Application mapping in NoC-Based many-cores

Many-core platforms based on Network-on-Chip (NoC [Benini and De Micheli 2002]) present an emerging technology in the real-time embedded domain. Although the idea to group the applications previously executed on separated single-core devices, and accommodate them on an individual many-core chip offers various options for power savings, cost reductions and contributes to the overall system flexibility, its implementation is a non-trivial task. In this paper we address the issue of application mapping onto a NoCbased many-core platform when considering fundamentals and trends of current many-core operating systems, specifically, we elaborate on a limited migrative application model encompassing a message-passing paradigm as a communication primitive. As the main contribution, we formulate the problem of real-time application mapping, and propose a three-stage process to efficiently solve it. Through analysis it is assured that derived solutions guarantee the fulfilment of posed time constraints regarding worst-case communication latencies, and at the same time provide an environment to perform load balancing for e.g. thermal, energy, fault tolerance or performance reasons.We also propose several constraints regarding the topological structure of the application mapping, as well as the inter- and intra-application communication patterns, which efficiently solve the issues of pessimism and/or intractability when performing the analysis.

Molecular mobility of n-ethylene glycol dimethacrylate glass formers upon free radical polymerization

Quando um líquido evita a cristalização durante o arrefecimento, diz-se que entra no estado sobrearrefecido. Se a temperatura continuar a diminuir, o consequente aumento da viscosidade reflecte-se na mobilidade molecular de tal maneira que os tempos característicos se tornam da mesma ordem de grandeza que os tempos acessíveis experimentalmente. Se o arrefecimento continuar, o líquido altamente viscoso acaba por vitrificar, i.e. entra no estado vítreo onde apenas os movimentos locais são permitidos. Os monómeros da família n -etileno glicol dimetacrilato ( n -EGDMA, para n = 1 até 4, que constituem o objecto deste estudo, facilmente evitam a cristalização, sendo pois bons candidatos para estudar a mobilidade molecular nos estados sobrearrefecido e vítreo. A Espectroscopia de Relaxação Dieléctrica (DRS) foi a técnica escolhida para obter informação detalhada sobre a sua dinâmica molecular (Capítulos 1 e 2). A primeira parte deste trabalho consistiu na caracterização dieléctrica dos processos de relaxação existentes acima e abaixo da temperatura de transição vítrea (g T ), a qual aumenta com o aumento do peso molecular (w M ), sendo este resultado confirmado por Calorimetria Diferencial de Varrimento (DSC). No que respeita ao processo cooperativo a , associado à transição vítrea, e ao processo secundário b, observa-se uma dependência com w M , enquanto que o outro processo secundário, g , aparenta ser independente deste factor (Capítulo 3). Nos capítulos seguintes, foram levadas a cabo diferentes estratégias com o objectivo de clarificar os mecanismos que estão na origem destas duas relaxações secundárias (b e g ), assim como conhecer a sua respectiva relação com a relaxação principal (a ). Do estudo, em tempo real, da polimerização isotérmica via radicais livres do TrEGDMA por Calorimetria de Varrimento Diferencial com Modulação de Temperatura (TMDSC), levado a cabo a temperaturas abaixo da g T do polímero final, concluem-se entre outros, dois importantes aspectos: i) que a vitrificação do polímero em formação conduz a graus de conversão relativamente baixos, e ii) que o monómero que está por reagir é expulso da rede polimérica que se forma, dando lugar a uma clara separação de fases (Capítulo 4). Com base nesta informação, o passo seguinte foi estudar separadamente a polimerização isotérmica do di-, tri- e tetra-EGDMA, dando especial atenção às alterações de mobilidade do monómero ainda por reagir. Com as restrições impostas pela formação de ligações químicas, as relaxações a e b detectadas no monómero tendem a desaparecer no novo polímero formado, enquanto que a relaxação g se mantém quase inalterada. Os diferentes comportamentos que aparecem durante a polimerização permitiram a atribuição da origem molecular dos processos secundários: o processo g foi associado ao movimento twisting das unidades etileno glicol, enquanto que a rotação dos grupos carboxilo foi relacionada com a relaxação b (Capítulo 5). No que respeita ao próprio polímero, um processo de relaxação adicional foi detectado, pol b , no poly-DEGDMA, poly-TrEGDMA e poly-TeEGDMA, com características similares ao encontrado nos poli(metacrilato de n -alquilo). Este processo foi confirmado e bem caracterizado aquando do estudo da copolimerização do TrEGDMA com acrilato de metilo (MA) para diferentes composições (Capítulo 6). Para finalizar, o EGDMA, o elemento mais pequeno da família de monómeros estudada, além de vitrificar apresenta uma marcada tendência para cristalizar quer a partir do estado líquido ou do estado vítreo. Durante a cristalização, a formação de uma fase rígida afecta principalmente o processo a , cuja intensidade diminui sem no entanto se observarem modificações significativas na dependência do tempo de relaxação característico com a temperatura. Por outro lado, o processo secundário b torna-se melhor definido e mais estreito, o que pode ser interpretado em termos de uma maior homogeneidade dos micro-ambientes associados aos movimentos locais(Capítulo 7).

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Is multidimensional scaling suitable for mapping the input respiratory impedance in subjects and patients?

This paper presents the application of multidimensional scaling (MDS) analysis to data emerging from noninvasive lung function tests, namely the input respiratory impedance. The aim is to obtain a geometrical mapping of the diseases in a 3D space representation, allowing analysis of (dis)similarities between subjects within the same pathology groups, as well as between the various groups. The adult patient groups investigated were healthy, diagnosed chronic obstructive pulmonary disease (COPD) and diagnosed kyphoscoliosis, respectively. The children patient groups were healthy, asthma and cystic fibrosis. The results suggest that MDS can be successfully employed for mapping purposes of restrictive (kyphoscoliosis) and obstructive (COPD) pathologies. Hence, MDS tools can be further examined to define clear limits between pools of patients for clinical classification, and used as a training aid for medical traineeship.

Molecular diversity of bla genes in Klebsiella pneumoniae and Escherichia coli isolates

Dissertation presented to obtain a Ph.D. degree in Biology, speciality Microbiology, by Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Molecular mobility, composition and structure analysis in glycerol plasticised chitosan films

This study was developed with the purpose to investigate the effect of polysaccharide/plasticiser concentration on the microstructure and molecular dynamics of polymeric film systems, using transmission electron microscope imaging (TEM) and nuclear magnetic resonance (NMR) techniques. Experiments were carried out in chitosan/glycerol films prepared with solutions of different composition. The films obtained after drying and equilibration were characterised in terms of composition, thickness and water activity. Results show that glycerol quantities used in film forming solutions were responsible for films composition; while polymer/total plasticiser ratio in the solution determined the thickness (and thus structure) of the films. These results were confirmed by TEM. NMR allowed understanding the films molecular rearrangement. Two different behaviours for the two components analysed, water and glycerol were observed: the first is predominantly moving free in the matrix, while glycerol is mainly bounded to the chitosan chain. (C) 2013 Elsevier Ltd. All rights reserved.

Diagnóstico molecular da tuberculose bovina

Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Fracionamento do veneno Crotalus durissus terrificus por cromatografia de exclusão molecular

Através da técnica de cromatografia de exclusão molecular utilizando Sephadex G-75 foram estudadas as diferentes frações do veneno de Crotalus durissus terrificus, uma das serpentes peçonhentas mais comuns no Brasil. Foram obtidos 4 picos (correspondentes às frações 32, 60, 86 e 103) com peso molecular variando de 4.000 a 150.000. As frações de todo o diagrama de gel filtração foram triadas através de reação de imunoeletroforese a fim de se verificar suas cargas e velocidade de migração. As linhas de precipitação encontradas foram comparadas às 11 linhas apresentadas pela reação de imunoeletroforese do veneno total contra o soro anti-crotálico. Constatou-se que as frações de um mesmo pico apresentavam características próprias com exceção da fração 54 (subida do pico II) que mostrou diferenças significativas em relação à fração 60. Após a triagem foram escolhidas as frações de cada pico onde as linhas de precipitação foram mais nítidas e intensas, para estudo de identidade através da reação de difusão radial dupla e letalidade comparada a concentração de 0,0625 mg/ml do veneno total que corresponde a DL50 em camundongo pelo método de SPEARM & KÄRBER. As frações 32, 86 e 103 correspondentes respectivamente aos picos I, III e IV apresentaram letalidade nula ou negligenciada e a fração II foi a mais tóxica.

Influence of constraining and confinement in the molecular mobility of low molecular weight materials

Dissertation presented to obtain a Ph.D. Degree in Chemical Physics

Biogeography, host specificity, and molecular phylogeny of the basidiomycetous yeast phaffia rhodozyma and its sexual form, xanthophyllomyces dendrorhous

Applied and Environmental Microbiology, Vol. 73, No.4

Bioecologia e caracterização molecular de Bulinus globosus de Angola

Parasitologia médica

Mapeamento da Responsabilidade Social em Portugal (The Mapping of Social Responsibility in Portugal)

Conferência multidisciplinar e multicultural.

Mapping and characterization of a green biofilm inside of Vilar de Frades Church (Portugal)

Vilar de Frades church is integrated in the Vilar de Frades Monastery, located in the North part of Portugal (Barcelos). The monastery, founded in 566, suffered several architectural modifications and restoration works, the most relevant was in the XVI century. The church, in granite, has one nave and six bays,holding ten chapels with vaults of crossed ribbings. Nowadays, the chapels present a severe biological colonization characterised by an intense green biofilm, which becoming apparent in other locations inside the church. In the course of a general survey concerning the conservation state of the church, an accurate campaign was planned in order to assess the main biodeterioration agents, map biological colonization and determine the environmental conditions. Laboratory analyses were accomplished with optical microscopy and spectrofluorometry. This study presents the results of this campaign. Details on conservation or preservation works that need to be implemented are also presented.

LADAR based mapping and obstacle detection system for service robots

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores