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.

Single-mode acceleration of matter waves in circular waveguides

Ultracold gases in ring geometries hold promise for significant improvements of gyroscopic sensitivity. Recent experiments have realized atomic and molecular storage rings with radii in the centimeter range, sizes whose practical use in inertial sensors requires velocities significantly in excess of typical recoil velocities. We use a combination of analytical and numerical techniques to study the coherent acceleration of matter waves in circular waveguides, with particular emphasis on its impact on single-mode propagation. In the simplest case we find that single-mode propagation is best maintained by the application of time-dependent acceleration force with the temporal profile of a Blackmann pulse. We also assess the impact of classical noise on the acceleration process.

Visualização interativa e manipulação de imagens 3D em tempo real usando métodos baseados na GPU

Este trabalho apresenta um conjunto de ferramentas que exploram as capacidades recentes das placas gráficas de computadores pessoais para prover a visualização e a interação com volumes de dados. O objetivo é oferecer ao usuário ferramentas que permitam a remoção interativa de partes não relevantes do volume. Assim, o usuário é capaz de selecionar um volume de interesse, o que pode tanto facilitar a compreensão da sua estrutura quanto a sua relação com os volumes circundantes. A técnica de visualização direta de volumes através do mapeamento de texturas é explorada para desenvolver estas ferramentas. O controle programável dos cálculos realizados pelo hardware gráfico para gerar a aparência de cada pixel na tela é usado para resolver a visibilidade de cada ponto do volume em tempo real. As ferramentas propostas permitem a modificação da visibilidade de cada ponto dentro do hardware gráfico, estendendo o benefício da visualização acelerada por hardware. Três ferramentas de interação são propostas: uma ferramenta de recorte planar que permite a seleção de um volume de interesse convexo; uma ferramenta do tipo “borracha”, para eliminar partes não relevantes da imagem; e uma ferramenta do tipo “escavadeira”, para remover camadas do volume Estas ferramentas exploram partes distintas do fluxo de visualização por texturas, onde é possível tomar a decisão sobre a visibilidade de cada ponto do volume. Cada ferramenta vem para resolver uma deficiência da ferramenta anterior. Com o recorte planar, o usuário aproxima grosseiramente o volume de interesse; com a borracha, ele refina o volume selecionado que, finalmente, é terminado com a escavadeira. Para aplicar as ferramentas propostas ao volume visualizado, são usadas técnicas de interação conhecidas, comuns nos sistemas de visualização 2D. Isto permite minimizar os esforços do usuário no treinamento do uso das ferramentas. Finalmente, são ilustradas as aplicações potenciais das ferramentas propostas para o estudo da anatomia do fígado humano. Nestas aplicações foi possível identificar algumas necessidades do usuário na visualização interativa de conjuntos de dados médicos. A partir destas observações, são propostas também novas ferramentas de interação, baseadas em modificações nas ferramentas propostas.

The risk of falling into the acceleration trap during a privatization process: a case study of a European telecommunication company

A privatização de uma empresa é uma mudança empresarial disruptiva que geralmente coincide com o fim de uma posição de monopólio e da subsequente entrada num ambiente competitivo. Os desafios que a privatização coloca são tão árduos que eles levam muitas vezes a liderança (leadership) para executar planos ambiciosos de mudança empresarial. No entanto, a literatura mostra que muitos deles falharam. Na verdade, esses planos preveem mudanças bruscas e importantes que tendem a empurrar a empresa privatizada na armadilha de aceleração (acceleration trap). Um tipo de “burnout organizacional” (organizational burnout) onde a exaustão e a resignação da força de trabalho afetam drasticamente o desempenho da empresa. A tese, portanto, focalizou em estudar a ligação entre um processo de privatização e o risco de cair na armadilha de aceleração. Uma investigação preliminar sobre a literatura das mudanças empresariais permitiu a concepção de um quadro preliminar teórico que sugere a existência de dois moderadores (moderators) deste relacionamento entre um processo de privatização e a armadilha de aceleração: um “choque cultural” (cultural clash) e um “fraco clima de liderança transformacional” (weak transformational leadership). Em seguida, um estudo de caso - baseado numa empresa de telecomunicações europeia e conduzido através de uma abordagem metodológico não puramente indutivo (non-purely inductive approach) - confirma, mas também aprofunda a compreensão da ação desses dois moderadores. A respeito do moderador “choque cultural” (cultural clash moderator), a análise de dados do estudo de caso da empresa de telecomunicações europeia mostra a importância exercitado tanto por um “choque de identidade corporativa” (corporate identity conflict) como por um “conflito de identidade gerencial” (management identity conflict). Quanto ao moderador “fraco liderança transformacional”, a análise dos dados destaca o papel da “falta de confiança na nova gerência” (lack of trust in the new management), mas também de “sentido do trabalho” (lack of job sense), principalmente através da perda de “orgulho no trabalho” (loss of proudness). Finalmente, a análise dos dados salienta que a “não aceitação do novo sistema de incentivos” (non-acceptance of the new incentive system) afeta significativamente a relação entre a privatização e a armadilha de aceleração, contribuindo tanto para um “choque cultural” como para um “fraco clima de liderança transformacional”.

Acceleration of the decomposition of Sicilian lemon leaves as an auxiliary measure in the control of citrus black spot

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

g-acceleration of gravity: its measurement from the shape of water by using a computerized rotational system

This paper proposes a different experimental setup compared with the traditional ones, in order to determine the acceleration of gravity, which is carried out by using a fluid at a constant rotation. A computerized rotational system-by using a data acquisition system with specific software, a power amplifier and a rotary motion sensor-is employed in order to evaluate the angular velocity and g. An equation to determine g is inferred from fluid mechanics. For this purpose, the fluid's parabolic shape inside a cylindrical receptacle is considered using a rotational movement.

Paralelização em GPU da segmentação vascular com extração de Centerlines por Height Ridges

The vascular segmentation is important in diagnosing vascular diseases like stroke and is hampered by noise in the image and very thin vessels that can pass unnoticed. One way to accomplish the segmentation is extracting the centerline of the vessel with height ridges, which uses the intensity as features for segmentation. This process can take from seconds to minutes, depending on the current technology employed. In order to accelerate the segmentation method proposed by Aylward [Aylward & Bullitt 2002] we have adapted it to run in parallel using CUDA architecture. The performance of the segmentation method running on GPU is compared to both the same method running on CPU and the original Aylward s method running also in CPU. The improvemente of the new method over the original one is twofold: the starting point for the segmentation process is not a single point in the blood vessel but a volume, thereby making it easier for the user to segment a region of interest, and; the overall gain method was 873 times faster running on GPU and 150 times more fast running on the CPU than the original CPU in Aylward

Glutamate-induced obesity leads to decreased sperm reserves and acceleration of transit time in the epididymis of adult male rats

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Acceleration of Sperm Transit Time and Reduction of Sperm Reserves in the Epididymis of Rats Exposed to Sibutramine

Sibutramine is a drug globally used for the treatment of obesity. The aim of this study was to investigate male reproductive disorders caused by sibutramine in adult rats. Wistar rats were treated for 28 consecutive days (gavage) with 10 mg/kg of sibutramine. Control animals received only vehicle (dimethylsulfoxide and saline). The rats were sacrificed for evaluation of body and reproductive organ weights, sperm parameters, hormone levels (luteinizing hormone, follicle-stimulating hormone, and testosterone), testicular and epididymal histopathology, sexual behavior, fertility and in vitro contractility of the epididymal duct. Sibutramine decreased (P < .05) weights of the epididymis and ventral prostate, but not of other reproductive organs. The sperm number and transit time in the epididymal cauda were decreased (P < .001), but the daily sperm production was not altered. Moreover, morphology and sperm motility, histopathology of the testes and epididymis, sexual behavior, fertility, and serum hormone levels were not altered by the treatment. Sibutramine increased the potency of norepinephrine and, per se, increased the mechanical activity of the epididymal duct in vitro. Thus, although sibutramine in these experimental conditions did not interfere with the reproductive process of rats, it provoked acceleration of the sperm transit time and a decrease in the sperm reserves in the epididymal cauda. This alteration is probably related to the sympathomimetic effect of this drug, as shown by the in vitro assays. In humans, use of this drug might present a threat for male fertility because sperm reserves in men are naturally lower than those in rats.

Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Consistent modified gravity: dark energy, acceleration and the absence of cosmic doomsday

We discuss modified gravity which includes negative and positive powers of curvature and provides gravitational dark energy. It is shown that in GR plus a term containing a negative power of curvature, cosmic speed-up may be achieved while the effective phantom phase (with w less than -1) follows when such a term contains a fractional positive power of curvature. Minimal coupling with matter makes the situation more interesting: even 1/R theory coupled with the usual ideal fluid may describe the (effective phantom) dark energy. The account of the R(2) term (consistent modified gravity) may help to escape cosmic doomsday.

Holographic dark energy and the universe expansion acceleration

By incorporating the holographic principle in a time-depending Lambda-term cosmology, new physical bounds on the arbitrary parameters of the model can be obtained. Considering then the dark energy as a purely geometric entity, for which no equation of state has to be introduced, it is shown that the resulting range of allowed values for the parameters may explain both the coincidence problem and the universe accelerated expansion, without resorting to any kind of additional structures. (C) 2006 Elsevier B.V. All rights reserved.