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

Application of hydrodynamic cavitation in brewing

Dissertação de mestrado em Engenharia Química e BiológicaA cerveja é uma bebida muito popular em todo o mundo e que tem uma grande história até aos dias de hoje, sendo a terceira bebida mais consumida em todo o mundo. É obtida por fermentação alcoólica, utilizando leveduras geralmente do género Saccharomyces, num mosto preparado a partir de malte de cereais, no qual foram adicionadas flores de lúpulo ou produtos de lúpulo e água potável. A indústria da cerveja, como a conhecemos, é o resultado de um longo desenvolvimento. A forma de produzir cerveja não é muito variável, pelo que esta indústria se baseia na criatividade para inovar nesta área. Além disso, atualmente várias investigações têm sido realizadas com vista a inovar tecnologicamente o processo. Uma das tecnologias mais investigadas neste campo, e o foco central deste estudo é a aplicação da cavitação hidrodinâmica no fabrico de cerveja, mais precisamente durante a fase de ebulição do mosto, a fim de poupar energia no processo. O fenómeno de cavitação consiste (com auxílio de maquinaria) na formação e colapso de pequenas bolhas de vapor que geram grandes quantidades de energia no meio. O principal objetivo deste estudo é fazer uso da tecnologia na ebulição do mosto, e compreender as condições que otimizam a isomerização dos ácidos alfa, bem como compreender se é possível reduzir os níveis de glúten na cerveja. As experiências foram realizadas num wort kettle com um volume de 50 L. Foram testadas diferentes temperaturas num intervalo de 70 a 90 °C, bem como diferentes números de cavitação sendo aplicados num intervalo de 0.062 a 0.15. Além disso, foi realizada uma experiência com pellets de lúpulo ao invés de extrato de lúpulo. Foram também realizadas experiências a 70 e 100 °C (temperatura de ebulição) sem cavitação, a fim de comparar os resultados com a utilização da tecnologia. A isomerização mais elevada (63 %) foi obtida a 90 °C aplicando um número de cavitação de 0.062. Esta foi superior à isomerização obtida para a experiência de ebulição tradicional (53.7 %). Os resultados mostraram que a temperatura de 90 °C, independentemente do número de cavitação, parece muito promissora e resulta numa melhor isomerização, ou pelo menos comparável à ebulição tradicional. Relativamente aos resultados de glúten, a cavitação hidrodinâmica mostrou diminuir a concentração de gliadina (proteína de glúten) no meio. No início da experiência foi detetada uma concentração de 65.3 ± 9.5 mg/L de gliadina enquanto no final 49.7 ± 7.2 mg/L.Beer is a very popular drink around the world, a beverage that has a great history until today, being the third most consumed drink in the entire world. It is obtained by alcoholic fermentation, using usually selected yeasts of the Saccharomyces genus, into a wort prepared from cereal malt, in which flowers of hops or hop products and potable water have been added. The beer industry as we know is the result of long development. The way of producing beer is not very variable, so this industry is based on creativity to innovate in this area. Furthermore, research is currently being carried out in order to technologically innovate the process. One of the most in-depth technologies in this field and the central focus of this study is the application of hydrodynamic cavitation in brewing, more precisely during the wort boiling stage, in order to save energy in the process. The cavitation phenomenon consists of (with support of machinery) the formation and collapse of small steam bubbles generating large amounts of energy in the medium. The main goal of this study is to make use of the application of the technology in wort boiling and understand the conditions that optimise the isomerisation of bitter alpha acids, as well as to understand if it is possible to reduce the levels of gluten in beer. The experiments were performed in a wort kettle with a volume of 50l. Different temperatures were tested in a range from 70 to 90 °C, as well as different cavitation numbers being applied in a range from 0.062 to 0.15. Furthermore, an experiment with hop pellets instead of hop extract was performed. Besides that, experiments at 70 and 100 °C (boiling temperature) without cavitation were also performed in order to compare the results with the use of the technology. The highest isomerization (63 %) was obtained at 90 °C applying 0.062 cavitation number. This was higher than the isomerization obtained for the experiment of traditional boiling (53.7 %). The results have shown that the use of 90 °C, regardless the cavitation number, seem very promising and results in isomerization better or comparable to traditional boiling. Regarding the gluten results, hydrodynamic cavitation has shown to decrease the concentration of gliadin (protein of gluten) in the medium. At the beginning of the experiment it was detected a concentration of 65.3 ± 9.5 mg/L gliadin while at the end 49.7 ± 7.2 mg/L