A multi-GPU algorithm for large-scale neuronal networks

Large-scale simulations of parts of the brain using detailed neuronal models to improve our understanding of brain functions are becoming a reality with the usage of supercomputers and large clusters. However, the high acquisition and maintenance cost of these computers, including the physical space, air conditioning, and electrical power, limits the number of simulations of this kind that scientists can perform. Modern commodity graphical cards, based on the CUDA platform, contain graphical processing units (GPUs) composed of hundreds of processors that can simultaneously execute thousands of threads and thus constitute a low-cost solution for many high-performance computing applications. In this work, we present a CUDA algorithm that enables the execution, on multiple GPUs, of simulations of large-scale networks composed of biologically realistic Hodgkin-Huxley neurons. The algorithm represents each neuron as a CUDA thread, which solves the set of coupled differential equations that model each neuron. Communication among neurons located in different GPUs is coordinated by the CPU. We obtained speedups of 40 for the simulation of 200k neurons that received random external input and speedups of 9 for a network with 200k neurons and 20M neuronal connections, in a single computer with two graphic boards with two GPUs each, when compared with a modern quad-core CPU. Copyright (C) 2010 John Wiley & Sons, Ltd.

Bayesian Estimation of the Logistic Positive Exponent IRT Model

A Bayesian inference approach using Markov Chain Monte Carlo (MCMC) is developed for the logistic positive exponent (LPE) model proposed by Samejima and for a new skewed Logistic Item Response Theory (IRT) model, named Reflection LPE model. Both models lead to asymmetric item characteristic curves (ICC) and can be appropriate because a symmetric ICC treats both correct and incorrect answers symmetrically, which results in a logical contradiction in ordering examinees on the ability scale. A data set corresponding to a mathematical test applied in Peruvian public schools is analyzed, where comparisons with other parametric IRT models also are conducted. Several model comparison criteria are discussed and implemented. The main conclusion is that the LPE and RLPE IRT models are easy to implement and seem to provide the best fit to the data set considered.

Multivariate measurement error models based on scale mixtures of the skew-normal distribution

Scale mixtures of the skew-normal (SMSN) distribution is a class of asymmetric thick-tailed distributions that includes the skew-normal (SN) distribution as a special case. The main advantage of these classes of distributions is that they are easy to simulate and have a nice hierarchical representation facilitating easy implementation of the expectation-maximization algorithm for the maximum-likelihood estimation. In this paper, we assume an SMSN distribution for the unobserved value of the covariates and a symmetric scale mixtures of the normal distribution for the error term of the model. This provides a robust alternative to parameter estimation in multivariate measurement error models. Specific distributions examined include univariate and multivariate versions of the SN, skew-t, skew-slash and skew-contaminated normal distributions. The results and methods are applied to a real data set.

Cellular automaton model for molecular traffic jams

We consider the time evolution of an exactly solvable cellular automaton with random initial conditions both in the large-scale hydrodynamic limit and on the microscopic level. This model is a version of the totally asymmetric simple exclusion process with sublattice parallel update and thus may serve as a model for studying traffic jams in systems of self-driven particles. We study the emergence of shocks from the microscopic dynamics of the model. In particular, we introduce shock measures whose time evolution we can compute explicitly, both in the thermodynamic limit and for open boundaries where a boundary-induced phase transition driven by the motion of a shock occurs. The motion of the shock, which results from the collective dynamics of the exclusion particles, is a random walk with an internal degree of freedom that determines the jump direction. This type of hopping dynamics is reminiscent of some transport phenomena in biological systems.

On estimation and influence diagnostics for the Grubbs` model under heavy-tailed distributions

The Grubbs` measurement model is frequently used to compare several measuring devices. It is common to assume that the random terms have a normal distribution. However, such assumption makes the inference vulnerable to outlying observations, whereas scale mixtures of normal distributions have been an interesting alternative to produce robust estimates, keeping the elegancy and simplicity of the maximum likelihood theory. The aim of this paper is to develop an EM-type algorithm for the parameter estimation, and to use the local influence method to assess the robustness aspects of these parameter estimates under some usual perturbation schemes, In order to identify outliers and to criticize the model building we use the local influence procedure in a Study to compare the precision of several thermocouples. (C) 2008 Elsevier B.V. All rights reserved.

A pharmacokinetic-pharmacodynamic model for duodenal levodopa infusion

Objective Levodopa in presence of decarboxylase inhibitors is following two-compartment kinetics and its effect is typically modelled using sigmoid Emax models. Pharmacokinetic modelling of the absorption phase of oral distributions is problematic because of irregular gastric emptying. The purpose of this work was to identify and estimate a population pharmacokinetic- pharmacodynamic model for duodenal infusion of levodopa/carbidopa (Duodopa®) that can be used for in numero simulation of treatment strategies. Methods The modelling involved pooling data from two studies and fixing some parameters to values found in literature (Chan et al. J Pharmacokinet Pharmacodyn. 2005 Aug;32(3-4):307-31). The first study involved 12 patients on 3 occasions and is described in Nyholm et al. Clinical Neuropharmacology 2003:26:156-63. The second study, PEDAL, involved 3 patients on 2 occasions. A bolus dose (normal morning dose plus 50%) was given after a washout during night. Plasma samples and motor ratings (clinical assessment of motor function from video recordings on a treatment response scale between -3 and 3, where -3 represents severe parkinsonism and 3 represents severe dyskinesia.) were repeatedly collected until the clinical effect was back at baseline. At this point, the usual infusion rate was started and sampling continued for another two hours. Different structural absorption models and effect models were evaluated using the value of the objective function in the NONMEM package. Population mean parameter values, standard error of estimates (SE) and if possible, interindividual/interoccasion variability (IIV/IOV) were estimated. Results Our results indicate that Duodopa absorption can be modelled with an absorption compartment with an added bioavailability fraction and a lag time. The most successful effect model was of sigmoid Emax type with a steep Hill coefficient and an effect compartment delay. Estimated parameter values are presented in the table. Conclusions The absorption and effect models were reasonably successful in fitting observed data and can be used in simulation experiments.

Uncertainties In Future Projections Of Extreme Rainfall: The Role Of Climate Model, Emission Scenario And Randomness

Climate change has resulted in substantial variations in annual extreme rainfall quantiles in different durations and return periods. Predicting the future changes in extreme rainfall quantiles is essential for various water resources design, assessment, and decision making purposes. Current Predictions of future rainfall extremes, however, exhibit large uncertainties. According to extreme value theory, rainfall extremes are rather random variables, with changing distributions around different return periods; therefore there are uncertainties even under current climate conditions. Regarding future condition, our large-scale knowledge is obtained using global climate models, forced with certain emission scenarios. There are widely known deficiencies with climate models, particularly with respect to precipitation projections. There is also recognition of the limitations of emission scenarios in representing the future global change. Apart from these large-scale uncertainties, the downscaling methods also add uncertainty into estimates of future extreme rainfall when they convert the larger-scale projections into local scale. The aim of this research is to address these uncertainties in future projections of extreme rainfall of different durations and return periods. We plugged 3 emission scenarios with 2 global climate models and used LARS-WG, a well-known weather generator, to stochastically downscale daily climate models’ projections for the city of Saskatoon, Canada, by 2100. The downscaled projections were further disaggregated into hourly resolution using our new stochastic and non-parametric rainfall disaggregator. The extreme rainfall quantiles can be consequently identified for different durations (1-hour, 2-hour, 4-hour, 6-hour, 12-hour, 18-hour and 24-hour) and return periods (2-year, 10-year, 25-year, 50-year, 100-year) using Generalized Extreme Value (GEV) distribution. By providing multiple realizations of future rainfall, we attempt to measure the extent of total predictive uncertainty, which is contributed by climate models, emission scenarios, and downscaling/disaggregation procedures. The results show different proportions of these contributors in different durations and return periods.

Software Tools For Large Scale Interactive Hydrodynamic Modeling

Running hydrodynamic models interactively allows both visual exploration and change of model state during simulation. One of the main characteristics of an interactive model is that it should provide immediate feedback to the user, for example respond to changes in model state or view settings. For this reason, such features are usually only available for models with a relatively small number of computational cells, which are used mainly for demonstration and educational purposes. It would be useful if interactive modeling would also work for models typically used in consultancy projects involving large scale simulations. This results in a number of technical challenges related to the combination of the model itself and the visualisation tools (scalability, implementation of an appropriate API for control and access to the internal state). While model parallelisation is increasingly addressed by the environmental modeling community, little effort has been spent on developing a high-performance interactive environment. What can we learn from other high-end visualisation domains such as 3D animation, gaming, virtual globes (Autodesk 3ds Max, Second Life, Google Earth) that also focus on efficient interaction with 3D environments? In these domains high efficiency is usually achieved by the use of computer graphics algorithms such as surface simplification depending on current view, distance to objects, and efficient caching of the aggregated representation of object meshes. We investigate how these algorithms can be re-used in the context of interactive hydrodynamic modeling without significant changes to the model code and allowing model operation on both multi-core CPU personal computers and high-performance computer clusters.

Model Prediction Control For Water Management Using Adaptive Prediction Accuracy

In the field of operational water management, Model Predictive Control (MPC) has gained popularity owing to its versatility and flexibility. The MPC controller, which takes predictions, time delay and uncertainties into account, can be designed for multi-objective management problems and for large-scale systems. Nonetheless, a critical obstacle, which needs to be overcome in MPC, is the large computational burden when a large-scale system is considered or a long prediction horizon is involved. In order to solve this problem, we use an adaptive prediction accuracy (APA) approach that can reduce the computational burden almost by half. The proposed MPC scheme with this scheme is tested on the northern Dutch water system, which comprises Lake IJssel, Lake Marker, the River IJssel and the North Sea Canal. The simulation results show that by using the MPC-APA scheme, the computational time can be reduced to a large extent and a flood protection problem over longer prediction horizons can be well solved.

Share bidding auctions, sliding scale royalty rates and the new brazilian regulatory framework for the pre-salt areas

O governo brasileiro recentemente aprovou uma legislação instituindo um novo marco regulatório para as reservas petrolíferas do pré-sal. Segundo as novas regras, estas áreas deverão ser licitadas mediante um leilão de partilha de lucro. Motivado por esta mudança, apresentamos um modelo de leilão de partilha sob afiliação, demonstrando a existência de um equilíbrio monótono em estratégias puras e caracterizando a solução. Alem disso, provamos que este mecanismo gera receita esperada maior ou igual a um leilão de primeiro preço usual. Em seguida, introduzimos no modelo uma função representando taxas de royalties que dependem do valor do objeto. Este instrumento permite uma elevação na receita esperada de ambos os modelos, fazendo com que a diferença entre eles encolha. Finalmente, analisando o novo marco regulatório sob o ponto de vista dos resultados obtidos, concluímos que o antigo modelo de concessão utilizado pelo governo brasileiro é mais adequado e lucrativo.

Mhealth entrepreneurship: an exploratory research for a managerial model for mhealth start ups in low and middle income countries

Since some years, mobile technologies in healthcare (mHealth) stand for the transformational force to improve health issues in low- and middle-income countries (LMICs). Although several studies have identified the prevailing issue of inconsistent evidence and new evaluation frameworks have been proposed, few have explored the role of entrepreneurship to create disruptive change in a traditionally conservative sector. I argue that improving the effectiveness of mHealth entrepreneurs might increase the adoption of mHealth solutions. Thus, this study aims at proposing a managerial model for the analysis of mHealth solutions from the entrepreneurial perspective in the context of LMICs. I identified the Khoja–Durrani–Scott (KDS) framework as theoretical basis for the managerial model, due to its explicit focus on the context of LMICs. In the subsequent exploratory research I, first, used semi-structured interviews with five specialists in mHealth, local healthcare systems and investment to identify necessary adaptations to the model. The findings of the interviews proposed that especially the economic theme had to be clarified and an additional entrepreneurial theme was necessary. Additionally, an evaluation questionnaire was proposed. In the second phase, I applied the questionnaire to five start-ups, operating in Brazil and Tanzania, and conducted semi-structured interviews with the entrepreneurs to gain practical insights for the theoretical development. Three of five entrepreneurs perceived that the results correlated with the entrepreneurs' expectations of the strengths and weaknesses of the start-ups. Main shortcomings of the model related to the ambiguity of some questions. In addition to the findings for the model, the results of the scores were analyzed. The analysis suggested that across the participating mHealth start-ups the ‘behavioral and socio-technical’ outcomes were the strongest and the ‘policy’ outcomes were the weakest themes. The managerial model integrates several perspectives, structured around the entrepreneur. In order to validate the model, future research may link the development of a start-up with the evolution of the scores in longitudinal case studies or large-scale tests.

Calculable lepton masses, seesaw relations, and four neutrino mixings in a 3-3-1 model with an extra U(1) symmetry

We propose a scheme in which the masses of the heavier leptons obey seesaw type relations. The light lepton masses, except the electron and the electron neutrino ones, are generated by one loop level radiative corrections. We work in a version of the 3-3-1 electroweak model that predicts singlets (charged and neutral) of heavy leptons beyond the known ones. An extra U(1)(Omega) symmetry is introduced in order to avoid the light leptons getting masses at the tree level. The electron mass induces an explicit symmetry breaking at U(1)(Omega). We discuss also the mixing matrix among four neutrinos. The new energy scale required is not higher than a few TeV.

Training on synthetic ethylene-vinyl acetate bench model allows novice medical students to acquire suture skills

PURPOSE: To assess the acquisition of suture skills by training on ethylene-vinyl acetate bench model in novice medical students.METHODS: Sixteen medical students without previous surgery experience (novices) were randomly divided into two groups. During one hour group A trained sutures on ethylene-vinyl acetate (EVA) bench model with feedback of instructors, while group B (control) received a faculty-directed training based on books and instructional videos. All students underwent a both pre-and post-tests to perform two-and three-dimensional sutures on ox tongue. All recorded performances were evaluated by two blinded evaluators, using the Global Rating Scale.RESULTS: Although both groups have had a better performance (p<0.05) in the post-test when compared with the pre-test, the analysis of post-test showed that group A (EVA) had a better performance (p<0.05) when compared with group B (control).CONCLUSION: The ethylene vinyl acetate bench model allowed the novice students to acquire suture skills faster when compared to the traditional model of teaching.

Does bench model fidelity interfere in the acquisition of suture skills by novice medical students?

OBJETIVO: Embora vários modelos de bancada inanimados tenham sido descritos para o treinamento de habilidades de sutura, até o momento, não existe um método ideal para esse ensino e aprendizagem durante a formação médica. O objetivo foi avaliar se a fidelidade dos modelos de bancada interfere na aquisição de habilidades de sutura em estudantes de medicina iniciantes na prática cirúrgica. MÉTODOS: 36 estudantes de medicina sem exposição prévia a habilidades cirúrgicas foram randomizados em três grupos (n = 12): treinamento de suturas baseado em materiais didáticos (controle); treinamento de suturas em modelo de baixa-fidelidade (modelo de bancada de etileno vinil acetato); ou treinamento de suturas em modelo de alta-fidelidade (modelo de bancada de pele de pata de porco). Foram aplicados pré e pós-testes (realização de pontos simples e pontos subdérmicos invertidos em língua de boi). Três ferramentas (Global Rating Scale com avaliação cega, tamanho do efeito e autopercepção da confiança baseada em uma escala de Likert) foram utilizadas para mensurar todas as performances de sutura. RESULTADOS: A análise após o treinamento demonstrou que os estudantes que treinaram nos modelos tiveram um melhor (p < 0.0000) desempenho na avaliação pela Global Rating Scale, quando comparados com o controle, independente da fidelidade do modelo. A magnitude do efeito (treinamento) foi considerada grande (> 0.80) em todas as mensurações. Após o treinamento os alunos sentiram-se mais confiantes (p < 0.0000) para executarem os dois tipos de suturas. CONCLUSÃO: A aquisição de habilidades de suturas no modelo de baixa fidelidade foi semelhante à prática no modelo de alta fidelidade, sendo que a melhora no desempenho dos participantes que treinaram nesses dois modelos foi superior à aprendizagem baseada em materiais didáticos.

Are large-scale distributional shifts of the blue-winged macaw (Primolius maracana) related to climate change?

Aim To evaluate whether observed geographical shifts in the distribution of the blue-winged macaw (Primolius maracana) are related to ongoing processes of global climate change. This species is vulnerable to extinction and has shown striking range retractions in recent decades, withdrawing broadly from southern portions of its historical distribution. Its range reduction has generally been attributed to the effects of habitat loss; however, as this species has also disappeared from large forested areas, consideration of other factors that may act in concert is merited.Location Historical distribution of the blue-winged macaw in Brazil, eastern Paraguay and northern Argentina.Methods We used a correlative approach to test a hypothesis of causation of observed shifts by reduction of habitable areas mediated by climate change. We developed models of the ecological niche requirements of the blue-winged macaw, based on point-occurrence data and climate scenarios for pre-1950 and post-1950 periods, and tested model predictivity for anticipating geographical distributions within time periods. Then we projected each model to the other time period and compared distributions predicted under both climate scenarios to assess shifts of habitable areas across decades and to evaluate an explanation for observed range retractions.Results Differences between predicted distributions of the blue-winged macaw over the twentieth century were, in general, minor and no change in suitability of landscapes was predicted across large areas of the species' original range in different time periods. No tendency towards range retraction in the south was predicted, rather conditions in the southern part of the species' range tended to show improvement for the species.Main conclusions Our test permitted elimination of climate change as a likely explanation for the observed shifts in the distribution of the blue-winged macaw, and points rather to other causal explanations (e.g. changing regional land use, emerging diseases).