A Case Study of OpenMP applied to Map/Reduce-style Computations

As data analytics are growing in importance they are also quickly becoming one of the dominant application domains that require parallel processing. This paper investigates the applicability of OpenMP, the dominant shared-memory parallel programming model in high-performance computing, to the domain of data analytics. We contrast the performance and programmability of key data analytics benchmarks against Phoenix++, a state-of-the-art shared memory map/reduce programming system. Our study shows that OpenMP outperforms the Phoenix++ system by a large margin for several benchmarks. In other cases, however, the programming model is lacking support for this application domain.

On the Assumption of Bivariate Normality in Selection Models: A Copula Approach Applied to Estimating HIV Prevalence

Background: Heckman-type selection models have been used to control HIV prevalence estimates for selection bias when participation in HIV testing and HIV status are associated after controlling for observed variables. These models typically rely on the strong assumption that the error terms in the participation and the outcome equations that comprise the model are distributed as bivariate normal.
Methods: We introduce a novel approach for relaxing the bivariate normality assumption in selection models using copula functions. We apply this method to estimating HIV prevalence and new confidence intervals (CI) in the 2007 Zambia Demographic and Health Survey (DHS) by using interviewer identity as the selection variable that predicts participation (consent to test) but not the outcome (HIV status).
Results: We show in a simulation study that selection models can generate biased results when the bivariate normality assumption is violated. In the 2007 Zambia DHS, HIV prevalence estimates are similar irrespective of the structure of the association assumed between participation and outcome. For men, we estimate a population HIV prevalence of 21% (95% CI = 16%–25%) compared with 12% (11%–13%) among those who consented to be tested; for women, the corresponding figures are 19% (13%–24%) and 16% (15%–17%).
Conclusions: Copula approaches to Heckman-type selection models are a useful addition to the methodological toolkit of HIV epidemiology and of epidemiology in general. We develop the use of this approach to systematically evaluate the robustness of HIV prevalence estimates based on selection models, both empirically and in a simulation study.

Solar coronal magnetic fields derived using seismology techniques applied to omnipresent sunspot waves

Sunspots on the surface of the Sun are the observational signatures of intense manifestations of tightly packed magnetic field lines, with near-vertical field strengths exceeding 6,000 G in extreme cases1. It is well accepted that both the plasma density and the magnitude of the magnetic field strength decrease rapidly away from the solar surface, making high-cadence coronal measurements through traditional Zeeman and Hanle effects difficult as the observational signatures are fraught with low-amplitude signals that can become swamped with instrumental noise2, 3. Magneto-hydrodynamic (MHD) techniques have previously been applied to coronal structures, with single and spatially isolated magnetic field strengths estimated as 9–55 G (refs 4,5,6,7). A drawback with previous MHD approaches is that they rely on particular wave modes alongside the detectability of harmonic overtones. Here we show, for the first time, how omnipresent magneto-acoustic waves, originating from within the underlying sunspot and propagating radially outwards, allow the spatial variation of the local coronal magnetic field to be mapped with high precision. We find coronal magnetic field strengths of 32 ± 5 G above the sunspot, which decrease rapidly to values of approximately 1 G over a lateral distance of 7,000 km, consistent with previous isolated and unresolved estimations. Our results demonstrate a new, powerful technique that harnesses the omnipresent nature of sunspot oscillations to provide magnetic field mapping capabilities close to a magnetic source in the solar corona.

A biological survey method applied to seafloor massive sulphides (SMS) with contagiously distributed hydrothermal-vent fauna

Strategies for mitigation of seafloor massive sulphide (SMS) extraction in the deep sea include establishment of suitable reference sites that allow for studies of natural environmental variability and that can serve as sources of larvae for re-colonisation of extracted hydrothermal fields. In this study, we characterize deep-sea vent communities in Manus Basin (Bismarck Sea, Papua New Guinea) and use macrofaunal data sets from a proposed reference site (South Su) and a proposed mine site (Solwara 1) to test the hypothesis that there was no difference in macrofaunal community structure between the sites. We used dispersion weighting to adjust taxa-abundance matrices to down-weight the contribution of contagious distributions of numerically abundant taxa. Faunal assemblages of 3 habitat types defined by biogenic taxa (2 provannid snails, Alviniconcha spp. and Ifremeria nautilei; and a sessile barnacle, Eochionelasmus ohtai) were distinct from one another and from the vent peripheral assemblage, but were not differentiable from mound-to-mound within a site or between sites. Mussel and tubeworm populations at South Su but not at Solwara 1 enhance the taxonomic and habitat diversity of the proposed reference site. © Inter-Research 2012.

Applied behaviour analysis: What do teachers of students with autism spectrum disorder know

With rising numbers of school-aged children with autism educated in mainstream classrooms and applied behaviour analysis (ABA) considered the basis of best practice, teachers’ knowledge in this field has become a key concern for inclusion. Self-reported knowledge of ABA of special needs teachers (n=165) was measured and compared to their actual knowledge of ABA demonstrated in accurate responses to a multiple-choice test. Findings reported here show that teachers’ self-perceived knowledge exceeded actual knowledge and that actual knowledge of ABA was not related to training received by government agency. Implications for teacher training are discussed.

Progress in the use of scanning electron microscopy (SEM) applied to the taxonomy of the genus Bursaphelenchus (Nematoda: Parasitaphelenchidae)

The scanning electron microscope (SEM) has been a major tool in detailed morphological observations of plant parasitic nematodes during the last 30 years, efficiently complementing light microscopical (LM) studies. Nematodes are extremely difficult to observe and characterize due to their small size (aprox. 1 mm long) and paucity of morphological characters, so detailed surface observations of several organs and nematode regions are of the highest value. Among plant parasitic nematodes, one of the most devastating species is the “pinewood nematode” (PWN), Bursaphelenchus xylophilus, which has been a major problem for forest species, and in particular pines, in Asia (Japan, China, Korea) and has been recently detected in the European Union (Portugal). B. xylophilus belongs to a closely related, morphologically similar group of species, within the genus Bursaphelenchus, and designated by the “xylophilus group”. SEM has become a crucial tool in observing several genital characters of males and females, such as male genital papillae, male copulatory spicules, female vulval flap and female genital papillae.s In this presentation, we will show how SEM has been utilized to observe and characterize the shape of the vulval flap, the presence/ absence of papillae near the flap, and confirm the presence and the arrangement of the male genital papillae. LM is also used in this work to show its value as a complementary tool to SEM, in both genital characteristics and other, general, characters of the genus Bursaphelenchus, such as the male bursa and cephalic region.

The Riemann-Hilbert method applied to the theory of orthogonal polynomials

Doutoramento em Matemática

A comunicação na promoção do termalismo em Viseu: novos meios para novos públicos

O Turismo apresenta-se, hoje, como uma área com imensas possibilidades de expansão na região de Viseu e mais ainda no que respeita ao termalismo, quer com a continuidade da qualidade do termalismo clássico quer com a consolidação do segmento de Saúde e Bem-estar. A comunicação, numa empresa, é muito importante, mas torna-se primordial que seja eficaz, e nisto, o recurso a línguas estrangeiras é fundamental, de modo a potenciar a competitividade internacional das empresas Portuguesas. De modo a respondermos à questão central deste estudo - o que é que as termas de Viseu estão a fazer de modo a comunicar eficazmente as suas valências aos diferentes públicos e qual a importância de iniciarem um esforço maior bem como de criarem instrumentos de comunicação mais eficazes e adequadas às aspirações de desenvolvimento económico e social – recorremos ao levantamento e à análise das fontes de informação utilizadas em termalismo, na região de Viseu, e da aplicação de questionários aos intervenientes no processo termal. Tendo em mente a questão fulcral desenvolveu-se um estudo composto por quatro capítulos, tendo um prévio, onde é apresentado o estudo. O primeiro é reservado ao enquadramento teórico, onde se cruzam as perspetivas de Linguística Sistémica Funcional, Turismo em Portugal e Comunicação de Informação. O segundo apresenta a metodologia de investigação adotada, o terceiro expõe a análise dos dados recolhidos, nos Sítios Web das estâncias termais Viseenses, nas brochuras, através dos questionários aplicados às rececionistas, à equipa médica, aos administradores das termas, aos presidentes das câmaras, aos aquistas e aos gabinetes de promoção termal. O terceiro capítulo termina com um diálogo de esclarecimento final efetuado aos presidentes camarários e aos administradores termais. No quarto e último capítulo são expostas as principais conclusões do estudo e é evidenciada a importância que as línguas estrangeiras têm na comunicação internacional dos produtos e serviços termais, bem como a necessidade do recurso a uma comunicação eficaz de modo a que as termas possam alcançar resultados mais proveitosos.

Optimal control and numerical optimization applied to epidemiological models

A relação entre a epidemiologia, a modelação matemática e as ferramentas computacionais permite construir e testar teorias sobre o desenvolvimento e combate de uma doença. Esta tese tem como motivação o estudo de modelos epidemiológicos aplicados a doenças infeciosas numa perspetiva de Controlo Ótimo, dando particular relevância ao Dengue. Sendo uma doença tropical e subtropical transmitida por mosquitos, afecta cerca de 100 milhões de pessoas por ano, e é considerada pela Organização Mundial de Saúde como uma grande preocupação para a saúde pública. Os modelos matemáticos desenvolvidos e testados neste trabalho, baseiam-se em equações diferenciais ordinárias que descrevem a dinâmica subjacente à doença nomeadamente a interação entre humanos e mosquitos. É feito um estudo analítico dos mesmos relativamente aos pontos de equilíbrio, sua estabilidade e número básico de reprodução. A propagação do Dengue pode ser atenuada através de medidas de controlo do vetor transmissor, tais como o uso de inseticidas específicos e campanhas educacionais. Como o desenvolvimento de uma potencial vacina tem sido uma aposta mundial recente, são propostos modelos baseados na simulação de um hipotético processo de vacinação numa população. Tendo por base a teoria de Controlo Ótimo, são analisadas as estratégias ótimas para o uso destes controlos e respetivas repercussões na redução/erradicação da doença aquando de um surto na população, considerando uma abordagem bioeconómica. Os problemas formulados são resolvidos numericamente usando métodos diretos e indiretos. Os primeiros discretizam o problema reformulando-o num problema de optimização não linear. Os métodos indiretos usam o Princípio do Máximo de Pontryagin como condição necessária para encontrar a curva ótima para o respetivo controlo. Nestas duas estratégias utilizam-se vários pacotes de software numérico. Ao longo deste trabalho, houve sempre um compromisso entre o realismo dos modelos epidemiológicos e a sua tratabilidade em termos matemáticos.

Soft-computing techniques applied to artificial tissue temperature estimation

Tese dout., Engenharia electrónica e computação - Processamento de sinal, Universidade do Algarve, 2008

The LOICZ biogeochemical budget approach applied to Ria Formosa lagoon, - Algarve, South Portugal

Dissertação mest., Gestão da Água e da Costa, Universidade do Algarve, 2007

Bacterial algorithm applied for fuzzy rule extraction

This paper presents a method of using the so-colled "bacterial algorithm" (4,5) for extracting a fuzzy rule base from a training set. The bewly proposed bacterial evolutionary algorithm (BEA) is shown. In our application one bacterium corresponds to a fuzzy rule system.

Electronic Journal of Applied Multivariate Statistics

The ecological sciences have experienced immense growth over the course of this century, and chances are that they will continue to grow well on into the next millennium. There are some good reasons for this – ecology encompasses some of the most pressing concerns facing humanity. With recent advances in data collection technology and ambitious field research, ecologists are increasingly calling upon multivariate statistics to explore and test for patterns in their data. The goal of FISH 560 (Applied Multivariate Statistics for Ecologists) at the University of Washington is to introduce graduate students to the multivariate statistical techniques necessary to carry out sophisticated analyses and to critically evaluate scientific papers using these approaches. It is a practical, hands-on course emphasizing the analysis and interpretation of multivariate analysis, and covers the majority of approaches in common use by ecologists. To celebrate the hard work of past students, I am pleased to announce the creation of the Electronic Journal of Applied Multivariate Statistics (EJAMS). Each year, students in FISH 560 are required to write a final paper consisting of a statistical analysis of their own multivariate data set. These papers are submitted to EJAMS at the end of quarter and are peer reviewed by two other class members. A decision on publication is based on the reviewers’ recommendations and my own reading the paper. In closing, there is a need for the rapid dissemination of ecological research using multivariate statistics at the University of Washington. EJAMS is committed to this challenge.