The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

Validation of three new measure-correlate-predict models for the long-term prospection of the wind resource

The estimation of the long-term wind resource at a prospective site based on a relatively short on-site measurement campaign is an indispensable task in the development of a commercial wind farm. The typical industry approach is based on the measure-correlate-predict �MCP� method where a relational model between the site wind velocity data and the data obtained from a suitable reference site is built from concurrent records. In a subsequent step, a long-term prediction for the prospective site is obtained from a combination of the relational model and the historic reference data. In the present paper, a systematic study is presented where three new MCP models, together with two published reference models �a simple linear regression and the variance ratio method�, have been evaluated based on concurrent synthetic wind speed time series for two sites, simulating the prospective and the reference site. The synthetic method has the advantage of generating time series with the desired statistical properties, including Weibull scale and shape factors, required to evaluate the five methods under all plausible conditions. In this work, first a systematic discussion of the statistical fundamentals behind MCP methods is provided and three new models, one based on a nonlinear regression and two �termed kernel methods� derived from the use of conditional probability density functions, are proposed. All models are evaluated by using five metrics under a wide range of values of the correlation coefficient, the Weibull scale, and the Weibull shape factor. Only one of all models, a kernel method based on bivariate Weibull probability functions, is capable of accurately predicting all performance metrics studied.

Transitions towards co-management: the process of marine resource management devolution in three east African countries

Communities are increasingly empowered with the ability and responsibility of working with national governments to make decisions about marine resources in decentralized co-management arrangements. This transition toward decentralized management represents a changing governance landscape. This paper explores the transition to decentralisation in marine resource management systems in three East African countries. The paper draws upon expert opinion and literature from both political science and linked social-ecological systems fields to guide exploration of five key governance transition concepts in each country: (1) drivers of change; (2) institutional arrangments; (3 institutional fit; (4) actor interactions; and (5) adaptive management. Key findings are that decentralized management in the region was largely donor-driven and only partly tranferred power to local stakeholders. However, increased accountability created a degree of democracy in regards to natural resource governance that was not previously present. Additionally, increased local-level adaptive management has emerged in most systems and, to date, this experimental management has helped to change resource user's views from metaphysical to more scientific cause-and-effect attribution of changes to resource conditions.

Artisanal gold mining at the margins of mineral resource governance : a case from Tanzania

This article discusses the character of mineral resource governance at the margins of the state in Tanzania and the way artisanal gold miners are incorporated into mineral sector transformation. The landscape of mineral resource exploitation has changed dramatically over the past 20 years: processes of economic liberalisation have heralded massive foreign investment in large-scale gold mining, while also stimulating artisanal activities. Against this background, the article shows how artisanal gold miners are affected by contradictory processes: some have become integrated with state institutions and legal processes, while others, the large majority, are either further excluded or incorporated in ways that exacerbate insecurity and exploitation, underpinned by socio-economic inequalities. These processes are compounded by the actions of large-scale and medium-scale gold mining companies and by poor local governance. It is open to debate whether this will bring improved integration and welfare for artisanal mining communities or new forms of exclusion, although evidence suggests the latter.

Groundwater residence time distributions in peatlands: implications for peat decomposition and accumulation

Peat soils consist of poorly decomposed plant detritus, preserved by low decay rates, and deep peat deposits are globally significant stores in the carbon cycle. High water tables and low soil temperatures are commonly held to be the primary reasons for low peat decay rates. However, recent studies suggest a thermodynamic limit to peat decay, whereby the slow turnover of peat soil pore water may lead to high concentrations of phenols and dissolved inorganic carbon. In sufficient concentrations, these chemicals may slow or even halt microbial respiration, providing a negative feedback to peat decay. We document the analysis of a simple, one-dimensional theoretical model of peatland pore water residence time distributions (RTDs). The model suggests that broader, thicker peatlands may be more resilient to rapid decay caused by climate change because of slow pore water turnover in deep layers. Even shallow peat deposits may also be resilient to rapid decay if rainfall rates are low. However, the model suggests that even thick peatlands may be vulnerable to rapid decay under prolonged high rainfall rates, which may act to flush pore water with fresh rainwater. We also used the model to illustrate a particular limitation of the diplotelmic (i.e., acrotelm and catotelm) model of peatland structure. Model peatlands of contrasting hydraulic structure exhibited identical water tables but contrasting RTDs. These scenarios would be treated identically by diplotelmic models, although the thermodynamic limit suggests contrasting decay regimes. We therefore conclude that the diplotelmic model be discarded in favor of model schemes that consider continuous variation in peat properties and processes.

Waste cooking oil as an energy resource: review of Chinese policies

Converting waste cooking oil into biofuel represents a three-win solution, dealing simultaneously with food security, pollution, and energy security. In this paper, we encode the policy documents of waste cooking oil refining biofuel in China based on content analysis, and explore the related policies from the two dimensions as basic policy tools and enterprises supply chain. Research indicates the weak institution coordination of policy issuing entities. Also, the findings show that tools of regulatory control and goal planning are overused. Policies of government procurement, outsourcing and biofuel consumption are relatively scarce. Generally, government focuses more on formulating policies from the strategic, administrative and regulatory aspects, while less on market-oriented initiatives as funding input and financial support.

Changing building user attitude and organisational policy towards sustainable resource use in healthcare

Health care provision is significantly impacted by the ability of the health providers to engineer a viable healthcare space to support care stakeholders needs. In this paper we discuss and propose use of organisational semiotics as a set of methods to link stakeholders to systems, which allows us to capture clinician activity, information transfer, and building use; which in tern allows us to define the value of specific systems in the care environment to specific stakeholders and the dependence between systems in a care space. We suggest use of a semantically enhanced building information model (BIM) to support the linking of clinician activity to the physical resource objects and space; and facilitate the capture of quantifiable data, over time, concerning resource use by key stakeholders. Finally we argue for the inclusion of appropriate stakeholder feedback and persuasive mechanism, to incentivise building user behaviour to support organisational level sustainability policy.

Enriching enterprise resource planning systems for strategic advantage: a semiotic motivated approach

Enterprise Resource Planning is often endorsed as a means to facilitate strategic advantage for businesses. The scarcity of resources is the method by which some businesses maintain their position. However, the ubiquitous trend towards the adoption of Enterprise Resourcing Planning systems coupled with market saturation makes the promise of advantage less compelling. Reported in this paper is a proposed solution based upon semiotic theory that takes a typical Enterprise Resource Planning deployment scenario and shapes it according to the needs of people in post-implementation contexts to leverage strategic advantage in different ways.

Doing more harm than good? Community based natural resource management and the neglect of local institutions in policy development

Approaches to natural resource management emphasise the importance of involving local people and institutions in order to build capacity, limit costs, and achieve environmental sustainability. Governments worldwide, often encouraged by international donors, have formulated devolution policies and legal instruments that provide an enabling environment for devolved natural resource management. However, implementation of these policies reveals serious challenges. This article explores the effects of limited involvement of local people and institutions in policy development and implementation. An in-depth study of the Forest Policy of Malawi and Village Forest Areas in the Lilongwe district provides an example of externally driven policy development which seeks to promote local management of natural resources. The article argues that policy which has weak ownership by national government and does not adequately consider the complexity of local institutions, together with the effects of previous initiatives on them, can create a cumulative legacy through which destructive resource use practices and social conflict may be reinforced. In short, poorly developed and implemented community based natural resource management policies can do considerably more harm than good. Approaches are needed that enable the policy development process to embed an in-depth understanding of local institutions whilst incorporating flexibility to account for their location-specific nature. This demands further research on policy design to enable rigorous identification of positive and negative institutions and ex-ante exploration of the likely effects of different policy interventions.

The coevolution of two phytoplankton species on a single resource: allelopathy as a pseudo-mixotrophy

Without the top-down effects and the external/physical forcing, a stable coexistence of two phytoplankton species under a single resource is impossible — a result well known from the principle of competitive exclusion. Here I demonstrate by analysis of a mathematical model that such a stable coexistence in a homogeneous media without any external factor would be possible, at least theoretically, provided (i) one of the two species is toxin producing thereby has an allelopathic effect on the other, and (ii) the allelopathic effect exceeds a critical level. The threshold level of allelopathy required for the coexistence has been derived analytically in terms of the parameters associated with the resource competition and the nutrient recycling. That the extra mortality of a competitor driven by allelopathy of a toxic species gives a positive feed back to the algal growth process through the recycling is explained. And that this positive feed back plays a pivotal role in reducing competition pressures and helping species succession in the two-species model is demonstrated. Based on these specific coexistence results, I introduce and explain theoretically the allelopathic effect of a toxic species as a ‘pseudo-mixotrophy’—a mechanism of ‘if you cannot beat them or eat them, just kill them by chemical weapons’. The impact of this mechanism of species succession by pseudo-mixotrophy in the form of alleopathy is discussed in the context of current understanding on straight mixotrophy and resource-species relationship among phytoplankton species.

Natural disaster accounting bias and its equivalence across genetic resource stocks

Two sources of bias arise in conventional loss predictions in the wake of natural disasters. One source of bias stems from neglect of accounting for animal genetic resource loss. A second source of bias stems from failure to identify, in addition to the direct effects of such loss, the indirect effects arising from implications impacting animal-human interactions. We argue that, in some contexts, the magnitude of bias imputed by neglecting animal genetic resource stocks is substantial. We show, in addition, and contrary to popular belief, that the biases attributable to losses in distinct genetic resource stocks are very likely to be the same. We derive the formal equivalence across the distinct resource stocks by deriving an envelope result in a model that forms the mainstay of enquiry in subsistence farming and we validate the theory, empirically, in a World-Society-for-the-Protection-of-Animals application

The drivers of multinational enterprise subsidiary entrepreneurship in China: a new resource-based view perspective

This paper extends the resource-based view (RBV) of the firm, as applied to multinational enterprises (MNEs), by distinguishing between two critical resource dimensions, namely relative resource superiority (capabilities) and slack. Both dimensions, in concert with specific environmental conditions, are required to increase entrepreneurial activities. We propose distinct configurations (three-way moderation effects) of capabilities, slack, and environmental factors (i.e. dynamism and hostility) to explain entrepreneurship. Using survey data from 66 Canadian subsidiaries operating in China, we find that higher subsidiary entrepreneurship requires both HR slack and strong downstream capabilities in subsidiaries, subject to the industry environment being dynamic and benign. However, high HR slack alone, in a dynamic and benign environment, but without the presence of strong capabilities, actually triggers the fewest initiatives, with HR slack redirected from entrepreneurial experimentation towards complacency and inefficiency. This paper has major implications for MNEs seeking to increase subsidiary entrepreneurship in fast growing emerging markets.

Enforcing service level agreements using an economically enhanced resource manager

Traditional resource management has had as its main objective the optimisation of throughput, based on parameters such as CPU, memory, and network bandwidth. With the appearance of Grid Markets, new variables that determine economic expenditure, benefit and opportunity must be taken into account. The SORMA project aims to allow resource owners and consumers to exploit market mechanisms to sell and buy resources across the Grid. SORMA’s motivation is to achieve efficient resource utilisation by maximising revenue for resource providers, and minimising the cost of resource consumption within a market environment. An overriding factor in Grid markets is the need to ensure that desired Quality of Service levels meet the expectations of market participants. This paper explains the proposed use of an Economically Enhanced Resource Manager (EERM) for resource provisioning based on economic models. In particular, this paper describes techniques used by the EERM to support revenue maximisation across multiple Service Level Agreements.