Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

'Flat phase' PID controllers

Flat Phase PID Controllers have the property that the phase of the transfer function round the associated feedback loop is constant or flat around the design frequency, with the aim that the phase margin and overshoot to a step response is unaffected when the gain of the device under control changes. Such designs have been achieved using Bode Integrals and by ensuring the phase is the same at two frequencies. This paper extends the ‘two frequency’ controller and describes a novel three frequency controller. The different design strategies arc compared.

Cortical hot spots and labyrinths: why cortical neuromodulation for episodic migraine with aura should be personalized

Stimulation protocols for medical devices should be rationally designed. For episodic migraine with aura we outline model-based design strategies toward preventive and acute therapies using stereotactic cortical neuromodulation. To this end, we regard a localized spreading depression (SD) wave segment as a central element in migraine pathophysiology. To describe nucleation and propagation features of the SD wave segment, we define the new concepts of cortical hot spots and labyrinths, respectively. In particular, we firstly focus exclusively on curvature-induced dynamical properties by studying a generic reaction-diffusion model of SD on the folded cortical surface. This surface is described with increasing level of details, including finally personalized simulations using patient's magnetic resonance imaging (MRI) scanner readings. At this stage, the only relevant factor that can modulate nucleation and propagation paths is the Gaussian curvature, which has the advantage of being rather readily accessible by MRI. We conclude with discussing further anatomical factors, such as areal, laminar, and cellular heterogeneity, that in addition to and in relation to Gaussian curvature determine the generalized concept of cortical hot spots and labyrinths as target structures for neuromodulation. Our numerical simulations suggest that these target structures are like fingerprints, they are individual features of each migraine sufferer. The goal in the future will be to provide individualized neural tissue simulations. These simulations should predict the clinical data and therefore can also serve as a test bed for exploring stereotactic cortical neuromodulation.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.

Crucial cytokine interactions in nitric oxide production induced by Mycoplasma arthritidis superantigen

Mycoplasma arthritidis causes autoimmune arthritis in rodents. It produces a superantigen (MAM) that simultaneously activates antigen presenting cells and T cells inducing nitric oxide and cytokine release. Nitric oxide is a key inducer and regulator of the immune system activation. Here, we investigated nitric oxide and cytokine production and interactions of these molecules in MAM-stimulated co-cultures of macrophages (J774A.1 cell line) with spleen lymphocytes. We found that: a) MAM-induced nitric oxide, interferon-gamma, membrane-associated tumor necrosis factor and interleukin-2 production in co-cultures of macrophages with lymphocytes from BALB/c and C3H/HePas but not from C57B1/6 mice; b) production of nitric oxide was dependent on interferon-gamma whereas that of interferon-gamma was dependent on interleukin-2 and membrane-associated tumor necrosis factor; c) these cytokines up regulated MAM-induced nitric oxide production. Unraveling the mechanisms of cell activation induced by MAM might be helpful to design strategies to prevent immune system activation by superantigens and therefore in seeking amelioration of associated immunopathologies. (C) 2008 Elsevier Masson SAS. All rights reserved.

Qualificação de edifícios residenciais verticais em Natal/RN à luz do regulamento técnico da qualidade para o nível de eficiência energética de edificações residenciais (RTQ-R)

The goal of the research was to investigate the energy performance of residential vertical buildings envelope in the hot and humid climate of Natal, capital of Rio Grande do Norte, based in the Technical Regulation of Quality for Energy Efficiency Level in Residential Buildings (RTQ -R), launched in 2010. The study pretends to contribute to the development of design strategies appropriate to the specific local climate and the increasing of energy efficiency level of the envelope. The methodological procedures included the survey in 22 (twenty two) residential buildings, the formulation of representative prototypes based on typological and constructives characters researched and the classification of the level of energy efficiency in the envelopment of these prototypes, using as a tool the prescriptive method of the RTQ-R and the parametric analyzes from assigning different values of the following variables: shape of the pavement type; distribution of housing compartments; orientation of the building; area and shading of openings; thermal transmittance, and solar absorptance of opaque materials of the frontage in order to evaluate the influence of these on the envelopment performance. The main results accomplished with this work includes the qualification of vertical residential buildings in Natal/RN; the verification of the adequacy of these buildings to local climate based from the diagnosis of the thermal energy of the envelopment performance, the identification of variables with more significant influence on the prescriptive methodology of RTQ-R and design solutions more favorable to obtain higher levels energy efficiency by this method. Finally, it was verified, that some of these solutions proved contradictory in relation to the recommendations contained in the theoretical approaches regarding environmental comfort in hot and humid weather, which indicates the need for improvement of the prescriptive method RTQ-R and further research on efficient design solutions

Layout, conforto e satisfação dos usuários em escritórios: uma avaliação pós-ocupação no edifício da sede administrativa do INPE-CRN

This research aimed to identify the link between the layout of workspaces in offices and the design strategies for environmental comfort. Strategies surveyed were focused on the thermal, visual and luminic comfort. In this research, visual comfort is related to issues of visual integration within and between the interior and exterior of the building. This is a case study conducted at the administrative headquarters of Centro Regional Nordeste do Instituto de Pesquisas Espaciais (INPE-CRN), located in Natal/RN. The methodological strategy used was the Post-Occupancy Evaluation, which combined the survey data on the building (layout of workspaces, bioclimatic strategies adopted in the design, use of these strategies) with some techniques aimed at acquiring qualitative information related to users. The workspace layout is primordial to satisfaction and productivity of workers. Issues such as concentration, communication, privacy, personal identity, density and space efficiency, barriers (access, visual and even ventilation and lighting), among others, are associated with the layout. The environmental comfort is one of the essential elements to maintaining life quality in workplace. Moreover, it is an important factor in user`s perception of the space in which he or she are inserted. Both layout and environmental comfort issues should be collected and analyzed in the establishment phase of the programming step. That way, it is possible to get adequate answers to these questions in subsequent project phases. It was found that changes in the program that occurred over time, especially concerning persons (number and characteristics), resulted in changes in layout, generating high density and inflexible environments. It turns difficult to adjust the furniture to the occupants` requirement, including comfort needs. However, the presence of strategies for environmental quality provides comfort to spaces, ensuring that, even in situations not considered optimal, users perceive the environment in a positive way. It was found that the relationship between environmental comfort and layout takes the following forms: in changing the perception of comfort, depending on the layout of the arrangements; adjustments in layout, due to needs for comfort; and the elevation of user satisfaction and environmental quality due to the presence of strategies comfort even in situations of inadequate layout

Estimativa da captura total: desenhos amostrais para pesca artesanal

Estimating total landings of artisanal fisheries in managed areas is essential for the development of programs aimed at the establishment of sustainable production systems. However, few experiences addressed the constraints of assessments targeted at multispecific and small scale fisheries with pulverized landings. Total annual production (fish, lobsters and octopus) at the Marine Extractive Reserve of Corumbau, Bahia, Brazil, in 2006, was estimated through yields recorded by fisherfolks, in the scope of a participatory fisheries monitoring program. Three designs were employed: 1) simple random sampling, 2) stratified random sampling by month and fishing frequency, 3) stratified random sampling by community, fishing frequency and months, resulting in estimates of 349t (95% confidence interval = 305-393), 330t (289-372) and 315t (279-351), respectively. This kind of information can help design strategies for aggregation of value to small scale fisheries production, and also for the dimensioning of the corresponding infrastructure. However, these estimates shall not be used to support fishing effort increase, as there is high uncertainty regarding the state of the stocks, as well as limitations related to the asymmetry in monthly landings per fisherfolk and to the sampling coverage in the different strata.

Open urban spaces quality: A study in a historical square in Bath - UK

The quality of open urban spaces is very important for urban vitality. Nowadays urban designers have to face the great challenge of designing urban spaces able to respond to people's need for liveable spaces. The success of these spaces depends on various aspects and the microclimatic condition has been recognized as one of the most influential. However, studies on thermal comfort in open space have shown that the user's thermal sensation does not depend only on microclimate parameters but also on other local qualitative aspects. Thus, environmental quality evaluation of successful public spaces can contribute to understand this issue. This paper focuses on a case study regarding Queen Square's environmental quality, a public space of historical importance in Bath-UK. The first stage of the research, a study on local characteristics and people observations, allowed a preliminary evaluation of the space performance, their social aspects, while it characterized and quantified the hourly variation of the space use in different days and seasons. In the second stage, short microclimatic surveys were carried out simultaneously with a perception survey through a questionnaire. The results show the strong vitality of the square and socioenvironmental significance, not only for its location in the urban context, but also for its historical value. The environmental quality of the square contributes to the users' sensation of comfort even in adverse climatic conditions. This research is part of a project that aims to investigate the impact of the environmental stimuli in the use of open spaces and intend to develop design strategies that aim to maximise the use of open spaces in different weather conditions.

Strengthening value chains as an industrial policy instrument. Methodology and experience of ECLAC in Central America

Foreword by Alicia Bárcena.

Análise de um regulador de velocidade digital para a Usina Hidroelétrica de Curuá-Una

Analisa uma proposta de um controlador digital para o regulador de velocidade da Usina Hidroelétrica de Curuá-Una, utilizando duas estratégias de projeto, a estratégia indireta com o projeto do controlador sendo feito no plano contínuo e depois discretizado e a estratégia direta, em que o controlador é projetado inteiramente no plano discreto. O conhecimento gerado no simulador é de grande importância, pois é uma das grandes ferramentas para avaliar o comportamento dos controladores digitais propostos, em ambiente seguro. O estudo dos controladores também permite uma substituição de equipamentos antigos, com produção descontinuada, por equipamentos novos que permitem a confecção de controladores modernos, digitais e inteligentes, que proporcionam uma substituição de técnicas antigas de controle por estratégias avançadas de controle, maximizando o rendimento do sistema em condições adversas de operação. O trabalho levanta as diferenças, vantagens e desvantagens de cada controlador, com o objetivo de auxiliar na escolha do controlador mais adequado para projetos de controladores avançados: tipo um controle adaptativo, controle fuzzy ou controle neural. As dificuldades de projeto e os resultados das simulações foram os principais indicadores na avaliações dos dois RV digitais projetados. De uma forma geral o RV digital direto apresentou melhor desempenho, estabilidade e menor esforço computacional, entretanto, o RV digital indireto mostrou desempenho similar, menor degradação devido às não linearidades e ao menor esforço de projeto.

Pesquisa epidemiológica e molecular do vírus respiratório sincicial humano (VSRH) em amostras de pacientes hospitalizados com pneumonia, na cidade de Belém

A pneumonia e a bronquiolite na infância são as principais causas de morbidade e mortalidade no mundo, sendo o Vírus Respiratório Sincicial Humano (VSRH) o principal agente viral. O VSRH está associado a surtos anuais de doenças respiratórias, onde a co-infecção bacteriana tem sido relatada. Este foi o primeiro estudo do VRSH em crianças hospitalizadas com Pneumonia Adquirida na Comunidade (PAC) em Belém, Pará (Norte do Brasil), que teve como objetivo determinar a prevalência da infecção pelo VSRH e avaliar as características clínicas e epidemiológicas dos pacientes. Métodos. Foi realizado um estudo prospectivo em oito hospitais no período de novembro de 2006 a outubro de 2007. Foram testadas 1.050 amostras de aspirado nasofaríngeo para o VRSH, obtidas de crianças hospitalizadas com até três anos de idade com diagnóstico de PAC, pelo método da imunofluorescência direta e da reação em cadeia por polimerase após transcrição reversa (RT-PCR) para identificação do subtipo viral. Foram obtidos resultados da dosagem de proteína C-reativa (PCR) e da cultura bacteriana. Resultados. A infecção pelo VSRH foi diagnosticada em 243 (23,1%) crianças. A idade média do grupo VRSH-positivo foi menor do que a do grupo VRSH-negativo (12,1 meses versus (vs) 15,5 meses, ambos com variância de 1-36 meses, p<0,001), enquanto que a distribuição por genero foi similar. O grupo VRSH-positivo apresentou menor dosagem (PCR) quando comparados ao grupo VRSH-negativo (15,3 vs 24.0 mg/dL, p<0,05). Os achados radiológicos confirmaram que 54,2% do grupo VRSH-positivo e 50,3% do grupo VRSH-negativo apresentavam infiltrado intersticial. A infecção bacteriana foi identificada predominantemente no grupo VRSH-positivo (10% vs 4,5%, p<0,05). Rinorréia e obstrução nasal foram predominantemente observadas no grupo VRSH-positivo. A co-circulação dos subtipos A e B foi observada, com predominância do subtipo B (209/227). A análise multivariada revelou que a idade de 1 ano (p<0,015), os níveis de PCR inferior a 48 mg/dL (p<0,001) e a co-infecção bacteriana (p<0,032) foram independentemente associados com a presença do VRSH em oposição ao grupo VRSH-negativo, e na análise dos sintomas, a obstrução nasal foi independentemente associada com o grupo VRSH-positivo (p<0,001). Conclusão. O presente estudo destaca a relevância da infecção por VSRH em casos hospitalizados de PAC em nossa região; nossos resultados justificam a realização de investigações adicionais que possam ajudar a elaborar estratégias para o controle da doença.

Polymeric micelles and molecular modeling applied to the development of radiopharmaceuticals

Micelles composed of amphiphilic copolymers linked to a radioactive element are used in nuclear medicine predominantly as a diagnostic application. A relevant advantage of polymeric micelles in aqueous solution is their resulting particle size, which can vary from 10 to 100 nm in diameter. In this review, polymeric micelles labeled with radioisotopes including technetium (99mTc) and indium (111In), and their clinical applications for several diagnostic techniques, such as single photon emission computed tomography (SPECT), gamma-scintigraphy, and nuclear magnetic resonance (NMR), were discussed. Also, micelle use primarily for the diagnosis of lymphatic ducts and sentinel lymph nodes received special attention. Notably, the employment of these diagnostic techniques can be considered a significant tool for functionally exploring body systems as well as investigating molecular pathways involved in the disease process. The use of molecular modeling methodologies and computer-aided drug design strategies can also yield valuable information for the rational design and development of novel radiopharmaceuticals.

A parallel community detection algorithm

Complex networks analysis is a very popular topic in computer science. Unfortunately this networks, extracted from different contexts, are usually very large and the analysis may be very complicated: computation of metrics on these structures could be very complex. Among all metrics we analyse the extraction of subnetworks called communities: they are groups of nodes that probably play the same role within the whole structure. Communities extraction is an interesting operation in many different fields (biology, economics,...). In this work we present a parallel community detection algorithm that can operate on networks with huge number of nodes and edges. After an introduction to graph theory and high performance computing, we will explain our design strategies and our implementation. Then, we will show some performance evaluation made on a distributed memory architectures i.e. the supercomputer IBM-BlueGene/Q "Fermi" at the CINECA supercomputing center, Italy, and we will comment our results.

Life cycle assessment in construction field: A life cycle cost analysis of reinforcement concrete bridge

The present work is included in the context of the assessment of sustainability in the construction field and is aimed at estimating and analyzing life cycle cost of the existing reinforced concrete bridge “Viadotto delle Capre” during its entire life. This was accomplished by a comprehensive data collection and results evaluation. In detail, the economic analysis of the project is performed. The work has investigated possible design alternatives for maintenance/rehabilitation and end-of-life operations, when structural, functional, economic and also environmental requirements have to be fulfilled. In detail, the economic impact of different design options for the given reinforced concrete bridge have been assessed, whereupon the most economically, structurally and environmentally efficient scenario was chosen. The Integrated Life-Cycle Analysis procedure and Environmental Impact Assessment were also discussed in this work. The scope of this thesis is to illustrate that Life Cycle Cost analysis as part of Life Cycle Assessment approach could be effectively used to drive the design and management strategy of new and existing structures. The final objective of this contribution is to show how an economic analysis can influence decision-making in the definition of the most sustainable design alternatives. The designers can monitor the economic impact of different design strategies in order to identify the most appropriate option.