Establishment of a Cross-European Field Site Network in the ALARM Project for Assessing Large-Scale Changes in Biodiversity

The field site network (FSN) plays a central role in conducting joint research within all Assessing Large-scale Risks for biodiversity with tested Methods (ALARM) modules and provides a mechanism for integrating research on different topics in ALARM on the same site for measuring multiple impacts on biodiversity. The network covers most European climates and biogeographic regions, from Mediterranean through central European and boreal to subarctic. The project links databases with the European-wide field site network FSN, including geographic information system (GIS)-based information to characterise the test location for ALARM researchers for joint on-site research. Maps are provided in a standardised way and merged with other site-specific information. The application of GIS for these field sites and the information management promotes the use of the FSN for research and to disseminate the results. We conclude that ALARM FSN sites together with other research sites in Europe jointly could be used as a future backbone for research proposals

Inclusion of nonlinear demand-supply relationships within large-scale partial equilibrium linear programming models

This paper presents a new method for the inclusion of nonlinear demand and supply relationships within a linear programming model. An existing method for this purpose is described first and its shortcomings are pointed out before showing how the new approach overcomes those difficulties and how it provides a more accurate and 'smooth' (rather than a kinked) approximation of the nonlinear functions as well as dealing with equilibrium under perfect competition instead of handling just the monopolistic situation. The workings of the proposed method are illustrated by extending a previously available sectoral model for the UK agriculture.

ALARM: Assessing large-scale environment risks for biodiversity with tested methods

The EU-funded research project ALARM will develop and test methods and protocols for the assessment of large-scale environmental risks in order to minimise negative human impacts. Research focuses on the assessment and forecast of changes in biodiversity and in the structure, function, and dynamics of ecosystems. This includes the relationships between society, the economy and biodiversity.

Large-scale functional expression of WT and truncated human adenosine A(2A) receptor in Pichia pastoris bioreactor cultures

Background: The large-scale production of G-protein coupled receptors (GPCRs) for functional and structural studies remains a challenge. Recent successes have been made in the expression of a range of GPCRs using Pichia pastoris as an expression host. P. pastoris has a number of advantages over other expression systems including ability to post-translationally modify expressed proteins, relative low cost for production and ability to grow to very high cell densities. Several previous studies have described the expression of GPCRs in P. pastoris using shaker flasks, which allow culturing of small volumes (500 ml) with moderate cell densities (OD600 similar to 15). The use of bioreactors, which allow straightforward culturing of large volumes, together with optimal control of growth parameters including pH and dissolved oxygen to maximise cell densities and expression of the target receptors, are an attractive alternative. The aim of this study was to compare the levels of expression of the human Adenosine 2A receptor (A(2A)R) in P. pastoris under control of a methanol-inducible promoter in both flask and bioreactor cultures. Results: Bioreactor cultures yielded an approximately five times increase in cell density (OD600 similar to 75) compared to flask cultures prior to induction and a doubling in functional expression level per mg of membrane protein, representing a significant optimisation. Furthermore, analysis of a C-terminally truncated A2AR, terminating at residue V334 yielded the highest levels (200 pmol/mg) so far reported for expression of this receptor in P. pastoris. This truncated form of the receptor was also revealed to be resistant to C-terminal degradation in contrast to the WT A(2A)R, and therefore more suitable for further functional and structural studies. Conclusion: Large-scale expression of the A(2A)R in P. pastoris bioreactor cultures results in significant increases in functional expression compared to traditional flask cultures.

A collaborative working environment for a large scale environmental model

Large scientific applications are usually developed, tested and used by a group of geographically dispersed scientists. The problems associated with the remote development and data sharing could be tackled by using collaborative working environments. There are various tools and software to create collaborative working environments. Some software frameworks, currently available, use these tools and software to enable remote job submission and file transfer on top of existing grid infrastructures. However, for many large scientific applications, further efforts need to be put to prepare a framework which offers application-centric facilities. Unified Air Pollution Model (UNI-DEM), developed by Danish Environmental Research Institute, is an example of a large scientific application which is in a continuous development and experimenting process by different institutes in Europe. This paper intends to design a collaborative distributed computing environment for UNI-DEM in particular but the framework proposed may also fit to many large scientific applications as well.

MIMO Wiener model identification for large scale fading of wireless mobile communications links

The large scale fading of wireless mobile communications links is modelled assuming the mobile receiver motion is described by a dynamic linear system in state-space. The geometric relations involved in the attenuation and multi-path propagation of the electric field are described by a static non-linear mapping. A Wiener system subspace identification algorithm in conjunction with polynomial regression is used to identify a model from time-domain estimates of the field intensity assuming a multitude of emitters and an antenna array at the receiver end.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

Recent patterns of change in vegetation structure and tree composition of British broadleaved woodland: evidence from large-scale surveys

Evidence is presented of widespread changes in structure and species composition between the 1980s and 2003–2004 from surveys of 249 British broadleaved woodlands. Structural components examined include canopy cover, vertical vegetation profiles, field-layer cover and deadwood abundance. Woods were located in 13 geographical localities and the patterns of change were examined for each locality as well as across all woods. Changes were not uniform throughout the localities; overall, there were significant decreases in canopy cover and increases in sub-canopy (2–10 m) cover. Changes in 0.5–2 m vegetation cover showed strong geographic patterns, increasing in western localities, but declining or showing no change in eastern localities. There were significant increases in canopy ash Fraxinus excelsior and decreases in oak Quercus robur/petraea. Shrub layer ash and honeysuckle Lonicera periclymenum increased while birch Betula spp. hawthorn Crataegus monogyna and hazel Corylus avellana declined. Within the field layer, both bracken Pteridium aquilinum and herbs increased. Overall, deadwood generally increased. Changes were consistent with reductions in active woodland management and changes in grazing and browsing pressure. These findings have important implications for sustainable active management of British broadleaved woodlands to meet silvicultural and biodiversity objectives.