A benchmark-driven modelling approach for evaluating deployment choices on a multi-core architecture

The complexity of current and emerging architectures provides users with options about how best to use the available resources, but makes predicting performance challenging. In this work a benchmark-driven model is developed for a simple shallow water code on a Cray XE6 system, to explore how deployment choices such as domain decomposition and core affinity affect performance. The resource sharing present in modern multi-core architectures adds various levels of heterogeneity to the system. Shared resources often includes cache, memory, network controllers and in some cases floating point units (as in the AMD Bulldozer), which mean that the access time depends on the mapping of application tasks, and the core's location within the system. Heterogeneity further increases with the use of hardware-accelerators such as GPUs and the Intel Xeon Phi, where many specialist cores are attached to general-purpose cores. This trend for shared resources and non-uniform cores is expected to continue into the exascale era. The complexity of these systems means that various runtime scenarios are possible, and it has been found that under-populating nodes, altering the domain decomposition and non-standard task to core mappings can dramatically alter performance. To find this out, however, is often a process of trial and error. To better inform this process, a performance model was developed for a simple regular grid-based kernel code, shallow. The code comprises two distinct types of work, loop-based array updates and nearest-neighbour halo-exchanges. Separate performance models were developed for each part, both based on a similar methodology. Application specific benchmarks were run to measure performance for different problem sizes under different execution scenarios. These results were then fed into a performance model that derives resource usage for a given deployment scenario, with interpolation between results as necessary.

Internal nanoparticle structure of temperature-responsive self-assembled PNIPAM-b-PEG-b-PNIPAM triblock copolymers in aqueous solutions: NMR, SANS and light scattering studies

In this study we report detailed information on the internal structure of PNIPAM-b-PEG-b-PNIPAM nanoparticles formed from self-assembly in aqueous solutions upon increase in temperature. NMR spectroscopy, light scattering and small-angle neutron scattering (SANS) were used to monitor different stages of nanoparticle formation as a function of temperature, providing insight into the fundamental processes involved. The presence of PEG in a copolymer structure significantly affects the formation of nanoparticles, making their transition to occur over a broader temperature range. The crucial parameter that controls the transition is the ratio of PEG/PNIPAM. For pure PNIPAM, the transition is sharp; the higher the PEG/PNIPAM ratio results in a broader transition. This behavior is explained by different mechanisms of PNIPAM block incorporation during nanoparticle formation at different PEG/PNIPAM ratios. Contrast variation experiments using SANS show that the structure of nanoparticles above cloud point temperatures for PNIPAM-b-PEG-b-PNIPAM copolymers is drastically different from the structure of PNIPAM mesoglobules. In contrast with pure PNIPAM mesoglobules, where solid-like particles and chain network with a mesh size of 1-3 nm are present; nanoparticles formed from PNIPAM-b-PEG-b-PNIPAM copolymers have non-uniform structure with “frozen” areas interconnected by single chains in Gaussian conformation. SANS data with deuterated “invisible” PEG blocks imply that PEG is uniformly distributed inside of a nanoparticle. It is kinetically flexible PEG blocks which affect the nanoparticle formation by prevention of PNIPAM microphase separation.

Distribution and abundance of ladybirds (Coleoptera : Coccinellidae) in non-crop habitats

The abundance and distribution of coccinellids in non-crop habitats was studied using removal sampling and visual observation. Coccinellids were most frequently found on grassland habitats. Coccinellid abundance appeared to be most strongly correlated with the percentage ground cover of thistle, grasses and nettles. The most commonly collected coccinellids were Coccinella septempunctata and Adalia bipunctata comprising 60% and 35% of the catches respectively. Most coccinellids were found on Rubus spp. with nettles (Urtica dioica) and grasses being the next most favoured plant species. Adalia bipunctata was the most commonly found coccinellid species on nettles and birch (Betula spp.) whereas C. septempunctata was the most commonly found species on grasses, Rubus spp, and oak (Quercus spp.). These results are discussed in light of current thinking on the importance of "island" habitats as pali of an integrated pest management programme.

Statistical inference of OH concentrations and air mass dilution rates from successive observations of non-methane hydrocarbons in single air masses

Bayesian inference has been used to determine rigorous estimates of hydroxyl radical concentrations () and air mass dilution rates (K) averaged following air masses between linked observations of nonmethane hydrocarbons (NMHCs) spanning the North Atlantic during the Intercontinental Transport and Chemical Transformation (ITCT)-Lagrangian-2K4 experiment. The Bayesian technique obtains a refined (posterior) distribution of a parameter given data related to the parameter through a model and prior beliefs about the parameter distribution. Here, the model describes hydrocarbon loss through OH reaction and mixing with a background concentration at rate K. The Lagrangian experiment provides direct observations of hydrocarbons at two time points, removing assumptions regarding composition or sources upstream of a single observation. The estimates are sharpened by using many hydrocarbons with different reactivities and accounting for their variability and measurement uncertainty. A novel technique is used to construct prior background distributions of many species, described by variation of a single parameter . This exploits the high correlation of species, related by the first principal component of many NMHC samples. The Bayesian method obtains posterior estimates of , K and following each air mass. Median values are typically between 0.5 and 2.0 × 106 molecules cm−3, but are elevated to between 2.5 and 3.5 × 106 molecules cm−3, in low-level pollution. A comparison of estimates from absolute NMHC concentrations and NMHC ratios assuming zero background (the “photochemical clock” method) shows similar distributions but reveals systematic high bias in the estimates from ratios. Estimates of K are ∼0.1 day−1 but show more sensitivity to the prior distribution assumed.

Comparison of subcellular partitioning, distribution, and internal speciation of Cu between Cu-tolerant and naive populations of Dendrodrilus rubidus Savigny

When considering contaminated site ecology and ecological risk assessment a key question is whether organisms that appear unaffected by accumulation of contaminants are tolerant or resistant to those contaminants. A population of Dendrodrilus rubidus Savigny earthworms from the Coniston Copper Mines, an area of former Cu mining, exhibit increased tolerance and accumulation of Cu relative to a nearby non-Cu exposed population. Distribution of total Cu between different body parts (posterior, anterior, body wall) of the two populations was determined after a 14 day exposure to 250 mg Cu kg(-1) in Cu-amended soil. Cu concentrations were greater in Coniston earthworms but relative proportions of Cu in different body parts were the same between populations. Cu speciation was determined using extended X-ray absorption fine structure spectroscopy (EXAFS). Cu was coordinated to 0 atoms in the exposure soil but to S atoms in the earthworms. There was no difference in this speciation between the different earthworm populations. In another experiment earthworms were exposed to a range of Cu concentrations (200-700 mg Cu kg(-1)). Subcellular partitioning of accumulated Cu was determined. Coniston earthworms accumulated more Cu but relative proportions of Cu in the different fractions (cytosol > granular > tissue fragments, cell membranes, and intact cells) were the same between populations. Results suggest that Coniston D. rubidus are able to survive in the Cu-rich Coniston Copper Mines soil through enlargement of the same Cu storage reservoirs that exist in a nearby non-Cu exposed population.

Endocranial lesions: their distribution and aetiology

Reactive new bone on the endocranial surface of the skull in non-adults has recently received a lot of attention in the palaeopathological literature. These features appear as layers of new bone on the original cortical surface, expanding around meningeal vessels, as isolated plaques, 'hair-on-end' extensions of the diploe or, as 'capillary' impressions extending into the inner lamina of the cranium. These lesions are commonly found on the occipital bone, outlining the cruciate eminence, but have also been recorded on the parietal and frontal bones, and appear to follow the areas of venous drainage. Although recognized as resulting from haemorrhage or inflammation, their precise aetiology is still a matter of controversy. This paper outlines their possible causes and examines their nature and distribution in a group of non-adults from four archaeological sites in England. It is recommended that, when recording these lesions in the future, additional skeletal pathologies, the age of the child, and nature and distribution of the lesions also be taken into account. Copyright (C) 2004 John Wiley Sons, Ltd.

Evaluating the risk of non-point source pollution from biosolids: integrated modelling of nutrient losses at field and catchment scales

A semi-distributed model, INCA, has been developed to determine the fate and distribution of nutrients in terrestrial and aquatic systems. The model simulates nitrogen and phosphorus processes in soils, groundwaters and river systems and can be applied in a semi-distributed manner at a range of scales. In this study, the model has been applied at field to sub-catchment to whole catchment scale to evaluate the behaviour of biosolid-derived losses of P in agricultural systems. It is shown that process-based models such as INCA, applied at a wide range of scales, reproduce field and catchment behaviour satisfactorily. The INCA model can also be used to generate generic information for risk assessment. By adjusting three key variables: biosolid application rates, the hydrological connectivity of the catchment and the initial P-status of the soils within the model, a matrix of P loss rates can be generated to evaluate the behaviour of the model and, hence, of the catchment system. The results, which indicate the sensitivity of the catchment to flow paths, to application rates and to initial soil conditions, have been incorporated into a Nutrient Export Risk Matrix (NERM).

Follicle-stimulating hormone isoforms and plasma concentrations of estradiol and inhibin A in dairy cows with ovulatory and non-ovulatory follicles during the first postpartum follicle wave

Following parturition, all cows display a wave of ovarian follicular growth, but a large proportion fail to generate a preovulatory rise in estradiol, and hence fail to ovulate. Follicle-stimulating hormone (FSH) exists as multiple isoforms in the circulation depending on the type and extent of glycosylation, and this has pronounced effects on its biological properties. This study examined differences in plasma FSH, estradiol, and inhibin A concentrations, and the distribution of FSH isoforms in cows with ovulatory or atretic dominant follicles during the first postpartum follicle wave. Plasma FSH isoform distribution was examined in both groups during the period of final development of the dominant follicle by liquid phase isoelectric focusing. Cows with an ovulatory follicle had higher circulating estradiol and inhibin A concentrations, and lower plasma FSH concentrations. The distribution of FSH isoforms displayed a marked shift toward the less acidic isoforms in cows with ovulatory follicles. A higher proportion of the FSH isoforms had a pl>5.0 in cows with ovulatory follicles compared to those with atretic follicles. In addition, cows with ovulatory follicles had greater dry matter intake, superior energy balance, elevated circulating concentrations of insulin and insulin-like growth factor-I, and lower plasma nonesterified fatty acids. The shift in FSH isoforms toward a greater abundance of the less acidic isoforms appears to be a key component in determining the capability for producing a preovulatory rise in estradiol, and this shift in FSH isoforms was associated with more favorable bioenergetic and metabolic status. (C) 2008 Elsevier Inc. All rights reserved.

Declining survival rates in a reintroduced population of the Mauritius kestrel: evidence for non-linear density dependence and environmental stochasticity

1. We studied a reintroduced population of the formerly critically endangered Mauritius kestrel Falco punctatus Temmink from its inception in 1987 until 2002, by which time the population had attained carrying capacity for the study area. Post-1994 the population received minimal management other than the provision of nestboxes. 2. We analysed data collected on survival (1987-2002) using program MARK to explore the influence of density-dependent and independent processes on survival over the course of the population's development. 3.We found evidence for non-linear, threshold density dependence in juvenile survival rates. Juvenile survival was also strongly influenced by climate, with the temporal distribution of rainfall during the cyclone season being the most influential climatic variable. Adult survival remained constant throughout. 4. Our most parsimonious capture-mark-recapture statistical model, which was constrained by density and climate, explained 75.4% of the temporal variation exhibited in juvenile survival rates over the course of the population's development. 5. This study is an example of how data collected as part of a threatened species recovery programme can be used to explore the role and functional form of natural population regulatory processes. With the improvements in conservation management techniques and the resulting success stories, formerly threatened species offer unique opportunities to further our understanding of the fundamental principles of population ecology.

Development of a method fon non-destructive testing of fruits using scanning laser vibrometry (SLV)

Quality control on fruits requires reliable methods, able to assess with reasonable accuracy and possibly in a non-destructive way their physical and chemical characteristics. More specifically, a decreased firmness indicates the presence of damage or defects in the fruit or else that the fruit has exceeded its “best before date”, becoming unsuitable for consumption. In high-value exotic fruits, such as mangoes, where firmness cannot be easily measured from a simple observation of texture, colour changes and unevenness of fruits surface, the use of non-destructive techniques is highly recommendable. In particular, the application of Laser vibrometry, based on the Doppler effect, a non-contact technique sensitive to differences in displacements inferior to the nanometre, appears ideal for a possible on-line control on food. Previous results indicated that a phase shift can be in a repeatable way associated with the presence of damage on the fruit, whilst a decreased firmness results in significant differences in the displacement of the fruits under the same excitation signal. In this work, frequency ranges for quality control via the application of a sound chirp are suggested, based on the measurement of the signal coherence. The variations of the average vibration spectrum of a grid of points, or of point-by-point signal velocity allows the go-no go recognition of “firm” and “over-ripe” fruits, with notable success in the particular case of mangoes. The future exploitation of this work will include the application of this method to allow on-line control during conveyor belt distribution of fruits.

Uniform versus discriminatory tariffs

We analyze the non-cooperative interaction between two exporting countries producing differentiated products and one importing country when governments use optimal policies to maximize welfare. The analysis includes product differentiation, asymmetric costs, and Bertrand competition. For identical exporting countries we demonstrate that the importing country always prefers a uniform tariff regime while both exporting countries prefer a discriminatory tariff regime for any degree of product differentiation. If countries are asymmetric in terms of production cost then the higher-cost exporter always prefers the discriminatory regime but the lower-cost exporter prefers the uniform regime if there is a significant cost differential. With cost asymmetry the announcement of a uniform tariff regime by the importer is not a credible strategy since there is an incentive to deviate to discrimination. This implies an international body can play a role in ensuring that tariff agreements are respected.

Non-testability of equal weights spatial dependence

We show that any invariant test for spatial autocorrelation in a spatial error or spatial lag model with equal weights matrix has power equal to size. This result holds under the assumption of an elliptical distribution. Under Gaussianity, we also show that any test whose power is larger than its size for at least one point in the parameter space must be biased.

The effect of triacylglycerol fatty acid positional distribution on postprandial plasma metabolite and hormone responses in normal adult men

The present study has examined the possibility that the positional distribution of fatty acids on dietary triacyglycerol (TAG) influences the postprandial response to a liquid meal in adult subjects. Postprandial TAG, non-esterified fatty acids (NEFA), ketones, glucose, insulin and gastric inhibitory polypeptide (GIP) responses were monitored in sixteen normal adult male subjects over 6 h following consumption of test meals containing dietary TAG in which palmitic acid was predominantly on the sn-1 (Control) or sn-2 positions (Betapol). Plasma total TAG, chylomicron-rich TAG and chylomicron-poor TAG concentrations were identical in response to the two test meals. The peak increase (mean (SD)) in chylomicron TAG was 0.85 (0.46) mmol/l after the Control meal and 0.85 (0.42) mmol/l after the Betapol meal. Plasma glucose, insulin, GIP, NEFA and ketone concentrations were also very similar following the two meals. It is concluded that dietary TAG containing saturated fatty acids on the sn-2 position appear in plasma at a similar level and over a similar timescale to TAG in which saturated fatty acids are predominantly located on sn-1 or sn-3 positions. The results reported in the present study demonstrate that the positional distribution of fatty acids on dietary TAG is not an important determinant of postprandial lipaemia in adult male subjects, but do not exclude the possibility that different responses may occur when these dietary TAG are given long term.

The distribution of the ring current: Cluster observations

Extending previous studies, a full-circle investigation of the ring current has been made using Cluster 4-spacecraft observations near perigee, at times when the Cluster array had relatively small separations and nearly regular tetrahedral configurations, and when the Dst index was greater than −30 nT (non-storm conditions). These observations result in direct estimations of the near equatorial current density at all magnetic local times (MLT) for the first time and with sufficient accuracy, for the following observations. The results confirm that the ring current flows westward and show that the in situ average measured current density (sampled in the radial range accessed by Cluster 4–4.5RE) is asymmetric in MLT, ranging from 9 to 27 nAm−2. The direction of current is shown to be very well ordered for the whole range of MLT. Both of these results are in line with previous studies on partial ring extent. The magnitude of the current density, however, reveals a distinct asymmetry: growing from 10 to 27 nAm−2 as azimuth reduces from about 12:00MLT to 03:00 and falling from 20 to 10 nAm−2 less steadily as azimuth reduces from 24:00 to 12:00MLT. This result has not been reported before and we suggest it could reflect a number of effects. Firstly, we argue it is consistent with the operation of region-2 field aligned-currents (FACs), which are expected to flow upward into the ring current around 09:00MLT and downward out of the ring current around 14:00MLT. Secondly, we note that it is also consistent with a possible asymmetry in the radial distribution profile of current density (resulting in higher peak at 4– 4.5RE). We note that part of the enhanced current could reflect an increase in the mean AE activity (during the periods in which Cluster samples those MLT).