Understanding the differentiation process of western Mediterranean butterflies: the case studies of Lycaena and Melanargia

Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2019The western Mediterranean region is responsible for generating and keeping a great amount of interspecific and intraspecific variation among numerous groups of species. Choosing butterflies as a model organism, this study aims to unravel the differentiation process of a few species from this Mediterranean region, belonging in two different genera: Lycaena and Melanargia. Therefore, the present work is divided in two case-studies, both focusing on different but complementary problematics: The first deals with the speciation and relationship between the two Sooty Copper butterflies, L. tityrus (the Sooty Copper, widespread in Europe) and L. bleusei (the Iberian Sooty Copper, an Iberian endemic), which has been considered as a subspecies of the former; the second studies the phylogenetic relationships and genetic differentiation of the whole subgenus Argeformia, belonging in the genus Melanargia, in particular the species Melanargia ines (widespread in Iberia and North Africa), M. occitanica (found in South of France + North Italy, Iberia, North Africa and Sicily) and M. arge (Italian endemic). While the first deals with two sister taxa and goes through different analyses (Genetics, Geometric Morphometrics and Species Distribution Modeling (SDM)) in one integrative study to infer if these should be considered as independent species, the second tries to confirm the current phylogenetic relationships among the species of Argeformia, and analyse the gene flow across the different land and sea barriers of the western Mediterranean region. Overall, each analysis conducted for Lycaena allowed us to clearly differentiate both Sooty Coppers and conclude that these should be considered as different species. Nonetheless, their reproductive barriers appear not to be fully developed and two L. tityrus specimens displayed introgressed L. bleusei genetic material. Additionally, the combination of Genetics and SDM results support the hypothesis of a post glacial population and genetic bottleneck for L. bleusei. Regarding Melanargia, our phylogeny agrees with the current classification and relationships within Argeformia, with M. occitanica sister to M. arge and both closely related to M. ines. The western Mediterranean barriers displayed different roles and capacities to isolate populations gene flow, with the Gibraltar Strait being the most influential barrier. Different evolutionary history scenarios are here presented for both the Sooty Coppers and Argeformia species, which seem to have a differentiation process fundamentally driven by isolation in allopatry across the geographic barriers and climatic oscillations in a first phase, and different ecological adaptations later

A Framework for Fast Image Deconvolution with Incomplete Observations

In image deconvolution problems, the diagonalization of the underlying operators by means of the FFT usually yields very large speedups. When there are incomplete observations (e.g., in the case of unknown boundaries), standard deconvolution techniques normally involve non-diagonalizable operators, resulting in rather slow methods, or, otherwise, use inexact convolution models, resulting in the occurrence of artifacts in the enhanced images. In this paper, we propose a new deconvolution framework for images with incomplete observations that allows us to work with diagonalized convolution operators, and therefore is very fast. We iteratively alternate the estimation of the unknown pixels and of the deconvolved image, using, e.g., an FFT-based deconvolution method. This framework is an efficient, high-quality alternative to existing methods of dealing with the image boundaries, such as edge tapering. It can be used with any fast deconvolution method. We give an example in which a state-of-the-art method that assumes periodic boundary conditions is extended, through the use of this framework, to unknown boundary conditions. Furthermore, we propose a specific implementation of this framework, based on the alternating direction method of multipliers (ADMM). We provide a proof of convergence for the resulting algorithm, which can be seen as a "partial" ADMM, in which not all variables are dualized. We report experimental comparisons with other primal-dual methods, where the proposed one performed at the level of the state of the art. Four different kinds of applications were tested in the experiments: deconvolution, deconvolution with inpainting, superresolution, and demosaicing, all with unknown boundaries.Comment: IEEE Trans. Image Process., to be published. 15 pages, 11 figures. MATLAB code available at https://github.com/alfaiate/DeconvolutionIncompleteOb

A convex formulation for hyperspectral image superresolution via subspace-based regularization

Hyperspectral remote sensing images (HSIs) usually have high spectral resolution and low spatial resolution. Conversely, multispectral images (MSIs) usually have low spectral and high spatial resolutions. The problem of inferring images which combine the high spectral and high spatial resolutions of HSIs and MSIs, respectively, is a data fusion problem that has been the focus of recent active research due to the increasing availability of HSIs and MSIs retrieved from the same geographical area. We formulate this problem as the minimization of a convex objective function containing two quadratic data-fitting terms and an edge-preserving regularizer. The data-fitting terms account for blur, different resolutions, and additive noise. The regularizer, a form of vector Total Variation, promotes piecewise-smooth solutions with discontinuities aligned across the hyperspectral bands. The downsampling operator accounting for the different spatial resolutions, the non-quadratic and non-smooth nature of the regularizer, and the very large size of the HSI to be estimated lead to a hard optimization problem. We deal with these difficulties by exploiting the fact that HSIs generally "live" in a low-dimensional subspace and by tailoring the Split Augmented Lagrangian Shrinkage Algorithm (SALSA), which is an instance of the Alternating Direction Method of Multipliers (ADMM), to this optimization problem, by means of a convenient variable splitting. The spatial blur and the spectral linear operators linked, respectively, with the HSI and MSI acquisition processes are also estimated, and we obtain an effective algorithm that outperforms the state-of-the-art, as illustrated in a series of experiments with simulated and real-life data.Comment: IEEE Trans. Geosci. Remote Sens., to be publishe

Tiago Guedes: o futuro do cinema passa por baixar muito os custos de produção

O projecto “Principais tendências no cinema português contemporâneo” nasceu no Departamento de Cinema da ESTC, com o objectivo de desenvolver investigação especializada a partir de um núcleo formado por alunos da Licenciatura em Cinema e do Mestrado em Desenvolvimento de Projecto Cinematográfico, a que se juntaram professores-investigadores membros do CIAC e convidados. O que agora se divulga corresponde a dois anos e meio de trabalho desenvolvido pela equipa de investigação, entre Abril de 2009 e Novembro de 2011. Dada a forma que ele foi adquirindo, preferimos renomeá-lo, para efeitos de divulgação, “Novas & velhas tendências no cinema português contemporâneo”.QUAIS SÃO, hoje, as principais características do desenvolvimento de projectos para cinema em Portugal? O que pensam realizadores cinematográficos, produtores, distribuidores e exibidores sobre o cinema português? Que conclusões tirar das suas opiniões, relatos de experiências e análises da situação contemporânea? Que novas tendências surgiram no cinema português, nos primeiros anos do séc. XXI?Fundação para a Ciência e Tecnologia, Centro de Investigação em Artes e Comunicação, Instituto do Cinema e do Audiovisual, Ministério da Cultura, Escola Superior de Teatro e Cinema

The role of short sea shipping and European rail corridors in intermodal freight transportation

This dissertation explores the possibility of combining short sea shipping with European Union rail corridors and inland waterways to carry freight towards regions located away from the coastline. The contributions of this dissertation is the expansion of a network model and the introduction of new transport chains in new areas not cov-ered before. A review of intermodal transport policies in the European Union and of transport cost and transit time models in intermodal transport chains is carried out. A network-based model of intermodal transport chains in the Atlantic façade of Europe is developed, including different combinations of modes of transportation (road, short sea shipping, rail and inland waterways). These models are applied to the quantification of total transport cost, transit time and a combination of both using value of time for creating a generalized transportation cost. Results are presented for transport chains from Porto and Bragança to 75 NUTS 2 regions (Nomenclature of ter-ritorial units for statistics) in northern Europe. The regions for which the different in-termodal combinations are more competitive are identified. Parametric variations of critical transport parameters are carried out, allowing the identification of changes in the scope of regions for which the different intermodal combinations are more com-petitive. The results obtained by the model identify the competitiveness of intermodal so-lutions using short sea shipping rail and inland waterways in the transport of freight. Intermodal solutions prove to be slow when comparing with road haulage, which proves to be cost competitive for certain regions.Esta dissertação explora a possibilidade de combinar o transporte marítimo de curta distância com os corredores ferroviários da União Europeia e vias navegáveis para transportar mercadorias para regiões distantes da costa. As contribuições desta dissertação são a expansão de um modelo de rede e a introdução de novas cadeias de transporte em novas áreas. É efetuada uma revisão das políticas de transporte intermo-dal na União Europeia e dos modelos de custos de transporte e de tempo de trânsito nas cadeias de transporte intermodal. É desenvolvido um modelo baseado em rede de cadeias de transporte intermodal na fachada atlântica da Europa, incluindo diferentes combinações de modos de trans-porte (rodoviário, marítimo de curta distância, ferroviário e vias fluviais). Estes mode-los são aplicados à quantificação do custo total de transporte, tempo de trânsito e uma combinação de ambos utilizando o valor do tempo para a criação de um custo genera-lizado de transporte. São apresentados resultados para cadeias de transporte entre o Porto e Bragança e 75 regiões NUTS 2 (Nomenclatura de unidades territoriais para es-tatísticas) do norte da Europa. São identificadas as regiões para as quais as diferentes combinações intermodais são mais competitivas. São realizadas variações paramétri-cas de parâmetros críticos de transporte, permitindo a identificação de mudanças no escopo de regiões para as quais as diferentes combinações intermodais são mais com-petitivas. Os resultados obtidos pelo modelo identificam a competitividade das soluções intermodais utilizando os modos marítimo, ferroviário e fluvial no transporte de mer-cadorias. As soluções intermodais mostram-se lentas quando comparadas com o trans-porte rodoviário, mas competitivas em termos de custos para determinadas regiões

Intelligent Routing for Software-Defined Media Networks

The multimedia market is an industry with an ever-growing demand coupled with strict requirements. Be it in live streaming services or file content broadcast, multimedia providers need to deliver the best possible quality in order to meet their costumer’s requirements and gain or keep their trust. Multimedia traffic has a high impact on networks and, due to its nature, is sensitive to congestion or hardware failure. Thus, it is frequently that multimedia providers resort to third-party software to monitor quality parameters. Skyline Communications’ DataMiner® offers network monitoring, orchestrating and automation capabilities across a broad range of applications and environments. These features are enabled by the emergence of Software-Defined Networking (SDN) which provides a global view of networks and the ability to change network properties through software applications. This contrasts with traditional networks which are rigid, static and difficult to scale-up. An application that greatly benefits from the global network view of SDN is routing optimization. Through routing optimization, a network can effectively deliver more traffic by efficiently balancing load across the different links and paths between end points of a service, reaching an increased performance in data transport. This dissertation comes to light with the goal of optimizing DataMiner’s routing mechanism by exploring the routing optimization possibilities enabled by its SDN-like architecture. Both link cost optimization-based and Machine Learning (ML) approaches are evaluated as possible solutions to Skyline’s problem and several experiments were conducted to compare them and understand their impact on network performance while transporting multimedia streams.O mercado audiovisual é uma indústria onde a procura está em constante crescimento, bem como a exigência. Tanto durante transmissões ao vivo como de conteúdo multimédia pré-gravado, os provedores de multimédia necessitam de garantir a melhor qualidade possível para corresponderem aos requisitos dos seus clientes e conquistarem ou manterem a sua confiança nos seus serviços. O tráfego multimédia tem um forte impacto nas redes que o transportam e, graças à sua natureza, é bastante sensível a congestão ou a falhas de equipamento. Por este motivo, é frequente os provedores de multimédia recorrerem a aplicações externas para monitorização de parâmetros de qualidade. O DataMiner®, desenvolvido pela Skyline Communications, oferece a capacidade de monitorizar e orquestrar redes de transporte de multimédia bem como de automatizar as suas funcionalidades num vasto conjunto de enquadramentos e ambientes. Tais funcionalidades são oferecidas pelo aparecimento de SDN que permite que se tenha uma visão global de uma rede e que se altere de forma flexível as suas definições através de aplicações. As características de redes deste tipo contrastam fortemente com as redes tradicionais marcadas pela sua rigidez, estaticidade e dificuldade de expansão. Uma área que beneficia bastante com a visão global de redes oferecida pela tecnologia de SDN é a otimização do transporte de dados. Desta forma, uma rede consegue transportar mais dados de forma eficiente através do balanceamento da carga a que é submetida pelas diferentes ligações entre elementos e caminhos que conectam pontos de entrada e saída da mesma, atingindo altos níveis de desempenho. A presente dissertação surge da intenção da Skyline de otimizar o seu algoritmo de encaminhamento através da exploração de métodos alternativos introduzidos pela tecnologia de SDN. Tanto métodos baseados em otimização do custo de ligações da rede como em aprendizagem automática são avaliados como possíveis soluções para o problema proposto e diversas simulações são conduzidas para as comparar e averiguar o seu impacto no desempenho de redes de transporte de dados multimédia

Terminal LTE flexível

Mstrado em Engenharia Eletrónica e TelecomunicaçõesAs redes móveis estão em constante evolução. A geração atual (4G) de redes celulares de banda larga e representada pelo standard Long Term Evolution (LTE), definido pela 3rd Generation Partnership Project (3GPP). Existe uma elevada procura/uso da rede LTE, com um aumento exponencial do número de dispositivos móveis a requerer uma ligação à Internet de alto débito. Isto pode conduzir à sobrelotação do espetro, levando a que o sinal tenha que ser reforçado e a cobertura melhorada em locais específicos, tal como em grandes conferências, festivais e eventos desportivos. Por outro lado, seria uma vantagem importante se os utilizadores pudessem continuar a usar os seus equipamentos e terminais em situações onde o acesso a redes 4G é inexistente, tais como a bordo de um navio, eventos esporádicos em localizações remotas ou em cenários de catástrofe, em que as infraestruturas que permitem as telecomunicações foram danificadas e a cobertura temporária de rede pode ser decisiva em processos de salvamento. Assim sendo, existe uma motivação clara por trás do desenvolvimento de uma infraestrutura celular totalmente reconfigurável e que preencha as características mencionadas anteriormente. Uma possível abordagem consiste numa plataforma de rádio definido por software (SDR), de código aberto, que implementa o standard LTE e corre em processadores de uso geral (GPPs), tornando possível construir uma rede completa investindo somente em hardware - computadores e front-ends de radiofrequência (RF). Após comparação e análise de várias plataformas LTE de código aberto foi selecionado o OpenAirInterface (OAI) da EURECOM, que disponibiliza uma implementação compatível com a Release 8.6 da 3GPP (com parte das funcionalidades da Release 10). O principal objectivo desta dissertação é a implementação de um User Equipment (UE) flexível, usando plataformas SDR de código aberto que corram num computador de placa única (SBC) compacto e de baixa potência, integrado com um front-end de RF - Universal Software Radio Peripheral (USRP). A transmissão de dados em tempo real usando os modos de duplexagem Time Division Duplex (TDD) e Frequency Division Duplex (FDD) é suportada e a reconfiguração de certos parâmetros é permitida, nomeadamente a frequência portadora, a largura de banda e o número de Resource Blocks (RBs) usados. Além disso, é possível partilhar os dados móveis LTE com utilizadores que estejam próximos, semelhante ao que acontece com um hotspot de Wi-Fi. O processo de implementação é descrito, incluindo todos os passos necessários para o seu desenvolvimento, englobando o port do UE de um computador para um SBC. Finalmente, a performance da rede é analisada, discutindo os valores de débitos obtidos.Mobile networks are constantly evolving. 4G is the current generation of broadband cellular network technology and is represented by the Long Term Evolution (LTE) standard, de ned by 3rd Generation Partnership Project (3GPP). There's a high demand for LTE at the moment, with the number of mobile devices requiring an high-speed Internet connection increasing exponentially. This may overcrowd the spectrum on the existing deployments and the signal needs to be reinforced and coverage improved in speci c sites, such as large conferences, festivals and sport events. On the other hand, it would be an important advantage if users could continue to use their equipment and terminals in situations where cellular networks aren't usually available, such as on board of a cruise ship, sporadic events in remote locations, or in catastrophe scenarios in which the telecommunication infrastructure was damaged and the rapid deployment of a temporary network can save lives. In all of these situations, the availability of exible and easily deployable cellular base stations and user terminals operating on standard or custom bands would be very desirable. Thus, there is a clear motivation for the development of a fully recon gurable cellular infrastructure solution that ful lls these requirements. A possible approach is an open-source, low-cost and low maintenance Software-De ned Radio (SDR) software platform that implements the LTE standard and runs on General Purpose Processors (GPPs), making it possible to build an entire network while only spending money on the hardware itself - computers and Radio-Frequency (RF) front-ends. After comparison and analysis of several open-source LTE SDR platforms, the EURECOM's OpenAirInterface (OAI) was chosen, providing a 3GPP standard-compliant implementation of Release 8.6 (with a subset of Release 10 functionalities). The main goal of this dissertation is the implementation of a exible opensource LTE User Equipment (UE) software radio platform on a compact and low-power Single Board Computer (SBC) device, integrated with an RF hardware front-end - Universal Software Radio Peripheral (USRP). It supports real-time Time Division Duplex (TDD) and Frequency Division Duplex (FDD) LTE modes and the recon guration of several parameters, namely the carrier frequency, bandwidth and the number of LTE Resource Blocks (RB) used. It can also share its LTE mobile data with nearby users, similarly to a Wi-Fi hotspot. The implementation is described through its several developing steps, including the porting of the UE from a regular computer to a SBC. The performance of the network is then analysed based on measured results of throughput