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.

SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

Impact of corporate social responsibility in the European pharmaceutical market

The objective of this master thesis is to evaluate the impact of CSR measures in the financial performance of the European pharmaceutical industry. By definition, CSR measures is quantified as corporate social disclosure considering the published CSR keywords on the annual reports of the selected companies, over four fiscal years (2010-2013). The financial performance of the companies were measured as return on assets (ROA) and Tobin’s Q. In order to defend the hypothesis developed, a multivariate regression is performed. The results obtained show no significant impact on the financial performance of a company nor in the short-time, nor in the long-time. Moreover, by comparison with other studies, it was possible to conclude that the financial performance is differently affected when considering different industries.

Overcoming the “European Paradox”: The role of Regional Innovation Systems (RIS) in translating R&D investments into economic and employment growth

The emergence of the so-called “European Paradox” shows that R&D investment is not maximally effective and that increasing the scale of public R&D expenditures is not sufficient to generate employment and sustained economic growth. Increasing Governmental R&D Investment is far from being a “panacea” for stagnant growth. It is worth noting that Government R&D Investment does not have a statistically significant impact on employment, indicating the need to assess the trade-offs of policies that could lead to significant increases in government expenditure. Surprisingly, Governmental R&D Employment does not contribute to “mass-market” employment, despite its quite important role in reducing Youth-Unemployment. Despite the negative side-effects of Governmental R&D Employment on both GVA and GDP, University R&D Employment appears to have a quite important role in reducing Unemployment, especially Youth-Unemployment, while it also does not have a downside in terms of economic growth. Technological Capacity enhancement is the most effective instrument for reducing Unemployment and is a policy without any downside regarding sustainable economical development. In terms of wider policy implications, the results reinforce the idea that European Commission Research and Innovation policies must be restructured, shifting from a transnational framework to a more localised, measurable and operational approach.

Price linkages in pharmaceutical markets

This paper studies the existing price linkage between generics and branded pharmaceuticals, in which the generic price must be a fraction of the latter. Using a vertical differentiation model, we look at the market equilibrium, the effects on the incentives for the brand producer to develop new products, and the possibility of predation by the brand producer over the generic firm. We find that the price linkage increases prices compared to no indexation and it may increase the incentives for the brand producer to expand its set of products. When prices are freely set, the branded firm may also want to expand a new product with a higher quality, but will prefer to remove the original one from the market. Predation may equally occur in both schemes but the price linkage may give fewer incentives for the branded firm to predate while compensating losses with a new drug.

Estudo de implementação da NP EN ISO 22000:2005 na Cooperativa de Olivicultores de Fátima, C. R.L.

O conceito de “Segurança Alimentar” faz sentido no momento em que o ser humano tem consciência de que o que ingere deve ser inócuo para a sua saúde e bem-estar. Para dar resposta a esta preocupação global, a indústria alimentar teve necessidade de adotar diretrizes orientadoras para a produção de alimentos seguros. Em consequência disso, surgiram as normas para os Sistemas de Gestão da Segurança Alimentar (SGSA) e a sua implementação é hoje em dia um elemento fundamental para a competitividade da empresa e dos produtos que comercializa. O trabalho desenvolvido na presente dissertação visa o estudo da implementação de um Sistema de Gestão da Segurança Alimentar com base no referencial de certificação NP EN ISO 22000:2005, na Cooperativa de Olivicultores de Fátima C. R. L.. A implementação de um sistema de gestão e a sua posterior certificação, é uma mais-valia para uma empresa. Ao obter a certificação, obtêm-se reconhecimento e satisfação dos clientes e outras partes interessadas, melhoria da imagem e prestigio, acesso a novos mercados, redução de custos de funcionamento através da melhoria do desempenho operacional e uma nova cultura com a sensibilização e motivação dos colaboradores, orientada para a melhoria continua e para a satisfação dos clientes e outras partes interessadas. Tendo por base os Códigos de Boas-práticas e HACCP existentes, fez-se a revisão e atualização de todo o sistema. Reapreciou-se o processo de fabrico e reavaliaram-se os pontos críticos. Reviram-se os Programas Pré-requisitos e melhorou-se o sistema HACCP. Os SGSA têm uma elevada relevância nas organizações associadas ao sector alimentar também nas indústrias produtoras de azeite, uma vez que estas devem implementar metodologias capazes de assegurar que os perigos para a saúde dos consumidores são eliminados ou reduzidos a níveis aceitáveis. Os principais perigos na indústria do azeite numa fase inicial são a presença de microrganismos patogénicos e parasitas da azeitona (Ex.: Bactrocera oleae) que se podem desenvolver devido ao excessivo tempo de espera até à operação ou por temperaturas inadequadas, podendo este perigo ser resolvido através do controlo na receção, de fornecedores, e do tempo de operação; boas práticas de fabrico e formação do pessoal. A presença de folhas, terra, pedras e metais diversos é outro dos perigos mais frequentes que são contornados através do controlo na receção; inspeção visual; avaliação dos fornecedores, limpeza e lavagem das azeitonas. Ao longo da produção e embalamento os principais perigos são os resíduos de produtos de higienização, incorporação de partículas estranhas ou restos de sujidade e a contaminação química por resíduos de massas e óleos de lubrificação, perigos estes que são colmatados através de boas práticas de fabrico; plano de higiene e de manutenção dos equipamentos e do uso de lubrificantes homologados para a indústria alimentar.

Estudo anatômico das madeiras dos gêneros Anisophyllea R. Brow ex. sabine e Polygonanthus Ducke. (Rhizophoraceae)

Neste trabalho, é feito o estudo dos caracteres anatômicos de 1 (uma) espécie do gênero Anlsophylleae de 2 (duas) espécies do gênero Polygonanthus(Rhizophoraceae) e para cada espécie são apresentadas: características gerais, descrição macro e microscópía, macro e microfotografias dos cortes transversal, tangencial e radial, histogramas da variação de freqüência de fibras e elementos vasculares, um quadro slinóptico com as principais características de cada espécie e uma ficha biométrlca dos elementos anatômicos, para cada espécie. As espécies estudadas foram: Anlisophylea manausensisPires & Rodrigues, Polygonanthus amazonicusDucke e P. punctulatusKuhlmann.

Biotransformation/separation routes to obtain pure enantiomers

The objective of the work presented in this thesis was the development of an innovative approach for the separation of enantiomers of secondary alcohols, combining the use of an ionic liquid (IL) - both as solvent for conducting enzymatic kinetic resolution and as acylating agent - with the use of carbon dioxide (CO2) as solvent for extraction. Menthol was selected for testing this reaction/separation approach due to the increasing demand for this substance, which is widely used in the pharmaceutical, cosmetics and food industries. With a view to using an ionic ester as acylating agent, whose conversion led to the release of ethanol, and due to the need to remove this alcohol so as to drive reaction equilibrium forward, a phase equilibrium study was conducted for the ehtanol/(±)-menthol/CO2 system, at pressures between 8 and 10 MPa and temperatures between 40 and 50 oC. It was found that CO2 is more selective towards ethanol, especially at the lowest pressure and highest temperature tested, leading to separation factors in the range 1.6-7.6. The pressure-temperature-composition data obtained were correlated with the Peng-Robinson equation of state and the Mathias-Klotz-Prausnitz mixing rule. The model fit the experimental results well, with an average absolute deviation (AAD) of 3.7 %. The resolution of racemic menthol was studied using two lipases, namely lipase from Candida rugosa (CRL) and immobilized lipase B from Candida antarctica (CALB), and two ionic acylating esters. No reaction was detected in either case. (R,S)-1-phenylethanol was used next, and it was found that with CRL low, nonselective, conversion of the alcohol took place, whereas CALB led to an enantiomeric excess (ee) of the substrate of 95%, at 30% conversion. Other acylating agents were tested for the resolution of (±)-menthol, namely vinyl esters and acid anhydrides, using several lipases and varying other parameters that affect conversion and enantioselectivity, such as substrate concentration, solvent and temperature. One such acylating agent was propionic anhydride. It was thus performed a phase equilibrium study on the propionic anhydride/CO2 system, at temperatures between 35 and 50 oC. This study revealed that, at 35 oC and pressures from 7 MPa, the system is monophasic for all compositions. The enzymatic catalysis studies carried out with propionic anhydride revealed that the extent of noncatalyzed reaction was high, with a negative effect on enantioselectivity. These studies showed also that it was possible to reduce considerably the impact of the noncatalyzed reaction relative to the reaction catalyzed by CRL by lowering temperature to 4 oC. Vinyl decanoate was shown to lead to the best results at conditions amenable to a process combining the use of supercritical CO2 as agent for post-reaction separation. The use of vinyl decanoate in a number of IL solvents, namely [bmim][PF6], [bmim][BF4], [hmim][PF6], [omim][PF6], and [bmim][Tf2N], led to an enantiomeric excess of product (eep) values of over 96%, at about 50% conversion, using CRL. In n-hexane and supercritical CO2, reaction progressed more slowly.(...)

Characterization of phenolic compounds and antioxidant properties of Glycyrrhiza glabra L. rhizomes and roots

The present work aims to characterize and quantify the phenolic composition and to evaluate the antioxidant activity of Glycyrrhiza glabra L. (commonly known as licorice) rhizomes and roots. The antioxidant potential of its methanol/water extract could be related with flavones (mainly apigenin derivatives), flavanones (mainly liquirintin derivatives), a methylated isoflavone and a chalcone, identified in the extract. Lipid peroxidation inhibition was the most pronounced antioxidant effect (EC50=0.24±0.01 µg/mL and 22.74±2.42 µg/mL in TBARS and -carotene/linoleate assays, respectively), followed by free radicals scavenging activity (EC50=111.54±6.04 µg/mL) and, finally, reducing power (EC50=128.63±0.21 µg/mL). In this sense, licorice extract could be used as a source of antioxidants for pharmaceutical, cosmetic and/or food industries.

Primeiro registro de Phanoxyla hystrix (R. Felder, [1874]) (Lepidoptera, Sphingidae) para o estado de Rondônia, Brasil

Um macho de Phanoxyla hystrix (R. Felder, [1874]) foi coletado em Porto Velho, representando o primeiro registro para o estado de Rondônia, Brasil.

A new and efficient synthesis of benzoimidazopurine derivatives

[Excerpt] Purine nucleobases are essential biomolecules in living organisms. Playing several key roles in the cell, they have been a significant inspiration for drug design.1 Benzimidazole nucleus is an important pharmacophore in the development of molecules with pharmaceutical or biological interest. Benzimidazoles have been reported to display significant pharmacological activities such as antiulcer, antifungal, antiparkinson, anticancer and antibiotic.2 Fused structures incorporating these two scaffolds might be important for medicinal chemistry and, to the best of our knowledge, there are no reports of these systems in the literature. In particular, benzo[4,5]imidazo[2,1]purines seem to be novel and must be important target molecules in the heterocyclic synthesis. (...)

Prediction of drug targets in human pathogens

The identification of new and druggable targets in bacteria is a critical endeavour in pharmaceutical research of novel antibiotics to fight infectious agents. The rapid emergence of resistant bacteria makes today's antibiotics more and more ineffective, consequently increasing the need for new pharmacological targets and novel classes of antibacterial drugs. A new model that combines the singular value decomposition technique with biological filters comprised of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of E. coli has been developed to predict potential drug targets in the Enterobacteriaceae family [1]. This model identified 99 potential target proteins amongst the studied bacterial family, exhibiting eight different functions that suggest that the disruption of the activities of these proteins is critical for cells. Out of these candidates, one was selected for target confirmation. To find target modulators, receptor-based pharmacophore hypotheses were built and used in the screening of a virtual library of compounds. Postscreening filters were based on physicochemical and topological similarity to known Gram-negative antibiotics and applied to the retrieved compounds. Screening hits passing all filters were docked into the proteins catalytic groove and 15 of the most promising compounds were purchased from their chemical vendors to be experimentally tested in vitro. To the best of our knowledge, this is the first attempt to rationalize the search of compounds to probe the relevance of this candidate as a new pharmacological target.

Acmella marajoensis G.A.R. Silva & J.U.M. Santos: uma nova espécie de Asteraceae para a Amazônia brasileira

Em decorrência dos estudos na subtribo Ecliptinae da Amazônia brasileira, é descrita uma nova espécie, Acmella marajoensis G.A.R. Silva & J.U.M. Santos. Até o presente momento, a espécie é considerada como endêmica da Ilha do Marajó. São apresentados diagnose em latim, descrição detalhada, comentários taxonômicos e ilustrações.