Many antibiotic resistance genes (ARGs) conferring resistance to a broad range of antibiotics have often been detected in aquatic environments such as untreated and treated wastewater, river and surface water. ARG proliferation in the aquatic environment could depend upon various factors such as geospatial variations, the type of aquatic body, and the type of wastewater (untreated or treated) discharged into these aquatic environments. Likewise, the strong interconnectivity of aquatic systems may accelerate the spread of ARGs through them. Hence a comparative and a holistic study of different aquatic environments is required to appropriately comprehend the problem of antibiotic resistance. Many studies approach this issue using molecular techniques such as metagenomic sequencing and metagenomic data analysis. Such analyses compare the broad spectrum of ARGs in water and wastewater samples, but these studies use comparisons which are limited to similarity/dissimilarity analyses. However, in such analyses, the discriminatory ARGs (associated ARGs driving such similarity/ dissimilarity measures) may not be identified. Consequentially, the reason which drives the dissimilarities among the samples would not be identified and the reason for antibiotic resistance proliferation may not be clearly understood. In this study, an effective methodology, using Extremely Randomized Trees (ET) Algorithm, was formulated and demonstrated to capture such ARG variations and identify discriminatory ARGs among environmentally derived metagenomes. In this study, data were grouped by: geographic location (to understand the spread of ARGs globally), untreated vs. treated wastewater (to see the effectiveness of WWTPs in removing ARGs), and different aquatic habitats (to understand the impact and spread within aquatic habitats). It was observed that there were certain ARGs which were specific to wastewater samples from certain locations suggesting that site-specific factors can have a certain effect in shaping ARG profiles. Comparing untreated and treated wastewater samples from different WWTPs revealed that biological treatments have a definite impact on shaping the ARG profile. While there were several ARGs which got removed after the treatment, there were some ARGs which showed an increase in relative abundance irrespective of location and treatment plant specific variables. On comparing different aquatic environments, the algorithm identified ARGs which were specific to certain environments. The algorithm captured certain ARGs which were specific to hospital discharges when compared with other aquatic environments. It was determined that the proposed method was efficient in identifying the discriminatory ARGs which could classify the samples according to their groups. Further, it was also effective in capturing low-level variations which generally get over-shadowed in the analysis due to highly abundant genes. The results of this study suggest that the proposed method is an effective method for comprehensive analyses and can provide valuable information to better understand antibiotic resistance. / MS

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We present the design, development, and test of three novel, distinct automatic target recognition (ATR) systems for the recognition of airplanes and, more specifically, non-cooperative airplanes, i.e. airplanes that do not provide information when interrogated, in the framework of passive bistatic radar systems. Passive bistatic radar systems use one or more illuminators of opportunity (already present in the field), with frequencies up to 1 GHz for the transmitter part of the systems considered here, and one or more receivers, deployed by the persons managing the system, and not co-located with the transmitters. The sole source of information are the signal scattered on the airplane and the direct-path signal that are collected by the receiver, some basic knowledge about the transmitter, and the geometrical bistatic radar configuration. The three distinct ATR systems that we built respectively use the radar images, the bistatic complex radar cross-section (BS-RCS), and the bistatic radar cross-section (BS-RCS) of the targets. We use data acquired either on scale models of airplanes placed in an anechoic, electromagnetic chamber or on real-size airplanes using a bistatic testbed consisting of a VOR transmitter and a software-defined radio (SDR) receiver, located near Orly airport, France. We describe the radar phenomenology pertinent for the problem at hand, as well as the mathematical underpinnings of the derivation of the bistatic RCS values and of the construction of the radar images.For the classification of the observed targets into pre-defined classes, we use either extremely randomized trees or subspace methods. A key feature of our approach is that we break the recognition problem into a set of sub-problems by decomposing the parameter space, which consists of the frequency, the polarization, the aspect angle, and the bistatic angle, into regions. We build one recognizer for each region. We first validate the extra-trees method on the radar images of the MSTAR dataset, featuring ground vehicles. We then test the method on the images of the airplanes constructed from data acquired in the anechoic chamber, achieving a probability of correct recognition up to 0.99.We test the subspace methods on the BS-CRCS and on the BS-RCS of the airplanes extracted from the data acquired in the anechoic chamber, achieving a probability of correct recognition up to 0.98, with variations according to the frequency band, the polarization, the sector of aspect angle, the sector of bistatic angle, and the number of (Tx,Rx) pairs used. The ATR system deployed in the field gives a probability of correct recognition of $0.82$, with variations according to the sector of aspect angle and the sector of bistatic angle.

Dans cette thèse, nous présentons la conception, le développement et le test de trois systèmes de reconnaissance automatique de cibles (ATR) visant à reconnaître des avions non-coopératifs, c’est-à-dire des avions ne fournissant par leur identité, en utilisant des signaux de radars passifs bistatiques. Les radars passifs bistatiques utilisent un ou plusieurs émetteurs d’opportunité (déjà présents sur le terrain), avec des fréquences allant jusqu’à 1 GHz pour les émetteurs considérés ici, et un ou plusieurs récepteurs déployés par le gestionnaire du système et non-colocalisés avec les émetteurs. Les seules informations utilisées sont les signaux réfléchis sur les avions et les signaux directement reçus qui sont tous les deux collectés par le récepteur, quelques informations concernant l’émetteur, et la configuration géométrique du radar bistatique.Les trois systèmes ATR que nous avons construits utilisent respectivement les images radar, les surfaces équivalentes radar (SER) complexes bistatiques et les SER réelles bistatiques. Nous utilisons des données acquises soit sur des modèles d’avions placés en chambre anéchoique à l’ONERA, soit sur des avions réels en utilisant un banc d’essai bistatique consistant en un émetteur VOR et un récepteur basé sur la radio-logicielle (SDR), et que nous avons déployé aux alentours de l’aéroport d’Orly. Nous décrivons d’abord la phénoménologie radar pertinente pour notre problème ainsi que les fondements mathématiques pour la dérivation de la SER bistatique d’un objet, et pour la construction d’images radar d’un objet.Nous utilisons deux méthodes pour la classification de cibles en classes prédéfinies : les arbres extrêmement aléatoires (extra-trees) et les méthodes de sous-espaces. Une caractéristique-clé de notre approche est que nous divisons le problème de reconnaissance global en un ensemble de sous-problèmes par décomposition de l’espace des paramètres (fréquence, polarisation, angle d’aspect et angle bistatique) en régions. Nous construisons un classificateur par région.Nous validons en premier lieu la méthode des extra-trees sur la base de données MSTAR, composée d’images radar de véhicules terrestres. Ensuite, nous testons cette méthode sur des images radar d’avions que nous avons construites à partir des données acquises en chambre anéchoique. Nous obtenons un pourcentage de classification allant jusqu’à 99%. Nous testons ensuite la méthode de sous-espaces sur les SER bistatiques (complexes et réelles) des avions que nous avons extraits des données de chambre anéchoique. Nous obtenons un pourcentage de classification allant jusqu’à 98%, avec des variations suivant la fréquence, la polarisation, l’angle d’aspect, l’angle bistatique et le nombre de paires émetteur-récepteur utilisées. Nous testons enfin la méthode de sous-espaces sur les SER bistatiques (réelles) extraites des signaux acquis par le banc d’essai déployé à Orly. Nous obtenons une probabilité de classification de 82%, avec des variations suivant l’angle d’aspect et l’angle bistatique. On a donc démontré dans cette thèse que l’on peut reconnaitre des cibles aériennes à partir de leur SER acquise en utilisant des signaux de radars passifs bistatiques. / We present the design, development, and test of three novel, distinct automatic target recognition (ATR) systems for the recognition of airplanes and, more specifically, non-cooperative airplanes, i.e. airplanes that do not provide information when interrogated, in the framework of passive bistatic radar systems. Passive bistatic radar systems use one or more illuminators of opportunity (already present in the field), with frequencies up to 1 GHz for the transmitter part of the systems considered here, and one or more receivers, deployed by the persons managing the system, and not co-located with the transmitters. The sole source of information are the signal scattered on the airplane and the direct-path signal that are collected by the receiver, some basic knowledge about the transmitter, and the geometrical bistatic radar configuration. The three distinct ATR systems that we built respectively use the radar images, the bistatic complex radar cross-section (BS-RCS), and the bistatic radar cross-section (BS-RCS) of the targets. We use data acquired either on scale models of airplanes placed in an anechoic, electromagnetic chamber or on real-size airplanes using a bistatic testbed consisting of a VOR transmitter and a software-defined radio (SDR) receiver, located near Orly airport, France. We describe the radar phenomenology pertinent for the problem at hand, as well as the mathematical underpinnings of the derivation of the bistatic RCS values and of the construction of the radar images.For the classification of the observed targets into pre-defined classes, we use either extremely randomized trees or subspace methods. A key feature of our approach is that we break the recognition problem into a set of sub-problems by decomposing the parameter space, which consists of the frequency, the polarization, the aspect angle, and the bistatic angle, into regions. We build one recognizer for each region. We first validate the extra-trees method on the radar images of the MSTAR dataset, featuring ground vehicles. We then test the method on the images of the airplanes constructed from data acquired in the anechoic chamber, achieving a probability of correct recognition up to 0.99.We test the subspace methods on the BS-CRCS and on the BS-RCS of the airplanes extracted from the data acquired in the anechoic chamber, achieving a probability of correct recognition up to 0.98, with variations according to the frequency band, the polarization, the sector of aspect angle, the sector of bistatic angle, and the number of (Tx,Rx) pairs used. The ATR system deployed in the field gives a probability of correct recognition of $0.82$, with variations according to the sector of aspect angle and the sector of bistatic angle.