Burrows-wheeler transform in secondary memory

Master’s Thesis in Computer EngineeringA suffix array is an index, a data structure that allows searching for sequences of characters. Such structures are of key importance for a large set of problems related to sequences of characters. An especially important use of suffix arrays is to compute the Burrows-Wheeler Transform, which can be used for compressing text. This procedure is the base of the UNIX utility bzip2. The Burrows-Wheeler transform is a key step in the construction of more sophisticated indexes. For large sequences of characters, such as DNA sequences of about 10 GB, it is not possible to calculate the Burrows-Wheeler transform in an average computer without using secondary memory. In this dissertation we will study the state-of-the-art algorithms to construct the Burrows-Wheeler transform in secondary memory. Based on this research we propose an algorithm and compare it against the previous ones to determine its relative performance. Our algorithm is based on the classical external Heapsort. The novelty lies in a heap that is especially designed for suffix arrays, which we call String Heap. This algorithm aims to be space-conscious, while trying to handle the disk access dominance over main memory access. We divide our solution in two parts, splitting and merging suffix arrays, the latter is the main application of the String Heap. The merging part produces the BWT, as a side effect of merging a set of partial suffix arrays of a text. We also compare its performance against the other algorithms. We also study a second version of the algorithm that accesses secondary memory in blocks

Chirikov diffusion in the asteroidal three-body resonance (5, −2, −2)

The theory of diffusion in many-dimensional Hamiltonian system is applied to asteroidal dynamics. The general formulation developed by Chirikov is applied to the Nesvorný-Morbidelli analytic model of three-body (three-orbit) mean-motion resonances (Jupiter-Saturn-asteroid). In particular, we investigate the diffusion along and across the separatrices of the (5, −2, −2) resonance of the (490) Veritas asteroidal family and their relationship to diffusion in semi-major axis and eccentricity. The estimations of diffusion were obtained using the Melnikov integral, a Hadjidemetriou-type sympletic map and numerical integrations for times up to 108 years.Facultad de Ciencias Astronómicas y GeofísicasInstituto de Astrofísica de La Plat

Chirikov diffusion in the asteroidal three-body resonance (5, −2, −2)

The theory of diffusion in many-dimensional Hamiltonian system is applied to asteroidal dynamics. The general formulation developed by Chirikov is applied to the Nesvorný-Morbidelli analytic model of three-body (three-orbit) mean-motion resonances (Jupiter-Saturn-asteroid). In particular, we investigate the diffusion along and across the separatrices of the (5, −2, −2) resonance of the (490) Veritas asteroidal family and their relationship to diffusion in semi-major axis and eccentricity. The estimations of diffusion were obtained using the Melnikov integral, a Hadjidemetriou-type sympletic map and numerical integrations for times up to 108 years.Facultad de Ciencias Astronómicas y GeofísicasInstituto de Astrofísica de La Plat

Inovações no estudo do comportamento das crianças com sensores de proximidade

A possibilidade de recolha contínua de dados massivos através de dispositivos digitais está a mudar a forma como estudamos o comportamento e o desenvolvimento da criança. Neste trabalho apresentamos um método inovador de mensuração que permite recolher e analisar de forma contínua e simultânea as dinâmicas de interação face-a-face, através de sensores de proximidade baseados em dispositivos de Identificação por Rádio-Frequência (RFID). Os sensores foram usados por 72 crianças (44 rapazes) de um Jardim de Infância com idades compreendidas entre os 53 e os 77 meses (M=63.2±4.9). O objetivo foi caracterizar os padrões de interação estabelecidos no recreio exterior em termos dos tempos médios em interação, da preferência por interações mediante o género do par e da preferência por interações em díade ou em grupo. As potencialidades e as limitações deste método de recolha e análise são discutidas na perspetiva do estudo do desenvolvimento da criança

Benchmarking de desempenho em igualdade de género nos países nórdicos : aplicação a Portugal

Mestrado em Economia e Políticas PúblicasA Dissertação tem como objetivo realizar uma análise comparativa entre Portugal e os Países Nórdicos (Dinamarca, Finlândia, Noruega e Suécia), no âmbito das políticas familiares e do bem-estar, com o propósito de levar a cabo um exercício de benchmarking. A análise empírica abarca a avaliação da cobertura e generosidade dos subsídios para serviços de cuidado infantil, políticas de licenças de maternidade, paternidade e parental e abonos de famílias e a crianças. Os resultados desta investigação permitiram concluir que as políticas familiares mais eficazes na promoção da igualdade género são aquelas que se focam mais concretamente no envolvimento dos homens na vida familiar, como a licença parental. Outras políticas que facilitem o retorno da mulher ao mercado de trabalho, como o alargamento da cobertura de serviços de cuidado infantil ou abonos de família generosos, são igualmente importantes para a garantia da independência económica das mulheres.The Dissertation aims to conduct a comparative analysis between Portugal and the Nordic Countries (Denmark, Finland, Norway and Sweden), within the scope of family policies and welfare, with the goal of pursuing a benchmarking exercise. The empirical analysis encompasses an evaluation of the coverage and generosity of childcare subsidies, maternity, paternity, paternal leave policies and family allowances. The results of this investigation revealed that the most effective policies regarding gender equality are those that focus more clearly in the involvement of men in the family life, such as parental leave. Other policies that facilitate women's return to the labour market, like extensive coverage of childcare services or generous family allowances, are equally important to secure women's economic independence.info:eu-repo/semantics/publishedVersio

Weak shock wave reflections due to transverse waves in a conventional shock tube

Previous experimental work, utilising a unique large scale shock tube, showed that the four-wave shock reflection pattern, known as the Guderley reflection existed for Mach numbers below 1.10 on wedge angles of 10° and 15°. The current study proves for the first time that these rare reflections can be produced in a conventional shock tube for Mach numbers ranging from 1.10 to 1.40 and for various disturbances in the flow. Two shock tube configurations were tested, the first consisted of a perturbation source on the floor of the tube, and the second utilised a variable diverging section (10°, 15°, and 20°). A new principle was applied where the developed Mach reflection undergoes successive reflections off the upper and lower walls of a tube to produce the desired reflection. The high resolution images captured using a sensitive schlieren system showed evidence of the fourth wave, namely the expansion fan, for the majority of the results for both shock tube configurations. A shocklet terminating the supersonic patch behind the reflected wave was interestingly only observed for Mach numbers of approximately 1.20. The wave structures were similar to those observed in previous experimental work, except no evidence of the second shocklet nor the multi-patch geometry was found. Multi-exposure images of the propagating shock superimposed on a single image frame, analysed with oblique shock equations, estimated the velocities near the triple point. It was shown that the reflected wave is very weak, and that the flow behind the Mach stem is supersonic confirming the shock reflections to be indeed Guderley reflections

Biomarcadores de aclimatação na saliva: estudo em vacas leiteiras com diferente potencial leiteiro

O ambiente térmico a que um animal está sujeito é um fator importante, que pode afetar a produção de leite. A saliva é cada vez mais utilizada como fonte de biomarcadores não invasivos, sendo o cortisol salivar o parâmetro mais frequentemente utilizado para avaliar stresse. No entanto, este último, isoladamente, apresenta algumas limitações. No presente trabalho foi feita uma comparação do perfil proteico da saliva de vacas Holstein, altas (AP) e baixas produtoras (BP), em três períodos diferentes: temperaturas elevadas (P1), temperaturas moderadas (P2) e temperaturas baixas (P3). Foram observados níveis de expressão das proteínas albumina e receptor polimérico de imunoglobulinas mais elevados em AP, nos P1 e P2. Os níveis de cortisol salivar não se observaram associados a stresse térmico. Ainda que necessitando de estudos futuros, os resultados obtidos reforçam o potencial da saliva na avaliação da capacidade de adaptação à temperatura, em animais produtores de leite; Salivary biomarkers of acclimatization – study in dairy cows with different milk yield potential Abstract: The thermal environment is one of the most important factors that can affect milk production. Saliva is increasingly used as a source of non-invasive biomarkers, with salivary cortisol being the parameter most commonly used to evaluate stress. However, cortisol evaluation, alone, has some limitations. In this study a comparison was made, in terms of saliva composition, among Holstein cows with high (AP) and low (BP) productive potential, in three different periods: high temperature (P1), moderate temperatures (P2) and low temperatures (P3). Expression levels of proteins albumin and polymeric immunoglobulin receptor were observed to be higher in AP in P1 and P2. Salivary cortisol levels were not observed to be associated with thermal stress. Although requiring further studies, the results support the potential of saliva for assessing the ability to adapt to temperature in milk-producing animals

Predefined pattern detection in large time series

Predefined pattern detection from time series is an interesting and challenging task. In order to reduce its computational cost and increase effectiveness, a number of time series representation methods and similarity measures have been proposed. Most of the existing methods focus on full sequence matching, that is, sequences with clearly defined beginnings and endings, where all data points contribute to the match. These methods, however, do not account for temporal and magnitude deformations in the data and result to be ineffective on several real-world scenarios where noise and external phenomena introduce diversity in the class of patterns to be matched. In this paper, we present a novel pattern detection method, which is based on the notions of templates, landmarks, constraints and trust regions. We employ the Minimum Description Length (MDL) principle for time series preprocessing step, which helps to preserve all the prominent features and prevents the template from overfitting. Templates are provided by common users or domain experts, and represent interesting patterns we want to detect from time series. Instead of utilising templates to match all the potential subsequences in the time series, we translate the time series and templates into landmark sequences, and detect patterns from landmark sequence of the time series. Through defining constraints within the template landmark sequence, we effectively extract all the landmark subsequences from the time series landmark sequence, and obtain a number of landmark segments (time series subsequences or instances). We model each landmark segment through scaling the template in both temporal and magnitude dimensions. To suppress the influence of noise, we introduce the concept oftrust region, which not only helps to achieve an improved instance model, but also helps to catch the accurate boundaries of instances of the given template. Based on the similarities derived from instance models, we introduce the probability density function to calculate a similarity threshold. The threshold can be used to judge if a landmark segment is a true instance of the given template or not. To evaluate the effectiveness and efficiency of the proposed method, we apply it to two real-world datasets. The results show that our method is capable of detecting patterns of temporal and magnitude deformations with competitive performance

Variações fisiológicas face à aclimatação sazonal – Estudo em vacas leiteiras com diferente potencial leiteiro

As alterações climáticas estão identificadas como uma das maiores ameaças ambientais, sociais e económicas para o planeta. O aumento de eventos climáticos extremos, como secas prolongadas, temperaturas extremas ou períodos com precipitação intensa e prolongada têm efeitos nos sistemas de produção animal (Avendaño-Reyes, 2012). Sabese que temperaturas elevadas afetam o bem-estar e o desempenho dos animais, pois provocam sérias alterações nas suas funções biológicas, como a diminuição na ingestão de matéria seca, na eficiência de utilização dos nutrientes e alterações metabólicas e hormonais (Marai et al., 2007). Nos bovinos leiteiros, estas mudanças culminam na redução da fertilidade, na diminuição da produção leiteira e da qualidade do leite, bem como na diminuição da resposta do sistema imunológico (Avendaño-Reyes, 2012). Segundo Kadzere et al. (2002), o progresso genético refletir-se-á em animais cada vez mais produtivos, uma vez que a seleção, em grande parte, tem vindo a ser efetuada pela quantidade de leite e não pela adaptabilidade às condições ambientais. Assim, as vacas de alta produção converteram-se em animais extremamente sensíveis a ambientes quentes (Cerqueira, 2013; Bernabucci et al., 2014). Quando expostos a um stresse térmico por calor prolongado, as vacas tendem a aclimatarem-se por forma a reajustarem a sua fisiologia para a menor aquisição de calor e à maior perda de calor (Horowitz, 2001), com efeitos negativos na produtividade do animal (Bernabucci et al., 2010). O objetivo deste estudo foi estudar o processo de aclimatação sazonal em vacas leiteira com distintos potenciais leiteiros. Pretendeu-se avaliar as respostas de vacas leiteiras de alto e baixo potencial leiteiro, aclimatadas ao Verão e ao Inverno, relativamente aos parâmetros composição do leite, temperatura retal, frequência respiratória, hemograma e triiodotironina

Academic Research on cattle’s acclimatisation process.

ACADEMIC RESEARCH ON CATTLE’S ACCLIMATISATION PROCESS Flávio Silva1, Cristina Conceição1,2, Liliana Cachucho3, Catarina Matos1, Ana Lúcia Garrido1, Ana Geraldo1,2, Elsa Lamy2, Fernando Capela e Silva2,4, Paulo Infante5 & Alfredo Pereira1,2, 1Departamento de Zootecnia, Universidade de Évora, Portugal; 2ICAAM, Universidade de Évora, Portugal; 3CEBAL, Beja, Portugal; 4Departamento de Biologia, Universidade de Évora, Portugal; 5Deparatamento de Matemática, Universidade de Évora, Portugal. ABSTRACT Animal’s welfare and performance is compromised by environmental heat stress, present during summer in the Mediterranean climate. Heat stress effects are well known and widely studied, although the mechanisms of season acclimatisation are less well understood. Throughout the last 20 years, we have been studying this process in the Mediterranean and tropical regions, aiming to understand it better, developing and improving methodologies and search for reliable biomarkers of thermal stress. The climatic changes, the more frequent extreme events and the increase of ambient temperature at the surface of the earth were identified as a problem to the animals in general and particularly under production systems conditions. Then, the main question is how those factors can affect the farm animals, especially those with higher genetic merit for production and lack of environmental adaptation. With these premises, were developed research projects on cattle’s acclimatisation process. These projects outcomes were: 2 PhD thesis and 5 Master dissertations, alongside ten articles peer-review and index journals and 20 publications in the book of abstracts and also several communications in national and international symposiums. Keywords: acclimatisation; heat stress; cattle