Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

How “intuition” exploded

Recent decades have seen a surge in interest in metaphilosophy. In particular there has been an interest in philosophical methodology. Various questions have been asked about philosophical methods. Are our methods any good? Can we improve upon them? Prior to such evaluative and ameliorative concerns, however, is the matter of what methods philosophers actually use. Worryingly, our understanding of philosophical methodology is impoverished in various respects. This article considers one particular respect in which we seem to be missing an important part of the picture. While it is a received wisdom that the word “intuition” has exploded across analytic philosophy in recent decades, the article presents evidence that the explosion is apparent across a broad swathe of academia (and perhaps beyond). It notes various implications for current methodological debates about the role of intuitions in philosophy.

Echoes of 1992: the NAFTA negotiations and North America now

Two decades ago, Canada, Mexico, and the United States created a continental economy. The road to integration from the signing of the North American Free Trade Agreement has not been a smooth one. Along the way, Mexico lived through a currency crisis, a democratic transition, and the rising challenge of Asian manufacturing. Canada stayed united despite surging Quebecois nationalism during the 1990s; since then, it has seen dramatic economic changes with the explosion of hydrocarbon production and a much stronger currency. The United States saw a stock-market bust, the shock of 9/11, and the near-collapse of its financial system. All of these events have transformed the relationships that emerged after NAFTA entered into force in 1994. Given the tremendous changes, one might be skeptical that the circumstances and details of the negotiation and ratification of NAFTA hold lessons for the future of North America. However, the road to NAFTA had its own difficulties, and many of the issues involved in the negotiations underpin today's challenges. NAFTA was conceived at a time of profound change in the international system. When Mexican leaders surveyed the world two decades ago, they saw emerging regional groupings in Europe, Asia, and South America. Faced with a lack of interest or compatibility, they instead doubled down on North America. How did Mexican leaders reconsider their national interests and redefine Mexico's role in the world in light of those transformations? Unpublished Mexican documents from SECOFI, the secretariate most involved in negotiating NAFTA, help illustrate Mexican thinking about its interests and role at that time. Combining those insights with analysis of newly available evidence from U.S. presidential archives, this paper sheds light on the negotiations that concluded two decades ago.

A mechanism for the formation of oxygen and iron bimodal radial distribution in the disc of our Galaxy

Recently, it has been proposed that there are two type Ia supernova progenitors: short-lived and long-lived. On the basis of this idea, we develop a theory of a unified mechanism for the formation of the bimodal radial distribution of iron and oxygen in the Galactic disc. The underlying cause for the formation of the fine structure of the radial abundance pattern is the influence of the spiral arms, specifically the combined effect of the corotation resonance and turbulent diffusion. From our modelling, we conclude that in order to explain the bimodal radial distributions simultaneously for oxygen and iron and to obtain approximately equal total iron output from different types of supernovae, the mean ejected iron mass per supernova event should be the same as quoted in the literature if the maximum mass of stars, which eject heavy elements, is 50 M(circle dot). For the upper mass limit of 70 M(circle dot), the production of iron by a type II supernova explosion should increase by about 1.5 times.

Hydrodynamical simulations of Galactic fountains - II. Evolution of multiple fountains

The ejection of gas out of the disc in late-type galaxies is related to star formation and is mainly due to the explosion of Type II supernovae (SN II). In a previous paper, we considered the evolution of a single Galactic fountain, that is, a fountain powered by a single SN cluster. Using three-dimensional hydrodynamical simulations, we studied in detail the fountain flow and its dependence with several factors, such as the Galactic rotation, the distance to the Galactic centre and the presence of a hot gaseous halo. As a natural followup, this paper investigates the dynamical evolution of multiple generations of fountains generated by similar to 100 OB associations. We have considered the observed size-frequency distribution of young stellar clusters within the Galaxy in order to appropriately fuel the multiple fountains in our simulations. Most of the results of the previous paper have been confirmed, like for example the formation of intermediate velocity clouds above the disc by the multiple fountains. Also, this work confirms the localized nature of the fountain flows: the freshly ejected metals tend to fall back close to the same Galactocentric region where they are delivered. Therefore, the fountains do not change significantly the radial profile of the disc chemical abundance. The multiple fountain simulations also allowed us to consistently calculate the feedback of the star formation on the halo gas. We found that the hot gas gains about 10 per cent of all the SN II energy produced in the disc. Thus, the SN feedback more than compensate for the halo radiative losses and allow for a quasi steady-state disc-halo circulation to exist. Finally, we have also considered the possibility of mass infall from the intergalactic medium and its interaction with the clouds that are formed by the fountains. Though our simulations are not suitable to reproduce the slow rotational pattern that is typically observed in the haloes around the disc galaxies, they indicate that the presence of an external gas infall may help to slow down the rotation of the gas in the clouds and thus the amount of angular momentum that they transfer to the coronal gas, as previously suggested in the literature.

Fault Coverage-Driven Incremental Test Generation

In this paper, we consider a classical problem of complete test generation for deterministic finite-state machines (FSMs) in a more general setting. The first generalization is that the number of states in implementation FSMs can even be smaller than that of the specification FSM. Previous work deals only with the case when the implementation FSMs are allowed to have the same number of states as the specification FSM. This generalization provides more options to the test designer: when traditional methods trigger a test explosion for large specification machines, tests with a lower, but yet guaranteed, fault coverage can still be generated. The second generalization is that tests can be generated starting with a user-defined test suite, by incrementally extending it until the desired fault coverage is achieved. Solving the generalized test derivation problem, we formulate sufficient conditions for test suite completeness weaker than the existing ones and use them to elaborate an algorithm that can be used both for extending user-defined test suites to achieve the desired fault coverage and for test generation. We present the experimental results that indicate that the proposed algorithm allows obtaining a trade-off between the length and fault coverage of test suites.

Previsão de volatilidade: uma comparação entre volatilidade implícita e realizada

Com origem no setor imobiliário americano, a crise de crédito de 2008 gerou grandes perdas nos mercados ao redor do mundo. O mês de outubro do mesmo ano concentrou a maior parte da turbulência, apresentando também uma explosão na volatilidade. Em meados de 2006 e 2007, o VIX, um índice de volatilidade implícita das opções do S&P500, registrou uma elevação de patamar, sinalizando o possível desequilíbrio existente no mercado americano. Esta dissertação analisa se o consenso de que a volatilidade implícita é a melhor previsora da volatilidade futura permanece durante o período de crise. Os resultados indicam que o VIX perde poder explicativo ao se passar do período sem crise para o de crise, sendo ultrapassado pela volatilidade realizada.

Internet e movimentos populares: um modelo de dados em painel

Nos últimos anos, o mundo vem assistindo a um maior número de mobilizações sociais, que ocorrem em todo o espectro de regimes de governo e níveis de desenvolvimento econômico: de países tradicionalmente democráticos e desenvolvidos, a países em desenvolvimento sob regimes autoritários. Tais mobilizações vêm ocorrendo simultaneamente a uma expansão acelerada das Tecnologias da Informação e Comunicação (TIC), mais notadamente o avanço da Internet e dos telefones celulares (ITU, 2014; CETIC, 2013), tornando mais rápido e fácil o acesso e difusão de informações sem o intermédio dos meios de comunicação de massa tradicionais; há os que defendem que o contexto de cada nação é o grande responsável por tais manifestações, enquanto outros citam a importância tanto das TIC quanto dos fatores contextuais como influenciadores. O objetivo desta pesquisa é identificar as variáveis explicativas da ocorrência de protestos, considerando aspectos tecnológicos, sociais e políticos, por meio da construção de modelos utilizando dados em painel. Para tal são utilizados dados do Banco Mundial, Fórum Econômico Mundial e ITU, desenvolvendo uma amostra de 124 países. O resultado desta análise revela que o percentual de usuários de Internet influencia positivamente a ocorrência de protestos e que países desenvolvidos possuem maior a chance de apresentarem manifestações.

Internet e movimentos populares: um modelo global de dados em painel

Nos últimos anos, o mundo vem assistindo a um maior número de mobilizações sociais, que ocorrem em todo o espectro de regimes de governo e níveis de desenvolvimento econômico: de países tradicionalmente democráticos e desenvolvidos, a países em desenvolvimento sob regimes autoritários. Tais mobilizações vêm ocorrendo simultaneamente a uma expansão acelerada das Tecnologias da Informação e Comunicação (TIC), mais notadamente o avanço da Internet e dos telefones celulares (ITU, 2014; CETIC, 2013), tornando mais rápido e fácil o acesso e difusão de informações sem o intermédio dos meios de comunicação de massa tradicionais; há os que defendem que o contexto de cada nação é o grande responsável por tais manifestações, enquanto outros citam a importância tanto das TIC quanto dos fatores contextuais como influenciadores. O objetivo desta pesquisa é identificar as variáveis explicativas da ocorrência de protestos, considerando aspectos tecnológicos, sociais e políticos, por meio da construção de modelos utilizando dados em painel. Para tal são utilizados dados do Banco Mundial, Fórum Econômico Mundial e ITU, desenvolvendo uma amostra de 124 países. O resultado desta análise revela que o percentual de usuários de Internet influencia positivamente a ocorrência de protestos e que países desenvolvidos possuem maior a chance de apresentarem manifestações.

Realidade aumentada aplicada em bibliotecas: multiplicidade no acesso a informação

Conceitua Realidade Aumentada do ponto de vista histórico de vários autores e como surgiu esse segmento através da evolução tecnológica até os dias atuais. Aborda seu funcionamento, como também, seus sistemas e aplicações em diversos campos de pesquisas e estudos científicos. Diferencia Realidade Aumentada de Realidade Virtual, visando melhor esclarecimento entre ambas na intenção de descaracterizá-las com uma única “realidade”. Apresenta a Realidade Aumentada e sua aplicação dentro de um contexto de uma unidade de informação, promovendo uma melhor interação com os usuários e as adaptações pelas quais as bibliotecas terão que passar futuramente para se adequarem a “explosão” tecnológica. Descreve o funcionamento da biblioteca ARToolKIT, baseada em RA e suas principais etapas de funcionamento para visualização de objetos virtuais em 3D. Exemplifica os benefícios que uma unidade de informação, que utiliza Realidade Aumentada, promove aos usuários portadores de deficiência, além de sua inclusão no meio digital e sua inserção no mercado de trabalho

Adsorção de Pb(II) utilizando adsorvente composto por montmorilonita e dolomita

The destructive impact of improper disposal of heavy metals in the environment increases as a direct result of population explosion, urbanization and industrial expansion and technological developments. Argil are potential materials for adsorption of inorganic and the pelletization of it is required for use in adsorptive columns of fixed bed. The low cost and the possibility of regeneration makes these materials attractive for use in the purification process, capable of removing inorganic compounds in contaminated aquatic environments. In this work was made pellets of a mixture of dolomite and montmorillonite by wet agglomeration, in different percentages. The removal of Pb (II) was investigated through experimental studies, and was modeled by kinetic models and isotherms of adsorption. The materials were characterized using the techniques of XRD, TG / DTA, FT-IR, and surface area by BET method. The results showed the adsorption efficiency of the contaminant by the composite material studied in synthetic solution. The study found that the adsorption follows the Langmuir model, and the kinetics of adsorption follows the model of pseudosecond order

Uma metodologia para a análise do desempenho sustentável dos postos de revenda de combustível na cidade de Natal/RN, com o uso de data envelopment analysis-DEA

The increasing use of fossil fuels in line with cities demographic explosion carries out to huge environmental impact in society. For mitigate these social impacts, regulatory requirements have positively influenced the environmental consciousness of society, as well as, the strategic behavior of businesses. Along with this environmental awareness, the regulatory organs have conquered and formulated new laws to control potentially polluting activities, mostly in the gas stations sector. Seeking for increasing market competitiveness, this sector needs to quickly respond to internal and external pressures, adapting to the new standards required in a strategic way to get the Green Badge . Gas stations have incorporated new strategies to attract and retain new customers whom present increasingly social demand. In the social dimension, these projects help the local economy by generating jobs and income distribution. In this survey, the present research aims to align the social, economic and environmental dimensions to set the sustainable performance indicators at Gas Stations sector in the city of Natal/RN. The Sustainable Balanced Scorecard (SBSC) framework was create with a set of indicators for mapping the production process of gas stations. This mapping aimed at identifying operational inefficiencies through multidimensional indicators. To carry out this research, was developed a system for evaluating the sustainability performance with application of Data Envelopment Analysis (DEA) through a quantitative method approach to detect system s efficiency level. In order to understand the systemic complexity, sub organizational processes were analyzed by the technique Network Data Envelopment Analysis (NDEA) figuring their micro activities to identify and diagnose the real causes of overall inefficiency. The sample size comprised 33 Gas stations and the conceptual model included 15 indicators distributed in the three dimensions of sustainability: social, environmental and economic. These three dimensions were measured by means of classical models DEA-CCR input oriented. To unify performance score of individual dimensions, was designed a unique grouping index based upon two means: arithmetic and weighted. After this, another analysis was performed to measure the four perspectives of SBSC: learning and growth, internal processes, customers, and financial, unifying, by averaging the performance scores. NDEA results showed that no company was assessed with excellence in sustainability performance. Some NDEA higher efficiency Gas Stations proved to be inefficient under certain perspectives of SBSC. In the sequence, a comparative sustainable performance and assessment analyzes among the gas station was done, enabling entrepreneurs evaluate their performance in the market competitors. Diagnoses were also obtained to support the decision making of entrepreneurs in improving the management of organizational resources and promote guidelines the regulators. Finally, the average index of sustainable performance was 69.42%, representing the efforts of the environmental suitability of the Gas station. This results point out a significant awareness of this segment, but it still needs further action to enhance sustainability in the long term

Projeto Prevenir: uma pesquisa acerca das mudanças no perfil das infecções por DST/AIDS, com a perspectiva de detectar pontos vulneráveis da prevenção

Rio Grande do Norte is among the Brazilian States where the tourism and sexual violence increasingly grow in the country, occupying 4th place in 2004. Associated to this fact, it comes the problematic one of the contamination of the women by Sexually Transmitted Disease (STD). Studies in Brazil have presented a considerable increase of the STDs, caused through lack of suitable protection in the sexual relationships. Due to the biological and psychosocial vulnerability, besides failures or inconsistencies in the condom use associated to the raised taxes of sexual activity with different partners, the STDs constitute the main risk of health. Many difficulties are found by the confrontation of this problem. In this context, this project had as aim to evaluate the vulnerability of this population of sexually active women in Natal-RN Ponta Negra neighbourhood to the infections by STDs, such as, Candida sp., Vaginoses Bacterial, Trichomonas Vaginalis and Chlamydia sp., arisen with the explosion of the sex market, showing a current statistical panorama. It was possible to detect vulnerable points in prevention through patient anamnesis, where the study it showed: high number of partners (8,3% with more than five), low age of first relationship and not the use of condoms (31,8% sometimes use and 45,8% had not used in the first relationship). Already consolidated by the preventive cytopathologic examination, these data were strengthened by high incidence of causing agents of STDs (58,6%). In this way, it is clear that the sexuality must to be thought on the context of the deep economic and socio-cultural transformations in which pass societies, and mainly the ones concerning to the sexuality exercise and to the sex market. With the profile change of the infections, new demands are placed in relation to the risk factors. Therefore, it can be concluded that the prevention vulnerable points detected as more important had been the deficiency in self-perception and wareness of the risk existence among the studied women

Enhancement of thermal stability, strength and extensibility of lipid-based polyurethanes with cellulose-based nanofibers

Cellulose was extracted from lignocellulosic fibers and nanocrystalline cellulose (NC) prepared by alkali treatment of the fiber, steam explosion of the mercerized fiber, bleaching of the steam exploded fiber and finally acid treatment by 5% oxalic acid followed again by steam explosion. The average length and diameter of the NC were between 200-250 nm and 4-5 nm, respectively, in a monodisperse distribution. Different concentrations of the NC (0.1, 0.5, 1.0, 1.5, 2.0 and 2.5% by weight) were dispersed non-covalently into a completely bio-based thermoplastic polyurethane (TPU) derived entirely from oleic acid. The physical properties of the TPU nanocomposites were assessed by Fourier Transform Infra-Red spectroscopy (FTIR), Thermo-Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), X-Ray Diffraction (XRD), Dynamic Mechanical Analysis (DMA) and Mechanical Properties Analysis. The nanocomposites demonstrated enhanced stress and elongation at break and improved thermal stability compared to the neat TPU. The best results were obtained with 0.5% of NC in the TPU. The elongation at break of this sample was improved from 178% to 269% and its stress at break from 29.3 to 40.5 MPa. In this and all other samples the glass transition temperature, melting temperature and crystallization behavior were essentially unaffected. This finding suggests a potential method of increasing the strength and the elongation at break of typically brittle and weak lipid-based TPUs without alteration of the other physico-chemical properties of the polymer. (C) 2012 Elsevier Ltd. All rights reserved.

Método não destrutivo de estimativa da área foliar de plantas daninhas de ambiente aquático: tanner-grass e capim-fino

The continuous inputs from agriculture areas and human or industrial sewer have been provided a widely demographic explosion of tropical tanner-grass and para grasss plants in the rivers and water reservoirs of Brazil. Considering the importance of these noxious weeds there is a vast necessity of basic studies on aspects related to reproduction, growing, development, nutritional requirements, responses to control systems and others. In most studies, leaf area knowledge is crucial and it is one of the most difficult characteristics to be measured because it usually requires expensive equipments or it uses a destructive technique. The objective of this work was to develop equations for leaf blade dimensional parameters to allow determination of the leaf area of African tanner-grass (Brachiaria subquadripara (Trin.) Hitchc) and para grass (Brachiaria mutica (Forsk.) Stapf.). Correlations between real leaf area and dimensional parameters of leaf blade such as length along the main vein (L) and maximum width (W) perpendicular to the main axis were studied. Only the linear equations allowed a good leaf area estimate. It is suggested to opt for a simple linear equation involving respective products of length times maximum width considering linear coefficient equal to zero. Thus, B. subquadripara (SS) and B. mutica (SM) non destructive leaf blade area estimates may be performed by the following formulas: SS = 0.7719 (L x W) and SM = 0.7479 (L x W), with coefficients of determination (R(2)) of 0.9594 and 0.9408, respectively.