Enabling sharing and reuse of scientific data

The purpose of this study was to develop an understanding of the current state of scientific data sharing that stakeholders could use to develop and implement effective data sharing strategies and policies. The study developed a conceptual model to describe the process of data sharing, and the drivers, barriers, and enablers that determine stakeholder engagement. The conceptual model was used as a framework to structure discussions and interviews with key members of all stakeholder groups. Analysis of data obtained from interviewees identified a number of themes that highlight key requirements for the development of a mature data sharing culture.

Information system evolvability, feedback and pattern languages

Information systems for business are frequently heavily reliant on software. Two important feedback-related effects of embedding software in a business process are identified. First, the system dynamics of the software maintenance process can become complex, particularly in the number and scope of the feedback loops. Secondly, responsiveness to feedback can have a big effect on the evolvability of the information system. Ways have been explored to provide an effective mechanism for improving the quality of feedback between stakeholders during software maintenance. Understanding can be improved by using representations of information systems that are both service-based and architectural in scope. The conflicting forces that encourage change or stability can be resolved using patterns and pattern languages. A morphology of information systems pattern languages has been described to facilitate the identification and reuse of patterns and pattern languages. The kind of planning process needed to achieve consensus on a system's evolution is also considered.

c-Cbl mediates ubiquitination, degradation, and down-regulation of human protease-activated receptor 2

Mechanisms that arrest G-protein-coupled receptor (GPCR) signaling prevent uncontrolled stimulation that could cause disease. Although uncoupling from heterotrimeric G-proteins, which transiently arrests signaling, is well described, little is known about the mechanisms that permanently arrest signaling. Here we reported on the mechanisms that terminate signaling by protease-activated receptor 2 (PAR(2)), which mediated the proinflammatory and nociceptive actions of proteases. Given its irreversible mechanism of proteolytic activation, PAR(2) is a model to study the permanent arrest of GPCR signaling. By immunoprecipitation and immunoblotting, we observed that activated PAR(2) was mono-ubiquitinated. Immunofluorescence indicated that activated PAR(2) translocated from the plasma membrane to early endosomes and lysosomes where it was degraded, as determined by immunoblotting. Mutant PAR(2) lacking intracellular lysine residues (PAR(2)Delta14K/R) was expressed at the plasma membrane and signaled normally but was not ubiquitinated. Activated PAR(2) Delta14K/R internalized but was retained in early endosomes and avoided lysosomal degradation. Activation of wild type PAR(2) stimulated tyrosine phosphorylation of the ubiquitin-protein isopeptide ligase c-Cbl and promoted its interaction with PAR(2) at the plasma membrane and in endosomes in an Src-dependent manner. Dominant negative c-Cbl lacking the ring finger domain inhibited PAR(2) ubiquitination and induced retention in early endosomes, thereby impeding lysosomal degradation. Although wild type PAR(2) was degraded, and recovery of agonist responses required synthesis of new receptors, lysine mutation and dominant negative c-Cbl impeded receptor ubiquitination and degradation and allowed PAR(2) to recycle and continue to signal. Thus, c-Cbl mediated ubiquitination and lysosomal degradation of PAR(2) to irrevocably terminate signaling by this and perhaps other GPCRs.

Development and exploitation of a controlled vocabulary in support of climate modelling

There are three key components for developing a metadata system: a container structure laying out the key semantic issues of interest and their relationships; an extensible controlled vocabulary providing possible content; and tools to create and manipulate that content. While metadata systems must allow users to enter their own information, the use of a controlled vocabulary both imposes consistency of definition and ensures comparability of the objects described. Here we describe the controlled vocabulary (CV) and metadata creation tool built by the METAFOR project for use in the context of describing the climate models, simulations and experiments of the fifth Coupled Model Intercomparison Project (CMIP5). The CV and resulting tool chain introduced here is designed for extensibility and reuse and should find applicability in many more projects.

Water reuse for irrigated agriculture in Jordan: challenges of soil sustainability and the role of management strategies

Reclaimed water provides an important contribution to the water balance in water-scarce Jordan, but the quality of this water presents both benefits and challenges. Careful management of reclaimed water is required to maximize the nutrient benefits while minimizing the salinity risks. This work uses a multi-disciplinary research approach to show that soil response to irrigation with reclaimed water is a function of the management strategies adopted on the farm by the water user. The adoption of management methods to maintain soil productivity can be seen to be a result of farmers’ awareness to potentially plant-toxic ions in the irrigation water (70% of Jordan Valley farmers identified salinization as a hazard from irrigation with reclaimed water). However, the work also suggests that farmers’ management capacity is affected by the institutional management of water. About a third (35%) of farmers in the Jordan Valley claimed that their ability to manage salinization was limited by water shortages. Organizational interviews revealed that institutional awareness of soil management challenges was quite high (34% of interviewees described salinization as a risk from water reuse), but strategies to address this challenge at the institutional level require greater development.

Synthesis of isomaltooligosaccharides and oligodextrans in a recycle membrane bioreactor by the combined use of dextransucrase and dextranase

A recycle ultrafiltration membrane reactor was used to develop a continuous synthesis process for the production of isomaltooligosaccharides (IMO) from sucrose, using the enzymes dextransucrase and dextranase. A variety of membranes were tested and the parameters affecting reactor stability, productivity, and product molecular weight distribution were investigated. Enzyme inactivation in the reactor was reduced with the use of a non-ionic surfactant but its use had severe adverse effects on the membrane pore size and porosity. During continuous isomaltooligosaccharide synthesis, dextransucrase inactivation was shown to occur as a result of the dextranase activity and it was dependent mainly on the substrate availability in the reactor and the hydrolytic activity of dextranase. Substrate and dextranase concentrations (50-200 mg/mL(-1) and 10-30 U/mL(-1), respectively) affected permeate fluxes, reactor productivity, and product average molecular weight. The oligodextrans and isomaltooligosaccharides formed had molecular weights lower than in batch synthesis reactions but they largely consisted of oligosaccharides with a degree of polymerization (DP) greater than 5, depending on the synthesis conditions. No significant rejection of the sugars formed was shown by the membranes and permeate flux was dependent on tangential flow velocity. (C) 2004 Wiley Periodicals, Inc.

Water reuse for irrigation in Jordan: plant beneficial nutrients, farmers’ awareness and management strategies

The reuse of treated wastewater (reclaimed water) is particularly well suited for irrigated agriculture as it often contains significant quantities of plant essential nutrients. This work has shown that reclaimed water in Jordan can have adequate concentrations of potassium, phosphate, sulphate and magnesium to meet all or part of the crop’s requirements. To fully benefit from these inputs farmers must have an awareness of the water quality and reduce the application of chemical fertilisers accordingly. Interviews with farmers have shown that 75 per cent of farmers indirectly using reclaimed water are aware of the nutrients. Farmers’ decision making as to the application of chemical fertilisers appears to be influenced by a range of factors which include the type of crops being cultivated, the provision of training on nutrient management and the availability of information on the nutrient content of the reclaimed water.

Planning for the reuse of redundant defence estate: disposal processes, policy frameworks and development impacts

This paper reviews recent research and other literature concerning the planning and development of redundant defence estate. It concentrates on UK sources but includes reference to material from Europe and the North America were it is relevant for comparative purposes. It introduces the topic by providing a brief review of the recent restructuring of the UK defence estate and then proceeds to examine the various planning policy issues generated by this process; the policy frameworks used to guide it; comparable approaches to surplus land disposal and the appraisal of impacts; and ending the main body of the review with an analyse of the economic, social and environmental impacts of military base closure and redevelopment. It concludes that there is a significant body of work focusing on the reuse and redevelopment of redundant defence estate in the UK and abroad, but that much of this work is based on limited research or on personal experience. One particular weakness of the current literature is that it does not fully reflect the institutional difficulties posed by the disposal process and the day-to-day pressures which MOD personnel have to deal with. In doing this, it also under-emphasises the embedded cultures of individuals and professional groups who are required to operationalise the policies, procedures and practices for planning and redeveloping redundant defence estate.

Towards effective water reuse: drivers, challenges and strategies shaping the organisational management of reclaimed water in Jordan

Treated wastewater or reclaimed water is gaining recognition as a valuable water resource around the world. To assess why, where and how water reuse takes place in Jordan, semi-structured interviews were conducted with representatives of 29 key organisations in 2008. The analysis reveals that water scarcity is a key driver for water reuse. However, despite such recognition, reuse was described positively by only a small proportion of the interviewees (n = 6). Negative and neutral perceptions regarding reuse dominated and the research found that this was related to two underlying challenges: (i) the requirement for more intensive management when using reclaimed water compared with freshwater and (ii) concern over societal acceptance of water reuse. These factors were found to be associated with the risks posed to humans and their environments, combined with negative emotional and cultural responses to human waste and its applications. Numerous strategies are identified that are employed by organisations to overcome these challenges. Wastewater treatment, regulation, monitoring, the mixing of treated effluent with freshwater and limited public discussion of water reuse are all employed to achieve maximum use of reclaimed water. Each strategy presents benefits of sort, but some may paradoxically also inhibit optimal use of reclaimed water. Careful modifications to the existing strategies of Jordanian agencies, such as more open discussion of reuse, could lead to greater social, economic and environmental gains.