Dans cette thèse, nous visons à formaliser les effets calculatoires. En effet, les langages de programmation les plus utilisés impliquent différentes sortes d'effets de bord: changement d'état, exceptions, entrées / sorties, non-déterminisme, etc. Ils peuvent apporter facilité et flexibilité dans le processus de codage. Cependant, le problème est de prendre en compte les effets lorsque l'on veut prouver des propriétés de programmes. La principale difficulté dans ce genre de preuve de programmes est le décalage entre la syntaxe des opérations avec effets de bord et leur interprétation. Typiquement, un fragment de programme avec des arguments de type X qui retourne une valeur de type Y n'est pas interprété comme une fonction de X vers Y , à cause des effets.L'approche algébrique la plus connue pour ce problème permet une interprétation des programmes, y compris ceux comportant des effets, en utilisant des monades : l'interprétation est une fonction de X vers T (Y ) où T est une monade. Cette approche a été étendue aux théories de Lawvere et aux "gestionnaires algébriques" (algebraic handlers). Une autre approche, appelée logique décorée, fournit une sémantique équationnelle pour ces programmes. Nous spécialisons l'approche de la logique décorée pour les effets liés à l'état de la mémoire et à la gestion des exceptions en définissant la logique décorée pour les états (L_st) et la logique décorée pour les exceptions (L_exc), respectivement. Elles nous permettent de prouver des propriétés de programmes impliquant de tels effets. Ensuite, nous formalisons ces logiques en Coq et certifions les preuves associées. Ces logiques sont construites de manière à être correctes. En outre, nous introduisons une notion de complétude syntaxique relative d'une théorie dans une logique donnée par rapport à une sous-logique. Nous montrons que la théorie décorée pour les états globaux ainsi que deux théories décorées pour les exceptions sont relativement complets relativement à leur sous-logique pure. Non seulement nous pouvons utiliser le système développé pour prouver des programmes comportant des effets, mais également nous utilisons cette formalisation pour certifier les résultats de complétude obtenus. / In this thesis, we aim to formalize the effects of a computation. Indeed, most used programming languages involve different sorts of effects: state change, exceptions, input/output, non-determinism, etc. They may bring ease and flexibility to the coding process. However, the problem is to take into account the effects when proving the properties of programs. The major difficulty in such kind of reasoning is the mismatch between the syntax of operations with effects and their interpretation. Typically, a piece of program with arguments in X that returns a value in Y is not interpreted as a function from X to Y , due to the effects. The best-known algebraic approach to the problem interprets programs including effects with the use of monads: the interpretation is a function from X to T(Y) where T is a monad. This approach has been extendedto Lawvere theories and algebraic handlers. Another approach called, the decorated logic, provides a sort of equational semantics for reasoning about programs with effects. We specialize the approach of decorated logic to the state and the exceptions effects by defining the decorated logic for states (L_st) and the decorated logic for exceptions (L_exc), respectively. This enables us to prove properties of programs involving such effects. Then, we formalize these logics in Coq and certify the related proofs. These logics are built so as to be sound. In addition, we introduce a relative notion of syntactic completeness of a theory in a given logic with respect to a sublogic. We prove that the decorated theory for the global states as well as two decorated theories for exceptions are syntactically complete relatively to their pure sublogics. These proofs are certified in Coq as applications of ourgeneric frameworks.

Les grottes sont un environnement particulier aux propriétés géophysiques singulières. C’est un milieu qui offre une conservation exceptionnelle et dans lequel s’inscrit, dans la matrice minérale, la marque du moindre geste qui y est réalisé. Assidument fréquentées au Paléolithique supérieur, de nombreuses cavités renferment des témoignages variés du passage des hommes. L’art pariétal est un des témoins, parfois spectaculaire, de cette fréquentation. D’autres vestiges (marques, objets, aménagements…) y sont aussi observables. Souvent moins visibles, moins spectaculaires car faisant entrer en jeu des éléments plus communs, l’intérêt de ces vestiges, dans la compréhension des comportements préhistoriques, a été reconnu tardivement dans l’histoire de la discipline. Parmi ces diverses traces d’activités humaines, et faisant suite aux travaux initiateurs sur le sujet (Bégouën et Clottes, 1981 ; Clottes 2007 et 2009), nous nous intéressons ici aux dépôts d’objets en paroi. Aucune étude approfondie et croisée à grande échelle de ce phénomène n’avait été conduite jusqu’ici. Les différentes matérialisations de ces gestes de dépôts, leurs constituants fondamentaux, les cultures et les territoires concernés ainsi que l’approfondissement de la connaissance des comportements humains en grottes ornées au travers de l’étude de ces gestes ont été les principaux axes de notre recherche.Nous avons ainsi identifié la présence de ces gestes de dépôts dans une quarantaine de sites ornés répartis sur l’espace franco-cantabrique durant tout le Paléolithique supérieur. Nous avons essentiellement basé la construction de notre méthode d’étude et notre analyse sur l’étude exhaustive et contextualisée de ces dépôts dans six sites français : Blanchard, Foissac, Gargas inférieure, Gargas supérieure, Le Mammouth et Le Pigeonnier. La priorité était pour nous de proposer une lecture interprétative des comportements à l’origine de ces dépôts. La matière dure animale (à l’état de fragments), et dans une moindre mesure le silex et l’ocre, sont les éléments essentiellement constitutifs de ces dépôts. Les résultats montrent que ces derniers sont omniprésents dans les grottes ornées. Ils ne sont cependant pas tous en tout point comparable. Nous avons pu mettre en évidence différentes catégories de gestes de dépôts. La plupart sont intentionnels mais sous-tendus par des motivations distinctes (symbolique, pragmatique, personnelle…). Nous avons identifié quatre pratiques symboliques où le dépôt est un medium permettant une connexion (« reliance ») avec l’Invisible par l’intermédiaire de la paroi-réceptacle.Ces pratiques (très fréquemment observées au Magdalénien et au Gravettien) sont des comportements symboliques fondamentaux qui motivent la fréquentation des cavités par ces populations préhistoriques durant tout le Paléolithique supérieur. Elles sont intimement reliées aux modes de vie, aux traditions culturelles et à la cosmogonie des sociétés préhistoriques. Ces pratiques préhistoriques peuvent être envisagées selon l’idée d’une possible affiliation à certains des grands universaux qui participent du fonds commun symbolique, et même spirituel, de l’humanité. / Caves are a particular environment with singular geophysics properties. It is an environment which offers an exceptional preservation and in which registers, in the mineral matrix, the mark of the slightest gesture which is realized there. Assidument frequented in the upper Palaeolithic, numerous cavities contain varied vestiges of the human passage.The parietal Art is one of the marks, sometimes spectacular, of this frequentation.Other vestiges (marks, objects, arrangements…) are there also observable. Often less visible, less spectacular because using more common elements, the interest of these vestiges, in the understanding of the prehistoric behavior, was late recognized in the history of the discipline. Among these diverse tracks of human activities, and following upon the works initiators on the subject (Bégouën et Clottes, 1981 ; Clottes 2007 et 2009), we are interested here in the deposits of objects in rock face. No in-depth and crossed study on a large scale of this phenomenon had been led up to here.The various realizations of these gestures of deposits, their fundamental constituents, the cultures and the concerned territories as well as the deepening of the knowledge of the human behavior in decorated caves through the study of these gestures were the main axes of our research.We so identified the presence of these gestures of deposits in about forty decorated sites distributed on the French-Catabric space during all the upper Palaeolithic. We essentially based the construction of our method of study and our analysis on the exhaustive and contextualised study of these deposits in six French sites : Blanchard, Foissac, Gargas inférieure, Gargas supérieure, Le Mammouth et Le Pigeonnier. The priority was for us to propose an interpretative reading of the behavior at the origin of these deposits. The animal hard material (in the state of fragments), and to a lesser extent the flint and the ochre, are the essentially constituent elements of these deposits. The results show that these last ones are omnipresent in the decorated caves. They are not however all completely comparable. We were able to bring to light various categories of gestures of deposits. Most are deliberate but underlain by different motivations (symbolic, pragmatic, personal…). We identified four symbolic practices where the deposit is a medium allowing a connection (« reliance ») with the Invisible through the rock face - receptacle.These practices (very frequently observed in the Magdalenian and in the Gravettian) are fundamental symbolic behavior which motivate the frequentation of cavities by these prehistoric populations during all the upper Palaeolithic. They are intimately bound with the lifestyles, with the cultural traditions and with the cosmogony of the prehistoric societies. These prehistoric practices can be envisaged according to the idea of a possible affiliation in some of the big universals which participate in the symbolic common fund, and even spiritual, in the humanity.

This essay examines the ways the decorated farmhouses known as hälsingegårdar of Hälsingland, Sweden, are depicted in art from the late nineteenth century Düsseldorf school of painting to contemporary pixel art and how the ways of depiction have changed over time. Three different works of art are analyzed with Erwin Panofsky’s model for iconographic and iconological analysis. Results show a gradual difference in technique and the artist's personal attitudes towards the hälsingegårdar. Starting with the genre painting’s idyllic interpretation of the peasant life as the height of nationalist values to the more provincialist cherry-picking of the late twentieth century naive painting and the final contemporary pixel art piece of ambivalence and distancing from the hälsingegårdar as a means of interpretation and understanding.

Mieux comprendre les mécanismes de la résistance aux antibiotique est un enjeu important dans la lutte contre les maladies infectieuses, qui fait face à la propagation de bactéries multi-résistantes. Les études d'association à l'échelle des génomes sont des outils puissants pour explorer les polymorphismes liés aux variations phénotypiques dans une population. Leur cadre méthodologique est très documenté pour les eucaryotes, mais leur application aux bactéries est très récente. Durant cette thèse, j'ai cherché à rendre ces outils mieux adaptés aux génomes plastiques des bactéries, principalement en travaillant sur la représentation des variations génétiques. En effet, parce que les bactéries ont la capacité à échanger du matériel génétique avec leur environnement, leurs génomes peuvent être trop différents au sein d'une espèce pour être alignés contre une référence. La description des variations par des fragments de séquence de longueur k, les k-mers, offre la flexibilité nécessaire mais ne permet pas une interprétation directe des résultats obtenus. La méthode mise au point teste l'association de ces k-mers avec le phénotype, et s'appuie sur un graphe de De Bruijn pour permettre la visualisation du contexte génomique des k-mers identifiés par le test, sous forme de graphes. Cette vue synthétique renseigne sur la nature de la séquence identifiée: il peut par exemple s'agir de polymorphisme local dans un gène ou de l'acquisition d'un gène dans un plasmide. Le type de variant représenté dans un graphe peut être prédit avec une bonne performance à partir de descripteurs du graphe, rendant plus opérationnelles les approches par k-mers pour l'étude des génomes bactériens / The emergence and spread of multi-drug resistance has become a major worldwide public health concern, calling for better understanding of the underlying resistance mechanisms. Genome-wide association studies are powerful tools to finely map the genetic polymorphism linked to the phenotypic variability observed in a population. However well documented for eukaryotic genome analysis, these studies were only recently applied to prokaryota.Through this PhD project, I searched how to better adapt these tools to the highly plastic bacterial genomes, mainly by working on the representation of the genetic variations in these genomes. Indeed, because the bacteria have the faculty to acquire genetic material by a means other than direct inheritance from a parent cell, their genomes can differ too much within a species to be aligned against a reference. A representation using sequence fragments of length k - the so-called k-mers - offers the required flexibility but generates redundancy and does not allow for a direct interpretation of the identified associations. The method we set up tests the association of these k-mers with the phenotype, and takes advantage of a De Bruijn graph (DBG) built over all genomes to remove the local redundancy of k-mers, and offer a visualisation of the genomic context of the k-mers identified by the test. This synthetic view as DBG subgraphs informs on the nature of the identified sequence: e.g. local polymorphism in a gene or gene acquired through a plasmid. The type of variant can be predicted correctly in 96% of the cases from descriptors of the subgraphs, providing a tractable framework for k-mer-based association studies

The main thrust of this thesis is the development of new triarylborane containing luminescent molecules as well as utilizing triarylboron center as a receptor for the selective detection of biologically, environmentally and industrially important anions such as fluoride and cyanide in aqueous and non-aqueous solutions. The thesis contains nine chapters. The contents of each chapter are described below. Chapter 1 The first chapter is an introduction to the theme of the thesis and presents a general review on the techniques, theories and photochemistry relevant to the present work with emphasis on photochemistry of triarylboranes and their importance in the field of anion sensor chemistry. A review on various boron based luminophores is also presented. Chapter 2 The second chapter deals with the general experimental techniques and synthetic procedures utilized in this work. Chapter 3 This chapter deals with the synthesis of boryl-BODIPY dyads (1-8) in which triarylborane acts as anion receptor and BODIPY as a signalling unit. The absorption spectra of all boryl-BODIPY dyads shows similar pattern. However, the fluorescence spectra of 1, 2, 3, 6 and 7 shows dual emission bands whereas 4, 5 and 8 exhibit a single emission band. These interesting photophysical properties of boryl-BODIPYs (1-8) depends on the dihedral angle between two chromophores and partial energy transfer from donor (triarylborane) to acceptor (BODIPY) unit. The energy transfer efficiency of compounds 4, 5 and 8 is higher (close to 100%) compared to other series of boryl-BODIPYs (1-3, 6 and 7), due to the orthogonal arrangement of chromophores with high dihedral angles. To better understand photophysical properties and energy transfer process, anion binding studies were carried out since triarylborane acts as receptor for fluoride and cyanide ions. Anion binding studies of boryl-BODIPYs were (1-5) carried out in dichloromethane solutions and using tetrabutylammonium salt of fluoride/cyanide. All boryl-BODIPY dyads (1-5) were sensitive and selective sensor of fluoride, whereas the presence of only excess amounts (20 equv or more amounts) of cyanide made any changes in absorption and emission spectra. Other anions even above 100 eq were unable to cause any change. The quenching efficiency of compounds 4 and 5 was found to be more than that of other boryl-BODIPYs (1 and 3). The binding of fluoride with boryl-BODIPY (1-5) was entirely reversible; addition of BF3•Et2O to the fluoride adducts of compounds (1-5) regenerated the parent compounds. Chapter 4 In chapter 3, it was established that linear boryl-BODIPY dyads (1-8) show dual/single fluorescence bands depending on the dihedral angle between triarylborane and BODIPY unit. This Chapter describes the synthesis of three new “V” shaped boryl-BODIPY dyads (9, 10 and 11) their optical properties, Compound 9-11 are structurally similar differing only in the number of methyl substituents on the BODIPY moiety which were found to play major role in determining their optical behavior. The dyads show rare forms of multiple channel emission characteristics arising from different extents of electronic energy transfer (EET) processes between the two covalently linked fluorescent chromophores (triarylborane and BODIPY units). Owing to the presence of Lewis acidic triarylborane moiety, the dyads function as highly selective and sensitive fluoride sensors with vastly different response behavior. Upon binding of fluoride to the tricoordinate borane centre, dyad 9 shows gradual quenching of its BODIPY dominated emission due to the cessation of (borane to BODIPY) EET process. Dyad 10 shows ratiometric changes in its emission behavior upon addition of fluoride. Dyad 11 forms fluoride induced nanoaggregates which result in fast and effective quenching of its emission intensity upon addition of even small quantities of analyte (i.e. 0.1 equivalent of fluoride). When the solution is allowed to stand, disaggregation of the molecules results in partial recovery of the initial fluorescence bands. Thus, small structural alterations in these three structurally close dyads (9-11) result in exceptionally versatile and unique photophysical behavior and remarkably diverse responses towards a single analyte i.e. fluoride anion. Chapter 5 This chapter deals with intermolecular charge transfer (ICT) process in borane containing donor-acceptor triads and tetrads to realize colorimetric response for small anions such as fluoride and cyanide. Triad 12 and tetrad 13 incorporating –B(Mes)2, BDY (borondipyrromethene), and TPA (triphenylamine) were synthesized. Introduction of two dissimilar acceptors (triarylborane and BODIPY) on a single donor (TPA) resulted in two distinct ICT process (amine to borane and amine to BDY). The absorption and emission properties of new triad and tetrad are highly dependent on individual building units. The nature of electronic communication among the individual fluorophore units has been comprehensively investigated and compared with building units. Compounds 12 and 13 showed chromogenic and fluorogenic response towards small anions such as fluoride and cyanide. Chapter 6 In the previous chapter, it was demonstrated that although triphenylamine-triarylborane-BODIPY donor-acceptor conjugates show colorimetric response towards fluoride and cyanide. They could not distinguish these two interfering anions. To overcome the anion interference peripherally triarylborane decorated porphyrin (14) and its Zn(II) complex (15) were designed and synthesized and this forms the subject matter of this Chapter. Compound 15 contains two different Lewis acidic binding sites (Zn(II) and boron centre). Unlike all previously known triarylborane based sensors, the optical responses of 15 towards fluoride and cyanide are distinctively different thus enabling the discrimination of these two interfering anions. Metalloporphyrin 15 shows a multiple channel fluorogenic response towards fluoride and cyanide and also a selective visual colorimetric response towards cyanide. By comparison with model systems and from detailed photophysical studies on 14 and 15, it was concluded that the preferential binding of fluoride occurs at the peripheral borane moieties resulting in the cessation of the EET (electronic energy transfer) process from triarylborane to porphyrin core and with negligible negative cooperative effects. On the other hand, cyanide binding occurs at the Zn(II) core leading to drastic changes in its absorption behavior which can be followed by the naked eye. Such changes are not observed when the boryl substituent is absent (e.g. tetraphenyl-Zn(II)-porphyrin or TPP). The conjugates 14 and 15 showed reversible binding interaction towards CN and F and they are capable of extracting fluoride from aqueous media. Chapter 7 This Chapter deals with the design of a sensor which can detect fluoride colorimetrically in aqueous medium. Detecting fluoride in aqueous solution is an important area of current research owing to both positive and negative health and environmental effects associated with the fluoride ion. Although numerous fluoride sensors are reported, the colorimetric sensing (visual detection without the need of costly equipment and complicated analytical of fluoride at recommended levels 0.7 ppm) has not realized. Here we report the design, optical and fluoride sensing ability of two new water soluble Lewis acidic triarylborane-triarylamine conjugates 16 and 17 (containing one or two ammonium cations (-C6H4-NMe3). Compound 17 shows selective colorimetric response for aqueous inorganic fluoride at as low a level as 0.1 ppm Chapter 8 The synthesis and optical properties of four new triarylborane–dipyrromethane (TAB– DPM) conjugates (19a–d) containing dual binding sites (hydrogen bond donor and Lewis acid) have been reported. The new compounds exhibit a selective fluorogenic response towards the F− ion. The NMR titrations show that the fluoride ions bind to the TAB–DPM conjugates via the Lewis acidic triarylborane centre in preference to the hydrogen bond donor (dipyrromethane) units. Chapter 9 A new triarylborane-aza-BODIPY conjugate is reported (22). The conjugate molecule consists of two blue emissive dimesitylarylborane moiety and a NIR (near infra-red) emissive aza-BOIDPY core and shows panchromatic absorption spanning over ~300-800 nm region. The presence of two different fluorophore units in the conjugate leads to a broad dual-emissive feature covering a large part of visible and NIR region. DFT computational studies suggest limited electronic communication between the individual fluorophore units which may be responsible for the intriguing optical features of the conjugate molecule. Further, the broadband emissive conjugate can act as a selective sensor for fluoride anion as a result of fluorescence quenching response in both visible as well as in NIR spectral region.

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