IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

The forms of bioavailability of phosphorus in integrated vertical flow constructed wetland with earthworms and different substrates

A sequential extraction method was utilized to analyze seven forms of P in an integrated vertical-flow constructed wetland (IVFCW) containing earthworms and different substrates. The aluminum-bound P (Al-P) content was found to be lower, and the occluded P (Oc-P) content was higher in the IVFCW. The addition of earthworms into the influent chamber of IVFCW increased the exchange P (Ex-P), iron-bound P (Fe-P), calcium bound P (Ca-P), Oc-P, detritus-bound (De-P) and organic P (Org-P) content in the influent chamber, and also enhanced P content uptake by wetland plants. A significantly positive correlation between P content of above-ground wetland plants and the Ex-P, Fe-P, Oc-P and Org-P content in the rhizosphere was found (P < 0.05), which indicated that the Ex-P, Fe-P, Oc-P and Org-P could be bio-available P. The Ex-P, Fe-P, De-P, Oc-P and Ca-P content of the influent chamber was higher where the substrate contained a mixture of Qing sand and river sand rather than only river sand. Also the IVFCW with earthworms and both Qing sand and river sand had a higher removal efficiency of P, which was related to higher P content uptake by wetland plants and P retained in IVFCW. These findings suggest that addition of earthworms in IVFCW increases the bioavailable P content, resulting in enhanced P content uptake by wetland plants.

The co-development of technology and new buildings: incorporating building integrated photovoltaics

Current approaches for the reduction of carbon emissions in buildings are often predicated on the integration of renewable technologies into building projects. Building integrated photovoltaics (BIPV) is one of these technologies and brings its own set of challenges and problems with a resulting mutual articulation of this technology and the building. A Social Construction of Technology (SCOT) approach explores how negotiations between informal groups of project actors with shared interests shape the ongoing specification of both BIPV and the building. Six main groups with different interests were found to be involved in the introduction of BIPV (Cost Watchers, Design Aesthetes, Green Guardians, Design Optimizers, Generation Maximizers and Users). Their involvement around three sets of issues (design changes from lack of familiarity with the technology, misunderstandings from unfamiliar interdependencies of trades and the effects of standard firm procedure) is followed. Findings underline how BIPV requires a level of integration that typically spans different work packages and how standard contractual structures inhibit the smooth incorporation of BIPV. Successful implementation is marked by ongoing (re-)design of both the building and the technology as informal fluid groups of project actors with shared interests address the succession of problems which arise in the process of implementation.

Perspectives on the specification of Building Integrated Photovoltaic (BIPV) technology in construction projects

Innovative, low carbon technologies are already available for use in the construction of buildings, but the impact of their specification on construction projects is unclear. This exploratory research identifies issues which arise following the specification of BIPV in non-residential construction projects. Rather than treating the inclusion of a new technology as a technical problem, the research explores the issue from a socio-technical perspective to understand the accommodations which the project team makes and their effect on the building and the technology. The paper is part of a larger research project which uses a Social Construction of Technology Approach (SCOT) to explore the accommodations made to working practices and design when Building Integrated PhotoVoltaic (BIPV) technology is introduced. The approach explores how the requirements of the technology from different groups of actors (Relevant Social Groups or RSG's) give rise to problems and create solutions. As such it rejects the notion of a rational linear view of innovation diffusion; instead it suggests that the variety and composition of the Relevant Social Groups set the agenda for problem solving and solutions as the project progresses. The research explores the experiences of three people who have extensive histories of involvement with BIPV in construction, looks at how SCOT can inform our understanding of the issues involved and identifies themes and issues in the specification of BIPV on construction projects. A key finding concerns the alignment of inflection points at which interviewees have found themselves changing from one RSG to another as new problems and solutions are identified. The points at which they change RSG often occurred at points which mirror conventional construction categories (in terms of project specification, tender, design and construction).

High Royds: an integrated, analytical approach for mapping the unmarked burials of a pauper cemetery

Applying geophysical techniques to detect and map the physical extent of individual unmarked graves proves difficult in many cases. The success of individual geophysical techniques for detecting unmarked graves may be due to a poor understanding of the nature of the graves themselves, the context in which they lie in, and temporal changes to the burial state. Given the unpredictability of these variables, it is surprising that grave prospection is often undertaken using only a single method. This paper presents a multi-methodological survey strategy for detecting unmarked burials and utilises an analytical approach for visualising and evaluating survey results.

A multi-instrument comparison of integrated water vapour measurements at a high latitude site

We compare measurements of integrated water vapour (IWV) over a subarctic site (Kiruna, Northern Sweden) from five different sensors and retrieval methods: Radiosondes, Global Positioning System (GPS), ground-based Fourier-transform infrared (FTIR) spectrometer, ground-based microwave radiometer, and satellite-based microwave radiometer (AMSU-B). Additionally, we compare also to ERA-Interim model reanalysis data. GPS-based IWV data have the highest temporal coverage and resolution and are chosen as reference data set. All datasets agree reasonably well, but the ground-based microwave instrument only if the data are cloud-filtered. We also address two issues that are general for such intercomparison studies, the impact of different lower altitude limits for the IWV integration, and the impact of representativeness error. We develop methods for correcting for the former, and estimating the random error contribution of the latter. A literature survey reveals that reported systematic differences between different techniques are study-dependent and show no overall consistent pattern. Further improving the absolute accuracy of IWV measurements and providing climate-quality time series therefore remain challenging problems.

Achieving customer satisfaction through integrated products and services: an exploratory study

Complex products such as manufacturing equipment have always needed maintenance and repair services. Increasingly, leading manufacturers are integrating products and services to generate increased revenues and achieve customer satisfaction. Designing integrated products and services requires a different approach to new product development and a clear understanding of how customers perceive the value they obtain from actual usage of products and services—so-called value-in-use. However, there is a lack of research on integrated products and services and how they impact customer satisfaction. An exploratory study was undertaken to understand customers’ views on integrated products and services and the value-in-use derived from such offerings. As value-in-use and its impacts are complicated concepts, a technique from psychology—Repertory Grid Technique—was used to gather data in 33 interviews. The interviews allowed a deep understanding of customer views on integrated products and services to be obtained, and a systematic analysis identified the key attributes of value-in-use. In order to probe further, the data were then analyzed using Honey’s procedure, which identified the impact of the attributes of value-in-use on customer satisfaction. Two key attributes—relational dynamic and access—were found to have the most influence on customer satisfaction. This paper contributes to the innovation field by identifying customer needs for integrated products and services and how these impact customer satisfaction. These are key points and need to be fully considered by managers during new product and service development. Similarly, the paper identifies a number of important areas for further research.

The BALTIMOS (BALTEX Integrated Model System) fi eld experiments: A comprehensive atmospheric boundary layer data set for model validation over the open and ice- covered Baltic Sea

A comprehensive atmospheric boundary layer (ABL) data set was collected in eight fi eld experiments (two during each season) over open water and sea ice in the Baltic Sea during 1998–2001 with the primary objective to validate the coupled atmospheric- ice-ocean-land surface model BALTIMOS (BALTEX Integrated Model System). Measurements were taken by aircraft, ships and surface stations and cover the mean and turbulent structure of the ABL including turbulent fl uxes, radiation fl uxes, and cloud conditions. Measurement examples of the spatial variability of the ABL over the ice edge zone and of the stable ABL over open water demonstrate the wide range of ABL conditions collected and the strength of the data set which can also be used to validate other regional models.