Automated tertiary structure prediction with accurate local model quality assessment using the IntFOLD-TS method

The IntFOLD-TS method was developed according to the guiding principle that the model quality assessment would be the most critical stage for our template based modelling pipeline. Thus, the IntFOLD-TS method firstly generates numerous alternative models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing quality assessment method – ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD-TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per-residue errors. This important information may help to make the 3D models that are produced by the IntFOLD-TS method more useful for guiding future experimental work

Mixed use urban regeneration at Brindleyplace, Birmingham and Gunwharf Quays, Portsmouth: an assessment of the impact on local and national economies

This independent research was commissioned by the British Property Federation. The report examines the local and national economic impact of two major, mixed use schemes in terms of tax revenue, household income, business rates and council tax and jobs creation. A regeneration balance sheet for each scheme is presented in the context of government policy and other related research. The report provides a comprehensive review of government policy and the role of retail and other land uses in regeneration. Highlighting the importance of national and local multiplier effects with detailed statistics drawn from a variety of sources, this fully illustrated colour research report builds up a detailed picture of economic impact of the mixed use regeneration schemes in the local economies of Birmingham and Portsmouth. The report will be of interest to property people, planners and all involved in regeneration and local economies.

An assessment of the impact of local processes on dust lifting in martian climate models

Simulation of the lifting of dust from the planetary surface is of substantially greater importance on Mars than on Earth, due to the fundamental role that atmospheric dust plays in the former’s climate, yet the dust emission parameterisations used to date in martian global climate models (MGCMs) lag, understandably, behind their terrestrial counterparts in terms of sophistication. Recent developments in estimating surface roughness length over all martian terrains and in modelling atmospheric circulations at regional to local scales (less than O(100 km)) presents an opportunity to formulate an improved wind stress lifting parameterisation. We have upgraded the conventional scheme by including the spatially varying roughness length in the lifting parameterisation in a fully consistent manner (thereby correcting a possible underestimation of the true threshold level for wind stress lifting), and used a modification to account for deviations from neutral stability in the surface layer. Following these improvements, it is found that wind speeds at typical MGCM resolution never reach the lifting threshold at most gridpoints: winds fall particularly short in the southern midlatitudes, where mean roughness is large. Sub-grid scale variability, manifested in both the near-surface wind field and the surface roughness, is then considered, and is found to be a crucial means of bridging the gap between model winds and thresholds. Both forms of small-scale variability contribute to the formation of dust emission ‘hotspots’: areas within the model gridbox with particularly favourable conditions for lifting, namely a smooth surface combined with strong near-surface gusts. Such small-scale emission could in fact be particularly influential on Mars, due both to the intense positive radiative feedbacks that can drive storm growth and a strong hysteresis effect on saltation. By modelling this variability, dust lifting is predicted at the locations at which dust storms are frequently observed, including the flushing storm sources of Chryse and Utopia, and southern midlatitude areas from which larger storms tend to initiate, such as Hellas and Solis Planum. The seasonal cycle of emission, which includes a double-peaked structure in northern autumn and winter, also appears realistic. Significant increases to lifting rates are produced for any sensible choices of parameters controlling the sub-grid distributions used, but results are sensitive to the smallest scale of variability considered, which high-resolution modelling suggests should be O(1 km) or less. Use of such models in future will permit the use of a diagnosed (rather than prescribed) variable gustiness intensity, which should further enhance dust lifting in the southern hemisphere in particular.

Development and assessment of a coupled crop-climate model

It is well established that crop production is inherently vulnerable to variations in the weather and climate. More recently the influence of vegetation on the state of the atmosphere has been recognized. The seasonal growth of crops can influence the atmosphere and have local impacts on the weather, which in turn affects the rate of seasonal crop growth and development. Considering the coupled nature of the crop-climate system, and the fact that a significant proportion of land is devoted to the cultivation of crops, important interactions may be missed when studying crops and the climate system in isolation, particularly in the context of land use and climate change. To represent the two-way interactions between seasonal crop growth and atmospheric variability, we integrate a crop model developed specifically to operate at large spatial scales (General Large Area Model for annual crops) into the land surface component of a global climate model (GCM; HadAM3). In the new coupled crop-climate model, the simulated environment (atmosphere and soil states) influences growth and development of the crop, while simultaneously the temporal variations in crop leaf area and height across its growing season alter the characteristics of the land surface that are important determinants of surface fluxes of heat and moisture, as well as other aspects of the land-surface hydrological cycle. The coupled model realistically simulates the seasonal growth of a summer annual crop in response to the GCM's simulated weather and climate. The model also reproduces the observed relationship between seasonal rainfall and crop yield. The integration of a large-scale single crop model into a GCM, as described here, represents a first step towards the development of fully coupled crop and climate models. Future development priorities and challenges related to coupling crop and climate models are discussed.

An assessment of the benefits and limitations of the shamba agroforestry system in Kenya and of management and policy requirements for its successful and sustainable reintroduction

The shamba system involves farmers tending tree saplings on state-owned forest land in return for being permitted to intercrop perennial food crops until canopy closure. At one time the system was used throughout all state-owned forest lands in Kenya, accounting for a large proportion of some 160,000 ha. The system should theoretically be mutually beneficial to both local people and the government. However the system has had a chequered past in Kenya due to widespread malpractice and associated environmental degradation. It was last banned in 2003 but in early 2008 field trials were initiated for its reintroduction. This study aimed to: assess the benefits and limitations of the shamba system in Kenya; assess the main influences on the extent to which the limitations and benefits are realised and; consider the management and policy requirements for the system's successful and sustainable operation. Information was obtained from 133 questionnaires using mainly open ended questions and six participatory workshops carried out in forest-adjacent communities on the western slopes of Mount Kenya in Nyeri district. In addition interviews were conducted with key informants from communities and organisations. There was strong desire amongst local people for the system's reintroduction given that it had provided significant food, income and employment. Local perceptions of the failings of the system included firstly mismanagement by government or forest authorities and secondly abuse of the system by shamba farmers and outsiders. Improvements local people considered necessary for the shamba system to work included more accountability and transparency in administration and better rules with respect to plot allocation and stewardship. Ninety-seven percent of respondents said they would like to be more involved in management of the forest and 80% that they were willing to pay for the use of a plot. The study concludes that the structural framework laid down by the 2005 Forests Act, which includes provision for the reimplementation of the shamba system under the new plantation establishment and livelihood improvement scheme (PELIS) [It should be noted that whilst the shamba system was re-branded in 2008 under the acronym PELIS, for the sake of simplicity the authors continue to refer to the 'shamba system' and 'shamba farmers' throughout this paper.], is weakened because insufficient power is likely to be devolved to local people, casting them merely as 'forest users' and the shamba system as a 'forest user right'. In so doing the system's potential to both facilitate and embody the participation of local people in forest management is limited and the long-term sustainability of the new system is questionable. Suggested instruments to address this include some degree of sharing of profits from forest timber, performance related guarantees for farmers to gain a new plot and use of joint committees consisting of local people and the forest authorities for long term management of forests.

Prediction of global and local model quality in CASP8 using the ModFOLD server

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0-an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/.

The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.

Assembling spatially explicit landscape models of pollen and spore dispersal by wind for risk assessment

Models of windblown pollen or spore movement are required to predict gene flow from genetically modified (GM) crops and the spread of fungal diseases. We suggest a simple form for a function describing the distance moved by a pollen grain or fungal spore, for use in generic models of dispersal. The function has power-law behaviour over sub-continental distances. We show that air-borne dispersal of rapeseed pollen in two experiments was inconsistent with an exponential model, but was fitted by power-law models, implying a large contribution from distant fields to the catches observed. After allowance for this 'background' by applying Fourier transforms to deconvolve the mixture of distant and local sources, the data were best fit by power-laws with exponents between 1.5 and 2. We also demonstrate that for a simple model of area sources, the median dispersal distance is a function of field radius and that measurement from the source edge can be misleading. Using an inverse-square dispersal distribution deduced from the experimental data and the distribution of rapeseed fields deduced by remote sensing, we successfully predict observed rapeseed pollen density in the city centres of Derby and Leicester (UK).

Assessment of the presence of Salmonella spp. in Egyptian dairy products using various detection media

Aims: To make a preliminary assessment of the incidence of Salmonella in Egyptian dairy products, and to investigate the effectiveness of various protocols for the detection of the pathogen in these products. Methods and Results: Samples of milk and related dairy products were randomly collected from local markets and examined for the presence of Salmonella. While most samples were free of the organism, isolates of Salmonella enterica subsp. enterica serovar Typhimurium PT 8 could be recovered from 'matared' cream specimens. These isolates were susceptible to antibiotics usually used to challenge infections caused by Salmonella. A combination of buffered peptone water, Muller-Kauffman tetrathionate broth, and brilliant green phenol red agar gave the best results for the detection of the pathogen. Selenite-cystine broth and Hektoen enteric agar were ineffective as an enrichment and a plating medium, respectively, in the isolation of Salmonella. A modified identification strategy that reduces the burden of serological testing of presumptive isolates is proposed. Conclusions, Significance and Impact of the Study: 'Matared' cream could be a vehicle for transmitting Salmonella. Using the above combination of media, beside the suggested modified confirmatory procedure, should increase the effectiveness and ease of the detection of Salmonella in milk and dairy products.

An assessment of aerosol‐cloud interactions in marine stratus clouds based on surface remote sensing

An assessment of aerosol-cloud interactions (ACI) from ground-based remote sensing under coastal stratiform clouds is presented. The assessment utilizes a long-term, high temporal resolution data set from the Atmospheric Radiation Measurement (ARM) Program deployment at Pt. Reyes, California, United States, in 2005 to provide statistically robust measures of ACI and to characterize the variability of the measures based on variability in environmental conditions and observational approaches. The average ACIN (= dlnNd/dlna, the change in cloud drop number concentration with aerosol concentration) is 0.48, within a physically plausible range of 0–1.0. Values vary between 0.18 and 0.69 with dependence on (1) the assumption of constant cloud liquid water path (LWP), (2) the relative value of cloud LWP, (3) methods for retrieving Nd, (4) aerosol size distribution, (5) updraft velocity, and (6) the scale and resolution of observations. The sensitivity of the local, diurnally averaged radiative forcing to this variability in ACIN values, assuming an aerosol perturbation of 500 c-3 relative to a background concentration of 100 cm-3, ranges betwee-4 and -9 W -2. Further characterization of ACI and its variability is required to reduce uncertainties in global radiative forcing estimates.

Thermal comfort assessment in a non-uniform thermal environment

This paper presents results for thermal comfort assessment in non-uniform thermal environments. Three types of displacement ventilation (DV) units that created stratified condition in an environmental test chamber have been selected to carry out the thermal comfort assessment: a flat diffuser (DV1), semi-circular diffuser (DV2), and floor swirl diffuser (DV3). The CBE (Center for the Built Environment at Berkeley) comfort model was implemented in this study to assess the occupant’s thermal comfort for the three DV types. The CBE model predicted the occupant’s mean skin as well as local skin temperatures very well when compared with measurements found in the literature, while it underestimated the occupant’s core temperature. The predicted occupant’s thermal sensation and thermal comfort for the case of (DV2) were the best. Therefore, the semi-circular diffuser (DV2) provided better thermal comfort for the occupant in comparison with the other two DV types.

Private investment in the countryside: an assessment of the role of new houses and estates in sustaining the rural economy and environment

The British countryside has been shaped and sustained over the years by the establishment of landed estates. Some of our best known, and now most protected, landmarks derive from this tradition by which money, that was often sourced from outside the rural economy, was invested in land. Whilst there was some reversal in this trend during the last century, there is again a widespread desire among people of means to invest in new country property. Paragraph 3.21 of Planning Policy Guidance Note 7: The Countryside - Environmental Quality and Economic and Social Development was introduced in 1997 as a means of perpetuating the historic tradition of innovation in the countryside through the construction of fine individual houses in landscaped grounds. That it was considered necessary to use a special provision of this kind reflects the prevailing presumption of planning authorities against allowing private residential development in open countryside. The Government is currently reviewing rural planning policy and is focusing on higher density housing, affordable homes and the use of brownfield sites. There is an underlying conception that individual private house developments contribute nothing and are seen as the least attractive option for most development sites. The purpose of paragraph 3.21 lies outside the government’s priorities and its particular provisions may therefore be excluded in forthcoming ‘policy statements’. This paper seeks to examine the role of private investors wishing to build new houses in the countryside, and the impact that that might have on local economies. It explores the interpretation placed on PPG7 through an investigation of appeal sites, and concludes by making recommendations for the review process, including the retention of some form of exceptions policy for new build houses.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.