Micoplasmas estão difundidos pela natureza e são caracterizados por um genoma relativamente pequeno, baixo conteúdo GC e ausência de parede celular e de algumas rotas biossintéticas. Mycoplasma hyopneumoniae é o agente etiológico da pneumonia enzoótica suína, capaz de colonizar o trato respiratório e seu crescimento in vitro, comparado com o de outros micoplasmas, é mais lento. Mycoplasma hyorhinis também é encontrado no trato respiratório de suínos. Devido à falta de algumas vias biossintéticas, micoplasmas são incapazes de sintetizar alguns nutrientes e componentes essenciais, sendo forçados a obtê-los do ambiente. Assim, um dos maiores empecilhos enfrentados na pesquisa e diagnóstico de micoplasma tem sido a dificuldade do cultivo in vitro. Portanto, o desenvolvimento de um meio de composição definida que sustente o crescimento celular serviria como uma ferramenta controladamente manipulável, permitindo a definição de suas vias metabólicas assim como análises genéticas. O objetivo do presente estudo foi analisar a viabilidade, taxa de crescimento e regulação gênica de M. hyopneumoniae e M. hyorhinis em diferentes meios de cultivo, assim como em diferentes condições de cultura. Neste trabalho, foi utilizado o meio Friis (1975) como meio complexo, e quatro meios definidos: (i) meio descrito para Mycoplasma pneumoniae por Yus et al. (2009); (ii) meio Yus sem adição de peptona; (iii) meio comercial CMRL e (iv) meio CMRL+ (complementado com lipídeos, aminoácidos e vitaminas). A viabilidade celular foi avaliada em todos os meios definidos e a taxa de crescimento de ambas as espécies nos cinco meios foi avaliada por citometria de fluxo. Os resultados demonstraram que a composição do meio influencia no crescimento da bactéria, uma vez que há diferença entre a concentração celular em cada meio testado. Entretanto, ambas as espécies apresentaram concentração celular semelhante em cada meio. Os resultados demonstram que, dentre os meios definidos testados, o meio CMRL+, desenvolvido no presente estudo, é o meio mais adequado, podendo ser considerado um meio de manutenção para estes microrganismos. Para a avaliação da regulação gênica através de qPCR, M. hyopneumoniae foi cultivado em meio Friis e CMRL+ sendo posteriormente submetido a condições de estresse (choque térmico e estresse oxidativo). Os resultados obtidos sugerem que M. hyopneumoniae altera seus níveis transcricionais mais rapidamente quando cultivado em meio CMRL+, provavelmente devido ao estresse duplo causado pela privação nutricional e estresse oxidativo ou choque térmico. Na condição de choque térmico, o tipo de regulação predominante diferiu entre os dois meios, enquanto que, quando submetido a estresse oxidativo, os genes apresentaram um padrão de regulação semelhante entre Friis e CMRL+. O meio de cultivo definido CMRL+ forneceu uma taxa de crescimento semelhante à do meio complexo Friis, e demonstrou presença de regulação gênica em M. hyopneumoniae em resposta à sua composição e às condições de estresse testadas. Portanto, este meio pode ser usado como uma ferramenta para o avanço da pesquisa com Mycoplasma. / Mycoplasmas are widespread in nature, and are characterized by a relative small genome, low GC content, absence of cell wall and lack of some biosynthetic pathways. Mycoplasma hyopneumoniae is the infective agent of enzootic pneumonia in swine, able to colonize the respiratory tract. Its growth is slower than other porcine mycoplasmas. Mycoplasma hyorhinis f y y . Ty y, ’ f mycoplasma that grows in culture, and its presence can frequently prevent the isolation of other Mycoplasma spp. Due to the lack of some biosynthetic pathways, mycoplasmas are incapable of synthesize some nutrients and essential compounds, being forced to obtain from the environment. Therefore, the major impediment to Mycoplasma research and laboratory diagnosis has been the difficulty of in vitro cultivation. Thus, the development of a defined medium that support mycoplasma growth would provide a tool that can be controllably manipulated to enable the definition of mycoplasmal metabolic pathways as well as genetic analysis. The aim of this work was to analyze viability, growth rate and gene regulation of M. hyopneumoniae and M. hyorhinis in different culture media, and cultivation conditions. In this work, we used Friss broth (1975) as a complex medium, and four different defined media: (i) a medium described for M. pneumoniae by Yus et al. (2009), (ii) defined Yus medium without peptone, (iii) commercial medium CMRL and (iv) CMRL+ medium (supplemented with lipids, amino acids and vitamins). All the defined media were tested towards cell viability and the growth rate of both species in the five media was assessed, through flow cytometry assay comparing between them. The results from flow cytometry assay showed that the composition of the media influences the bacterial growth, once cell concentration in each of the tested media was different. However, both species presented similar cell concentration in each media. The results demonstrate that, amongst the defined media tested, CMRL+ broth, developed in this study, b , g ’ y b . To gene regulation assessment, M. hyopneumoniae was cultivated in Friis and CMRL+ and underwent two stress conditions (heat shock and oxidative stress). Results suggest that M. hyopneumoniae alters the transcriptional levels of some genes more promptly when cultivated in CMRL+ broth, probably due to the dual stress caused by the combination of nutrients deprivation in CMRL+ broth plus heat shock or oxidative stress. In the heat shock condition, the prevailing kind of regulation differed between the two media, while when submitted to oxidative stress, genes presented similar pattern of regulation between Friis and CMRL+. CMRL+ medium provided a growth rate resembling the complex broth and M. hyopneumoniae showed to have gene expression regulation in response to its composition and to the culture conditions tested. Thus, it can be used as a tool that can be controllably manipulated enabling the definition of mycoplasmal nutritional requirements and metabolic pathways as well as genetic analysis, such as gene regulation.

This research is related to computer networks. In this thesis, three main issues are addressed which affect the performance of any computer network: congestion, efficient resources utilization and link failure. Those issues are related to each other in many situations. Many approaches have been suggested to deal with those issues as well as many solutions were applied. Despite all the improvements of the technology and the proposed solutions, those issues continue to be a burden on the system’s performance. This effect is related to the increase of the Quality of Service (QoS) requirements in modern networks. The basic idea of this research is evolving the intelligence of a conventional computer network when dealing with those issues by adding some features of the Software Defined Networking (SDN). This adoption upgrades the conventional computer network system to be more dynamic and higher self-organizing when dealing with those issues. This idea is applied on a system represented by a computer network that uses the Open Shortest Path First (OSPF) routing protocol. The first improvement deals with the distribution of Internet Protocol (IP) routed flows. The second improvement deals with tunnel establishment that serves Multi-Protocol Label Switching (MPLS) routed flows and the third improvement deals with bandwidth reservation when applying network restoration represented by Fast Re-route (FRR) mechanism to sooth the effect of link failure in OSPF/MPLS routed network. This idea is also applied on another system that uses the Enhanced Interior Gateway Routing Protocol (EIGRP) to improve the performance of its routing algorithm. Adopting the SDN notion is achieved by adding an intelligent controller to the system and creating a dialog of messages between the controller and the conventional routers. This requires upgrading the routers to respond to the new modified system. Our proposed approaches are presented with simulations of different configurations which produce fine results.

As the demands of communication systems have become more complex and varied, software defined radios (SDR) have become increasingly popular. With behavior that can be modified in software, SDR's provide a highly flexible and configurable development environment. Despite its programmable behavior, the maximum performance of an SDR is still rooted in its hardware. This limitation and the desire for the use of SDRs in different applications have led to the rise of various pieces of hardware to serve as SDR platforms. These platforms vary in aspects such as their performance limitations, implementation details, and cost. In this way the choice of SDR platform is not solely based on the cost of the hardware and should be closely examined before making a final decision. This thesis examines the various SDR platform families available on the market today and compares the advantages and disadvantages present for each during development. As many different types of hardware can be considered an option to successfully implement an SDR, this thesis specifically focuses on general purpose processors, system on chip, and field-programmable gate array implementations. When examining these SDR families, the Freescale BSC9131 is chosen to represent the system on chip implementation, while the Nutaq PicoSDR 2x2 Embedded with Virtex6 SX315 is used for the remaining two options. In order to test each of these platforms, a Viterbi algorithm is implemented on each and the performance measured. This performance measurement considers both how quickly the platform is able to perform the decoding, as well as its bit error rate performance in order to ascertain the implementations' accuracy. Other factors considered when comparing each platform are its flexibility and the amount of options available for development. After testing, the details of each implementation are discussed and guidelines for choosing a platform are suggested.

This thesis describes a real-time software-defined-radio implementation of a two source distributed beamformer. The technique in this thesis can be used to synchronize the carriers of two single antenna wireless transmitters (i.e. ``sources") with independent local clocks so that their bandpass transmissions arrive in-phase at an intended receiver (i.e. ``destination"). Synchronization is achieved via: (i) an unmodulated beacon transmitted by the destination to the sources and (ii) a pair of secondary unmodulated beacons between the sources. No explicit channel state information is exchanged between the sources and/or the destination. Using this method, it is possible to realize a two-source distributed beamformer that provides a reduction in overall transmit energy and increased security due to the directionality of the transmitted signal. System characterization results are provided along with experimental results for both time-invariant and time-varying channels. The experimental results in this thesis confirm the theoretical predictions and also provide explicit guidelines for a real-time implementation of a two-source distributed beamforming system.

Reliable wireless networks for high speed trains require a significant amount of data communications for enabling safety features such as train collision avoidance and railway management. Cognitive radio integrates heterogeneous wireless networks that will be deployed in order to achieve intelligent communications in future railway systems. One of the primary technical challenges in achieving reliable communications for railways is the handling of high mobility environments involving trains, which includes significant Doppler shifts in the transmission as well as severe fading scenarios that makes it difficult to estimate wireless spectrum utilization. This thesis has two primary contributions: (1) The creation of a Heterogeneous Cooperative Spectrum Sensing (CSS) prototype system, and (2) the derivation of a Long Term Evolution for Railways (LTE-R) system performance analysis. The Heterogeneous CSS prototype system was implemented using Software-Defined Radios (SDRs) possessing different radio configurations. Both soft and hard-data fusion schemes were used in order to compare the signal source detection performance in real-time fading scenarios. For future smart railways, one proposed solution for enabling greater connectivity is to access underutilized spectrum as a secondary user via the dynamic spectrum access (DSA) paradigm. Since it will be challenging to obtain an accurate estimate of incumbent users via a single-sensor system within a real-world fading environment, the proposed cooperative spectrum sensing approach is employed instead since it can mitigate the effects of multipath and shadowing by utilizing the spatial and temporal diversity of a multiple radio network. Regarding the LTE-R contribution of this thesis, the performance analysis of high speed trains (HSTs) in tunnel environments would provide valuable insights with respect to the smart railway systems operating in high mobility scenarios in drastically impaired channels.

Modern computer networks allow server resources to be shared. While this multiplexing is the unsung hero of scalability and performance, the fact that clients are sharing resources and each client’s network traffic is transmitted in a larger pool of the total network traffic, poses distinct challenges for security. By adopting multiplexing so broadly, the networking and systems communities have implicitly favored performance over security. When servers multiplexing clients are compromised, the attack is able to spread by exploiting unsuspecting clients sharing the resource. Drive-by-downloads are an example of an attack where a Web server is compromised and begins distributing malware to connecting clients. As a result of using today’s many-to-one client-server network model, current approaches are inadequate at protecting the network and its resources. We propose a redesign of the modern network infrastructure. Our approach involves moving from the current many-to-one client-server model to a one-to-one client-server model. In redesigning the network, we provide a means of better accountability for traffic between clients and servers. With accountability, we enable the ability to quickly determine which client is responsible for an attack. This allows us to quickly repair the affected entities. To accomplish this accountability, we separate each client’s communication into separate flows. A flow is identified by various network features, such as IP addresses and ports. Further, instead of allowing multiple clients to be multiplexed at the same server, we use a technique that allows each client to communicate with a server that is logically separate from all other clients. Accordingly, a server compromise only effects a single client. We create a one-to-one client-server model using virtualization techniques and OpenFlow, a software-defined network (SDN) protocol. We complete our model in three phases. In the first, we deploy a physical SDN using physical machines and a commodity network switch that supports OpenFlow to gain an initial understanding of SDNs. The next phase involves implementation of Choreographer, a DNS access control mechanism, in a virtualized SDN environment for better scalability over our physical configuration. Finally, we leverage Choreographer to dynamically instantiate a server for each client and create network flows that allow a client to reach the requested server.

This thesis describes a real-time software-defined-radio implementation of the time-slotted round-trip carrier synchronization protocol in two-source and three-source communication systems. The techniques developed in this thesis can be used to synchronize the carriers of two or three single-antenna wireless transmitters with independent local oscillators so that their band-pass transmissions combine constructively at an intended receiver. Synchronization is achieved via the time-slotted transmission of (i) an unmodulated primary beacon from the destination to the sources and (ii) a series of secondary unmodulated beacons between the sources. Explicit channel state information is not exchanged between the sources and/or the destination. When synchronized, the single-antenna sources are able to cooperatively transmit as a distributed beamformer and achieve increased transmission range, reduced transmission energy, and/or increased security. The experimental results in this thesis confirm the theoretical predictions and also provide explicit guidelines for the real-time implementation of a carrier synchronization technique suitable for distributed transmit beamforming.

Os Pontos de Troca de Tráfego participam de maneira substancial e crítica no ecossistema da Internet, possibilitando conexões entre múltiplos Sistemas Autônomos (ASes, do inglês Autonomous Systems). O gerenciamento das redes de PTT possui como objetivos primários, o gerenciamento dos chamados fluxos elefante (do inglês, elephant flows). Fluxos elefante tendem a existir em número reduzido, porém correspondem à maioria do tráfego em uma infraestrutura de rede. O gerenciamento dos fluxos elefante envolve uma adequada identificação e quando necessário, um redirecionamento destes fluxos para caminhos mais apropriados, de forma a minimizar os possíveis impactos sobre os outros fluxos ativos na rede. Além disso, o gerenciamento de fluxos elefante tornou-se um importante objeto de discussão em PTTs baseados em redes SDN, principalmente porque estas redes dispõem de controladores que possuem uma visão consistente da rede subjacente, o que permite uma gerência destes fluxos de forma refinada. Nesta dissertação, será proposto, desenvolvido e avaliado um sistema de identificação dos fluxos elefante e seus respectivos caminhos de rede, em conjunto com um sistema de recomendação, que possui o objetivo de sugerir configurações alternativas para os fluxos elefante identificados anteriormente nas redes de PTTs baseadas em SDN. Neste sistema, o operador do PTT pode definir templates que em última instância definem como os caminhos dos fluxos elefante serão modificados para atender objetivos específicos. Por fim, será demonstrado que o sistema proposto pode auxiliar o operador do PTT a identificar, gerenciar e mitigar o impacto dos fluxos elefante da rede do PTT. / Internet Exchange Points (IXPs) play a key role in the current Internet architecture enabling cost-effective connections among multiple autonomous systems (ASes). Management of IXP networks is primarily concerned with the management of the so-called elephant flows. Such flows represent a small portion of the total flows of a IXP network but usually have high impact on the overall traffic. Managing elephant flows involves adequate identification and eventually rerouting of such flows to more appropriate locations to minimize the possible negative impact on the other (mice) flows active in the network. Elephant flow management becomes more important in SDN-based IXPs that require controllers to have a consistent view of the underlying network to allow fine-grained adjustment. In this master thesis, we propose, develop, and evaluate an identification system to identify elephant flows and their respectively paths, as well as a recommendation system to suggest alternative configurations to previously identified elephant flows in an SDN-based IXP network. In this solution, the IXP operator can define templates that ultimately define how elephant flows can be reconfigured to achieve a specific objective. We demonstrate that our system can help IXP operators to identify, handle and mitigate the impact of elephant flows in the IXP network.

O projeto de mecanismos flexíveis e eficientes para o posicionamento e encadeamento de funções virtualizadas de rede (VNFs) é essencial para o sucesso de Virtualização de Funções de Rede (Network Function Virtualization, NFV). A maioria das soluções existentes, no entanto, considera custos fixos (e imutáveis) de processamento de fluxos e de largura de banda ao posicionar as VNFs em Pontos de Presença da Rede (N-PoPs). Essa limitação torna-se crítica em redes NFV com fluxos cujos comportamentos são altamente dinâmicos e nas quais os requisitos de processamento e os recursos disponíveis nos NPoPs mudam constantemente. Para preencher essa lacuna, propõe-se o NFV-PEAR, uma plataforma para o posicionamento e encadeamento adaptativo de VNFs. O NFV-PEAR visa (re)organizar periodicamente os posicionamentos e encadeamentos de VNFs previamente determinados, objetivando-se manter um desempenho fim-a-fim aceitável mesmo durante flutuações nos custos de processamento e nos requisitos dos fluxos. Paralelamente, busca-se minimizar as mudanças na rede (por exemplo, a realocação de VNFs ou de fluxos) realizadas para cumprir esse objetivo. Os resultados obtidos, a partir de uma avaliação experimental, mostram que o NFV-PEAR tem potencial para reduzir significativamente o número de mudanças na rede necessárias para assegurar o desempenho fim-a-fim esperado para os fluxos, garantindo assim o funcionamento estável dos serviços. / The design of flexible and efficient mechanisms for proper placement and chaining of virtual network functions (VNFs) is key for the success of Network Function Virtualization (NFV). Most state-of-the-art solutions, however, consider fixed (and immutable) flow processing and bandwidth requirements when placing VNFs in the Network Points of Presence (N-PoPs). This limitation becomes critical in NFV-enabled networks having highly dynamic flow behavior, and in which flow processing requirements and available N-PoP resources change constantly. To bridge this gap, we present NFV-PEAR, a platform for adaptive VNF placement and chaining. In NFV-PEAR, network operators may periodically (re)arrange previously determined placement and chaining of VNFs, with the goal of maintaining acceptable end-to-end flow performance despite fluctuations of flow processing costs and requirements. In parallel, NFV-PEAR seeks to minimize network changes (e.g., reallocation of VNFs or network flows). The results obtained from an experimental evaluation provide evidence that NFV-PEAR has potential to deliver more stable operation of network services, while significantly reducing the number of network changes required to ensure end-to-end flow performance.

Redes definidas por software (SDN) são uma abordagem recente para o projeto e operação de redes de computadores. Este paradigma é empregado com sucesso em cenários de datacenter, no entanto redes de acesso definidas por software (SDAN) ainda são raras em operadoras de telefonia e provedores de Internet. Isso deve-se em grande parte à inexistência de uma arquitetura de referência, algo que diversos projetos tentaram suprir nos últimos anos. Independente da vertente escolhida, a opção por uma mudança tão disruptiva como o SDN precisa ser justificada. Modelos tecno-econômicos são comumente utilizados para estimar o impacto da mudança na rentabilidade da operação. O custo total de propriedade (TCO) é uma métrica utilizada para esse fim. O presente trabalho desenvolveu um modelo simplificado de comparação de arquiteturas de rede, que diferentemente dos demais, tem foco nos serviços oferecidos ao assinante e no custo de gerenciamento dos mesmos. A análise é realizada em duas dimensões. Na primeira o esforço de operar a rede é estimado através de uma análise qualitativa, de forma similar ao realizado por outros modelos. O segundo eixo é a quantidade de recursos exigida para provisionar e monitorar cada serviço. Essa estimativa é gerada através do uso de simulação de tempo discreto dos elementos e protocolos relevantes. A combinação das duas análises permite identificar as tendências de comportamento dos serviços geradas pela adoção de uma nova arquitetura de rede, e avaliar a conveniência dessa migração. O uso de simulação neste trabalho demandou a construção de modelos dos equipamentos e protocolos envolvidos. Elegeu-se o pacote NS-3 como ferramenta de simulação. Definir e implementar modelos para todos os serviços analisados poderia tornar-se tão oneroso quanto as técnicas que desejávamos suplantar, e por isso utilizou-se uma abordagem indireta. São simulados apenas os componentes essenciais, e os custos de cada serviço são inferidos a partir deles. O modelo de rede SDAN utilizado, denominado SDCN, é inspirado no SplitArchitecture, proposto pelo projeto SPARC. / Software defined networks are a novel approach to design and operation of computer networks. Although this paradigm is employed successfully in many data-centers and campus, software defined access networks (SDAN) are still in their infancy. Carriers and ISPs have not converged on a standard architecture to build their infrastructure upon, a problem many initiatives are trying to solve. Regardless of the chosen model, the option for such a disruptive change as SDN needs to be justified. Techno-economic models are commonly used to estimate the impact of a change in the operation. The Total Cost of Ownership (TCO) is a metric commonly used for this purpose. The present work developed a simplified evaluation model for network architectures, which focuses on the services offered to the subscriber and on the cost of managing them. The analysis is performed in two dimensions. In the first, the effort to operate the network is estimated through a qualitative analysis, similar to the one performed by other existing models. The second axis is the amount of resources required to provision and monitor each service. This estimation is produced through the use of discrete time simulation of selected elements and protocols. The combination of the analyzes allows us to identify the behavioral trends provoked by the adoption of a new network architecture, and to evaluate the convenience of such migration. The simulation in this work demanded models for the equipment and protocols involved. The package NS-3 was the chosen simulation tool. Defining and implementing models for all services analyzed could become as costly as the techniques we wish to overcome, so an indirect approach has been used. Only the essential components are simulated, and the costs of each service are inferred from them. The SDAN model evaluated in this work, called SDCN, is a simplification of the SplitArchitecture proposed by the SPARC project.