The ParaWise expert assistant - widening accessibility to efficient and scalable tool Generated OpenMP code

Despite the apparent simplicity of the OpenMP directive shared memory programming model and the sophisticated dependence analysis and code generation capabilities of the ParaWise/CAPO tools, experience shows that a level of expertise is required to produce efficient parallel code. In a real world application the investigation of a single loop in a generated parallel code can soon become an in-depth inspection of numerous dependencies in many routines. The additional understanding of dependencies is also needed to effectively interpret the information provided and supply the required feedback. The ParaWise Expert Assistant has been developed to automate this investigation and present questions to the user about, and in the context of, their application code. In this paper, we demonstrate that knowledge of dependence information and OpenMP are no longer essential to produce efficient parallel code with the Expert Assistant. It is hoped that this will enable a far wider audience to use the tools and subsequently, exploit the benefits of large parallel systems.

Using an interactive software environment for the parallelization of real-world scientific applications

The parallelization of real-world compute intensive Fortran application codes is generally not a trivial task. If the time to complete the parallelization is to be significantly reduced then an environment is needed that will assist the programmer in the various tasks of code parallelization. In this paper the authors present a code parallelization environment where a number of tools that address the main tasks such as code parallelization, debugging and optimization are available. The ParaWise and CAPO parallelization tools are discussed which enable the near automatic parallelization of real-world scientific application codes for shared and distributed memory-based parallel systems. As user involvement in the parallelization process can introduce errors, a relative debugging tool (P2d2) is also available and can be used to perform nearly automatic relative debugging of a program that has been parallelized using the tools. A high quality interprocedural dependence analysis as well as user-tool interaction are also highlighted and are vital to the generation of efficient parallel code and in the optimization of the backtracking and speculation process used in relative debugging. Results of benchmark and real-world application codes parallelized are presented and show the benefits of using the environment

Explicit finite volume modeling of aircraft anti-icing and de-icing

In this paper, a runback water and ice prediction model is extended to anti-icing and thermal de-icing situations. The resulting coupled equations that govern thin-film flow, ice accretion, and heat conduction in the multilayered system substrate-ice-water are solved using an explicit finite volume approach. The procedure is implemented in the three-dimensional icing code ICECREMO2, and both structured and unstructured grids can be considered. Numerical results are presented to compare the present code simulations to some data provided by other ice prediction codes and to show the capabilities of the present numerical tool.

Super-villains of the "real world": the political use of the characterization of villains in Chistopher Nolan's "Dark Knight Trilogy"

It is almost a tradition that celluloid (or digital) villains are represented with some characteristics that remind us the real political enemies of the producer country of the film, or even enemies within the country according to the particular ideology that sustains the film. The case of Christopher Nolan The Dark Knight trilogy, analyzed here, is representative of this trend for two reasons. First, because it gets marked by political radicalization conducted by the US government after the attack of September 11, 2001. Secondly, because it offers a profuse gallery of villains who are outside the circle of friends as the new doctrine “either with us or against us” opened by George Bush for the XXI century. This gallery includes from the very terrorists who justify the War on Terror (Ra's al Ghul, the Joker), to the “radical left” (Bane, Talia al Ghul) including liberal politicians (Harvey Dent), and corrupt that take advantage of the softness of the law to commit crimes with impunity (Dr. Crane, the Scarecrow).

Spanish Sociology and Anti-Semitism Between passed prejudice and key to civilization

There is a significant lack of sociological research in Spain about anti-Semitism. At the same time there are alarming anti-Semitic tendencies and anti-Jewish stereotypes which are above the European average. This article aims to explain this lack of sociological research about anti-Semitism in Spain. Therefore two types of explications are offered: on the one hand side some structural problems will be shown which sociology in general had since its beginnings and which complicate the understanding of anti-Semitism. Furthermore explications regarding the specific social and historic situation in Spain and of Spanish sociology in particular will be exposed. It will be shown that for its rationalistic character and with the exception of very few authors – who are considered marginalized for practical research – sociology in general has had enormous problems in understanding anti-Semitism. The specific historic situation, Francoism, the dispute about the historic memory and the delayed institutionalisation of sociology could also explain the lack of sociological interest in the topic especially in Spain. The article shows that the study of anti-Semitism is not only relevant for struggling against this burden of society in many of its variants. Furthermore, thinking about anti-Semitism can help sociology to recognise its own epistemological problems. It can serve to criticise and improve instruments of sociological research by showing the limitations of the sociological approach and to uncover the importance of interdisciplinary research for understanding specific social phenomena. In that sense, anti-Semitism, far from being a marginal subject, can be considered a key topic in the process of civilisation and it can help us to decipher the contemporary Spanish society.

A Firm Perspective of Anti-dumping and Countervailing Duty Cases in the United States

The role played by firms in the prosecution of anti-dumping and countervailing duty cases in the United States is understudied. This article provides greater understanding of the challenges faced by firms during the process of prosecuting anti-dumping and countervailing duty cases in the United States. This is achieved by applying a theoretical model of corporate political activity to data collected through interviews with 24 trade attorneys in Washington, D.C., practising in the area of antidumping and countervailing duty law. Anti-dumping and countervailing duty cases are found to require significant resource commitments from firms in the participating industries, as well as requiring individual firms to make a number of strategic decisions. The value of an affirmative decision and imposition of duties to the domestic and foreign industry is found to be more nuanced than previous studies have suggested. Non-duty effects of AD and CVD cases are also confirmed. Finally a clearer understanding of the role of individual firms in anti-dumping and countervailing duty cases is shown to have the potential to improve how industry influence is taken account of in future research.

Collaborative artistic laboratories. Transfrontier spaces of cultural production

The appearance of the open code paradigm and the demands of social movements have permeated the ways in which today’s cultural institutions are organized. This article analyzes the birth of a new critical and cooperative spatiality and how it is transforming current modes of cultural research and production. It centers on the potential for establishing the new means of cooperation that are being tested in what are defined as collaborative artistic laboratories. These are hybrid spaces of research and creation based on networked and cooperative structures producing a new societal-technical body that forces us to reconsider the traditional organic conditions of the productive scenarios of knowledge and artistic practice.

Toxicity of non-steroidal anti-inflammatory drugs to Gyps vultures:a new threat from ketoprofen

Three Gyps vulture species are on the brink of extinction in South Asia owing to the veterinary non-steroidal anti-inflammatory drug (NSAID) diclofenac. Carcasses of domesticated ungulates are the main food source for Asia's vultures and birds die from kidney failure after consuming diclofenac-contaminated tissues. Here, we report on the safety testing of the NSAID ketoprofen, which was not reported to cause mortality in clinical treatment of scavenging birds and is rapidly eliminated from livestock tissues. Safety testing was undertaken using captive non-releasable Cape griffon vultures (Gyps coprotheres) and wild-caught African white-backed vultures (G. africanus), both previously identified as susceptible to diclofenac and suitable surrogates. Ketoprofen doses ranged from 0.5 to 5 mg kg(-1) vulture body weight, based upon recommended veterinary guidelines and maximum levels of exposure for wild vultures (estimated as 1.54 mg kg(-1)). Doses were administered by oral gavage or through feeding tissues from cattle dosed with ketoprofen at 6 mg kg(-1) cattle body weight, before slaughter. Mortalities occurred at dose levels of 1.5 and 5 mg kg(-1) vulture body weight (within the range recommended for clinical treatment) with the same clinical signs as observed for diclofenac. Surveys of livestock carcasses in India indicate that toxic levels of residual ketoprofen are already present in vulture food supplies. Consequently, we strongly recommend that ketoprofen is not used for veterinary treatment of livestock in Asia and in other regions of the world where vultures access livestock carcasses. The only alternative to diclofenac that should be promoted as safe for vultures is the NSAID meloxicam.

Apparent tolerance of turkey vultures (Cathartes aura) to the non-steroidal anti-inflammatory drug diclofenac

The nonsteroidal anti-inflammatory drug diclofenac is extremely toxic to Old World Gyps vultures (median lethal dose -0.1-0.2 mg/kg), evoking visceral gout, renal necrosis, and mortality within a few days of exposure. Unintentional secondary poisoning of vultures that fed upon carcasses of diclofenac-treated livestock decimated populations in the Indian subcontinent. Because of the widespread use of diclofenac and other cyclooxygenase-2 inhibiting drugs, a toxicological study was undertaken in turkey vultures (Cathartes aura) as an initial step in examining sensitivity of New World scavenging birds. Two trials were conducted entailing oral gavage of diclofenac at doses ranging from 0.08 to 25 mg/kg body weight. Birds were observed for 7 d, blood samples were collected for plasma chemistry (predose and 12, 24, and 48 h and 7 d postdose), and select individuals were necropsied. Diclofenac failed to evoke overt signs of toxicity, visceral gout, renal necrosis, or elevate plasma uric acid at concentrations greater than 100 times the estimated median lethal dose reported for Gyps vultures. For turkey vultures receiving 8 or 25 mg/kg, the plasma half-life of diclofenac was estimated to be 6 h, and it was apparently cleared after several days as no residues were detectable in liver or kidney at necropsy. Differential sensitivity among avian species is a hallmark of cyclooxygenase-2 inhibitors, and despite the tolerance of turkey vultures to diclofenac, additional studies in related scavenging species seem warranted.

Effects of Gold Nanoparticle and Enzyme Precipitation on Enhancement of Surface Plasmon Resonance Immunoassay: A Super Sensitive Measurement of Anti- Glutamic Acid Decarboxylase Antibody

Introduction: In this study, colloidal gold nanoparticle and precipitation of an insoluble product formed by HRP-biocatalyzed oxidation of 3,3'-diaminobenzidine (DAB) in the presence of H2O2 were used to enhance the signal obtained from the surface plasmon resonance biosensor.

Methods: The colloidal gold nanoparticle was synthesized as described by Turkevitch et al., and their surface was firstly functionalized with HS(CH2)11(OCH2CH2)3COOH (OEG3¬-COOH) by self assembling technique. Thereafter, those OEG3-COOH functionalized nanoparticles were covalently conjugated with horseradish peroxidase (HRP) and anti-IgG antibody (specific to the Fc portion of all human IgG subclasses) to form an enzyme-immunogold complex. Characterization was performed by several methods: UV-Vis absorption, dynamic light scattering (DLS), transmission electron microscopy (TEM) and FTIR. The as-prepared enzyme-immunogold complex has been applied in enhancement of SPR immunoassay. A sensor chip used in the experiment was constructed by using 1:10 molar ratio of HS(CH2)11(OCH2CH2)6COOH and HS(CH2)11(OCH2CH2)3OH. The capture protein, GAD65 (autoantigen) which is recognized by anti-GAD antibody (autoantibody) in the sera of insulin-dependent diabetes mellitus patients, was immobilized onto the 1:10 surface via biotin-streptavidin interaction.

Results and conclusions: In the research, we reported the influences of gold nanoparticle and enzyme precipitation on the enhancement of SPR signal. Gold nanoparticle showed its enhancement as being consistent with other previous studies, while the enzyme precipitation using DAB substrate was applied for the first time and greatly amplified the SPR detection. As the results, anti-GAD antibody could be detected at pg/ml level which is far higher than that of commercial ELISA detection kit. This study indicates another way to enhance SPR measurement, and it is generally applicable to other SPR-based immunoassays.

In Vitro and In Vivo Anti-Schistosomal Activity of the Alkylphospholipid Analog Edelfosine

Background: Schistosomiasis is a parasitic disease caused by trematodes of the genus Schistosoma. Five species of Schistosoma are known to infect humans, out of which S. haematobium is the most prevalent, causing the chronic parasitic disease schistosomiasis that still represents a major problem of public health in many regions of the world and especially in tropical areas, leading to serious manifestations and mortality in developing countries. Since the 1970s, praziquantel (PZQ) is the drug of choice for the treatment of schistosomiasis, but concerns about relying on a single drug to treat millions of people, and the potential appearance of drug resistance, make identification of alternative schistosomiasis chemotherapies a high priority. Alkylphospholipid analogs (APLs), together with their prototypic molecule edelfosine (EDLF), are a family of synthetic antineoplastic compounds that show additional pharmacological actions, including antiparasitic activities against several protozoan parasites.

Methodology/Principal Findings: We found APLs ranked edelfosine> perifosine> erucylphosphocholine> miltefosine for their in vitro schistosomicidal activity against adult S. mansoni worms. Edelfosine accumulated mainly in the worm tegument, and led to tegumental alterations, membrane permeabilization, motility impairment, blockade of male-female pairing as well as induction of apoptosis-like processes in cells in the close vicinity to the tegument. Edelfosine oral treatment also showed in vivo schistosomicidal activity and decreased significantly the egg burden in the liver, a key event in schistosomiasis.

Conclusions/Significance: Our data show that edelfosine is the most potent APL in killing S. mansoni adult worms in vitro. Edelfosine schistosomicidal activity seems to depend on its action on the tegumental structure, leading to tegumental damage, membrane permeabilization and apoptosis-like cell death. Oral administration of edelfosine diminished worm and egg burdens in S. mansoni-infected CD1 mice. Here we report that edelfosine showed promising antischistosomal properties in vitro and in vivo.

Against divisiveness: Digital workers of the world unite! A rejoinder to César Bolaño and Eloy Vieira

This piece is a short rejoinder to César Bolaño’s paper The Political Economy of the Internet and related articles (e.g., Comor, Foley, Huws, Reveley, Rigi and Prey, Robinson) that center around the relevance of Marx’s labor theory of value for understanding social media. I argue that Dallas Smythe’s assessment of advertising was made to distinguish his approach from the one by Baran and Sweezy. Smythe developed the idea of capital’s exploitation of the audience at a time when both feminist and anti-imperialist Marxists challenged the orthodox idea that only white factory workers are exploited. The crucial question is how to conceptualize productive labor. This is a theoretical, normative, and political question. A mathematical example shows the importance of the “crowdsourcing” of value-production on Facebook. I also point out parallels of the contemporary debate to the Soviet question of who is a productive or unproductive worker in the Material Product System.

Desenvolvimento de um Code Set para a escrita manual baseado na classificação internacional de funcionalidade versão crianças e jovens

Compreender a funcionalidade de uma criança é um desafio persistente em contextos de saúde e educação. Na tentativa de superar esse desafio, em 2007, a Organização Mundial de Saúde desenvolveu a Classificação Internacional de Funcionalidade, Incapacidade e Saúde para Crianças e Jovens (CIF-CJ) como o primeiro sistema de classificação universal para documentar a saúde e funcionalidade da criança. Apesar de a CIF-CJ não ser um instrumento de avaliação e intervenção, tem, no entanto, a capacidade de servir de enquadramento para o desenvolvimento de ferramentas adaptadas às necessidades dos seus utilizadores. Considerando que no contexto escolar, a escrita manual encontra-se entre as atividades mais requeridas para a participação plena de uma criança, parece ser pertinente a definição de um conjunto de códigos destinados a caracterizar o perfil de funcionalidade de uma criança, no que se refere à escrita manual. O objetivo deste estudo foi, pois, o desenvolvimento de um conjunto preliminar de códigos baseado na CIF-CJ que possa vir a constituir um code set para a escrita manual. Dada a complexidade do tema e atendendo a que se pretende alcançar consenso entre os especialistas sobre quais as categorias da CIF-CJ que devem ser consideradas, optou-se pela utilização da técnica de Delphi. A escolha da metodologia seguiu a orientação dos procedimentos adotados pelo projeto Core Set CIF. De dezoito profissionais contactados, obtiveram-se respostas de sete terapeutas ocupacionais com experiência em pediatria, que participaram em todas as rondas. No total, três rondas de questionários foram realizadas para atingir um consenso, com um nível de concordância, previamente definido, de 70%. Deste estudo resultou um conjunto preliminar de códigos com 54 categorias da CIF-CJ (16 categorias de segundo nível, 14 categorias de terceiro nível e uma categoria de quarto nível), das quais 31 são categorias das funções do corpo, uma categoria das estruturas do corpo, 12 categorias de atividades e participação e 10 categorias de fatores ambientais. Este estudo é um primeiro passo para o desenvolvimento de um code set para a escrita manual baseado na CIF-CJ , sendo claramente necessário a realização de mais pesquisas no contexto do desenvolvimento e da validação deste code set.

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.