GPU Acceleration of Partial Differential Equation Solvers

Differential equations are often directly solvable by analytical means only in their one dimensional version. Partial differential equations are generally not solvable by analytical means in two and three dimensions, with the exception of few special cases. In all other cases, numerical approximation methods need to be utilized. One of the most popular methods is the finite element method. The main areas of focus, here, are the Poisson heat equation and the plate bending equation. The purpose of this paper is to provide a quick walkthrough of the various approaches that the authors followed in pursuit of creating optimal solvers, accelerated with the use of graphical processing units, and comparing them in terms of accuracy and time efficiency with existing or self-made non-accelerated solvers.

Mutagenesis of RpoE-like sigma factor genes in Bdellovibrio reveals differential control of groEL and two groES genes

BACKGROUND: Bdellovibrio bacteriovorus HD100 must regulate genes in response to a variety of environmental conditions as it enters, preys upon and leaves other bacteria, or grows axenically without prey. In addition to "housekeeping" sigma factors, its genome encodes several alternate sigma factors, including 2 Group IV-RpoE-like proteins, which may be involved in the complex regulation of its predatory lifestyle.

RESULTS: We find that one sigma factor gene, bd3314, cannot be deleted from Bdellovibrio in either predatory or prey-independent growth states, and is therefore possibly essential, likely being an alternate sigma 70. Deletion of one of two Group IV-like sigma factor genes, bd0881, affects flagellar gene regulation and results in less efficient predation, although not due to motility changes; deletion of the second, bd0743, showed that it normally represses chaperone gene expression and intriguingly we find an alternative groES gene is expressed at timepoints in the predatory cycle where intensive protein synthesis at Bdellovibrio septation, prior to prey lysis, will be occurring.

CONCLUSIONS: We have taken the first step in understanding how alternate sigma factors regulate different processes in the predatory lifecycle of Bdellovibrio and discovered that alternate chaperones regulated by one of them are expressed at different stages of the lifecycle.

Differential evolution combined with clonal selection for dynamic economic dispatch

Dynamic economic load dispatch (DELD) is one of the most important steps in power system operation. Various optimisation algorithms for solving the problem have been developed; however, due to the non-convex characteristics and large dimensionality of the problem, it is necessary to explore new methods to further improve the dispatch results and minimise the costs. This article proposes a hybrid differential evolution (DE) algorithm, namely clonal selection-based differential evolution (CSDE), to solve the problem. CSDE is an artificial intelligence technique that can be applied to complex optimisation problems which are for example nonlinear, large scale, non-convex and discontinuous. This hybrid algorithm combines the clonal selection algorithm (CSA) as the local search technique to update the best individual in the population, which enhances the diversity of the solutions and prevents premature convergence in DE. Furthermore, we investigate four mutation operations which are used in CSA as the hyper-mutation operations. Finally, an efficient solution repair method is designed for DELD to satisfy the complicated equality and inequality constraints of the power system to guarantee the feasibility of the solutions. Two benchmark power systems are used to evaluate the performance of the proposed method. The experimental results show that the proposed CSDE/best/1 approach significantly outperforms nine other variants of CSDE and DE, as well as most other published methods, in terms of the quality of the solution and the convergence characteristics.

Differential ecological impacts of an invader and a native under environmental change are revealed by comparative functional responses.

Predicting the ecological impacts of damaging invasive species under relevant environmental contexts is a major challenge, for which comparative functional responses (the relationship between resource availability and consumer uptake rate) have great potential. Here, the functional responses of Gammarus pulex, an ecologically damaging invader in freshwaters in Ireland and other islands, were compared with those of a native trophic equivalent Gammarus duebeni celticus. Experiments were conducted at two dissolved oxygen concentrations (80 and 50 % saturation), representative of anthropogenic water quality changes, using two larval prey, blackfly (Simuliidae spp.) and mayfly (Baetis rhodani). Overall, G. pulex had higher Type II functional responses and hence predatory impacts than G. d. celticus and the functional responses of both predators were reduced by lowered oxygen concentration. However, this reduction was of lower magnitude for the invader as compared to the native. Further, the invader functional response at low oxygen was comparable to that of the native at high oxygen. Attack rates of the two predators were similar, with low oxygen reducing these attack rates, but this effect occurred more strongly for blackfly than mayfly prey. Handling times were significantly lower for the invader compared with the native, and significantly higher at low oxygen, however, the effect of lowered oxygen on handling times was minimal for the invader and pronounced for the native. Maximum feeding rates were significantly greater for the invader compared with the native, and significantly reduced at low oxygen, with this effect again lesser for the invader as compared to the native. The greater functional responses of the invader corroborate with its impacts on recipient macroinvertebrate communities when it replaces the native. Further, our experiments predict that the impact of the invader will be less affected than the native under altered oxygen regimes driven by anthropogenic influences.

Is differential phytochelatin production related to decreased arsenate influx in arsenate tolerant Holcus lanatus?

Phytochelatins (PCs) are required for arsenic (As) detoxification in nontolerant plants. In addition, a role for PCs in arsenate tolerance has recently been proven, with tolerant plants able to accumulate significantly higher concentrations of As-PC complexes at equivalent levels of stress than nontolerant plants. The relationship between arsenate influx and PC production in tolerant and non-tolerant Holcus lanatus plants was determined in this study, along with an investigation of the effect of inhibition of PC synthesis by buthionine sulfoximine (BSO) on arsenate tolerance. A strong correlation between PC production and arsenate influx was demonstrated in arsenate-tolerant plants. In addition, inhibition of PC synthesis by BSO in tolerant plants increased arsenate sensitivity to that of the nontolerant clone. This dramatic reduction in tolerance proves that PC production is an essential component of the arsenate tolerance mechanism in H. lanatus. This study proposes that while there is a single major gene for arsenate tolerance, hypostatic modifiers are also in operation, affecting the expression of the tolerance character. © New Phytologist (2002).

Copper- and arsenate-induced oxidative stress in Holcus lanatus L. clones with differential sensitivity

The biochemical responses of Holcus lanatus L. to copper and arsenate exposure were investigated in arsenate-tolerant and -non-tolerant plants from uncontaminated and arsenic/copper-contaminated sites. Increases in lipid peroxidation, superoxide dismutase (SOD) activity and phytochelatin (PC) production were correlated with increasing copper and arsenate exposure. In addition, significant differences in biochemical responses were observed between arsenate-tolerant and -non-tolerant plants. Copper and arsenate exposure led to the production of reactive oxygen species, resulting in significant lipid peroxidation in non-tolerant plants. However, SOD activity was suppressed upon metal exposure, possibly due to interference with metallo-enzymes. It was concluded that in non-tolerant plants, rapid arsenate influx resulted in PC production, glutathione depletion and lipid peroxidation. This process would also occur in tolerant plants, but by decreasing the rate of influx, they were able to maintain their constitutive functions, detoxify the metals though PC production and quench reactive oxygen species by SOD activity.

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

The Development and Testing of a New Version of the Cognitive Reflection Test Applying Item Response Theory (IRT)

The cognitive reflection test (CRT) is a short measure of a person's ability to resist intuitive response tendencies and to produce a normatively correct response, which is based on effortful reasoning. Although the CRT is a very popular measure, its psychometric properties have not been extensively investigated. A major limitation of the CRT is the difficulty of the items, which can lead to floor effects in populations other than highly educated adults. The present study aimed at investigating the psychometric properties of the CRT applying item response theory analyses (a two-parameter logistic model) and at developing a new version of the scale (the CRT-long), which is appropriate for participants with both lower and higher levels of cognitive reflection. The results demonstrated the good psychometric properties of the original, as well as the new scale. The validity of the new scale was also assessed by measuring correlations with various indicators of intelligence, numeracy, reasoning and decision-making skills, and thinking dispositions. Moreover, we present evidence for the suitability of the new scale to be used with developmental samples. Finally, by comparing the performance of adolescents and young adults on the CRT and CRT-long, we report the first investigation into the development of cognitive reflection.

Differential efficiency of the endocytic machinery in tonic and phasic synapses

Efficient synaptic vesicle membrane recycling is one of the key factors required to sustain neurotransmission. We investigated potential differences in the compensatory endocytic machineries in two glutamatergic synapses with phasic and tonic patterns of activity in the lamprey spinal cord. Post-embedding immunocytochemistry demonstrated that proteins involved in synaptic vesicle recycling, including dynamin, intersectin, and synapsin, occur at higher levels (labeling per vesicle) in tonic dorsal column synapses than in phasic reticulospinal synapses. Synaptic vesicle protein 2 occurred at similar levels in the two types of synapse. After challenging the synapses with high potassium stimulation for 30 min the vesicle pool in the tonic synapse was maintained at a normal level, while that in the phasic synapse was partly depleted along with expansion of the plasma membrane and accumulation of clathrin-coated intermediates at the periactive zone. Thus, our results indicate that an increased efficiency of the endocytic machinery in a synapse may be one of the factors underlying the ability to sustain neurotransmission at high rates.

Can less be more? Comparison of an 8-item placement quality measure with the 50-item Dundee Ready Educational Environment Measure (DREEM)

Clinical clerks learn more than they are taught and not all they learn can be measured. As a result, curriculum leaders evaluate clinical educational environments. The quantitative Dundee Ready Environment Measure (DREEM) is a de facto standard for that purpose. Its 50 items and 5 subscales were developed by consensus. Reasoning that an instrument would perform best if it were underpinned by a clearly conceptualized link between environment and learning as well as psychometric evidence, we developed the mixed methods Manchester Clinical Placement Index (MCPI), eliminated redundant items, and published validity evidence for its 8 item and 2 subscale structure. Here, we set out to compare MCPI with DREEM. 104 students on full-time clinical placements completed both measures three times during a single academic year. There was good agreement and at least as good discrimination between placements with the smaller MCPI. Total MCPI scores and the mean score of its 5-item learning environment subscale allowed ten raters to distinguish between the quality of educational environments. Twenty raters were needed for the 3-item MCPI training subscale and the DREEM scale and its subscales. MCPI compares favourably with DREEM in that one-sixth the number of items perform at least as well psychometrically, it provides formative free text data, and it is founded on the widely shared assumption that communities of practice make good learning environments.