Accessing biodiversity resources in computational environments from workflow applications

In the Biodiversity World (BDW) project we have created a flexible and extensible Web Services-based Grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. The current Web Servicesbased Grid environment enables execution of the BDW workflow tasks in remote nodes but with a limited scope. The next step in the evolution of the BDW architecture is to enable workflow tasks to utilise computational resources available within and outside the BDW domain. We describe the present BDW architecture and its transition to a new framework which provides a distributed computational environment for mapping and executing workflows in addition to bringing together heterogeneous resources and analytical tools.

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.

The measurement of maternal plasma corticotropin-releasing factor (CRF) and CRF-binding protein improves the early prediction of preeclampsia

In the present study we measured maternal plasma concentrations of two placental neurohormones, corticotropin-releasing factor (CRF) and CRF-binding protein (CRF-BP), in 58 at-risk pregnant women consecutively enrolled between 28 and 29 wk of pregnancy to evaluate whether their evaluation may predict third trimester-onset preeclampsia ( PE). The statistical significance was assessed by t test. The cut-off points for defining altered CRF and CRF-BP levels for prediction of PE were chosen by receiving operator characteristics curve analysis, and the probability of developing PE was calculated for several combinations of hormone testing results. CRF and CRF-BP levels were significantly ( both P < 0.0001) higher and lower, respectively, in the patients (n = 20) who later developed PE than in those who did not present PE at follow-up. CRF at the cut-off 425.95 pmol/liter achieved a sensitivity of 94.8% and a specificity of 96.9%, whereas CRF-BP at the cut-off 125.8 nmol/liter combined a sensitivity of 92.5% and a specificity of 82.5% as single markers for prediction of PE. The probability of PE was 34.5% in the whole study population, 93.75% when both CRF and CRF-BP levels were changed, and 0% if both hormone markers were unaltered. The measurement of CRF and CRF-BP levels may add significant prognostic information for predicting PE in at-risk pregnant women.

Design, synthesis and computational modelling of aromatic tweezer-molecules as models for chain-folding polymer blends

Novel 'tweezer-type' complexes that exploit the interactions between pi-electron-rich pyrenyl groups and pi-electron deficient diimide units have been designed and synthesised. The component molecules leading to complex formation were accessed readily from commercially available starting materials through short and efficient syntheses. Analysis of the resulting complexes, using the visible charge-transfer band, revealed association constants that increased sequentially from 130 to 11,000 M-1 as increasing numbers of pi-pi-stacking interactions were introduced into the systems. Computational modelling was used to analyse the structures of these complexes, revealing low-energy chain-folded conformations for both components, which readily allow close, multiple pi-pi-stacking and hydrogen bonding to be achieved. In this paper, we give details of our initial studies of these complexes and outline how their behaviour could provide a basis for designing self-healing polymer blends for use in adaptive coating systems. (C) 2008 Elsevier Ltd. All rights reserved.

Geometrical isomers of [TEAH][Co(L-Se)(2)]center dot xH(2)O: synthesis, structural, spectroscopic and computational studies

Trans-1, [HNEt3][Co-III(L-Se)(2)]center dot H2O and cis-1, [HNEt3][Co-III(L-Se)(2)]center dot 3H(2)O have been synthesized and characterized by single-crystal X-ray studies. The counter ion Et3NH+ plays a crucial role in the crystal packing leading to the formation of two distinctly different supramolecular assemblies in the two complexes. In trans-1, Co-bisphenolate units and triethylamine molecules are arranged in a linear fashion leading to a supramolecular columnar assembly along the crystallographic a-axis. In this assembly, triethylammonium ions are sandwiched between successive Co-bisphenolate units and act as gluing agents joining Co-bisphenolate units on either side through C-H center dot center dot center dot pi interactions. In sharp contrast to trans-1, Co-bisphenolate units and triethylammonium ions in cis-1 are arranged in a helical supramolecular assembly through similar C-H center dot center dot center dot pi interactions along the crystallographic b-axis. The Se center dot center dot center dot Se van der Waals interactions may be responsible for the predominant occurrence of the cis-isomer. The cyclic voltammetric studies showed quasi-reversible waves for the cobalt(III) -> cobalt(II) reductions with E-1/2 = 0.635 and 0.628 V vs. Ag/AgCl for cis-1 (at similar to 5 degrees C) and trans-1 (at similar to 25 degrees C), respectively. DFT calculations show that the trans-form is the thermodynamic product with higher stability than the cis-one, which is consistent with the variable temperature H-1 NMR studies

Ab initio prediction of the infrared-absorption spectrum of the C2Cl radical

The three lowest (1(2)A('), 2(2)A('), and 1(2)A(')) potential-energy surfaces of the C2Cl radical, correlating at linear geometries with (2)Sigma(+) and (2)Pi states, have been studied ab initio using a large basis set and multireference configuration-interaction techniques. The electronic ground state is confirmed to be bent with a very low barrier to linearity, due to the strong nonadiabatic electronic interactions taking place in this system. The rovibronic energy levels of the (CCCl)-C-12-C-12-Cl-35 isotopomer and the absolute absorption intensities at a temperature of 5 K have been calculated, to an upper limit of 2000 cm(-1), using diabatic potential-energy and dipole moment surfaces and a recently developed variational method. The resulting vibronic states arise from a strong mixture of all the three electronic components and their assignments are intrinsically ambiguous. (c) 2005 American Institute of Physics.

Ab initio prediction of the infrared absorption spectrum of the C2Br radical

The first three electronic states (1(2)A', 2(2)A', 1(2)A '') of the C2Br radical, correlating at linear geometries with (2)Sigma(+) and (2)Pi states, have been studied ab initio, using Multi Reference Configuration Interaction techniques. The electronic ground state is found to have a bent equilibrium geometry, R-CC = 1.2621 angstrom, R-CBr = 1.7967 angstrom, < CCBr 156.1 degrees, with a very low barrier to linearity. Similarly to the valence isoelectronic radicals C2F and C2Cl, this anomalous behaviour is attributed to a strong three-state non-adiabatic electronic interaction. The Sigma, Pi(1/2), Pi(3/2) vibronic energy levels and their absolute infrared absorption intensities at a temperature of 5K have been calculated for the (CCBr)-C-12-C-12-Br-79 isotopomer, to an upper limit of 2000 cm(-1), using ab initio diabatic potential energy and dipole moment surfaces and a recently developed variational method.

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C( 9)-H groups of adjacent molecules. In the liquid phase, the presence of C-(HO)-O-... bonded forms is revealed by both vibrational and NMR spectroscopy. A Delta H value of - 8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-(HO)-O-... contacts relative to the C(9)-(HO)-O-... ones.

Achieving quality through statistical prediction for building services systems

The application of prediction theories has been widely practised for many years in many industries such as manufacturing, defence and aerospace. Although these theories are not new, their application has not been widely used within the building services industry. Collectively, the building services industry should take a deeper look at these approaches in comparison with the traditional deterministic approaches currently being practised. By extending the application into this industry, this paper seeks to provide the industry with an overview of how simplified stochastic modelling coupled with availability and reliability predictions using historical data compiled from various sources could enhance the quality of building services systems.

Prediction of Parkinson's disease tremor onset using artificial neural networks

In this paper we present the initial results using an artificial neural network to predict the onset of Parkinson's Disease tremors in a human subject. Data for the network was obtained from implanted deep brain electrodes. A tuned artificial neural network was shown to be able to identify the pattern of the onset tremor from these real time recordings.

A swarm intelligence method for feature tracking in AMV derivation

Feature tracking is a key step in the derivation of Atmospheric Motion Vectors (AMV). Most operational derivation processes use some template matching technique, such as Euclidean distance or cross-correlation, for the tracking step. As this step is very expensive computationally, often shortrange forecasts generated by Numerical Weather Prediction (NWP) systems are used to reduce the search area. Alternatives, such as optical flow methods, have been explored, with the aim of improving the number and quality of the vectors generated and the computational efficiency of the process. This paper will present the research carried out to apply Stochastic Diffusion Search, a generic search technique in the Swarm Intelligence family, to feature tracking in the context of AMV derivation. The method will be described, and we will present initial results, with Euclidean distance as reference.