A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

The European storm Kyrill in January 2007: synoptic evolution, meteorological impacts and some considerations with respect to climate change

The synoptic evolution and some meteorological impacts of the European winter storm Kyrill that swept across Western, Central, and Eastern Europe between 17 and 19 January 2007 are investigated. The intensity and large storm damage associated with Kyrill is explained based on synoptic and mesoscale environmental storm features, as well as on comparisons to previous storms. Kyrill appeared on weather maps over the US state of Arkansas about four days before it hit Europe. It underwent an explosive intensification over the Western North Atlantic Ocean while crossing a very intense zonal polar jet stream. A superposition of several favourable meteorological conditions west of the British Isles caused a further deepening of the storm when it started to affect Western Europe. Evidence is provided that a favourable alignment of three polar jet streaks and a dry air intrusion over the occlusion and cold fronts were causal factors in maintaining Kyrill's low pressure very far into Eastern Europe. Kyrill, like many other strong European winter storms, was embedded in a pre-existing, anomalously wide, north-south mean sea-level pressure (MSLP) gradient field. In addition to the range of gusts that might be expected from the synoptic-scale pressure field, mesoscale features associated with convective overturning at the cold front are suggested as the likely causes for the extremely damaging peak gusts observed at many lowland stations during the passage of Kyrill's cold front. Compared to other storms, Kyrill was by far not the most intense system in terms of core pressure and circulation anomaly. However, the system moved into a pre-existing strong MSLP gradient located over Central Europe which extended into Eastern Europe. This fact is considered determinant for the anomalously large area affected by Kyrill. Additionally, considerations of windiness in climate change simulations using two state-of-the-art regional climate models driven by ECHAM5 indicate that not only Central, but also Eastern Central Europe may be affected by higher surface wind speeds at the end of the 21st century. These changes are partially associated with the increased pressure gradient over Europe which is identified in the ECHAM5 simulations. Thus, with respect to the area affected, as well as to the synoptic and mesoscale storm features, it is proposed that Kyrill may serve as an interesting study case to assess future storm impacts.

On the radius of centrality in evolving communication networks

In this article, we investigate how the choice of the attenuation factor in an extended version of Katz centrality influences the centrality of the nodes in evolving communication networks. For given snapshots of a network, observed over a period of time, recently developed communicability indices aim to identify the best broadcasters and listeners (receivers) in the network. Here we explore the attenuation factor constraint, in relation to the spectral radius (the largest eigenvalue) of the network at any point in time and its computation in the case of large networks. We compare three different communicability measures: standard, exponential, and relaxed (where the spectral radius bound on the attenuation factor is relaxed and the adjacency matrix is normalised, in order to maintain the convergence of the measure). Furthermore, using a vitality-based measure of both standard and relaxed communicability indices, we look at the ways of establishing the most important individuals for broadcasting and receiving of messages related to community bridging roles. We compare those measures with the scores produced by an iterative version of the PageRank algorithm and illustrate our findings with two examples of real-life evolving networks: the MIT reality mining data set, consisting of daily communications between 106 individuals over the period of one year, a UK Twitter mentions network, constructed from the direct \emph{tweets} between 12.4k individuals during one week, and a subset the Enron email data set.

Formation and circulation of the cold intermediate layer in the Gulf of Saint Lawrence

[ 1] The local heat content and formation rate of the cold intermediate layer (CIL) in the Gulf of Saint Lawrence are examined using a combination of new in situ wintertime observations and a three-dimensional numerical model. The field observations consist of five moorings located throughout the gulf over the period of November 2002 to June 2003. The observations demonstrate a substantially deeper surface mixed layer in the central and northeast gulf than in regions downstream of the buoyant surface outflow from the Saint Lawrence Estuary. The mixed-layer depth in the estuary remains shallow (< 60 m) throughout winter, with the arrival of a layer of near-freezing waters between 40 and 100 m depth in April. An eddy-permitting ice-ocean model with realistic forcing is used to hindcast the period of observation. The model simulates well the seasonal evolution of mixed-layer depth and CIL heat content. Although the greatest heat losses occur in the northeast, the most significant change in CIL heat content over winter occurs in the Anticosti Trough. The observed renewal of CIL in the estuary in spring is captured by the model. The simulation highlights the role of the northwest gulf, and in particular, the separation of the Gaspe Current, in controlling the exchange of CIL between the estuary and the gulf. In order to isolate the effects of inflow through the Strait of Belle Isle on the CIL heat content, we examine a sensitivity experiment in which the strait is closed. This simulation shows that the inflow has a less important effect on the CIL than was suggested by previous studies.

A comparison of energy use in conventional and integrated arable farming systems in the UK

The LINK Integrated Farming Systems (LINK-IFS) Project (1992-1997) was setup to compare conventional and integrated arable farming systems (IAFS), concentrating on practical feasibility and economic viability, but also taking into account the level of inputs used and environmental impact. As part of this, an examination into energy use within the two systems was also undertaken. This paper presents the results from that analysis. The data used is from the six sites within the LINK-IFS Project, spread through the arable production areas of England and from the one site in Scotland, covering the 5 years of the project. The comparison of the energy used is based on the equipment and inputs used to produce I kg of each crop within the conventional and integrated rotations, and thereby the overall energy used for each system. The results suggest that, in terms of total energy used, the integrated system appears to be the most efficient. However, in terms of energy efficiency, energy use per kilogram of output, the results are less conclusive. (C) 2003 Elsevier Science B.V. All rights reserved.

Technical note: A proposed method to determine the extent of degradation of a feed in the rumen from the degradation profile obtained with the in vitro gas production technique using feces as the inoculum

A method is proposed to determine the extent of degradation in the rumen involving a two-stage mathematical modeling process. In the first stage, a statistical model shifts (or maps) the gas accumulation profile obtained using a fecal inoculum to a ruminal gas profile. Then, a kinetic model determines the extent of degradation in the rumen from the shifted profile. The kinetic model is presented as a generalized mathematical function, allowing any one of a number of alternative equation forms to be selected. This method might allow the gas production technique to become an approach for determining extent of degradation in the rumen, decreasing the need for surgically modified animals while still maintaining the link with the animal. Further research is needed before the proposed methodology can be used as a standard method across a range of feeds.

Modelling the partitioning of evapotranspiration in a maize-sunflower intercrop

The primary purpose of this study was to model the partitioning of evapotranspiration in a maize-sunflower intercrop at various canopy covers. The Shuttleworth-Wallace (SW) model was extended for intercropping systems to include both crop transpiration and soil evaporation and allowing interaction between the two. To test the accuracy of the extended SW model, two field experiments of maize-sunflower intercrop were conducted in 1998 and 1999. Plant transpiration and soil evaporation were measured using sap flow gauges and lysimeters, respectively. The mean prediction error (simulated minus measured values) for transpiration was zero (which indicated no overall bias in estimation error), and its accuracy was not affected by the plant growth stages, but simulated transpiration during high measured transpiration rates tended to be slightly underestimated. Overall, the predictions for daily soil evaporation were also accurate. Model estimation errors were probably due to the simplified modelling of soil water content, stomatal resistances and soil heat flux as well as due to the uncertainties in characterising the 2 micrometeorological conditions. The SW’s prediction of transpiration was most sensitive to parameters most directly related to the canopy characteristics such as the partitioning of captured solar radiation, canopy resistance, and bulk boundary layer resistance.

Use of auditory cues for wayfinding assistance in virtual environment: music aids route decision

This paper addresses the crucial problem of wayfinding assistance in the Virtual Environments (VEs). A number of navigation aids such as maps, agents, trails and acoustic landmarks are available to support the user for navigation in VEs, however it is evident that most of the aids are visually dominated. This work-in-progress describes a sound based approach that intends to assist the task of 'route decision' during navigation in a VE using music. Furthermore, with use of musical sounds it aims to reduce the cognitive load associated with other visually as well as physically dominated tasks. To achieve these goals, the approach exploits the benefits provided by music to ease and enhance the task of wayfinding, whilst making the user experience in the VE smooth and enjoyable.

Effects of a novel galactooligosaccharide on the faecal microbiota of healthy and inflammatory bowel disease cats during a randomized, double-blind, cross-over feeding study

Inflammatory bowel disease (IBD) is a common gastrointestinal disorder of cats with no known aetiological agent. Previous work has suggested that the faecal microbiota of IBD cats is significantly different from that of healthy cats, including significantly lower bifidobacteria, bacteroides and total counts in IBD cats and significantly lower levels of sulfate-reducing bacteria in healthy cats. Prebiotics, including galactooligosaccharides (GOS), have been shown to elicit a bifidogenic effect in humans and other animals. The purpose of the current study was to examine the impact of a novel GOS supplementation on the faecal microbiota of healthy and IBD cats during a randomized, double-blind, cross-over feeding study. Eight oligonucleotide probes targeting specific bacterial populations and DAPI stain (total bacteria) were used to monitor the feline faecal microbiota. Overall, inter-animal variation was high; while a trend of increased bifidobacterial levels was seen with GOS supplementation it was not statistically significant in either healthy or IBD cats. No significant differences were observed in the faecal microbiota of IBD cats and healthy cats fed the same diet. Members of the family Coriobacteriaceae (Atopobium cluster) were found to be the most abundant bacteria in the feline microbiota.

Impact of age and menopausal status on the postprandial triacylglycerol response in healthy women

Objective: To examine the impact of age and the natural menopause on the postprandial triacylglycerol (TAG) response in healthy women. Methods and results: Thirty-seven premenopausal and sixty-one postmenopausal women underwent a sequential meal postprandial investigation, in which blood samples were taken at regular intervals after a test breakfast and lunch given at 0 and 330 min respectively. Lipids and glucose were measured in the fasting sample, with TAG analysed in the postprandial samples. Postmenopausal women were shown to have higher fasting total cholesterol, low density lipoprotein cholesterol (LDL-C) and glucose (P < 0.02). Marked differences in the postprandial TAG response were evident between the groups, with a greater incremental area under the curve (IAUC) and maximum TAG concentration in the postmenopausal women (P < 0.04). Multivariate regression analysis revealed both age and fasting TAG to be independently associated with the summary measures of the postprandial TAG response in the premenopausal women only. Interestingly, sub-division of the women into both younger and older pre- and postmenopausal subgroups, showed the most marked difference in TAG-IAUC to be between the younger and the older premenopausal women, whereas differences in fasting LDL-C were most evident between the older premenopausal and the younger postmenopausal women. Conclusions: Our results suggest a divergence in the relationship of age and menopausal status with fasting LDL-C and postprandial TAG which may reflect differences in the metabolic effects of age and the menopause on these lipid risk markers or a greater impact of early oestrogen decline on pathways of TAG rather than LDL metabolism.