800 resultados para DISTRIBUTED STRAIN
Resumo:
In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids.
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We present a general Multi-Agent System framework for distributed data mining based on a Peer-to-Peer model. Agent protocols are implemented through message-based asynchronous communication. The framework adopts a dynamic load balancing policy that is particularly suitable for irregular search algorithms. A modular design allows a separation of the general-purpose system protocols and software components from the specific data mining algorithm. The experimental evaluation has been carried out on a parallel frequent subgraph mining algorithm, which has shown good scalability performances.
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Recently, two approaches have been introduced that distribute the molecular fragment mining problem. The first approach applies a master/worker topology, the second approach, a completely distributed peer-to-peer system, solves the scalability problem due to the bottleneck at the master node. However, in many real world scenarios the participating computing nodes cannot communicate directly due to administrative policies such as security restrictions. Thus, potential computing power is not accessible to accelerate the mining run. To solve this shortcoming, this work introduces a hierarchical topology of computing resources, which distributes the management over several levels and adapts to the natural structure of those multi-domain architectures. The most important aspect is the load balancing scheme, which has been designed and optimized for the hierarchical structure. The approach allows dynamic aggregation of heterogenous computing resources and is applied to wide area network scenarios.
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This paper focuses on improving computer network management by the adoption of artificial intelligence techniques. A logical inference system has being devised to enable automated isolation, diagnosis, and even repair of network problems, thus enhancing the reliability, performance, and security of networks. We propose a distributed multi-agent architecture for network management, where a logical reasoner acts as an external managing entity capable of directing, coordinating, and stimulating actions in an active management architecture. The active networks technology represents the lower level layer which makes possible the deployment of code which implement teleo-reactive agents, distributed across the whole network. We adopt the Situation Calculus to define a network model and the Reactive Golog language to implement the logical reasoner. An active network management architecture is used by the reasoner to inject and execute operational tasks in the network. The integrated system collects the advantages coming from logical reasoning and network programmability, and provides a powerful system capable of performing high-level management tasks in order to deal with network fault.
Resumo:
In real world applications sequential algorithms of data mining and data exploration are often unsuitable for datasets with enormous size, high-dimensionality and complex data structure. Grid computing promises unprecedented opportunities for unlimited computing and storage resources. In this context there is the necessity to develop high performance distributed data mining algorithms. However, the computational complexity of the problem and the large amount of data to be explored often make the design of large scale applications particularly challenging. In this paper we present the first distributed formulation of a frequent subgraph mining algorithm for discriminative fragments of molecular compounds. Two distributed approaches have been developed and compared on the well known National Cancer Institute’s HIV-screening dataset. We present experimental results on a small-scale computing environment.
Resumo:
The effects of uniform straining and shearing on the stability of a surface quasi-geostrophic temperature filament are investigated. Straining is shown to stabilize perturbations for wide filaments but only for a finite time until the filament thins to a critical width, after which some perturbations can grow. No filament can be stabilized in practice, since there are perturbations that can grow large for any strain rate. The optimally growing perturbations, defined as solutions that reach a certain threshold amplitude first, are found numerically for a wide range of parameter values. The radii of the vortices formed through nonlinear roll-up are found to be proportional to θ/s, where θ is the temperature anomaly of the filament and s the strain rate, and are not dependent on the initial size of the filament. Shearing is shown to reduce the normal-mode growth rates, but it cannot stabilize them completely when there are temperature discontinuities in the basic state; smooth filaments can be stabilized completely by shearing and a simple scaling argument provides the shear rate required. Copyright © 2010 Royal Meteorological Society
Resumo:
An attenuated strain (263) of the tick-borne encephalitis virus, isolated from field ticks, was either serially subcultured, 5 times in mice, or at 40 degrees C in PS cells, producing 2 independent strains, 263-m5 and 263-TR with identical genomes; both strains exhibited increased plaque size, neuroinvasiveness and temperature-resistance. Sequencing revealed two unique amino acid substitutions, one mapping close to the catalytic site of the viral protease. These observations imply that virus adaptation from ticks to mammals occurs by selection of pre-existing virulent variants from the quasispecies population rather than by the emergence of new random mutations. The significance of these observations is discussed. (c) 2008 Elsevier Inc. All rights reserved.
Resumo:
In the absence of added thiamine, Rhizobium leguminosarum bv. viciae strain 3841 does not grow in liquid medium and forms only "pin" colonies on agar plates, which contrasts with the good growth of Sinorhizobium meliloti 1021, Mesorhizobium loti 303099, and Rhizobium etli CFN42. These last three organisms have thiCOGE genes, which are essential for de novo thiamine synthesis. While R. leguminosarum bv. viciae 3841 lacks thiCOGE, it does have thiMED. Mutation of thiM prevented formation of pin colonies on agar plates lacking added thiamine, suggesting thiamine intermediates are normally present. The putative functions of ThiM, ThiE, and ThiD are 4-methyl-5-(beta-hydroxyethyl) thiazole (THZ) kinase, thiamine phosphate pyrophosphorylase, and 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) kinase, respectively. This suggests that a salvage pathway operates in R. leguminosarum, and addition of HMP and THZ enabled growth at the same rate as that enabled by thiamine in strain 3841 but elicited no growth in the thiM mutant (RU2459). There is a putative thi box sequence immediately upstream of the thiM, and a gfp-mut3.1 fusion to it revealed the presence of a promoter that is strongly repressed by thiamine. Using fluorescent microscopy and quantitative reverse transcription-PCR, it was shown that thiM is expressed in the rhizosphere of vetch and pea plants, indicating limitation for thiamine. Pea plants infected by RU2459 were not impaired in nodulation or nitrogen fixation. However, colonization of the pea rhizosphere by the thiM mutant was impaired relative to that of the wild type. Overall, the results show that a thiamine salvage pathway operates to enable growth of Rhizobium leguminosarum in the rhizosphere, allowing its survival when thiamine is limiting.
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Lipid deposits occur more frequently downstream of branch points than upstream in immature rabbit and human aortas but the opposite pattern is seen in mature vessels. These distributions correlate spatially with age-related patterns of aortic permeability, observed in rabbits, and may be determined by them. The mature but not the immature pattern of permeability is dependent on endogenous nitric oxide synthesis. Although the transport patterns have hitherto seemed robust, recent studies have given the upstream pattern in some mature rabbits but the downstream pattern in others. Here we show that transport in mature rabbits is significantly skewed to the downstream pattern in the afternoon compared with the morning (P < 0.05), and switches from a downstream to an upstream pattern at around 21 months in rabbits of the Murex strain, but at twice this age in Highgate rabbits (P < 0.001). The effect of time of day was not explained by changes in nitric oxide production, assessed from plasma levels of nitrate and nitrate, nor did it correlate with conduit artery tone, assessed from the shape of the peripheral pulse wave. The effect of strain could not be explained by variation in nitric oxide production nor by differences in wall structure. The effects of time of day and rabbit strain on permeability patterns explain recent discrepancies, provide a useful tool for investigating underlying mechanisms and may have implications for human disease.
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We present results on the growth of damage in 29 fatigue tests of human femoral cortical bone from four individuals, aged 53–79. In these tests we examine the interdependency of stress, cycles to failure, rate of creep strain, and rate of modulus loss. The behavior of creep rates has been reported recently for the same donors as an effect of stress and cycles (Cotton, J. R., Zioupos, P., Winwood, K., and Taylor, M., 2003, "Analysis of Creep Strain During Tensile Fatigue of Cortical Bone," J. Biomech. 36, pp. 943–949). In the present paper we first examine how the evolution of damage (drop in modulus per cycle) is associated with the stress level or the "normalized stress" level (stress divided by specimen modulus), and results show the rate of modulus loss fits better as a function of normalized stress. However, we find here that even better correlations can be established between either the cycles to failure or creep rates versus rates of damage than any of these three measures versus normalized stress. The data indicate that damage rates can be excellent predictors of fatigue life and creep strain rates in tensile fatigue of human cortical bone for use in practical problems and computer simulations.
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During fatigue tests of cortical bone specimens, at the unload portion of the cycle (zero stress) non-zero strains occur and progressively accumulate as the test progresses. This non-zero strain is hypothesised to be mostly, if not entirely, describable as creep. This work examines the rate of accumulation of this strain and quantifies its stress dependency. A published relationship determined from creep tests of cortical bone (Journal of Biomechanics 21 (1988) 623) is combined with knowledge of the stress history during fatigue testing to derive an expression for the amount of creep strain in fatigue tests. Fatigue tests on 31 bone samples from four individuals showed strong correlations between creep strain rate and both stress and “normalised stress” (σ/E) during tensile fatigue testing (0–T). Combined results were good (r2=0.78) and differences between the various individuals, in particular, vanished when effects were examined against normalised stress values. Constants of the regression showed equivalence to constants derived in creep tests. The universality of the results, with respect to four different individuals of both sexes, shows great promise for use in computational models of fatigue in bone structures.
Resumo:
A novel strain of Bifidobacterium bifidum NCIMB 41171, isolated from a faecal sample from a healthy human volunteer and able to express beta-galactosidase activity, was used in synthesis reactions for the production of galactooligosaccharide from lactose. The beta-galactosidase activity of whole bifidobacterial cells showed an optimum activity at pH 6.8-7.0 and 40 degrees C. The transgalactosylation activity of the B. bifidum cells from 50% (w/w) lactose resulted in a galactooligosaccharide mixture (20% w/w) comprising (w/w): 25% disaccharides, 35% trisaccharides, 25% tetrasaccharides and 15% pentasaccharides. Using different initial lactose concentrations, the conversion rate to galactooligosaccharides was maximum (35%) when 55% (w/w) lactose was used. In fermentation experiments, B. bifidum showed an increased preference towards the produced galactooligosaccharide mixture, displaying higher growth rate and short-chain fatty acid production when compared with commercially available oligosaccharides.