Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

The relationship between diffuse spectral reflectance of the soil and its cation exchange capacity is scale-dependent

Diffuse reflectance spectroscopy (DRS) is increasingly being used to predict numerous soil physical, chemical and biochemical properties. However, soil properties and processes vary at different scales and, as a result, relationships between soil properties often depend on scale. In this paper we report on how the relationship between one such property, cation exchange capacity (CEC), and the DRS of the soil depends on spatial scale. We show this by means of a nested analysis of covariance of soils sampled on a balanced nested design in a 16 km × 16 km area in eastern England. We used principal components analysis on the DRS to obtain a reduced number of variables while retaining key variation. The first principal component accounted for 99.8% of the total variance, the second for 0.14%. Nested analysis of the variation in the CEC and the two principal components showed that the substantial variance components are at the > 2000-m scale. This is probably the result of differences in soil composition due to parent material. We then developed a model to predict CEC from the DRS and used partial least squares (PLS) regression do to so. Leave-one-out cross-validation results suggested a reasonable predictive capability (R2 = 0.71 and RMSE = 0.048 molc kg− 1). However, the results from the independent validation were not as good, with R2 = 0.27, RMSE = 0.056 molc kg− 1 and an overall correlation of 0.52. This would indicate that DRS may not be useful for predictions of CEC. When we applied the analysis of covariance between predicted and observed we found significant scale-dependent correlations at scales of 50 and 500 m (0.82 and 0.73 respectively). DRS measurements can therefore be useful to predict CEC if predictions are required, for example, at the field scale (50 m). This study illustrates that the relationship between DRS and soil properties is scale-dependent and that this scale dependency has important consequences for prediction of soil properties from DRS data

Hydrochemical variations and contaminant load in the Rio Tinto (Spain) during flood events

The aim of this work is to study the hydrochemical variations during flood events in the Rio Tinto, SW Spain. Three separate rainfall/flood events were monitored in October 2004 following the dry season. In general, concentrations markedly increased following the first event (Fe from 99 to 1130 mg/L; Q(max) = 0.78 m(3)/s) while dissolved loads peaked in the second event (Fe = 7.5 kg/s, Cu = 0.83 kg/s, Zn = 0.82 kg/s; Q(max) = 77 m(3)/s) and discharge in the third event (Q(max) = 127 m(3)/s). This pattern reflects a progressive depletion of metals and sulphate stored in the dry summer as soluble evaporitic salt minerals and concentrated pore fluids, with dilution by freshwater becoming increasingly dominant as the month progressed. Variations in relative concentrations were attributed to oxyhydroxysulphate Fe precipitation, to relative changes in the sources of acid mine drainage (e.g. salt minerals, mine tunnels, spoil heaps etc.) and to differences in the rainfall distributions along the catchment. The contaminant load carried by the river during October 2004 was enormous, totalling some 770 t of Fe, 420 t of Al, 100 t of Cu, 100 t of Zn and 71 t of Mn. This represents the largest recorded example of this flush-out process in an acid mine drainage setting. Approximately 1000 times more water and 1408 200 times more dissolved elements were carried by the river during October 2004 than during the dry, low-flow conditions of September 2004, highlighting the key role of flood Events in the annual pollutant transport budget of semi-arid and and systems and the need to monitor these events in detail in order to accurately quantify pollutant transport. (c) 2007 Elsevier B.V. All rights reserved.

Incorporation of cis-9,trans-11 or trans-10,cis-12 conjugated linoleic acid into plasma and cellular lipids in healthy men

This study investigated the incorporation of cis-9,trans-11 conjugated linoleic acid (c9,t11 CLA) and trans-10,cis-12-CLA (t10,c12 CLA) into plasma and peripheral blood mononuclear cell (PBMC) lipids when consumed as supplements highly enriched in these isomers. Healthy men (n = 49, age 31 +/- 8 years) consumed one, two, and four capsules containing similar to600 mg of either c9,t11 CIA or t10,c12 CLA per capsule for sequential 8 week periods followed by a 6 week washout before consuming the alternative isomer. Both isomers were incorporated in a dosedependent manner into plasma phosphatidylcholine (PC) (c9,t11 CLA r = 0.779, t10,c12 CLA r = 0.738; P < 0.0001) and cholesteryl ester (CE) (c9,t11 CLA r = 0.706, t10,c12 CLA r = 0.788; P < 0.0001). Only t10,c12 CLA was enriched in plasma nonesterified fatty acids. Both c9,t11 CIA and t10,c12 CLA were incorporated linearly into PBMC total lipids (r = 0.285 and r = 0.273, respectively; P < 0.0005). The highest concentrations of c9,t11 CLA and t10,c12 CLA in PBMC lipids were 3- to 4-fold lower than those in plasma PC and CE. These data suggest that the level of intake is a major determinant of plasma and PBMC CLA content, although PBMCs appear to incorporate both CLA isomers less readily.

Incorporation of cis-9, trans-11 conjugated linoleic acid and vaccenic acid (trans-11 18 : 1) into plasma and leucocyte lipids in healthy men consuming dairy products naturally enriched in these fatty acids

The present study investigated whether consuming dairy products naturally enriched in cis-9, trans-11 (c9,t11) conjugated linoleic acid (CLA) by modification of cattle feed increases the concentration of this isomer in plasma and cellular lipids in healthy men. The study had a double-blind cross-over design. Subjects aged 34-60 years consumed dairy products available from food retailers for 1 week and then either control (0.17 g c9,t11 CLA/d; 0.31 g trans-vaccenic acid (tVA)/d) or CLA-enriched (1.43 g c9,t11 CLA/d; 4.71 g tVA/d) dairy products for 6 weeks. After 7 weeks washout, this was repeated with the alternate products. c9,t11 CLA concentration in plasma lipids was lower after consuming the control products, which may reflect the two-fold greater c9,t11 CLA content of the commercial products. Consuming the CLA-enriched dairy products increased the c9,t11 CLA concentration in plasma phosphatidylcholine (PC) (38 %; P=0.035), triacylglycerol (TAG) (22 %; P < 0.0001) and cholesteryl esters (205 %; P < 0.0001), and in peripheral blood mononuclear cells (PBMC) (238 %; P < 0.0001), while tVA concentration was greater in plasma PC (65 %; P=0.035), TAG (98 %; P=0.001) and PBMC (84 %; P=0.004). Overall, the present study shows that consumption of naturally enriched dairy products in amounts similar to habitual intakes of these foods increased the c9,t11 CLA content of plasma and cellular lipids.

An ex-ante evaluation of the economic impact of Bt cotton adoption by spanish farmers facing the EU cotton sector reform

Cotton production in the European Union (EU) is limited to areas of Greece and Southern Spain (Andalusia). The 2004 reform of the EU cotton policy severely affected the profitability of the crop. In this article we analyze how the introduction of genetically modified (GM), insect-resistant cotton varieties (Bt cotton) might help EU cotton farmers to increase profitability and therefore face the cotton policy reform. We first study farmers’ attitudes toward adoption of Bt cotton varieties through a survey conducted in Andalusia (Southern Spain). The results show a positive attitude of Andalusian cotton farmers toward the Bt cotton varieties. Second, we perform an ex-ante analysis of the effects of introducing Bt cotton in Andalusia. Finally, we integrate the analysis of the effects of Bt cotton with the analysis of the EU cotton reform. Our results show that despite the significant economic benefits of Bt cotton, the current policy reform is likely to jeopardize the profitability of cotton production in the EU.

Pharmacological analysis of a dopamine D-2Short: G(alpha o) fusion protein expressed in Sf9 cells

A dopamine D-2Short receptor:G(alphao) fusion protein was expressed in Sf9 cells using the baculovirus expression system. [H-3]Spiperone bound to D-2Short:G(alphao) with a pK(d) approximate to 10. Dopamine stimulated the binding of [S-35]guanosine-5'-O-(3-thio)triphosphate (GTPgammaS) to D-2Short:G(alphao) expressed with Gbeta(1)gamma(2) (E-max > 460%; pEC(50) 5.43 +/- 0.06). Most of the putative D-2 antagonists behaved as inverse agonists (suppressing basal [S-35]GTPgammaS binding) at D-2Short:G(alphao)/Gbeta(1)gamma(2) although (-)-suipiride and ziprasidone were neutral antagonists. Competition of [H-3]spiperone binding by dopamine and 10,11-dihydroxy-N-n-propylnorapo-morphine revealed two, binding sites of different affinities, even in the presence of GTP (100 muM). The D-2Short:G(alphao) fusion protein is therefore a good model for characterising D-2 receptors. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Interaction of the D-2short dopamine receptor with G proteins: analysis of receptor G protein selectivity

The human D-2short (D-2S) dopamine receptor has been expressed together with the G proteins Gi2 and Go in insect cells using the baculovirus system. Levels of receptor were determined using [H-3]spiperone binding. Levels of G protein heterotrimer were determined using quantitative Western blot and using [S-35]GTPgammaS saturation binding experiments. Levels of the receptor and G protein and the receptor/G protein ratio were similar in the two preparations. Stimulation of [S-35]GTPgammaS binding by a range of agonists occurred with higher relative efficacy and in some cases higher potency in the preparation expressing Go, indicating that interaction of the D-2S receptor is more efficient with this G protein. The effects of various G protein-selective agents on 10,11-dihydroxy-N-n-propylnorapomorphine ([H-3]NPA) binding were used to examine the receptor/G protein complex in the two preparations. Suramin inhibited [H-3]NPA binding with slightly higher potency in the Gi2 preparation, whereas GppNHp inhibited [H-3]NPA binding with greater potency (similar to6-fold) in the Go preparation. This may imply that the G protein is more readily activated in the D-2S/Go preparation. [H-3]Spiperone binding occurred with an increased B-max in the presence of suramin in the Go preparation but not in the Gi2 preparation, suggesting a higher affinity interaction between the free receptor and this G protein. It is concluded that the higher efficiency activation of Go by the D-2S receptor may be a function of higher affinity receptor/G protein interaction as well as a greater ability to activate the G protein. (C) 2003 Elsevier Science Inc. All rights reserved.

Dinuclear complexes of M-II thiocyanate (M = Ni and Cu) containing a tridentate Schiff-base ligand: synthesis, structural diversity and magnetic properties

A dinuclear Ni-II complex, [Ni-2(L)(2)(H2O)(NCS)(2)]center dot 3H(2)O (1) in which the metal atoms are bridged by one water molecule and two mu(2)-phenolate ions, and a thiocyanato-bridged dimeric Cull complex, [Cu(L)NCS](2) (2) [L = tridentate Schiff-base ligand, N-(3-aminopropyl)salicylaldimine, derived from 1:1 condensation of salicylaldehyde and 1,3-diaminopropane], have been synthesized and characterized by IR and UV/Vis spectroscopy, cyclic voltammetry and single-crystal X-ray diffraction studies. The structure of 1 consists of dinuclear units with crystallographic C-2 symmetry in which each Ni-II atom is in a distorted octahedral environment. The Ni-O distance and the Ni-O-Ni angle, through the bridged water molecule, are 2.240(11) angstrom and 82.5(5)degrees, respectively. The structure of 2 consists of dinuclear units bridged asymmetrically by di-mu(1,3)-NCS ions; each Cull ion is in a square-pyramidal environment with tau = 0.25. Variable-temperature magnetic susceptibility studies indicate the presence of dominant ferromagnetic exchange coupling in complex 1 with J = 3.1 cm(-1), whereas complex 2 exhibits weak antiferromagnetic coupling between the Cu-II centers with J = -1.7 cm(-1). ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

21-Deoxycortisone (17 alpha-hydroxy4-pregnene-3,11,20-trione)

The title compound, C21H28O4, a synthetic glucocorticoid, crystallizes with a single molecule in the asymmetric unit. Ring A is almost in a half-chair conformation, rings B and C are almost in chair conformations, and ring D is between a twist and a 13 beta-envelope conformation. The A/B ring junction is quasi-trans, whereas the B/C and C/D ring junctions both approach trans characteristics. The molecule as a whole is slightly convex towards the beta side, with an angle of 9.60 (2)degrees between the C10-C19 and C13-C18 vectors. Molecular-packing and hydrogen-bonding (both intra- and inter-molecular) interactions play a major role in the structural association of the compound.

Water-soluble tripeptide A beta(9-11) forms amyloid-like fibrils and exhibits neurotoxicity

A water-soluble, hydrophilic tripeptide GYE, having sequence identity with the N-terminal segment of amyloid peptides A,beta(9-11), upon self-association exhibits amyloid-like fibrils and significant neurotoxicity towards the Neuro2A cell line. However, the tripeptides GFE and GWE, in which the centrally located tyrosine residue has been replaced by phenylalanine or tryptophan, fail to show amyloidogenic behavior and exhibit little or no neurotoxicity.

Opposing effects of cis-9,trans-11 and trans-10,cis-12 conjugated linoleic acid on blood lipids in healthy humans

Background: Conjugated linoleic acid (CLA) is reported to have weight-reducing and antiatherogenic properties when fed to laboratory animals. However, the effects of CLA on human health and, in particular, the effects of individual CLA isomers are unclear. Objective: This study investigated the effects of 3 doses of highly enriched cis-9,trans-11 (0.59, 1.19, and 2.38 g/d) or trans-10,cis-12 (0.63, 1.26, and 2.52 g/d) CLA preparations on body composition, blood lipid profile, and markers of insulin resistance in healthy men. Design: Healthy men consumed 1, 2, and 4 capsules sequentially, containing either 80% cis-9,trans-11 CLA or 80% trans-10,cis-12 CLA for consecutive 8-wk periods. This phase was followed by a 6-wk washout and a crossover to the other isomer. Results: Body composition was not significantly affected by either isomer of CLA. Mean plasma triacylglycerol concentration was higher during supplementation with trans-10,cis-12 CLA than during that with cis-9,trans-11 CLA, although there was no influence of dose. There were significant effects of both isomer and dose on plasma total cholesterol and LDL-cholesterol concentrations but not on HDL-cholesterol concentration. The ratios of LDL to HDL cholesterol and of total to HDL cholesterol were higher during supplementation with trans-10,cis-12 CLA than during that with cis-9,trans-11 CLA. CLA supplementation had no significant effect on plasma insulin concentration, homeostasis model for insulin resistance, or revised quantitative insulin sensitivity check index. Conclusion: Divergent effects of cis-9,trans-11 CLA and trans10,cis-12 CLA appear on the blood lipid profile in healthy humans: trans-10,cis-12 CLA increases LDL:HDL cholesterol and total:HDL cholesterol, whereas cis-9,trans-11 CLA decreases them.