Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

MOTIVATION: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering or consensus based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ - a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilising the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead. RESULTS: The ModFOLDclustQ method is competitive with leading clustering based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over 5 times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction. AVAILABILITY: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from: http://www.reading.ac.uk/bioinf/downloads/ CONTACT: l.j.mcguffin@reading.ac.uk.

Gene flow, risk assessment and the environmental release of transgenic plants

The release of genetically modified plants is governed by regulations that aim to provide an assessment of potential impact on the environment. One of the most important components of this risk assessment is an evaluation of the probability of gene flow. In this review, we provide an overview of the current literature on gene flow from transgenic plants, providing a framework of issues for those considering the release of a transgenic plant into the environment. For some plants gene flow from transgenic crops is well documented, and this information is discussed in detail in this review. Mechanisms of gene flow vary from plant species to plant species and range from the possibility of asexual propagation, short- or long-distance pollen dispersal mediated by insects or wind and seed dispersal. Volunteer populations of transgenic plants may occur where seed is inadvertently spread during harvest or commercial distribution. If there are wild populations related to the transgenic crop then hybridization and eventually introgression in the wild may occur, as it has for herbicide resistant transgenic oilseed rape (Brassica napus). Tools to measure the amount of gene flow, experimental data measuring the distance of pollen dispersal, and experiments measuring hybridization and seed survivability are discussed in this review. The various methods that have been proposed to prevent gene flow from genetically modified plants are also described. The current "transgenic traits'! in the major crops confer resistance to herbicides and certain insects. Such traits could confer a selective advantage (an increase in fitness) in wild plant populations in some circumstances, were gene flow to occur. However, there is ample evidence that gene flow from crops to related wild species occurred before the development of transgenic crops and this should be taken into account in the risk assessment process.

Population-level assessment of risks of pesticides to birds and mammals in the UK

It is generally acknowledged that population-level assessments provide,I better measure of response to toxicants than assessments of individual-level effects. population-level assessments generally require the use of models to integrate potentially complex data about the effects of toxicants on life-history traits, and to provide a relevant measure of ecological impact. Building on excellent earlier reviews we here briefly outline the modelling options in population-level risk assessment. Modelling is used to calculate population endpoints from available data, which is often about Individual life histories, the ways that individuals interact with each other, the environment and other species, and the ways individuals are affected by pesticides. As population endpoints, we recommend the use of population abundance, population growth rate, and the chance of population persistence. We recommend two types of model: simple life-history models distinguishing two life-history stages, juveniles and adults; and spatially-explicit individual-based landscape models. Life-history models are very quick to set up and run, and they provide a great deal or insight. At the other extreme, individual-based landscape models provide the greatest verisimilitude, albeit at the cost of greatly increased complexity. We conclude with a discussion of the cations of the severe problems of parameterising models.

Making sense of research quality assessment

Purpose – For many academics in UK universities the nature and orientation of their research is overwhelmingly determined by considerations of how that work will be graded in research assessment exercises (RAEs). The grades awarded to work in a particular subject area can have a considerable impact on the individual and their university. There is a need to better understand those factors which may influence these grades. The paper seeks to address this issue. Design/methodology/approach – The paper considers relationships between the grades awarded and the quantitative information provided to the assessment panels for the 1996 and 2001 RAEs for two subject areas, built environment and town and country planning, and for three other subject areas, civil engineering, geography and archaeology, in the 2001 RAE. Findings – A simple model demonstrating strong and consistent relationships is established. RAE performance relates to numbers of research active staff, the production of books and journal papers, numbers of research studentships and graduations, and research income. Important differences between subject areas are identified. Research limitations/implications – Important issues are raised about the extent to which the new assessment methodology to be adopted for the 2008 RAE will capture the essence of good quality research in architecture and built environment. Originality/value – The findings provide a developmental perspective of RAEs and show how, despite a changed methodology, various research activities might be valued in the 2008 RAE. The basis for a methodology for reviewing the credibility of the judgements of panels is proposed.

Does gym use impact upon nutritional knowledge?

Purpose - The purpose of this paper is to investigate gym and non-gym users' use and understanding of nutrition labels. Design/methodology/approach - A consumer survey in the form of a questionnaire conducted in the Greater London area in February/March 2005. Subject recruitment process took place in both a gym and university setting. Frequency tables and chi(2)-test are used to assess relationships between variables (p = 0.05). Findings - The resulting sample consisted of 187 subjects, with predominance of females and gym users. Of the subjects, 88 per cent reported to at least occasionally read nutrition labels, with higher reading rates amongst women, irrespective of gym user status. Total and saturated fats are the most often information viewed on labels, however the overall knowledge of the calorie content of fat is low, with 53 per cent of subjects responding saturated fat contains more calories per gram when compared with other types of fats. This paper does not find significant differences in the use and understanding of nutrition labels between gym and non-gym users, but highlights the publics' continued lack of understanding of nutrition labels. Originality/value - This paper is unique as it investigates whether there is any difference between gym/non-gym users' use and interpretation of use of nutrition labels. It finds gender impacted more on nutritional labels knowledge than gym user's status. This points to a gender issue and questions the quality of information available to the general public. This paper is valuable as it highlights and identifies an area that requires further research and assessment, and is therefore useful to key stakeholders responsible for public health nutrition.

Probiotics: their potential to impact human health

Probiotics—live microorganisms that when administered in adequate amounts confer a health benefit on the host—have been studied for both human and animal applications, and worldwide research on this topic has accelerated in recent years. This paper reviews the literature on probiotics, describes how probiotics work in human ecosystems, and outlines the impact of probiotics on human health and disease. The paper also addresses safety issues of probiotic use, suggests future developments in the field of probiotics, and provides research and policy recommendations. Product considerations and potential future developments regarding probiotics also are discussed. The authors conclude that controlled human studies have revealed a diverse range of health benefits from consumption of probiotics, due largely to their impact on immune function or on microbes colonizing the body. Additional, well-designed and properly controlled human and mechanistic studies with probiotics will advance the essential understanding of active principles, mechanisms of action, and degree of effects that can be realized by specific consumer groups. Recommendations include establishment of a standard of identity for the term “probiotic,” adoption of third-party verification of label claims, use of probiotics selectively in clinical conditions, and use of science-based assessment of the benefits and risks of genetically engineered probiotic microbes.

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.

Case studies to demonstrate the range of applications of the Southampton Hand Assessment Procedure

The Southampton Hand Assessment Procedure (SHAP) was devised to assess quantitatively the functional range of injured and healthy adult hands. It was designed to be a practical tool for use in a busy clinical setting; thus, it was made simple to use and easy to interpret. This paper describes four examples of its use: before and after a surgical procedure, to observe the impact of an injury, use with prostheses, and during recovery following a fracture. The cases show that the SHAP is capable of monitoring progress and recovery, identifying functional abilities in prosthetic hands and comparing the capabilities of different groups of injuries.

An assessment of eye-gaze potential within immersive virtual environments

In collaborative situations, eye gaze is a critical element of behavior which supports and fulfills many activities and roles. In current computer-supported collaboration systems, eye gaze is poorly supported. Even in a state-of-the-art video conferencing system such as the access grid, although one can see the face of the user, much of the communicative power of eye gaze is lost. This article gives an overview of some preliminary work that looks towards integrating eye gaze into an immersive collaborative virtual environment and assessing the impact that this would have on interaction between the users of such a system. Three experiments were conducted to assess the efficacy of eye gaze within immersive virtual environments. In each experiment, subjects observed on a large screen the eye-gaze behavior of an avatar. The eye-gaze behavior of that avatar had previously been recorded from a user with the use of a head-mounted eye tracker. The first experiment was conducted to assess the difference between users' abilities to judge what objects an avatar is looking at with only head gaze being viewed and also with eye- and head-gaze data being displayed. The results from the experiment show that eye gaze is of vital importance to the subjects, correctly identifying what a person is looking at in an immersive virtual environment. The second experiment examined whether a monocular or binocular eye-tracker would be required. This was examined by testing subjects' ability to identify where an avatar was looking from their eye direction alone, or by eye direction combined with convergence. This experiment showed that convergence had a significant impact on the subjects' ability to identify where the avatar was looking. The final experiment looked at the effects of stereo and mono-viewing of the scene, with the subjects being asked to identify where the avatar was looking. This experiment showed that there was no difference in the subjects' ability to detect where the avatar was gazing. This is followed by a description of how the eye-tracking system has been integrated into an immersive collaborative virtual environment and some preliminary results from the use of such a system.

Adapting to climate change impacts on water resources in England - an assessment of draft Water Resources Management Plans

Climate change is expected to produce reductions in water availability in England, potentially necessitating adaptive action by the water industry to maintain supplies. As part of Ofwat's fifth Periodic Review (PR09), water companies recently released their draft Water Resources Management Plans, setting out how each company intends to maintain the balance between the supply and demand for water over the next 25 years, following Environment Agency guidelines. This paper reviews these plans to determine company estimates of the impact of climate change on water supply relative to other resource pressures. The approaches adopted for incorporating the impact in the plans and the proposed management solutions are also identified. Climate change impacts for individual resource zones range from no reductions in deployable output to greater than 50% over the planning period. The estimated national aggregated loss of deployable output under a “core” climate scenario is ~520 Ml/d (3% of deployable output) by 2034/35, the equivalent of the supply of one entire water company (South West Water). Climate change is the largest single driver of change in water supplies over the planning period. Over half of the climate change impact is concentrated in southern England. In extreme cases, climate change uncertainty is of the same magnitude as the change under the core scenario (up to a loss of ~475 Ml/d). 44 of the 68 resource zones with available data are estimated to have a climate change impact. In 35 of these climate change has the greatest impact although in 10 zones sustainability reductions have a greater impact. Of the overall change in downward pressure on the supply-demand balance over the planning period, ~56% is accounted for by increased demand (620 Ml/d) and supply side climate change accounts for ~37% (407 Ml/d). Climate change impacts have a cumulative impact in concert with other changing supply side reducing components increasing the national pressure on the supply-demand balance. Whilst the magnitude of climate change appears to justify its explicit consideration, it is rare that adaptation options are planned solely in response to climate change but as a suite of options to provide a resilient supply to a range of pressures (including significant demand side pressures). Supply-side measures still tend to be considered by water companies to be more reliable than demand-side measures.

Assessment of a climate model to reproduce rainfall variability and extremes over Southern Africa

It is increasingly accepted that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. A change in the distribution and magnitude of extreme rainfall events (associated with changing variability), such as droughts or flooding, may have a far greater impact on human and natural systems than a changing mean. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The sub-continent is considered especially vulnerable to and ill-equipped (in terms of adaptation) for extreme events, due to a number of factors including extensive poverty, famine, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of ability of a state of the art climate model to simulate climate at daily timescales is carried out using satellite-derived rainfall data from the Microwave Infrared Rainfall Algorithm (MIRA). This dataset covers the period from 1993 to 2002 and the whole of southern Africa at a spatial resolution of 0.1° longitude/latitude. This paper concentrates primarily on the ability of the model to simulate the spatial and temporal patterns of present-day rainfall variability over southern Africa and is not intended to discuss possible future changes in climate as these have been documented elsewhere. Simulations of current climate from the UKMeteorological Office Hadley Centre’s climate model, in both regional and global mode, are firstly compared to the MIRA dataset at daily timescales. Secondly, the ability of the model to reproduce daily rainfall extremes is assessed, again by a comparison with extremes from the MIRA dataset. The results suggest that the model reproduces the number and spatial distribution of rainfall extremes with some accuracy, but that mean rainfall and rainfall variability is underestimated (over-estimated) over wet (dry) regions of southern Africa.

The impact of large scale atmospheric circulation patterns on wind power generation and its potential predictability: a case study over the UK

Over recent years there has been an increasing deployment of renewable energy generation technologies, particularly large-scale wind farms. As wind farm deployment increases, it is vital to gain a good understanding of how the energy produced is affected by climate variations, over a wide range of time-scales, from short (hours to weeks) to long (months to decades) periods. By relating wind speed at specific sites in the UK to a large-scale climate pattern (the North Atlantic Oscillation or "NAO"), the power generated by a modelled wind turbine under three different NAO states is calculated. It was found that the wind conditions under these NAO states may yield a difference in the mean wind power output of up to 10%. A simple model is used to demonstrate that forecasts of future NAO states can potentially be used to improve month-ahead statistical forecasts of monthly-mean wind power generation. The results confirm that the NAO has a significant impact on the hourly-, daily- and monthly-mean power output distributions from the turbine with important implications for (a) the use of meteorological data (e.g. their relationship to large scale climate patterns) in wind farm site assessment and, (b) the utilisation of seasonal-to-decadal climate forecasts to estimate future wind farm power output. This suggests that further research into the links between large-scale climate variability and wind power generation is both necessary and valuable.

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.

Assessment of evaluations made to healthy eating policies in Europe: a review within the EATWELL Project

Objective: To identify and assess healthy eating policies at national level which have been evaluated in terms of their impact on awareness of healthy eating, food consumption, health outcome or cost/benefit. Design: Review of policy documents and their evaluations when available. Setting: European Member States. Subjects: One hundred and twenty-one policy documents revised, 107 retained. Results: Of the 107 selected interventions, twenty-two had been evaluated for their impact on awareness or knowledge and twenty-seven for their impact on consumption. Furthermore sixteen interventions provided an evaluation of health impact, while three actions specifically measured any cost/benefit ratio. The indicators used in these evaluations were in most cases not comparable. Evaluation was more often found for public information campaigns, regulation of meals at schools/canteens and nutrition education programmes. Conclusions: The study highlights the need not only to develop harmonized and verifiable procedures but also indicators for measuring effectiveness and success and for comparing between interventions and countries. EU policies are recommended to provide a set of indicators that may be measured consistently and regularly in all countries. Furthermore, public information campaigns should be accompanied by other interventions, as evaluations may show an impact on awareness and intention, but rarely on consumption patterns and health outcome.

Assessment of day-to-day functioning in prodromal and early Huntington disease

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess functional impact in day-to-day activities in prHD and early HD individuals.