Salamandra salamandra (Amphibia: Caudata: Salamandridae) in Portugal: not all black and yellow

The fire salamander complex is quite diverse in the Iberian Peninsula where nine subspecies of Salamandra salamandra are currently recognized. Here, we analysed the geographical distribution of the subspecies S. s. gallaica and S. s. crespoi using partial sequences of the mitochondrial cytochrome b gene of 168 individuals from 12 locations in Portugal. Our results support the existence of a deep lineage divergence between the two subspecies, with non-overlapping geographical distributions except in two contact zones: one in Sesimbra on the western coast, and another in Alcoutim on the southeastern border with Spain. Moreover, S. s. crespoi displays signs of gene flow among the sampled locations whereas S. s. gallaica shows evidence of some restriction to gene flow. Present-day genetic make-up of S. s. gallaica and S. s. crespoi is a result of past historical events, fine-tuned by contemporary Iberian geoclimate. Humid mountain areas were found to harbour increased genetic diversity possibly acting as past refugia during drier interglacial periods. To analyse wider geographical patterns and lineage splitting events within S. salamandra we performed a Bayesian dating analysis completing our data set with previously published sequences. The observed divergences were associated to successive biogeographic scenarios, and to other Iberian species showing similar trends.

Distributional Similarity of Words with Different Frequencies

Distributional semantics tries to characterize the meaning of words by the contexts in which they occur. Similarity of words hence can be derived from the similarity of contexts. Contexts of a word are usually vectors of words appearing near to that word in a corpus. It was observed in previous research that similarity measures for the context vectors of two words depend on the frequency of these words. In the present paper we investigate this dependency in more detail for one similarity measure, the Jensen-Shannon divergence. We give an empirical model of this dependency and propose the deviation of the observed Jensen-Shannon divergence from the divergence expected on the basis of the frequencies of the words as an alternative similarity measure. We show that this new similarity measure is superior to both the Jensen-Shannon divergence and the cosine similarity in a task, in which pairs of words, taken from Wordnet, have to be classified as being synonyms or not.

Evolution of the rbcS gene family in Solanaceae: concerted evolution and gain and loss of introns, with a description of new statistical guidelines for determining the number of unique gene copies.

Thesis (Ph.D.)--University of Washington, 2014

Custo histórico versus justo valor

Oriêntador: Mestre Carlos Pedro

Estudo da divergência entre duas vias que curvam em sentidos contrários

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

Modelação do viaduto do Corgo durante o ensaio de carga estático

Trabalho Final de Mestrado elaborado no Laboratório Nacional de Engenharia Civil (LNEC) para a obtenção do grau de Mestre em Engenharia Civil pelo Instituto Superior de Engenharia de Lisboa no âmbito do protocolo de cooperação entre o ISEL e o LNEC

Análise de um veículo todo o terreno do tipo KARTCROSS

O presente trabalho descreve a análise feita a um veículo de todo o terreno. O kartcross/buggy em estudo é usado em provas do tipo Baja, sendo estas provas longas e com traçados sinuosos. O veículo, já construído, foi testado através de softwares, a nível estrutural e ciclístico, pretendendo-se assim efetuar engenharia inversa sobre o mesmo. No decorrer da sua utilização normal o kartcross/buggy sofre vários tipos de solicitações, como sejam aceleração, travagem e força centrípta em curva. Portanto, o veículo deve ser capaz de suportar estes esforços e ter uma boa habilidade. Além dos testes em uso corrente foi analisada também a rigidez torsional do quadro do veículo e do veículo completo, podendo-se assim melhorar estes valores. A nível ciclístico foram analisados os parâmetros das suspensões como o camber, convergência/divergência, caster, entre outros. Da análise destes parâmetros e possível fazerem-se melhorias de forma a que o veículo tenha um melhor desempenho. Para validar os testes computacionais efetuados foi reproduzido experimentalmente o teste da rigidez torsional. No final, compararam-se os valores numéricos com os experimentais e aferir se o modelo se encontra bem representado.

Integer and Fractional Order Entropy Analysis of Earthquake Data-series

This paper studies the statistical distributions of worldwide earthquakes from year 1963 up to year 2012. A Cartesian grid, dividing Earth into geographic regions, is considered. Entropy and the Jensen–Shannon divergence are used to analyze and compare real-world data. Hierarchical clustering and multi-dimensional scaling techniques are adopted for data visualization. Entropy-based indices have the advantage of leading to a single parameter expressing the relationships between the seismic data. Classical and generalized (fractional) entropy and Jensen–Shannon divergence are tested. The generalized measures lead to a clear identification of patterns embedded in the data and contribute to better understand earthquake distributions.

Fractional State Space Analysis of Economy Systems

This paper examines modern economic growth according to the multidimensional scaling (MDS) method and state space portrait (SSP) analysis. Electing GDP per capita as the main indicator for economic growth and prosperity, the long-run perspective from 1870 to 2010 identifies the main similarities among 34 world partners’ modern economic growth and exemplifies the historical waving mechanics of the largest world economy, the USA. MDS reveals two main clusters among the European countries and their old offshore territories, and SSP identifies the Great Depression as a mild challenge to the American global performance, when compared to the Second World War and the 2008 crisis.

Macroeconomic impacts of politics and policy: Applications to financial and real markets

A PhD Dissertation, presented as part of the requirements for the Degree of Doctor of Philosophy from the NOVA - School of Business and Economics

Ressocialização no meio prisional

This paper examine the purpose of rehabilitation while main purpose of imprisonment application, and the divergence between its central role assumed in legislation and what is being practiced in the institutional dimension. This study aims to determine the expected outcome of this dialectical opposition, in pursuit of preventive purposes that guide the criminal reactions of Portuguese criminal - legal system. To this end, the sentence of imprisonment shall be framed in the main politico- criminal traits of our country, analyzing the standards and principles that underlie and underpin our legal – criminal system. The guiding principles of the prison sentence and the respective legislation will be presented, such as the prison system and treatment provided to achieve the above desideratum. Finally material factors and legislative contradictions that oppose the rehabilitation in prisons will be presented. The dissertation does not intend to expose the solution to this paradox insurmountable, but rather present the main factors that hinder the achievement of the objectives intended to be achieved with the prison sentence.

When orthologs diverge between human and mouse.

Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse orthologous genes, and discuss it in the context of biomedical research.

Sympatric speciation in palms on an oceanic island.

The origin of species diversity has challenged biologists for over two centuries. Allopatric speciation, the divergence of species resulting from geographical isolation, is well documented. However, sympatric speciation, divergence without geographical isolation, is highly controversial. Claims of sympatric speciation must demonstrate species sympatry, sister relationships, reproductive isolation, and that an earlier allopatric phase is highly unlikely. Here we provide clear support for sympatric speciation in a case study of two species of palm (Arecaceae) on an oceanic island. A large dated phylogenetic tree shows that the two species of Howea, endemic to the remote Lord Howe Island, are sister taxa and diverged from each other well after the island was formed 6.9 million years ago. During fieldwork, we found a substantial disjunction in flowering time that is correlated with soil preference. In addition, a genome scan indicates that few genetic loci are more divergent between the two species than expected under neutrality, a finding consistent with models of sympatric speciation involving disruptive/divergent selection. This case study of sympatric speciation in plants provides an opportunity for refining theoretical models on the origin of species, and new impetus for exploring putative plant and animal examples on oceanic islands.

Oligocene CO2 decline promoted C4 photosynthesis in grasses.

C4 photosynthesis is an adaptation derived from the more common C3 photosynthetic pathway that confers a higher productivity under warm temperature and low atmospheric CO2 concentration [1, 2]. C4 evolution has been seen as a consequence of past atmospheric CO2 decline, such as the abrupt CO2 fall 32-25 million years ago (Mya) [3-6]. This relationship has never been tested rigorously, mainly because of a lack of accurate estimates of divergence times for the different C4 lineages [3]. In this study, we inferred a large phylogenetic tree for the grass family and estimated, through Bayesian molecular dating, the ages of the 17 to 18 independent grass C4 lineages. The first transition from C3 to C4 photosynthesis occurred in the Chloridoideae subfamily, 32.0-25.0 Mya. The link between CO2 decrease and transition to C4 photosynthesis was tested by a novel maximum likelihood approach. We showed that the model incorporating the atmospheric CO2 levels was significantly better than the null model, supporting the importance of CO2 decline on C4 photosynthesis evolvability. This finding is relevant for understanding the origin of C4 photosynthesis in grasses, which is one of the most successful ecological and evolutionary innovations in plant history.

Are there two species of Pygmy Shrews (Sorex)? Revisiting the question using DNA sequence data

Pygmy Shrews in North America have variously been considered to be one species (Sorex hoyi) or two species (S. hoyi and S. thompsoni). Currently, only S. hoyi is recognized. In this study, we examine mitochondrial DNA sequence data for the cytochrome b gene to evaluate the level of differentiation and phylogeographic relationships among eleven samples of Pygmy Shrews from across Canada. Pygmy Shrews from eastern Canada (i.e., Ontario, Quebec, New Brunswick, Nova Scotia, and Prince Edward Island) are distinct from Pygmy Shrews from western Canada (Alberta, Yukon) and Alaska. The average level of sequence divergence between these clades (3.3%) falls within the range of values for other recognized pairs of sister species of shrews. A molecular clock based on third position transversion substitutions suggests that these two lineages diverged between 0.44 and 1.67 million years ago. These molecular phylogenetic data. combined with a reinterpretation of previously published morphological data, are suggestive of separate species status for S. hoyi and S. thompsoni as has been previously argued by others. Further analysis of specimens from geographically intermediate areas (e.g., Manitoba. northern Ontario) is required to determine if there is secondary contact and/or introgression between these two putative species.