Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

An analysis of UK policies for domestic energy reduction using an agent based tool

This paper introduces a new agent-based model, which incorporates the actions of individual homeowners in a long-term domestic stock model, and details how it was applied in energy policy analysis. The results indicate that current policies are likely to fall significantly short of the 80% target and suggest that current subsidy levels need re-examining. In the model, current subsidy levels appear to offer too much support to some technologies, which in turn leads to the suppression of other technologies that have a greater energy saving potential. The model can be used by policy makers to develop further scenarios to find alternative, more effective, sets of policy measures. The model is currently limited to the owner-occupied stock in England, although it can be expanded, subject to the availability of data.

Effects of noise and by-catch on a Danish harbour porpoise population

Ships and wind turbines generate noise, which can have a negative impact on marine mammal populations by scaring animals away. Effective modelling of how this affects the populations has to take account of the location and timing of disturbances. Here we construct an individual-based model of harbour porpoises in the Inner Danish Waters. Individuals have their own energy budgets constructed using established principles of physiological ecology. Data are lacking on the spatial distribution of food which is instead inferred from knowledge of time-varying porpoise distributions. The model produces plausible patterns of population dynamics and matches well the age distribution of porpoises caught in by-catch. It estimates the effect of existing wind farms as a 10% reduction in population size when food recovers fast (after two days). Proposed new wind farms and ships do not result in further population declines. The population is however sensitive to variations in mortality resulting from by-catch and to the speed at which food recovers after being depleted. If food recovers slowly the effect of wind turbines becomes negligible, whereas ships are estimated to have a significant negative impact on the population. Annual by-catch rates ≥10% lead to monotonously decreasing populations and to extinction, and even the estimated by-catch rate from the adjacent area (approximately 4.1%) has a strong impact on the population. This suggests that conservation efforts should be more focused on reducing by-catch in commercial gillnet fisheries than on limiting the amount of anthropogenic noise. Individual-based models are unique in their ability to take account of the location and timing of disturbances and to show their likely effects on populations. The models also identify deficiencies in the existing database and can be used to set priorities for future field research.

Processes controlling atmospheric dispersion through city centres

We develop a process-based model for the dispersion of a passive scalar in the turbulent flow around the buildings of a city centre. The street network model is based on dividing the airspace of the streets and intersections into boxes, within which the turbulence renders the air well mixed. Mean flow advection through the network of street and intersection boxes then mediates further lateral dispersion. At the same time turbulent mixing in the vertical detrains scalar from the streets and intersections into the turbulent boundary layer above the buildings. When the geometry is regular, the street network model has an analytical solution that describes the variation in concentration in a near-field downwind of a single source, where the majority of scalar lies below roof level. The power of the analytical solution is that it demonstrates how the concentration is determined by only three parameters. The plume direction parameter describes the branching of scalar at the street intersections and hence determines the direction of the plume centreline, which may be very different from the above-roof wind direction. The transmission parameter determines the distance travelled before the majority of scalar is detrained into the atmospheric boundary layer above roof level and conventional atmospheric turbulence takes over as the dominant mixing process. Finally, a normalised source strength multiplies this pattern of concentration. This analytical solution converges to a Gaussian plume after a large number of intersections have been traversed, providing theoretical justification for previous studies that have developed empirical fits to Gaussian plume models. The analytical solution is shown to compare well with very high-resolution simulations and with wind tunnel experiments, although re-entrainment of scalar previously detrained into the boundary layer above roofs, which is not accounted for in the analytical solution, is shown to become an important process further downwind from the source.

Using mobile devices to enhance undergraduate field research

Mobile devices can enhance undergraduate research projects and students’ research capabilities. The use of mobile devices such as tablet computers will not automatically make undergraduates better researchers, but their use should make investigations, writing, and publishing more effective and may even save students time. We have explored some of the possibilities of using “tablets” and “smartphones” to aid the research and inquiry process in geography and bioscience fieldwork. We provide two case studies as illustration of how students working in small research groups use mobile devices to gather and analyze primary data in field-based inquiry. Since April 2010, Apple’s iPad has changed the way people behave in the digital world and how they access their music, watch videos, or read their email much as the entrepreneurs Steve Jobs and Jonathan Ive intended. Now with “apps” and “the cloud” and the ubiquitous references to them appearing in the press and on TV, academics’ use of tablets is also having an impact on education and research. In our discussion we will refer to use of smartphones such as the iPhone, iPod, and Android devices under the term “tablet”. Android and Microsoft devices may not offer the same facilities as the iPad/iphone, but many app producers now provide versions for several operating systems. Smartphones are becoming more affordable and ubiquitous (Melhuish and Falloon 2010), but a recent study of undergraduate students (Woodcock et al. 2012, 1) found that many students who own smartphones are “largely unaware of their potential to support learning”. Importantly, however, students were found to be “interested in and open to the potential as they become familiar with the possibilities” (Woodcock et al. 2012). Smartphones and iPads could be better utilized than laptops when conducting research in the field because of their portability (Welsh and France 2012). It is imperative for faculty to provide their students with opportunities to discover and employ the potential uses of mobile devices in their learning. However, it is not only the convenience of the iPad or tablet devices or smartphones we wish to promote, but also a way of thinking and behaving digitally. We essentially suggest that making a tablet the center of research increases the connections between related research activities.

Leaf trapping and retention of particles by holm oak and other common tree species in Mediterranean urban environments

Holm oak (Quercus ilex), a widespread urban street tree in the Mediterranean region, is widely used as biomonitor of persistent atmospheric pollutants, especially particulate-bound metals. By using lab- and field-based experimental approaches, we compared the leaf-level capacity for particles’ capture and retention between Q. ilex and other common Mediterranean urban trees: Quercus cerris, Platanus × hispanica, Tilia cordata and Olea europaea. All applied methods were effective in quantifying particulate capture and retention, although not univocal in ranking species performances. Distinctive morphological features of leaves led to differences in species’ ability to trap and retain particles of different size classes and to accumulate metals after exposure to traffic in an urban street. Overall, P. × hispanica and T. cordata showed the largest capture potential per unit leaf area for most model particles (Na+ and powder particles), and street-level Cu and Pb, while Q. ilex acted intermediately. After wash-off experiments, P. × hispanica leaves had the greatest retention capacity among the tested species and O. europaea the lowest. We concluded that the Platanus planting could be considered in Mediterranean urban environments due to its efficiency in accumulating and retaining airborne particulates; however, with atmospheric pollution being typically higher in winter, the evergreen Q. ilex represents a better year-round choice to mitigate the impact of airborne particulate pollutants.

On the Casimir energy for a massive quantum scalar field and the cosmological constant

We present a rigorous, regularization-independent local quantum field theoretic treatment of the Casimir effect for a quantum scalar field of mass mu not equal 0 which yields closed form expressions for the energy density and pressure. As an application we show that there exist special states of the quantum field in which the expectation value of the renormalized energy-momentum tensor is, for any fixed time, independent of the space coordinate and of the perfect fluid form g(mu,nu)rho with rho > 0, thus providing a concrete quantum field theoretic model of the cosmological constant. This rho represents the energy density associated to a state consisting of the vacuum and a certain number of excitations of zero momentum, i.e., the constituents correspond to lowest energy and pressure p <= 0. (C) 2009 Elsevier Inc. All rights reserved.

Spacetime noncommutativity with a bifermionic parameter

We consider a Moyal plane and propose to make the noncommutativity parameter Theta(mu nu) bifermionic, i.e. composed of two fermionic (Grassmann odd) parameters. The Moyal product then contains a finite number of derivatives, which avoid the difficulties of the standard approach. As an example, we construct a two-dimensional noncommutative field theory model based on the Moyal product with a bifermionic parameter and show that it has a locally conserved energy-momentum tensor. The model has no problem with the canonical quantization and appears to be renormalizable.

Three-dimensional, fully adaptive simulations of phase-field fluid models

We present an efficient numerical methodology for the 31) computation of incompressible multi-phase flows described by conservative phase-field models We focus here on the case of density matched fluids with different viscosity (Model H) The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow`s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin-Helmholtz instability, and flow-induced drop coalescence (C) 2010 Elsevier Inc. All rights reserved

A simplified heat pump model for use in solar plus heat pump system simulation studies

Solar plus heat pump systems are often very complex in design, with sometimes special heat pump arrangements and control. Therefore detailed heat pump models can give very slow system simulations and still not so accurate results compared to real heat pump performance in a system. The idea here is to start from a standard measured performance map of test points for a heat pump according to EN 14825 and then determine characteristic parameters for a simplified correlation based model of the heat pump. By plotting heat pump test data in different ways including power input and output form and not only as COP, a simplified relation could be seen. By using the same methodology as in the EN 12975 QDT part in the collector test standard it could be shown that a very simple model could describe the heat pump test data very accurately, by identifying 4 parameters in the correlation equation found. © 2012 The Authors.

In search of exchange rate predictability : a study about accuracy, consistency, and granger causality of forecasts generated by a Taylor Rule Model

Este estudo investiga o poder preditivo fora da amostra, um mês à frente, de um modelo baseado na regra de Taylor para previsão de taxas de câmbio. Revisamos trabalhos relevantes que concluem que modelos macroeconômicos podem explicar a taxa de câmbio de curto prazo. Também apresentamos estudos que são céticos em relação à capacidade de variáveis macroeconômicas preverem as variações cambiais. Para contribuir com o tema, este trabalho apresenta sua própria evidência através da implementação do modelo que demonstrou o melhor resultado preditivo descrito por Molodtsova e Papell (2009), o “symmetric Taylor rule model with heterogeneous coefficients, smoothing, and a constant”. Para isso, utilizamos uma amostra de 14 moedas em relação ao dólar norte-americano que permitiu a geração de previsões mensais fora da amostra de janeiro de 2000 até março de 2014. Assim como o critério adotado por Galimberti e Moura (2012), focamos em países que adotaram o regime de câmbio flutuante e metas de inflação, porém escolhemos moedas de países desenvolvidos e em desenvolvimento. Os resultados da nossa pesquisa corroboram o estudo de Rogoff e Stavrakeva (2008), ao constatar que a conclusão da previsibilidade da taxa de câmbio depende do teste estatístico adotado, sendo necessária a adoção de testes robustos e rigorosos para adequada avaliação do modelo. Após constatar não ser possível afirmar que o modelo implementado provém previsões mais precisas do que as de um passeio aleatório, avaliamos se, pelo menos, o modelo é capaz de gerar previsões “racionais”, ou “consistentes”. Para isso, usamos o arcabouço teórico e instrumental definido e implementado por Cheung e Chinn (1998) e concluímos que as previsões oriundas do modelo de regra de Taylor são “inconsistentes”. Finalmente, realizamos testes de causalidade de Granger com o intuito de verificar se os valores defasados dos retornos previstos pelo modelo estrutural explicam os valores contemporâneos observados. Apuramos que o modelo fundamental é incapaz de antecipar os retornos realizados.

Problematizando a Reforma Psiquiátrica na atualidade: a saúde mental como campo da práxis

Mental Health, in the form of the Psychiatric Reform, and the Anti-Asylum Movement do not ignore the production of knowledge about that field, mainly due to the consolidation of Public Health as a field of knowledge. The article explores some authors who consider Mental Health as a new field of knowledge, introducing a new paradigm in the perception of health - Disease and Care -; however, the goal is to introduce Psychosocial Care as a means to enforce the transdisciplinary and multiprofessional practices. The possibility is that mental health produces developments in Health, consolidating the public policies. In practice, the hospital-centered and drug-based model still predominates, and there are setbacks to be overcome by taking advantage of loopholes capable of breaking with what is instituted.

Extração automática de contornos de telhados usando dados de varredura a laser e campos randômicos de Markov

This paper proposes a methodology for automatic extraction of building roof contours from a Digital Elevation Model (DEM), which is generated through the regularization of an available laser point cloud. The methodology is based on two steps. First, in order to detect high objects (buildings, trees etc.), the DEM is segmented through a recursive splitting technique and a Bayesian merging technique. The recursive splitting technique uses the quadtree structure for subdividing the DEM into homogeneous regions. In order to minimize the fragmentation, which is commonly observed in the results of the recursive splitting segmentation, a region merging technique based on the Bayesian framework is applied to the previously segmented data. The high object polygons are extracted by using vectorization and polygonization techniques. Second, the building roof contours are identified among all high objects extracted previously. Taking into account some roof properties and some feature measurements (e. g., area, rectangularity, and angles between principal axes of the roofs), an energy function was developed based on the Markov Random Field (MRF) model. The solution of this function is a polygon set corresponding to building roof contours and is found by using a minimization technique, like the Simulated Annealing (SA) algorithm. Experiments carried out with laser scanning DEM's showed that the methodology works properly, as it delivered roof contours with approximately 90% shape accuracy and no false positive was verified.

Processos cognitivos que operam na configuração de narrativas: uma pesquisa exploratória dos fenômenos que subjazem à compreensão de textos

This paper investigates the cognitive processes that operate in understanding narratives in this case, the novel Macunaíma, by Mário de Andrade. Our work belongs to the field of Embodied-based Cognitive Linguistics and, due to its interdisciplinary nature, it dialogues with theoretical and methodological frameworks of Psycholinguistics, Cognitive Psychology and Neurosciences. Therefore, we adopt an exploratory research design, recall and cloze tests, adapted, with postgraduation students, all native speakers of Brazilian Portuguese. The choice of Macunaíma as the novel and initial motivation for this proposal is due to the fact it is a fantastic narrative, which consists of events, circumstances and characters that are clearly distant types from what is experienced in everyday life. Thus, the novel provides adequate data to investigate the configuration of meaning, within an understanding-based model. We, therefore, seek, to answer questions that are still, generally, scarcely explored in the field of Cognitive Linguistics, such as to what extent is the activation of mental models (schemas and frames) related to the process of understanding narratives? How are we able to build sense even when words or phrases are not part of our linguistic repertoire? Why do we get emotionally involved when reading a text, even though it is fiction? To answer them, we assume the theoretical stance that meaning is not in the text, it is constructed through language, conceived as a result of the integration between the biological (which results in creating abstract imagery schemes) and the sociocultural (resulting in creating frames) apparatus. In this sense, perception, cognitive processing, reception and transmission of the information described are directly related to how language comprehension occurs. We believe that the results found in our study may contribute to the cognitive studies of language and to the development of language learning and teaching methodologies

A Markovian model market-Akerlof's lemons and the asymmetry of information

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)