Echantillonnage adaptatif optimal dans les champs de Markov, application à l'échantillonnage d'une espèce adventice

Ce travail de thèse propose deux contributions: (i) la formalisation et la résolution approchée du problème d'échantillonnage adaptatif optimal dans les champs de Markov et (ii) la modélisation du problème d'échantillonnage d'une espèce adventice au sein d'une parcelle cultivée et la conception de stratégies d'échantillonnage adaptatives de cette espèce. Pour le premier point, nous avons d'abord formulé le problème du choix d'une stratégie d'échantillonnage adaptative optimale comme un Processus Décisionnel de Markov (PDM) à horizon fini. Nous avons ensuite proposé un algorithme de résolution approchée de tout PDM à horizon fini dont le modèle est connu. Cet algorithme, nommé Least Square Dynamic Programming (LSDP), combine les concepts de programmation dynamique et d'apprentissage par renforcement. Il a ensuite été adapté pour la conception de stratégies d'échantillonnage adaptatives pour tout type de champ de Markov et tout type de coût d'observation. En pratique, l'algorithme LSDP permet une résolution approchée de problèmes d'échantillonnage de plus grande taille qu'avec la plupart des algorithmes classiques d'apprentissage par renforcement. Pour le deuxième point, nous avons d'abord modélisé la répartition spatiale d'une espèce adventice à l'aide des champs de Markov. Un modèle de coût d'échantillonnage d'une espèce adventice a également été proposé. Ces deux modèles ont ensuite été utilisés pour concevoir de nouvelles stratégies d'échantillonnage adaptatives d'une espèce. Une étude sur données réelles a démontré la supériorité des stratégies adaptatives sur des stratégies statiques, classiquement utilisées en échantillonnage adventice.This work is divided into two parts: (i) the theoretical study of the problem of adaptive sampling in Markov Random Fields (MRF) and (ii) the modeling of the problem of weed sampling in a crop field and the design of adaptive sampling strategies for this problem. For the first point, we first modeled the problem of finding an optimal sampling strategy as a finite horizon Markov Decision Process (MDP). Then, we proposed a generic algorithm for computing an approximate solution to any finite horizon MDP with known model. This algorithm, called Least-Squared Dynamic Programming (LSDP), combines the concepts of dynamic programming and reinforcement learning. It was then adapted to compute adaptive sampling strategies for any type of MRF distributions and observations costs. An experimental evaluation of this algorithm was performed on simulated problems. For the second point, we first modeled the weed spatial repartition in the MRF framework. Second, we have built a cost model adapted to the weed sampling problem. Finally, both models were used together to design adaptive sampling strategies with the LSDP algorithm. Based on real world data, these strategies were compared to a simple heuristic and to static sampling strategies classically used for weed sampling

Leukocytes migrating in lymph from the oro-nasal mucosae : interest for vaccination and immune tolerance

We developed a novel sheep model of lymphatic catheterisation to collect, in real time, cells circulating in the afferent lymph draining mainly the mucosae in the head. With this model, we were able to collect migrating leukocytes, either in their baseline condition, or after the administration of a vaccine antigen, from the oro-nasal mucosa to the draining lymph nodes where the immune response takes place. We showed that particulate antigens, such as bacteria, are taken from the tissues to the lymph nodes mainly by two types of cells, the monocytes and the granulocytes, and only occasionally by dendritic cells (DC). This finding challenges the general view, common among immunologists, whereby dendritic cells capture the antigen in the tissues before taking it to the lymph node. In addition, our study identified the permanent migration of a subset of DC - expressing the CD26 molecule – which carries cell-derived apoptotic bodies of self. This DC subset could be responsible for self-tolerance, a mechanism involved in control of transplant rejection, autoimmune diseases and vaccination.Un modèle original de cathétérisme lymphatique chez l'ovin, développé dans notre laboratoire, permet d'accéder en temps réel aux cellules en migration dans la lymphe drainant principalement les muqueuses de la tête de l'animal. Ainsi, à l'état basal ou après administration d'un antigène vaccinal, il est possible de collecter des cellules leucocytaires migrant depuis les muqueuses oro-nasales vers les ganglions, sites décisionnels de la réponse immune. Grâce à ce modèle, nous avons montré que des antigènes particulaires, notamment des bactéries, étaient transportés dans la lymphe essentiellement par deux types de cellules, les monocytes et les granulocytes et plus marginalement par les cellules dendritiques (DC). Ces résultats modifient la vision linéaire communément admise selon laquelle les DC capturent, transportent et présentent les antigènes aux lymphocytes naïfs; ils suggèrent que d'autres populations phagocytaires, impliquées dans le transport antigénique, pourraient moduler la réponse immune. Par ailleurs, nous avons mis en évidence la migration permanente d'une sous-population de DC, identifiée par la molécule CD26, qui transporte des débris de cellules du soi. Ce phénomène pourrait être impliqué dans la tolérance périphérique, mécanisme d'importance dans le rejet des greffes, les maladies auto-immunes et la vaccination

A Combine On-Line Acoustic Flowmeter and Fluorocarbon Coolant Mixture Analyzer for The ATLAS Silicon Tracker

An upgrade to the ATLAS silicon tracker cooling control system may require a change from C3F8 (octafluoro-propane) to a blend containing 10-30% of C2F6 (hexafluoro-ethane) to reduce the evaporation temperature and better protect the silicon from cumulative radiation damage with increasing LHC luminosity. Central to this upgrade is a new acoustic instrument for the real-time measurement of the C3F8/C2F6 mixture ratio and flow. The instrument and its Supervisory, Control and Data Acquisition (SCADA) software are described in this paper. The instrument has demonstrated a resolution of 3.10-3 for C3F8/C2F6 mixtures with ~20%C2F6, and flow resolution of 2% of full scale for mass flows up to 30gs-1. In mixtures of widely-differing molecular weight (mw), higher mixture precision is possible: a sensitivity of < 5.10-4 to leaks of C3F8 into the ATLAS pixel detector nitrogen envelope (mw difference 160) has been seen. The instrument has many potential applications, including the analysis of mixtures of hydrocarbons, vapours for semi-conductor manufacture and anaesthesia

Closedness of star products and cohomologies

We first review the introduction of star products in connection with deformations of Poisson brackets and the various cohomologies that are related to them. Then we concentrate on what we have called ``closed star products" and their relations with cyclic cohomology and index theorems. Finally we shall explain how quantum groups, especially in their recent topological form, are in essence examples of star products.Comment: 16 page

Development of a custom on-line ultrasonic vapour analyzer/flowmeter for the ATLAS inner detector, with application to gaseous tracking and Cherenkov detectors

Precision sound velocity measurements can simultaneously determine binary gas composition and flow. We have developed an analyzer with custom electronics, currently in use in the ATLAS inner detector, with numerous potential applications. The instrument has demonstrated ~0.3% mixture precision for C3F8/C2F6 mixtures and < 10-4 resolution for N2/C3F8 mixtures. Moderate and high flow versions of the instrument have demonstrated flow resolutions of +/- 2% F.S. for flows up to 250 l.min-1, and +/- 1.9% F.S. for linear flow velocities up to 15 ms-1; the latter flow approaching that expected in the vapour return of the thermosiphon fluorocarbon coolant recirculator being built for the ATLAS silicon tracker.Comment: Paper submitted to TWEPP2012; Topical Workshop on Electronics for Particle Physics, Oxford, UK, September 17-21, 2012. KEYWORDS: Sonar; Saturated fluorocarbons; Flowmetry; Sound velocity, Gas mixture analysis. 8 pages, 7 figure

Implementation of ultrasonic sensing for high resolution measurement of binary gas mixture fractions

We describe an ultrasonic instrument for continuous real-time analysis of the fractional mixture of a binary gas system. The instrument is particularly well suited to measurement of leaks of a high molecular weight gas into a system that is nominally composed of a single gas. Sensitivity &#60; 5 × 10−5 is demonstrated to leaks of octaflouropropane (C3F8) coolant into nitrogen during a long duration (18 month) continuous study. The sensitivity of the described measurement system is shown to depend on the difference in molecular masses of the two gases in the mixture. The impact of temperature and pressure variances on the accuracy of the measurement is analysed. Practical considerations for the implementation and deployment of long term, in situ ultrasonic leak detection systems are also described. Although development of the described systems was motivated by the requirements of an evaporative fluorocarbon cooling system, the instrument is applicable to the detection of leaks of many other gases and to processes requiring continuous knowledge of particular binary gas mixture fractions

Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads.

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population. (Résumé d'auteur

CNTN6 mutations are risk factors for abnormal auditory sensory perception in autism spectrum disorders

Contactin genes CNTN5 and CNTN6 code for neuronal cell adhesion molecules that promote neurite outgrowth in sensory-motor neuronal pathways. Mutations of CNTN5 and CNTN6 have previously been reported in individuals with autism spectrum disorders (ASDs), but very little is known on their prevalence and clinical impact. In this study, we identified CNTN5 and CNTN6 deleterious variants in individuals with ASD. Among the carriers, a girl with ASD and attention-deficit/hyperactivity disorder was carrying five copies of CNTN5. For CNTN6, both deletions (6/1534 ASD vs 1/8936 controls; P=0.00006) and private coding sequence variants (18/501 ASD vs 535/33480 controls; P=0.0005) were enriched in individuals with ASD. Among the rare CNTN6 variants, two deletions were transmitted by fathers diagnosed with ASD, one stop mutation CNTN6W923X was transmitted by a mother to her two sons with ASD and one variant CNTN6P770L was found de novo in a boy with ASD. Clinical investigations of the patients carrying CNTN5 or CNTN6 variants showed that they were hypersensitive to sounds (a condition called hyperacusis) and displayed changes in wave latency within the auditory pathway. These results reinforce the hypothesis of abnormal neuronal connectivity in the pathophysiology of ASD and shed new light on the genes that increase risk for abnormal sensory perception in ASD

Verifiable Delay Functions

We study the problem of building a verifiable delay function (VDF). A VDF requires a specified number of sequential steps to evaluate, yet produces a unique output that can be efficiently and publicly verified. VDFs have many applications in decentralized systems, including public randomness beacons, leader election in consensus protocols, and proofs of replication. We formalize the requirements for VDFs and present new candidate constructions that are the first to achieve an exponential gap between evaluation and verification time

Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments.

International audienceSHANK genes code for scaffold proteins located at the post-synaptic density of glutamatergic synapses. In neurons, SHANK2 and SHANK3 have a positive effect on the induction and maturation of dendritic spines, whereas SHANK1 induces the enlargement of spine heads. Mutations in SHANK genes have been associated with autism spectrum disorders (ASD), but their prevalence and clinical relevance remain to be determined. Here, we performed a new screen and a meta-analysis of SHANK copy-number and coding-sequence variants in ASD. Copy-number variants were analyzed in 5,657 patients and 19,163 controls, coding-sequence variants were ascertained in 760 to 2,147 patients and 492 to 1,090 controls (depending on the gene), and, individuals carrying de novo or truncating SHANK mutations underwent an extensive clinical investigation. Copy-number variants and truncating mutations in SHANK genes were present in ∼1% of patients with ASD: mutations in SHANK1 were rare (0.04%) and present in males with normal IQ and autism; mutations in SHANK2 were present in 0.17% of patients with ASD and mild intellectual disability; mutations in SHANK3 were present in 0.69% of patients with ASD and up to 2.12% of the cases with moderate to profound intellectual disability. In summary, mutations of the SHANK genes were detected in the whole spectrum of autism with a gradient of severity in cognitive impairment. Given the rare frequency of SHANK1 and SHANK2 deleterious mutations, the clinical relevance of these genes remains to be ascertained. In contrast, the frequency and the penetrance of SHANK3 mutations in individuals with ASD and intellectual disability-more than 1 in 50-warrant its consideration for mutation screening in clinical practice