Η διδακτορική διατριβή με τίτλο «Σχεδιασμός και υλοποίηση συστήματος διαχείρισης και ενοποίησης διαφορετικών ταυτοτήτων χρηστών σε δίκτυα νέας γενιάς» πραγματεύεται την οργάνωση και διαχείριση των ταυτοτήτων χρηστών σε ένα ενοποιημένο δικτυακό περιβάλλον αποτελούμενο από διαφορετικά δίκτυα, τεχνολογίες και υπηρεσίες. Η διατριβή, αρχικά εξετάζει τις προτεινόμενες αρχιτεκτονικές και υπηρεσίες του Μελλοντικού Διαδικτύου και ανάμεσα στα προβλήματα που παρουσιάζονται επικεντρώνεται στην επίλυση της Διαχείρισης Ψηφιακών Ταυτοτήτων (Identity Management – IdM). Μέχρι τώρα οι προτεινόμενες λύσεις είναι λειτουργικές μόνο κάτω από συγκεκριμένες συνθήκες, όπως π.χ. την εφαρμογή νέων παγκόσμιων προσδιοριστικών ή τη δημιουργία μεγάλων ομοσπονδιών εμπιστοσύνης. Στην πράξη όμως τέτοιες πρακτικές δεν μπορούν να υιοθετηθούν από μεγάλης κλίμακας δίκτυα. Σε αντίθεση με αυτές τις προσεγγίσεις, η συγκεκριμένη διατριβή προτείνει τον σχεδιασμό ενός συστήματος που θα έχει ως σκοπό να βοηθάει τα εκάστοτε πλαίσια (δίκτυα, ομοσπονδίες, παρόχους κ.τ.λ.) να αντιμετωπίζουν μόνα τους τα προβλήματα διαχείρισης ταυτοτήτων που παρουσιάζονται στις υπηρεσίες τους. Για να επιτευχθεί αυτό, αρχικά αποδεικνύεται πως είναι αναγκαίος ο διαχωρισμός της διαδικασίας ανακάλυψης δεδομένων που σχετίζονται με τις ψηφιακές ταυτότητες, από τις υπόλοιπες διαδικασίες διαχείρισης (π.χ. ανταλλαγή δεδομένων μεταξύ παρόχων). Με βάση αυτή την προσέγγιση δημιουργήθηκε το σύστημα DIMANDS, το οποίο δίνει την δυνατότητα στους παρόχους να ανακαλύπτουν τα δεδομένα ταυτότητας που απαιτούνται για την ολοκλήρωση μιας δεδομένης υπηρεσίας, ενώ παράλληλα τους επιτρέπει να διαχειρίζονται αυτόνομα τις υπόλοιπες διαδικασίες που σχετίζονται με την υπηρεσία αυτή. Το σύστημα πληροί όλες τις απαιτήσεις ασφάλειας, εμπιστοσύνης, διαφύλαξης ιδιοαπόρρητου και απόδοσης ενός μεγάλης κλίμακας συστήματος διαχείρισης ψηφιακών ταυτοτήτων. Αυτό αποδεικνύεται από προσομοιώσεις που έγιναν στο περιβάλλον εξομοίωσης OPNET. Τέλος σημειώνεται πως ένα δοκιμαστικό σενάριο χρήσης του συστήματος υλοποιήθηκε σε περιβάλλον Ruby on Rails. / This PhD thesis entitled “Design and implementation of a system for the management and unification of users’ diverse identities in next generation networks” examines the organization and management of users’ identity data in a unified network environment composed by diverse networks, technologies and services. The dissertation, initially examines the proposed future Internet architectures and services and among the identified problems, it focuses on the management of Digital Identities (Identity Management – IdM). Until now, the proposed solutions are only functional if specific conditions are met, such as the implementation of new global identifiers or creating large scale federations of trust. In practice though, these conditions cannot be enforced in large-scale networks. Contrary to these approaches, this dissertation proposes the design of a system capable of helping the individual contexts (federations, networks, service providers, etc.) to independently deal with their own identity management problems that appear in their services. To achieve this, initially we prove that it is necessary to separate the process of discovering identity related data from the all the rest of the identity management procedures (e.g. data exchange between providers). Based on this approach we created DIMANDS, a system which allows providers to discover the necessary data required to complete a specific service, while enabling them to manage autonomously the remaining procedures associated with this service. The system meets all the requirements of security, trust, privacy and performance of a large scale identity management system. This is evidenced by simulations made in the OPNET simulation environment. Finally it must be noted that a demo based on the system’s functionality was implemented in Ruby on Rails environment.

Στην παρούσα διατριβή προτείνονται Μηχανισμοί Ασφάλειας για την ανάπτυξη ασφαλών και αξιόπιστων διάχυτων υπηρεσιών υγείας πάνω σε Δίκτυα Επόμενης Γενιάς (Next Generation Networks – NGN). Οι προτεινόμενοι Μηχανισμοί Ασφάλειας έχουν ως στόχο να λειτουργήσουν προσθετικά στο επίπεδο ασφάλειας που προσφέρουν οι υπάρχοντες μηχανισμοί ασφάλειας που υποστηρίζονται από το NGN. Αυτό είναι αναγκαίο καθώς οι διάχυτες υπηρεσίες υγείας εμπεριέχουν ιδιαιτέρως ευαίσθητη πληροφορία. Επιπρόσθετα, στην παρούσα διατριβή προτείνεται ένα γενικό πλαίσιο εφαρμογής, το οποίο υποστηρίζει τους προτεινόμενους Μηχανισμούς Ασφάλειας, προκειμένου να επιτυγχάνεται γρήγορη και αποτελεσματική ανάπτυξη ασφαλών και αξιόπιστων διάχυτων υπηρεσιών υγείας πάνω σε NGN. Πιο συγκεκριμένα, το προτεινόμενο πλαίσιο βασίζεται στην αρχιτεκτονική του προτύπου ETSI/Parlay και επεκτείνει το σύνολο των Διεπαφών των Χαρακτηριστικών Ικανότητας Υπηρεσίας (Service Capability Features Interfaces – SCFs Interfaces) και το σύνολο των μηχανισμών που υποστηρίζει το Πλαίσιο ETSI/Parlay. Το προτεινόμενο πλαίσιο επεκτείνει το σύνολο των Διεπαφών των Χαρακτηριστικών Ικανότητας Υπηρεσίας προκειμένου αυτό να περιλαμβάνει όχι μόνο τις διεπαφές που σχετίζονται με τις υπηρεσίες του υποκείμενου δικτύου (NGN), αλλά και επιπλέον διεπαφές που δίνουν τη δυνατότητα σε διάχυτες υπηρεσίες υγείας να έχουν πρόσβαση σε ικανότητες επαίσθησης (sensing capabilities) δικτύων αισθητήρων που είναι υπεύθυνα για τη συλλογή πληροφορίας περιβάλλοντος καθώς και βιοπληροφορίας. Επίσης, το προτεινόμενο πλαίσιο επεκτείνει το σύνολο των μηχανισμών που υποστηρίζει το Πλαίσιο ETSI/Parlay προκειμένου να είναι δυνατή η παροχή σε διάχυτες υπηρεσίες υγείας όχι μόνο των βασικών μηχανισμών, που υποστηρίζονται από το προτυποποιημένο Πλαίσιο ETSI/Parlay, αλλά και των Μηχανισμών Δικτύων Αισθητήρων καθώς και των Μηχανισμών Ασφάλειας, οι οποίοι προτείνονται στην παρούσα διατριβή. Οι Μηχανισμοί Ασφάλειας, οι οποίοι προτείνονται, στοχεύουν στην παροχή ασφάλειας στα δεδομένα των τελικών χρηστών καθώς και στην ασφαλή πρόσβαση στις διάχυτες υπηρεσίες υγείας και στην ασφαλή χρήση τους. Πιο συγκεκριμένα, οι προτεινόμενοι Μηχανισμοί Ασφάλειας επικεντρώνονται στη διασφάλιση της εμπιστευτικότητας των δεδομένων, της ακεραιότητας των δεδομένων, της πιστοποίησης αυθεντικότητας καθώς και του ελέγχου πρόσβασης των οντοτήτων που συμμετέχουν σε διάχυτες υπηρεσίες υγείας. Για τη διασφάλιση της εμπιστευτικότητας των δεδομένων προτείνεται ένα γενικό σχήμα κρυπτογράφησης. Αυτό το σχήμα επιτρέπει το σχεδιασμό και την υλοποίηση ασφαλών εξατομικευμένων κρυπτογραφικών αλγορίθμων τμήματος για την κρυπτογράφηση δεδομένων διάχυτων υπηρεσιών υγείας, όπως οι ιατρικοί φάκελοι των ασθενών. Επίσης, προτείνεται ένας μηχανισμός για διασφάλιση της ακεραιότητας των δεδομένων για σύστημα ιατρικής τηλε-παρακολούθησης. Αυτό το σύστημα τηλε-παρακολούθησης λειτουργεί σε περιβάλλον έξυπνου σπιτιού και υποστηρίζει τη μεταφορά βιοσημάτων του ασθενή από τον ασθενή στη Μονάδα Παροχής Υπηρεσιών Υγείας. Επιπρόσθετα, προτείνονται δύο μηχανισμοί για διασφάλιση της πιστοποίησης αυθεντικότητας. Ο πρώτος μηχανισμός είναι ένας ευφυής μηχανισμός πιστοποίησης αυθεντικότητας για εφαρμογές e-Hospital πάνω σε WLAN μέσα σε νοσοκομείο. Ο δεύτερος μηχανισμός είναι ένας μηχανισμός συμφωνίας κλειδιού ομάδας και ανάκτησης σε ad hoc δίκτυα, που χρησιμοποιούνται κατά τη διαχείριση ιατρικών συμβάντων έκτακτης ανάγκης σε περιοχές στις οποίες δεν υπάρχει σταθερή τηλεπικοινωνιακή υποδομή. Τέλος, προτείνεται μία υποδομή PKI σε ένα ιατρικό δίκτυο μεγάλης κλίμακας που συνδέει ένα ευρύ φάσμα από Μονάδες Παροχής Υπηρεσιών Υγείας. Η προτεινόμενη υποδομή PKI εστιάζεται στη διασφάλιση της πιστοποίησης αυθεντικότητας και του ελέγχου πρόσβασης των επαγγελματιών του χώρου της υγείας που επιθυμούν να αποκτήσουν πρόσβαση σε υπηρεσίες που σχετίζονται με αυτούς καθώς και σε υπηρεσίες υγείας που σχετίζονται με τον ασθενή. / In this dissertation, Security Mechanisms are proposed for the development of secure and reliable pervasive healthcare services over Next Generation Networks (NGN). The proposed Security Mechanisms aim at increasing the security level provided by the existing security mechanisms supported by NGN. It is essential since pervasive healthcare services include extremely sensitive information. Furthermore, in this dissertation, a generic application framework is proposed supporting the proposed Security Mechanisms in order the rapid and efficient development of secure and reliable pervasive healthcare services over NGN to be achieved. In particular, the proposed framework is based on the ETSI/Parlay architecture and extends the set of the Service Capability Features Interfaces (SCFs Interfaces) as well as the set of mechanisms supported by the ETSI/Parlay Framework. The proposed framework extends the set of the SCFs Interfaces in order to integrate not only the interfaces related to the services of the underlying network (NGN), but also additional interfaces enabling pervasive healthcare services to access sensing capabilities of sensor networks which are responsible for gathering context and bio information. Moreover, the proposed framework extends the set of mechanisms supported by the ETSI/Parlay Framework to provide pervasive healthcare services not only with the basic mechanisms supported by the standardized ETSI/Parlay Framework, but also with the Sensor Networks Mechanisms and the Security Mechanisms proposed in this dissertation. The proposed Security Mechanisms aim at securing the end-user data as well as the access to the pervasive healthcare services and the use of them. In particular, the proposed Security Mechanisms focus on ensuring data confidentiality, data integrity, authentication and access control of entities participating in pervasive healthcare services. To ensure data confidentiality, a generic encryption schema is proposed. This schema enables the design and implementation of secure personalized block ciphers for encryption of data included in pervasive healthcare services such as patients’ medical records. Moreover, a data integrity mechanism for a tele-monitoring system is proposed. This tele-monitoring system operates in a smart home environment and supports transmission of patient’s biosignals from the patient to the Healthcare Center. Additionally, two authentication mechanisms are proposed. The first mechanism is an intelligent authentication mechanism for e-Hospital applications over WLAN in a hospital. The second mechanism is a group key agreement and recovery mechanism in ad hoc networks used for handling emergency medical incidents in areas without fixed telecommunications infrastructure. Finally, a PKI infrastructure in a large-scale healthcare network connecting a wide spectrum of Healthcare Centers is proposed. The proposed PKI infrastructure focuses on ensuring authentication and access control of healthcare professionals willing to access services related to them as well as healthcare services related to patient.

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / Title page: Dept. of Genetics, Faculty of Science / ENGLISH ABSTRACT: Next-generation sequencing technologies are increasingly used in metagenomic studies, largely due to the high sequence data throughput capacity and unbiased approach in determining the genetic composition of an unknown environmental sample. This study investigated the applicability of the Illumina next-generation sequencing platform for metagenomic sequencing of grapevine viruses to provide the first complete viral profile, or virome, of a diseased vineyard. Leaf material was harvested from 44 randomly selected vines in a leafroll-diseased vineyard in South Africa. Sample material was pooled and double-stranded RNA extracted. The dsRNA was sequenced as a paired-end sequencing run using the Illumina sequencing-by-synthesis technique, and more than 19 million sequence reads, equivalent to approximately 837 megabases of metagenomic sequence data, were obtained. Of these data, approximately 400 megabases could be assembled into 449 scaffolds, using the de novo assembler Velvet. These scaffolds were subjected to BLAST searches against the NCBI databases and top hit scores were used for virus identification. Based on the BLAST results, suitable sequences were selected from the NCBI database and used as reference sequence in MAQ mapping assemblies. The bioinformatic analyses allowed for the determination of the virus species present, the most prominent variants, and the relative abundance of each. Four known grapevine viral pathogens were identified. Grapevine leafroll-associated virus 3, representing 59% of the analyzed short read sequence data, was identified as the most prominent virus species. Three variants of this virus were detected: GP18 was the most abundant, followed by a minor Cl766/NY1 variant and a potential novel grapevine leafroll-associated ampelovirus. A single Grapevine rupestris stem pitting ]associated virus variant, similar to SG1, and a Grapevine virus A variant, a member of molecular group III, were identified. This study is also the first to report the presence of Grapevine virus E (GVE) in South African vineyards. Grapevine virus E was further genetically characterized and the genome sequence of GVE isolate SA94 determined. The GVE SA94 genome sequence, 7568 nucleotides in length, is the first complete genome sequence for the virus species. The genome organization of GVE SA94 is typical of vitiviruses, but in contrast to other RNA viruses, the AlkB domain is located within the helicase domain in open reading frame 1 (ORF 1). Grapevine virus E SA94 shares nearly 100% nucleotide identity with the Japanese TvP15 isolate and GVE 3404, a de novo scaffold generated from the metagenomic sequence data. Bioinformatic analysis of metagenomic sequence data further revealed the presence of three fungus-infecting viral families, Chrysoviridae, Totiviridae and the unclassified dsRNA virus, Fusarium graminearum dsRNA mycovirus 4. A virus from the family Chrysoviridae, similar to Penicillium chrysogenum virus, was the second most abundant virus detected. We demonstrated the successful application of a short read sequencing technology, such as the Illumina platform, for viral profiling of an infected vineyard. To our knowledge this is the first application of the Illumina technology for this purpose. / AFRIKAANSE OPSOMMING: Volgende-generasie tegnologie om basis volgordes van nukleiensure te bepaal, word al meer gebruik in metagenomiese studies. Dit is veral weens die hoe data-omset kapasiteit en onbevooroordeelde aanslag in die bepaling van die genetiese samestelling van onbekende omgewingsmonsters. Hierdie studie het die aanwending van die Illumina volgende-generasie volgorde-bepalingsplatform in 'n metagenomiese studie van wingerdvirusse, ondersoek. Dit het ten doel gehad om die eerste volledige virus profiel, of viroom, van 'n geinfekteerde wingerd saam te stel. Blaarmateriaal is verkry vanaf 44 lukraak-gekose wingerdstokke in 'n rolblad-geinfekteerde wingerd in Suid-Afrika. Monster materiaal is saamgevoeg en dubbelstring-RNS geekstraheer. Die dubbelstring-RNS is onderwerp aan gepaarde-ent volgorde-bepaling deur gebruik te maak van die Illumina volgorde-bepaling-deur-sintese tegniek. Meer as 19 miljoen volgorde reekse, ekwivalent aan ongeveer 837 megabasisse volgorde data, is verkry. Van hierdie data kon ongeveer 400 megabasisse saamgevoeg word in 449 konstrukte ("scaffolds"), deur gebruik te maak van die de novo samesteller Velvet. Hierdie konstrukte is onderwerp aan BLAST soektogte teen die NCBI databasisse en die hoogste trefslag-telling is gebruik vir virus identifikasie. Op grond van die "BLAST" resultate is geskikte volgordes geselekteer vanaf die NCBI databasis en gebruik as verwysingvolgordes in MAQ kartering-analises. Met die bioinfomatika analises kon die virus spesies teenwoordig, asook die mees prominente variante en relatiewe voorkoms van elk, bepaal word. Vier bekende virus wingerdpatogene is geidentifiseer. Grapevine leafroll-associated virus 3, verteenwoordig deur 59% van die geanaliseerde kort-reeks volgorde data, is identifiseer as die mees prominente virus spesie. Drie variante van die virus is in die wingerdmonster opgespoor: GP18 kom die mees algemeen voor, gevolg deur 'n CL-766/NY1 variant en 'n potensiele nuwe wingerd rolblad-geassosieerde ampelovirus. 'n Enkele Grapevine rupestris stem pitting-associated virus variant, soortgelyk aan SG1, en 'n Grapevine virus A variant, 'n lid van molekulere groep III, is geidentifiseer. Hierdie studie is ook die eerste om die teenwoordigheid van Grapevine virus E (GVE) in Suid-Afrikaanse wingerde te rapporteer. Grapevine virus E is verder geneties gekarakteriseer en die genoomvolgorde van GVE isolaat SA94 is bepaal. Die GVE SA94 genoomvolgorde, 7568 nukleotiede lank, is die eerste volledige genoomvolgorde vir hierdie virus spesie. Die genoomorganisasie is tipies van vitivirusse, maar in kontras met ander RNA virusse is die AlkB domein binne-in die helikase domein van oopleesraam 1 (ORF 1) geleë. Grapevine virus E SA94 deel byna 100% nukleotied identiteit met die Japannese TvP15 isolaat en GVE 3404, 'n de novo konstruk gegenereer vanaf die metagenomiese volgorde data. Bioinformatika analises van die metagenomiese volgorde data het verder die teenwoordigheid van drie swam-infekterende virus families, die Chrysoviridae, Totiviridae en ongeklassifiseerde dubbelstring-RNS virus, Fusarium graminearum dsRNA mycovirus 4, aangetoon. 'n Virus van die Chrysoviridae familie, soortgelyk aan Penicillium chrysogenum virus, het die tweede meeste voorgekom in die wingerd monster. Hierdie studie demonstreer die suksesvolle toepassing van 'n kort reeks volgorde-bepalingstegnologie soos die Illumina platform, vir die opstel van 'n virusprofiel van 'n geinfekteerde wingerd. Sover ons kennis strek is hierdie die eerste aanwending van die Illumina tegnologie vir hierdie doel.

Orientador: Erick da Cruz Castelli / Resumo: O Complexo Principal de Histocompatibilidade (MHC) é um complexo gênico que está intimamente envolvido com a regulação do sistema imune. Esse complexo comporta o sistema de Antígenos Leucocitários Humano (HLA), cuja principal importância está relacionada com o reconhecimento do que é próprio ou não do organismo. HLA-C é o gene polimórfico menos variável dos genes HLA clássicos e o que tem menor expressão nos tecidos, exceto na interface materno-fetal, em que é o único gene clássico expresso. A molécula codificada por esse gene possui significante função na apresentação antigênica e regulação da atividade de células NK, o que permite uma íntima associação com situações fisiológicas, como gestação, e patológicas, como doenças infecciosas, autoimunes, inflamatórias, neoplasias e rejeições a enxertos transplantados. Sua porção gênica mais estudada é a que codifica a fenda de ligação a peptídeos antigênicos, devido sua destacada importância na apresentação de antígenos a células T citotóxicas. No entanto, outras regiões do gene, que são negligenciadas nos estudos de variabilidade, também merecem destaque por influenciarem na sinalização e modulação da citotoxicidade de células efetoras, na ancoragem e estabilidade da molécula na membrana plasmática e na internalização e reciclagem da molécula HLA-C. Desta maneira, nós exploramos a variabilidade dos segmentos que codificam α3 (éxon 4), transmembrana (éxon 5) and cauda citoplasmática (éxon 6 and éxon 7) da molécula HLA-C em uma popu... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The Major Histocompatibility Complex (MHC) is a gene complex closely involved in the regulation of the immune system. This complex includes the Human Leukocyte Antigen (HLA) system, whose main role is related to the recognition of self/non-self structures of humans. HLA-C is the least variable polymorphic gene of classical HLA genes and has the lowest expression in tissues, except at the maternal-fetal interface, where it is the only classical HLA class I expressed gene. The molecule encoded by this gene has a significant role in the antigen presentation and regulation of NK cells activities, which allows an intimate association with physiological conditions, such as pregnancy, and pathological conditions like infectious, autoimmune, and inflammatory diseases, cancer, and transplantation rejection. The most studied HLA-C portion is that encoding the peptide-binding groove, due to its outstanding importance in presentation of antigens to cytotoxic T cells. However, other regions of the gene, which are neglected in the variability studies, are also important in influencing the signaling and modulation of effector cell cytotoxicity, in the anchorage and stability of the molecule on the cell surface, and in the internalization and recycling of the HLA-C molecule. Here, we explore the variability of the segments encoding the α3 (exon 4), transmembrane (exon 5) and cytoplasmic tail (exon 6 and exon 7) domains of the HLA-C molecule in an admixed population sample from Southeastern B... (Complete abstract click electronic access below) / Mestre

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En ville, les systèmes de récupération et d'infiltration des eaux pluviales dans le sous-sol ont pour conséquence d'augmenter la connectivité hydrologique entre la surface et la nappe phréatique. Ces pratiques d'infiltration produisent de nombreuses perturbations physico-chimiques au niveau de la nappe (ex. augmentation des variations thermiques, baisse des concentrations en oxygène dissous, enrichissement de la nappe en matière organique dissoute) mais les conséquences sur le compartiment microbien restent peu connues. L'objectif principal de la thèse est de déterminer les effets de l'infiltration des eaux pluviales sur les communautés microbiennes des nappes phréatiques, aussi bien en termes d'abondance, d'activités que de diversité génétique bactérienne. En se basant sur les changements environnementaux associés à l'infiltration des eaux pluviales et l'analyse des communautés bactériennes, un objectif fondamental est d'évaluer l'importance des phénomènes de dispersion (ex. transferts) et de sélection par des facteurs abiotiques (ex. disponibilité des ressources nutritives) sur les assemblages bactériens au sein des nappes phréatiques. Ces travaux ont été axés sur des expérimentations de terrain utilisant deux approches d'échantillonnage : une méthode active (prélèvements d'eau) et une méthode passive (incubation de substrats artificiels). La description des communautés a été effectuée par une méthode de séquençage de nouvelle génération (i.e. Illumina MiSeq) en se basant sur le gène rrs. Les résultats de ce travail mettent en avant une influence significative des pratiques d'infiltration sur les bactériomes d'un aquifère. En effet, le développement, les activités et la diversité des micro-organismes retrouvés dans la nappe ont été stimulés significativement par l'enrichissement en carbone organique dissous biodégradable engendré par ces pratiques. Néanmoins, cet impact est fortement réduit dans les systèmes étudiés où la zone non saturée est épaisse (> 10 m) et agit comme un filtre physique, chimique et biologique efficace entre le bassin d'infiltration et l'aquifère. Les faibles similarités entre les structures génétiques des bactériomes des eaux d'infiltration et dans la nappe indiquent que la zone non saturée joue un rôle efficace sur la rétention des bactéries dans les systèmes étudiés. En conclusion, cette thèse constitue la première étude d'envergure visant à quantifier la réponse du compartiment microbien des aquifères à des perturbations engendrées par l'infiltration des eaux pluviales en milieu urbain. Elle ouvre aussi de nouvelles perspectives sur les méthodes et outils d'évaluation de la qualité des nappes phréatiques / In urban area, managed aquifer recharge (MAR) systems raises hydrological connectivity between surface and groundwater. These infiltration practices are the cause of many disturbances in groundwaters (e.g. increase of thermal variations, decrease of dissolved oxygen or enrichment in organic matter) but associated consequences on microbial compartment remains unclear. The main aim of the thesis is to determine the effects of stormwater runoff infiltration on microbial communities of groundwater, in terms of abundance, activities and bacterial diversity. Based on environmental changes associated to MAR practices and bacterial community analyses, a fundamental question is to assess the importance of dispersal (e.g. transfers) and selection by abiotic factors (e.g. nutrients availability) on groundwater communities assemblage. This study is based on field experiments with two complementary strategies of sampling: an active one (i.e. groundwater sampling) and a passive one (incubation of artificial substrate). Communities’ description was made by next-generation sequencing (i.e. Illumina MiSeq) of rrs gene. The results showed a significant influence of MAR practices on microbial communities. Growth, activities and diversity of groundwater micro-organisms were mainly stimulated by biodegradable dissolved organic carbon enrichment associated to MAR practices. Nonetheless, this impact was reduced in systems where the vadose zone is thick (> 10 m) and acts as a physical, chemical and biological filter between the infiltration basin and the aquifer. Low similarities between bacterial communities of infiltration waters and bacterial communities of groundwaters reveal that vadose zone is effective on the retention of bacteria in studied systems. To conclude, this thesis constitutes the first major study that aimed to quantify microbial compartment response to disturbances caused by MAR practices in urban area. It also opens new perspectives on assessment tool for groundwater quality

L'identification de gènes ayant permis à des populations de s'adapter à leur environnement local constitue une des problématiques majeures du domaine de la génétique des populations. Les méthodes statistiques actuelles répondant à cette problématique ne sont plus adaptées aux données de séquençage nouvelle génération (NGS). Nous proposons dans cette thèse de nouvelles statistiques adaptées à ces nouveaux volumes de données, destinées à la détection de gènes sous sélection. Nos méthodes reposent exclusivement sur l'Analyse en Composantes Principales, dont nous justifierons l'utilisation en génétique des populations. Nous expliquerons également les raisons pour lesquelles nos approches généralisent les méthodes statistiques existantes et démontrons l'intérêt d'utiliser une approche basée sur l'Analyse en Composantes Principales en comparant nos méthodes à celles de l'état de l'art. Notre travail a notamment abouti au développement de pcadapt, une librairie R permettant l'utilisation de nos statistiques de détection sur des données génétiques variées. / Identifying genes involved in local adaptation is of major interest in population genetics. Current statistical methods for genome scans are no longer suited to the analysis of Next Generation Sequencing (NGS) data. We propose new statistical methods to perform genome scans on massive datasets. Our methods rely exclusively on Principal Component Analysis which use in population genetics will be discussed extensively. We also explain the reasons why our approaches can be seen as extensions of existing methods and demonstrate how our PCA-based statistics compare with state-of-the-art methods. Our work has led to the development of pcadapt, an R package designed for outlier detection for various genetic data.

Magister Scientiae - MSc / Providing carrier grade characteristics for Internet Protocol (IP) communication applications is a significant problem for IP application providers in order to offer integrated services that span IP and telecommunication networks. This thesis addresses the provision of life-cycle management, which is only one carrier grade characteristic, for a SoftBridge application, which is an example of IP communication applications. A SoftBridge provides semi-synchronous multi-modal IP-based communication. The work related to IP-Telecommunication integrated services and the SoftBridge is analyzed with respect to life-cycle management in a literature review. It is suggested to use an Application Server in a Next Generation Network (NGN) to provide life-cyclemanagement functionality for IP-Telecommunication applications. In this thesis, the Application Server is represented by a JAIN Service Logic Execution Environment(JSLEE), in which a SoftBridge application can be deployed, activated, deactivated, uninstalled and upgraded online.Two methodologies are applied in this research: exploratory prototyping, which evolves the development of a SoftBridge application, and empirical comparison, which is concerned with the empirical evaluation of a SoftBridge application in terms of carriergrade capabilities. A SoftBridge application called SIMBA provides a Deaf Telephony service similar to aprevious Deaf Telephony SoftBridge, However, SIMBA’s SoftBridge design and implementation are unique to this thesis. In order to test the life-cycle management ability of SIMBA, an empirical evaluation is carried out including the experiments oflife-cycle management and call-processing performance. The final experimental results of the evaluation show that a JSLEE is able to provide life-cycle management for SIMBA without causing a significant decrease in performance. In conclusion, the life-cycle management can be provided or a SoftBridge application by using an Application Server such as a JSLEE. Futhermore, the results indicate that approach of using Application Server (JSLEE) integration should be sufficiently general to provide life cycle management, and indeed other carrier grade capabilities, for other IP communication applications. This allows IP communication applications to be integrated into an NGN.Providing carrier grade characteristics for Internet Protocol (IP) communication applications is a significant problem for IP application providers in order to offer integrated services that span IP and telecommunication networks. This thesis addresses the provision of life-cycle management, which is only one carrier grade characteristic, for a SoftBridge application, which is an example of IP communication applications. A SoftBridge provides semi-synchronous multi-modal IP-based communication. The work related to IP-Telecommunication integrated services and the SoftBridge is analyzed with respect to life-cycle management in a literature review. It is suggested to use an Application Server in a Next Generation Network (NGN) to provide life-cyclemanagement functionality for IP-Telecommunication applications. In this thesis, the Application Server is represented by a JAIN Service Logic Execution Environment(JSLEE), in which a SoftBridge application can be deployed, activated, deactivated, uninstalled and upgraded online.Two methodologies are applied in this research: exploratory prototyping, which evolves the development of a SoftBridge application, and empirical comparison, which is concerned with the empirical evaluation of a SoftBridge application in terms of carriergrade capabilities. A SoftBridge application called SIMBA provides a Deaf Telephony service similar to aprevious Deaf Telephony SoftBridge, However, SIMBA’s SoftBridge design and implementation are unique to this thesis. In order to test the life-cycle management ability of SIMBA, an empirical evaluation is carried out including the experiments oflife-cycle management and call-processing performance. The final experimental results of the evaluation show that a JSLEE is able to provide life-cycle management for SIMBA without causing a significant decrease in performance. In conclusion, the life-cycle management can be provided or a SoftBridge application by using an Application Server such as a JSLEE. Futhermore, the results indicate that approach of using Application Server (JSLEE) integration should be sufficiently general to provide life cycle management, and indeed other carrier grade capabilities, for other IP communication applications. This allows IP communication applications to be integrated into an NGN. / South Africa

Magister Scientiae - MSc / Telecommunication companies, service providers and large companies are now adapting converged multi-service Next Generation Networks (NGNs). Network management is shifting from managing Network Elements (NE) to managing services. This paradigm shift coincides with the rapid development of Quality of Service (QoS) protocols for IP networks. NEs and services are managed with Policy Based Network Management (PBNM) which is most concerned with managing services that require QoS using the Common Open Policy Service (COPS) Protocol. These services include Voice over IP (VoIP), video conferencing and video streaming. It follows that legacy NEs without support for QoS need to be replaced and/or excluded from the network. However, since most of these services run over IP, and legacy NEs easily supports IP, it may be unnecessary to throw away legacy NEs if it can be made to fit within a PBNM approach. Our approach enables an existing PBNM system to include legacy NEs in its management paradigm. The Proxy-Policy Enforcement Point (P-PEP) and Queuing Policy Enforcement Point (Q-PEP) can enforce some degree of traffic shaping on a gateway to the legacy portion of the network. The P-PEP utilises firewall techniques using the common legacy and contemporary NE management protocol Simple Network Management Protocol (SNMP) while the Q-PEP uses queuing techniques in the form Class Based Queuing (CBQ) and Random Early Discard (RED) for traffic control. / South Africa

Glycopeptides are the so-called last-resort antibiotics in clinical practice used to treat heavier, predominantly nosocomial infections caused by multi-resistant coagulase-negative staphylococci. The origin and genetic basis of resistance to glycopeptide antibiotics has not yet been elucidated within coagulase-negative staphylococci. Research on Staphylococcus aureus has shown, that intermediate resistance to glycopeptide antibiotics is associated with the presence of one or more mutations, rather than being conditioned by the support of a particular genetic element, such as in enterococci. By using various types of in vitro resistant mutant selection, we were able to obtain isogenic pairs of glycopeptide sensitive and resistant strains of Staphylococcus epidermidis and Staphylococcus haemolyticus. By sequencing the genomes of these pairs, one nucleotide polymorphisms were identified and predominantly found in metabolic and cell wall control systems. Phenotypic analysis did not reveal a direct association of glycopeptide resistance with increased biofilm formation. In clinical practice, the cross-resistance of glycopeptides and other antibiotics is problematic. For the non-glycopeptide antibiotics imipenem and rifampicin, the incidence of cross-resistance with glycopeptide antibiotics in S. aureus...