Genetic studies on the mosquito vector Culex pipiens.

As duas espécies do complexo Culex pipiens com maior distribuição geográfica, Culex quinquefasciatus e Culex pipiens sensu stricto, são importantes vectores de filárias e arbovírus. Culex pipiens s.s. apresenta categorias intra-específicas definidas por características ecológicas e fisiológicas, das quais as formas pipiens e molestus têm sido implicadas na transmissão do vírus da Febre do Nilo Ocidental na Europa e América do Norte. Hibridação entre Cx. quinquefasciatus e Cx. pipiens s.s. foi documentada em algumas regiões geográficas onde ambas espécies coexistem simpatricamente. Este fenómeno também foi descrito entre as formas molestus e pipiens, em áreas de simpatria e quando existe contacto limitado em certas épocas do ano. No entanto, o impacto da hibridação na divergência genética entre as espécies ou formas está por clarificar. Além disso, a hibridação pode afectar características ecológicas/fisiológicas das espécies/formas, que podem influenciar a sua capacidade vectorial. Neste contexto, foram analisadas populações do complexo Cx. pipiens da Europa, EUA e da Macaronésia com objectivo de determinar níveis de diferenciação genética e taxas de hibridação entre os membros do complexo. As amostras de mosquitos foram obtidas por diferentes métodos de colheita no terreno e a partir de colónias laboratoriais, entre 2005 e 2011. As análises genéticas realizadas foram baseadas em microssatélites e por polimorfismos de comprimento de fragmentos amplificados. Foram efectuadas comparações abordando questões específicas a diferentes níveis taxonómicos, que estão descritas nos cinco capítulos de resultados da tese. A distribuição e níveis de hibridação entre Cx. quinquefasciatus e Cx. pipiens s.s. foram avaliados nas ilhas da Macaronésia, o que permitiu detectar híbridos (~40%) em duas ilhas do arquipélago de Cabo Verde. A distribuição destas espécies na região reflecte a biogeografia e aspectos históricos da colonização humana. A coexistência em habitats de superfície das formas molestus e pipiens na região da Comporta (Portugal), foi demostrada pela combinação de análises fenotípicas e genéticas. As análises moleculares também sugerem a existência de um padrão de introgressão assimétrica, de molestus para pipiens. Estudos adicionais, sugerem uma maior tendência da forma molestus para explorar habitats intradomiciliares/antropogénicos quando comparada com a forma pipiens. Em ambas as formas, mais de 90% das refeições sanguíneas foram realizadas em aves. Foi ainda efectuada a primeira análise genómica focada na divergência entre os genomas das formas molestus e pipiens. Esta análise indicou uma baixa divergência entre os dois genomas (1,4%–3,1%), o que é consistente com um processo de especiação simpátrica com fluxo génico. Finalmente, foram realizadas análises genéticas em amostras de Cx. pipiens s.s. colhidas na Grécia durante um surto de Febre do Nilo Ocidental, em 2010. Populações simpátricas de molestus e pipiens com introgressão assimétrica foram identificadas na região onde o surto ocorreu, enquanto uma população homogénea de molestus foi encontrada numa região sem transmissão do vírus. Estes resultados evidenciam a importância da caracterização da variação genética e das relações evolutivas entre os membros do complexo Cx. pipiens para entender o seu potencial como vectores de doenças. Também abrem novas perspectivas para a investigação da ecologia e evolução deste complexo de espécies com importância médica.The two widespread species of the Culex pipiens complex, Culex quinquefasciatus and Culex pipiens sensu stricto, are major vectors of filarial worms and arboviruses. Culex pipiens s.s. is also divided into intraspecific categories defined by ecological and physiological traits. Of these, two forms, denoted pipiens and molestus, have been implicated in West Nile virus transmission in Europe and North America. Inter-specific hybridisation between Cx. quinquefasciatus and Cx. pipiens s.s.has been documented in some geographic regions where both species occur sympatrically. Likewise, hybridisation between molestus and pipiens forms has been described in areas of sympatry or when the forms become in contact during certain times of the year. However, the impact of hybridisation on the extent of genetic divergence between species or forms remains uncertain. Moreover, hybridisation may affect ecological and physiological traits of the species/forms, which may influence their vectorial capacity. In this context, the degree of genetic differentiation and hybridisation between members of the Cx. pipiens complex was studied in populations from Europe, USA and Macaronesian islands. Mosquito samples were obtained from field collections or laboratory colonies between 2005 and 2011. Genetic analyses were based on microsatellite genotypes and amplified fragment length polymorphisms. Comparisons were made at different taxonomic levels, addressing specific questions. These are described in the five results chapters of this thesis. The distribution and hybridisation between Cx. quinquefasciatus and Cx. pipiens s.s. were assessed in Macaronesian islands. Hybrid rates ~40% were detected in two islands of the Cape Verde archipelago. The distribution of the species reflects both the islands' biogeography and historical aspects of human colonization. A combination of phenotypic and genetic analyses conducted in Comporta (Portugal) revealed the co-occurrence of molestus and pipiens forms of Cx. pipiens s.s. in aboveground habitats.Moreover, a pattern of asymmetric introgression from molestus into pipiens was found. Subsequent molecular and ecological analyses carried out in the same region suggested that the molestus form has a higher tendency to explore indoor/anthropogenic habitats, when compared with the sympatric pipiens form. In both forms, over 90% of blood meals were made on avian hosts. The first genomic scan addressing levels of genome divergence between molestus and pipiens forms was implemented. Low levels of inter-form genomic divergence (1.4%–3.1%) were detected, consistent with a process of sympatric speciation with gene flow. Finally, Cx. pipiens s.s. samples collected in Greece during a WNV outbreak in 2010 were genetically characterised. Sympatric molestus and pipiens populations with asymmetric introgression were detected in the region where the outbreak occurred, whereas a more genetically homogenous molestus population was found in a region with no WNV transmission. These results highlight the importance of characterizing patterns of genetic variation and evolutionary relations among members of the Cx. pipiens complex as a requirement for understanding the potential of these species to act as disease vectors. They also open new perspectives for further research on the ecology and evolution of this species complex of medical importance

Exploiting partial reconfiguration through PCIe for a microphone array network emulator

The current Microelectromechanical Systems (MEMS) technology enables the deployment of relatively low-cost wireless sensor networks composed of MEMS microphone arrays for accurate sound source localization. However, the evaluation and the selection of the most accurate and power-efficient network’s topology are not trivial when considering dynamic MEMS microphone arrays. Although software simulators are usually considered, they consist of high-computational intensive tasks, which require hours to days to be completed. In this paper, we present an FPGA-based platform to emulate a network of microphone arrays. Our platform provides a controlled simulated acoustic environment, able to evaluate the impact of different network configurations such as the number of microphones per array, the network’s topology, or the used detection method. Data fusion techniques, combining the data collected by each node, are used in this platform. The platform is designed to exploit the FPGA’s partial reconfiguration feature to increase the flexibility of the network emulator as well as to increase performance thanks to the use of the PCI-express high-bandwidth interface. On the one hand, the network emulator presents a higher flexibility by partially reconfiguring the nodes’ architecture in runtime. On the other hand, a set of strategies and heuristics to properly use partial reconfiguration allows the acceleration of the emulation by exploiting the execution parallelism. Several experiments are presented to demonstrate some of the capabilities of our platform and the benefits of using partial reconfiguration

Performance and resource modeling for FPGAs using high-level synthesis tools

High-performance computing with FPGAs is gaining momentum with the advent of sophisticated High-Level Synthesis (HLS) tools. The performance of a design is impacted by the input-output bandwidth, the code optimizations and the resource consumption, making the performance estimation a challenge. This paper proposes a performance model which extends the roofline model to take into account the resource consumption and the parameters used in the HLS tools. A strategy is developed which maximizes the performance and the resource utilization within the area of the FPGA. The model is used to optimize the design exploration of a class of window-based image processing application

Runtime reconfigurable beamforming architecture for real-time sound-source localization

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Plataforma de software para gestão dos doentes mentais internados em instituições do setor social no Hospital Fernando Fonseca.

Projecto final para obtenção do Grau de Mestre em Engenharia Informática e de Computadores.O Hospital Fernando Fonseca e uma organização que trabalha com doentes com doenças mentais os quais são enviados para Casa de Saúde de modo a serem cuidados durante 24 horas por dia. Estes pacientes podem ser enviados para as Casas de Saúde por parte do próprio HFF ou por instituições externas. Quando um paciente entra numa Casa de Saúde, o HFF ou a instituição que enviou o paciente, é responsável pelo pagamento dos cuidados diários deste paciente. Já dentro da Casa de Saúde, pode ser necessário que um paciente visite outras instituições, por exemplo hospitais. Durante este período, o HFF não pode ser cobrado pelo cuidado destes pacientes uma vez que estes não estão na Casa de Saúde. Dado que o HFF não controla estas saídas, podem ser cobrados dias nos quais o paciente não esteve na Casa de Saúde. O processo atual de referenciação de um paciente para uma Casa de Saúde, bem como a gestão do mesmo, e realizado de forma manual, através do envio de emails entre departamentos. Este processo pode ser lento e sujeito a falhas. O desenvolvimento deste projeto tem como objetivo a criação de uma aplicação que facilite a comunicação entre os diferentes departamentos envolvidos no processo de internamento, bem como simplificar a criação e gestão do processo e garantir que o HFF esta a ser cobrado o valor real dos cuidados. Neste documento serão apresentadas as diferentes fases de desenvolvimento do projeto tais como o levantamento de requisitos, a criação de mock-ups para exposição de ideias, criação de modelos de base de dados, criação da aplicação, testes realizados e por fim o deployment.Hospital Fernando Fonseca is an organization that manages patients with mental diseases sent to Care Houses that are able to take care of them for 24 hours a day. These patients can be sent to the Care Houses by the hospital itself or by other institutions. Once a patient has entered a Care House, the HFF is responsible for the payment of the daily cares of the patient. In case the patient comes from another institution, then it is the institution’s responsibility to make these payments. Once in the Care House, a patient might need to go to other institutions, such as hospitals, for other health related reasons. During these days, the care of the patients should not be billed since they are not in the Care House. This however, poses a problem because the HFF cannot track these visits since they are only managed by the Care House, which can lead to the days being billed without the knowledge of the HFF. The current process of referring a patient to a Care House and managing their internment is made manually, and the communication between the HFF and the Care Houses is made via e-mail. This makes the process slow and prone to failure. The development of this project has the goal of creating and application that will allow the different departments that take part in this process to communicate better with each other in order to simplify the process and guarantee the correct billing for the care of the patients. This document will present the different stages of the development of the project, such as defining the requirements, creating a set of mock-ups to explain the ideas to the HFF, developing the database models, creating the application, testing it and finally deploying it.N/

Evaluation of classical machine learning techniques towards urban sound recognition embedded systems

Automatic urban sound classification is a desirable capability for urban monitoring systems, allowing real-time monitoring of urban environments and recognition of events. Current embedded systems provide enough computational power to perform real-time urban audio recognition. Using such devices for the edge computation when acting as nodes of Wireless Sensor Networks (WSN) drastically alleviates the required bandwidth consumption. In this paper, we evaluate classical Machine Learning (ML) techniques for urban sound classification on embedded devices with respect to accuracy and execution time. This evaluation provides a real estimation of what can be expected when performing urban sound classification on such constrained devices. In addition, a cascade approach is also proposed to combine ML techniques by exploiting embedded characteristics such as pipeline or multi-thread execution present in current embedded devices. The accuracy of this approach is similar to the traditional solutions, but provides in addition more flexibility to prioritize accuracy or timing

Design exploration and performance strategies towards power-efficient FPGA-based achitectures for sound source localization

Many applications rely on MEMS microphone arrays for locating sound sources prior to their execution. Those applications not only are executed under real-time constraints but also are often embedded on low-power devices. These environments become challenging when increasing the number of microphones or requiring dynamic responses. Field-Programmable Gate Arrays (FPGAs) are usually chosen due to their flexibility and computational power. This work intends to guide the design of reconfigurable acoustic beamforming architectures, which are not only able to accurately determine the sound Direction-Of-Arrival (DoA) but also capable to satisfy the most demanding applications in terms of power efficiency. Design considerations of the required operations performing the sound location are discussed and analysed in order to facilitate the elaboration of reconfigurable acoustic beamforming architectures. Performance strategies are proposed and evaluated based on the characteristics of the presented architecture. This power-efficient architecture is compared to a different architecture prioritizing performance in order to reveal the unavoidable design trade-offs

FPGA-based architectures for acoustic beamforming with microphone arrays : trends, challenges and research opportunities

Over the past decades, many systems composed of arrays of microphones have been developed to satisfy the quality demanded by acoustic applications. Such microphone arrays are sound acquisition systems composed of multiple microphones used to sample the sound field with spatial diversity. The relatively recent adoption of Field-Programmable Gate Arrays (FPGAs) to manage the audio data samples and to perform the signal processing operations such as filtering or beamforming has lead to customizable architectures able to satisfy the most demanding computational, power or performance acoustic applications. The presented work provides an overview of the current FPGA-based architectures and how FPGAs are exploited for different acoustic applications. Current trends on the use of this technology, pending challenges and open research opportunities on the use of FPGAs for acoustic applications using microphone arrays are presented and discussed