A distributed platform for the volunteer execution of workflows on a local area network

Thesis submitted in fulfilment of the requirements for the Degree of Master of Science in Computer Science

Heterogeneous computing with an algorithmic skeleton framework

The Graphics Processing Unit (GPU) is present in almost every modern day personal computer. Despite its specific purpose design, they have been increasingly used for general computations with very good results. Hence, there is a growing effort from the community to seamlessly integrate this kind of devices in everyday computing. However, to fully exploit the potential of a system comprising GPUs and CPUs, these devices should be presented to the programmer as a single platform. The efficient combination of the power of CPU and GPU devices is highly dependent on each device’s characteristics, resulting in platform specific applications that cannot be ported to different systems. Also, the most efficient work balance among devices is highly dependable on the computations to be performed and respective data sizes. In this work, we propose a solution for heterogeneous environments based on the abstraction level provided by algorithmic skeletons. Our goal is to take full advantage of the power of all CPU and GPU devices present in a system, without the need for different kernel implementations nor explicit work-distribution.To that end, we extended Marrow, an algorithmic skeleton framework for multi-GPUs, to support CPU computations and efficiently balance the work-load between devices. Our approach is based on an offline training execution that identifies the ideal work balance and platform configurations for a given application and input data size. The evaluation of this work shows that the combination of CPU and GPU devices can significantly boost the performance of our benchmarks in the tested environments, when compared to GPU-only executions.

Definição e execução de computações dinâmicas numa linguagem de programação orientada-a-serviços

Os serviços inicialmente idealizados para o mundo dos negócios, têm actualmente um espectro de utilização muito mais lato, facilitando assim a incorporação de software do exterior, sob a representação de serviço, por parte das aplicações. Os principais contribuidores para a emergente utilização de serviços são a proliferação dos dispositivos móveis, a crescente popularidade da computação da nuvem e a ubiquidade da Internet. Apesar deste estado da arte, a abstracção dos serviços continua, maioritariamente, a ser relegada para a camada do middleware. Consequentemente, este confinamento obstem o programador de ter privilégios para interagir com os serviços ao nível da linguagem. A inexistência deste nível de abstracção dificulta o deployment de aplicações dinâmicas. Como medida para tal, o objectivo do nosso trabalho é garantir suporte ao dinamismo e deployment de arquitecturas orientadas a serviços. Com esse propósito, vamos endereçar os problemas de incorporação dos serviços acessíveis pela Web e permitir operações de reconfiguração dos mesmos, nomeadamente, a ligação dinâmica, substituição do fornecedor de serviços e a gestão dinâmica de conjuntos de fornecedores de serviços.

Towards an algorithmic skeleton framework for programming the Intel R Xeon PhiTM processor

The Intel R Xeon PhiTM is the first processor based on Intel’s MIC (Many Integrated Cores) architecture. It is a co-processor specially tailored for data-parallel computations, whose basic architectural design is similar to the ones of GPUs (Graphics Processing Units), leveraging the use of many integrated low computational cores to perform parallel computations. The main novelty of the MIC architecture, relatively to GPUs, is its compatibility with the Intel x86 architecture. This enables the use of many of the tools commonly available for the parallel programming of x86-based architectures, which may lead to a smaller learning curve. However, programming the Xeon Phi still entails aspects intrinsic to accelerator-based computing, in general, and to the MIC architecture, in particular. In this thesis we advocate the use of algorithmic skeletons for programming the Xeon Phi. Algorithmic skeletons abstract the complexity inherent to parallel programming, hiding details such as resource management, parallel decomposition, inter-execution flow communication, thus removing these concerns from the programmer’s mind. In this context, the goal of the thesis is to lay the foundations for the development of a simple but powerful and efficient skeleton framework for the programming of the Xeon Phi processor. For this purpose we build upon Marrow, an existing framework for the orchestration of OpenCLTM computations in multi-GPU and CPU environments. We extend Marrow to execute both OpenCL and C++ parallel computations on the Xeon Phi. We evaluate the newly developed framework, several well-known benchmarks, like Saxpy and N-Body, will be used to compare, not only its performance to the existing framework when executing on the co-processor, but also to assess the performance on the Xeon Phi versus a multi-GPU environment.

Capacidade antioxidante e triagem farmacológica de extratos brutos de folhas de Byrsonima crassifolia e de Inga edulis

Com o objetivo de avaliar o efeito de duas espécies amazônicas em doenças relacionadas aos processos de oxidação, determinou-se a capacidade antioxidante (método Oxygen Radical Absorbance Capacity), o teor de polifenóis totais (método Folin-Ciocalteu - PT), bem como os efeitos farmacológicos in vitro (efeito antiproliferativo) e in vivo (antinociceptivo, antiinflamatório, antiulcerogênico) dos extratos hidroalcoólicos (65:35; v/v; etanol:água) das folhas de Byrsonima crassifolia (BC) e Inga edulis (IE). Os extratos de BC e IE apresentaram elevada capacidade antioxidante (1.422 e 694 µmol de Trolox Equivalente g-1 de folha seca - FS, respectivamente) e um valor relativamente alto de PT (35,93 e 24,50 mg Equivalente ácido gálico g-1 FS, respectivamente). Essa atividade antioxidante não teve relação direta com o teor de compostos fenólicos dos extratos, sugerindo a contribuição de outros grupos químicos nessa atividade. Em cultura de células tumorais humanas (nove linhagens), os extratos não apresentaram atividade antiproliferativa significante, com efeito citotóxico somente na concentração mais elevada. Em modelo de nocicepção induzida pelo calor (placa quente), o extrato de IE apresentou efeito antinociceptivo (P < 0,05) após 30 (250 e 500 mg kg-1) e 60 min (125 e 500 mg kg-1) de sua administração oral. Nos modelos de inflamação houve somente redução do edema para IE na concentração de 500 mg kg-1. Os extratos das duas espécies reduziram as lesões ulcerativas produzidas por etanol em até 84% (P < 0,05), sugerindo uma possível ligação com a atividade antioxidante observada e indicando a necessidade de estudos para a elucidação do mecanismo de ação envolvido.

Fatores de risco cardiovascular em adolescentes com diferentes níveis de gasto energético

FUNDAMENTO: A inatividade física na adolescência está relacionada com o acúmulo de gordura corporal, o que aparentemente pode aumentar a probabilidade do surgimento e desenvolvimento das alterações metabólicas. OBJETIVO: Verificar a predisposição dos fatores de risco para doenças cardiovasculares em adolescentes com diferentes níveis de gasto energético. MÉTODOS: Foram selecionados 108 rapazes e 132 moças, com idades entre 12 e 17 anos. O gasto energético diário foi obtido pelo questionário proposto por Bouchard e cols. Previamente dividiu-se amostra através dos quartis de gasto energético (kcal/kg/dia) para composição dos grupos: sedentário (GS), moderadamente ativo (GM) e ativo (GA). Para avaliar as concentrações de colesterol total (CT), HDL-C e triglicérides (TG), utilizou-se o método enzimático-colorimétrico. O LDL-C foi calculado pela fórmula de Friedewald e cols. Para análise estatística utilizou-se a análise de variância de um fator, adotando p<0,05. RESULTADOS: Para o sexo masculino, foram encontradas diferenças significativas entre os grupos na variável CT (mg/dl), sendo o GA (121,56±19,15) diferente do GM (142,70±27,65) e do GS (145,63±36,54), assim como o GM diferiu do GS (F=3,70 e p=0,03). Para a variável TG (mg/dl), o GA (65,69±18,95) diferiu-se do GM (82,25±33,73) e do GS (97,44±45,95), assim como o GM diferiu do GS (F=3,40 e p=0,04). Para o sexo feminino não foram encontradas diferenças significativas em razão do gasto energético diário. CONCLUSÃO: Os rapazes mais ativos apresentam menores concentrações de CT e TG quando comparados aos seus pares moderadamente ativos e sedentários.

Atividade física, consumo de lipídios e fatores de risco para aterosclerose em adolescentes

FUNDAMENTO: A aterosclerose é a doença coronariana que acomete com maior frequência a população adulta brasileira. Embora seja uma doença predominantemente adulta, os fatores de risco associados podem surgir em indivíduos jovens. OBJETIVO: Verificar a associação do nível de atividade física (NAF) e o consumo de lipídios com os fatores de risco para aterosclerose em adolescentes. MÉTODOS: Foram avaliados 260 meninos e 237 meninas com idades entre 10-18 anos. O nível de atividade física foi estimado através do recordatório proposto por Bouchard e cols.. O consumo de lipídios foi avaliado através do inquérito alimentar desenvolvido por Sichieri e Everhart. A pressão arterial foi mensurada utilizando um esfigmomanômetro de coluna de mercúrio. O colesterol total, o HDL-C e os triglicérides foram determinados através do método enzimático-colorimétrico. O LDL-C foi calculado pela fórmula de Friedewald. Na análise estatística, foi empregada a regressão logística, com nível de significância estipulado em p < 0,05. RESULTADOS: Quanto ao NAF, 17,3% dos meninos e 22,6% das meninas foram classificados como sedentários. Para os hábitos alimentares, 54% e 48,6% dos meninos e meninas, respectivamente, apresentaram consumo de lipídios acima das recomendações. Meninos com níveis elevados de colesterol total e de LDL-C tiveram maior razão de chances de serem sedentários do que seus pares mais ativos. Apresentar níveis elevados de LDL-C esteve associado ao consumo excessivo de gordura saturada em ambos os sexos. CONCLUSÃO: Os resultados avigoram as evidências prévias de que jovens devem ser encorajados desde cedo à adoção de um estilo de vida fisicamente mais ativo associado a uma ingestão alimentar apropriada.

Magasin de zoologie, d'anatomie comparée et de palaeontologie.

ser. 2, v. 7 (1845)

Magasin de zoologie, d'anatomie comparée et de palaeontologie.

ser. 2, v. 1-3 (1831-41)

Liquid chromatography-tandem mass spectrometry (LC/APCI-MS/MS) methods for the quantification of captan and folpet phthalimide metabolites in human plasma and urine.

Captan and folpet are fungicides largely used in agriculture. They have similar chemical structures, except that folpet has an aromatic ring unlike captan. Their half-lives in blood are very short, given that they are readily broken down to tetrahydrophthalimide (THPI) and phthalimide (PI), respectively. Few authors measured these biomarkers in plasma or urine, and analysis was conducted either by gas chromatography coupled to mass spectrometry or liquid chromatography with UV detection. The objective of this study was thus to develop simple, sensitive and specific liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry (LC/APCI-MS/MS) methods to quantify both THPI and PI in human plasma and urine. Briefly, deuterated THPI was added as an internal standard and purification was performed by solid-phase extraction followed by LC/APCI-MS/MS analysis in negative ion mode for both compounds. Validation of the methods was conducted using spiked blank plasma and urine samples at concentrations ranging from 1 to 250 μg/L and 1 to 50 μg/L, respectively, along with samples of volunteers and workers exposed to captan or folpet. The methods showed a good linearity (R (2) > 0.99), recovery (on average 90% for THPI and 75% for PI), intra- and inter-day precision (RSD, <15%) and accuracy (<20%), and stability. The limit of detection was 0.58 μg/L in urine and 1.47 μg/L in plasma for THPI and 1.14 and 2.17 μg/L, respectively, for PI. The described methods proved to be accurate and suitable to determine the toxicokinetics of both metabolites in human plasma and urine.

Coevolution of restriction factors and retroviruses

Les virus exploitent la machinerie cellulaire de l'hôte pour se répliquer. Ils doivent s'adapter pour infecter la cellule hôte de manière optimale tout en échappant à la vigilance du système de défense de l'hôte. Ainsi l'hôte et les virus se livrent à de constantes batailles évolutives. Mon travail de thèse a porté sur l'étude des signatures évolutives de facteurs de l'hôte agissant comme des 'facteurs de restriction' en bloquant la réplication rétrovirale chez les primates. Plus spécifiquement, mon travail a visé à utiliser des données évolutives pour renseigner les analyses fonctionnelles et la biologie. Nous avons étudié le facteur anti-VIH-1 nommé TRIM5a (i) chez les prosimiens pour mieux comprendre son rôle dans le contrôle d'un lentivirus endogène, (ii) dans son activité contre d'autres anciennes infections représentées par des rétrovirus endogènes humains et (iii) en tant que protéine capable de générer des mutants de la capside. Premièrement nous nous sommes intéressés à TRIM5a chez deux espèces de lémuriens dont Microcebus murinus qui porte le lentivirus endogène PSIV dans son génome depuis plusieurs millions d'années,. Nous avons observé que TRIM5a chez M. murinus a un spectre d'activité antivirale réduit à l'opposé de TRIM5a chez le Lemur catta - non porteur du PSIV endogène - qui bloque une large variété de rétrovirus dont le PSIV. De ce fait TRIM5a aurait pu contribuer à protéger certaines espèces de lémuriens vis-à-vis d'anciennes infections par le PSIV. A l'inverse du PSIV, des virus dérivés des rétrovirus endogènes humains HERV-K and HERV-H se sont révélés largement résistants à l'inhibition par TRIM5a. Ces données illustrent une absence de protection par TRIM5a face à d'autres anciennes infections rétrovirales. Puis, pour évaluer l'impact de la protéine TRIM5a humaine sur le VIH-1, nous avons testé l'effet de mutations des résidues sous sélection positive dans la capside du VIH-1 sur l'inhibition par TRIM5a. Nos résultats montrent que TRIM5a ne jouerait pas un rôle significatif dans l'évolution de la capside du VIH-1. Enfin notre travail a porté sur le facteur anti-VIH-1 SAMHD1 récemment découvert, que nous avons séquencé chez 25 espèces de primates. L'analyse évolutive des sites sous sélection positive et des expériences fonctionnelles ont permis d'identifier le domaine de SAMHD1 interagissant avec la protéine lentivirale Vpx. De même que d'autres protéines virales contrecarrent les facteurs de restriction en les menant à la dégradation, nous avons observé que Vpx induit la dégradation de SAMHD1 de manière spécifique à l'espèce. Ces découvertes contribuent à comprendre comment les facteurs de restriction et les virus co-évoluent pour se neutraliser l'un l'autre. - Viruses hijack the host cellular machinery to replicate. They adapt to infect optimally host cells while escaping host defense systems. Viruses and the host coevolve in an evolutionary struggle. My thesis work has been devoted to study the evolutionary signatures of host factors acting as restriction factors that block retroviral replication in primates. Specifically, my work aimed at using evolutionary data to inform functional analyses and biology. We studied the anti-HIV-1 factor TRIM5a (i) in prosimians to better understand its possible role in the control of an endogenous lentivirus, (ii) in its activity against other ancient infections - as represented by HERVs, and (iii) as a protein capable of generating escape mutants in the viral capsid. First, my work focused on two lemur species, one of which was the gray mouse lemur that carries the endogenous lentivirus PSIV integrated in its genome for several million years. TRIM5a from gray mouse lemur exhibited a limited antiviral spectrum as opposed to TRIM5a from ring-tailed lemur - not a host of PSIV - that is able to block diverse retroviruses notably PSIV. These results support the possible contribution of TRIM5a in protecting lemur species from ancient infection by PSIV. In contrast, chimeric viruses derived from two human endogenous retroviruses were broadly resistant to TRIM5a-mediated restriction, suggesting TRIM5a lack of activity against other types of ancient infections. To evaluate the recent impact of human TRIM5a on HIV-1 evolution, we tested whether variants at positively selected sites in the HIV-1 capsid affected the ability of human TRIM5a alleles to restrict HIV-1. Our results indicate that TRIM5a does not play a significant role in the evolution of HIV1 capsid. At last, our work concentrated on the newly discovered anti-HIV-1 restriction factor SAMHD1. We determined its coding sequence in a panel of 25 species of primates. Evolutionary analyses of positively selected sites in SAMHD1 domains and functional assays identified the domain of SAMHD1 interacting with the lentiviral protein Vpx. Similar to other viral countermeasures targeting cellular restriction factors, Vpx was responsible of the degradation of SAMHD1 orthologs in a species-specific manner. These findings contributed to understanding how restriction factors and viruses evolve to counteract each other.

La voix-over du Roman d'un tricheur et sa postérité dans Providence. A propos de la résurgence de pratiques "bonimentorielles".

Partant de la réception internationale du film Le Roman d'un tricheur de Sacha Guitry dans laquelle la voix du cinéaste est fréquemment rapprochée de celle du "bonimenteur" de l'époque muette, cette étude examine les particularités de ce film en termes de positionnement du narrateur over par rapport aux images et par rapport au spectateur. Une filiation est posée entre ce film et Providence de Resnais au niveau des manifestations de l'oralité: là aussi, le narrateur occupe la place d'instigateur du monde filmique et de spectateur des images qu'il commente.

Physical activity attenuates the influence of FTO variants on obesity risk: a meta-analysis of 218,166 adults and 19,268 children.

BACKGROUND: The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA) may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute unambiguously whether PA attenuates the association of FTO with obesity risk, we meta-analyzed data from 45 studies of adults (n = 218,166) and nine studies of children and adolescents (n = 19,268). METHODS AND FINDINGS: All studies identified to have data on the FTO rs9939609 variant (or any proxy [r(2)>0.8]) and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active) in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were performed within each study by including the FTO×PA interaction term in an additive model, adjusting for age and sex. Subsequently, random effects meta-analysis was used to pool the interaction terms. In adults, the minor (A-) allele of rs9939609 increased the odds of obesity by 1.23-fold/allele (95% CI 1.20-1.26), but PA attenuated this effect (p(interaction)  = 0.001). More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio  = 1.22/allele, 95% CI 1.19-1.25) than in the inactive group (odds ratio  = 1.30/allele, 95% CI 1.24-1.36). No such interaction was found in children and adolescents. CONCLUSIONS: The association of the FTO risk allele with the odds of obesity is attenuated by 27% in physically active adults, highlighting the importance of PA in particular in those genetically predisposed to obesity.