Towards data warehousing and mining of protein unfolding simulation data

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

A longitudinal study of carbon disclosure strategy: evidence from utility, energy and mining industries in the UK

The paper investigates how energy-intensive industries respond to the recent government-led carbon emission schemes through the content analysis of 306 annual and standalone reports of 25 UK listed companies from 2004 to 2012. This period of reporting captures the trend and development of corporate disclosures on carbon emissions after the launch of EU Emissions Trading Schemes (ETS) and Climate Change Act (CCA) 2008. It is found that in corresponding to strategic legitimacy theory, there is an increase in both the quality and quantity of carbon disclosures as a response to these initiatives. However, the change is gradual, which reflects in the achievement of peak disclosure period two years after the launch. It indicates that the new legislations have a lasting impact on the discourses rather than an immediate legitimacy threat from the perspective of institutional legitimacy theory. The results also show that carbon disclosures are an institutionalised practice as companies in the same industries and/or with same carbon trading account status appear to imitate and adopt the industry’s ‘best practice’ disclosure strategy to maintain legitimacy. The trend analysis suggests that the overall disclosure practice is still in its infant stage, especially in the reporting of quantitative and monetary items. The paper contributes to the social and environmental accounting literature by adopting both strategic and institutional view of legitimacy, which explains why carbon disclosures evolve in a specific way to meet the expectation of various stakeholders.

The economics of enhanced landfill mining: private and societal performance drivers

This paper addresses the economics of Enhanced Landfill Mining (ELFM) both from a private point of view as well as from a society perspective. The private potential is assessed using a case study for which an investment model is developed to identify the impact of a broad range of parameters on the profitability of ELFM. We found that especially variations in Waste-to-Energy (WtE efficiency, electricity price, CO2-price, WtE investment and operational costs) and ELFM support explain the variation in economic profitability measured by the Internal Rate of Return. To overcome site-specific parameters we also evaluated the regional ELFM potential for the densely populated and industrial region of Flanders (north of Belgium). The total number of potential ELFM sites was estimated using a 5-step procedure and a simulation tool was developed to trade-off private costs and benefits. The analysis shows that there is a substantial economic potential for ELFM projects on the wider regional level. Furthermore, this paper also reviews the costs and benefits from a broader perspective. The carbon footprint of the case study was mapped in order to assess the project’s net impact in terms of greenhouse gas emissions. Also the impacts of nature restoration, soil remediation, resource scarcity and reduced import dependence were valued so that they can be used in future social cost-benefit analysis. Given the complex trade-off between economic, social and environmental issues of ELFM projects, we conclude that further refinement of the methodological framework and the development of the integrated decision tools supporting private and public actors, are necessary.

The Geology and Mineralogy of the Independence Mining District

From 1888 until 1893 the district was a booming mining camp. Seven stamp mills were running and ore was be­ing mined from the Independence, King Solomon, Poorman, Golden, Hidden Treasure and Crown claims. The town of Independence, which was on the Boulder River at the fork of Basin Creek, boasted a population of 400 people.

Geology and Ore Deposits of the Clinton Mining District

This report includes the results of geological investigation of the Clinton Mining District and the Hidden Treasure Mine.The Clinton Mining District is an unorganized mining dis­trict situated in the Garnet Range two and one-half miles northeast of the town of Clinton, Montana, which is on the Northern Pacific Railway and the Chicago, Milwaukee, St. Paul, and Pacific Railroad seventeen miles east of the city of Missoula. The district is in the same range of mountains as the Gar­net Mining District and the drainage from the district covered is to the south into the Hell Gate or Clarks Fork of the Colum­bia River. The main stream is known as Trail creek, which runs in a southerly direction from the area studied.