.006 mmol/min per g (Figure 1D). The 5-15N Gln peak (_271 ppm) was visible in the first and all subsequent scans, whereas the 2-15N Gln/Glu peak (_342 ppm) appeared after B1.5 h (Figure 1C). From the in vivo 5-15N Gln time course, Vsyn = 0.29±0.1 mmol/min per g and a plasma NH3 fractional enrichment of 71%±6% were calculated. Vnt was 0.26±0.1 mmol/min/g, obtained assuming a negligible Gln efflux.5 Vsyn and Vnt were within the range of 13C NMR measurements.6 Conclusion: The combination of 1H and 15N NMR allowed for the first time a direct and localized measurement of Vnt and apparent glutamine synthesis rate. Vnt is approximately one order of magnitude faster than the net glutamine accumulation.