Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

Online dietary intake estimation: The Food4Me food frequency questionnaire

Background: Dietary assessment methods are important tools for nutrition research. Online dietary assessment tools have the potential to become invaluable methods of assessing dietary intake because, compared with traditional methods, they have many advantages including the automatic storage of input data and the immediate generation of nutritional outputs. Objective: The aim of this study was to develop an online food frequency questionnaire (FFQ) for dietary data collection in the “Food4Me” study and to compare this with the validated European Prospective Investigation of Cancer (EPIC) Norfolk printed FFQ. Methods: The Food4Me FFQ used in this analysis was developed to consist of 157 food items. Standardized color photographs were incorporated in the development of the Food4Me FFQ to facilitate accurate quantification of the portion size of each food item. Participants were recruited in two centers (Dublin, Ireland and Reading, United Kingdom) and each received the online Food4Me FFQ and the printed EPIC-Norfolk FFQ in random order. Participants completed the Food4Me FFQ online and, for most food items, participants were requested to choose their usual serving size among seven possibilities from a range of portion size pictures. The level of agreement between the two methods was evaluated for both nutrient and food group intakes using the Bland and Altman method and classification into quartiles of daily intake. Correlations were calculated for nutrient and food group intakes. Results: A total of 113 participants were recruited with a mean age of 30 (SD 10) years (40.7% male, 46/113; 59.3%, 67/113 female). Cross-classification into exact plus adjacent quartiles ranged from 77% to 97% at the nutrient level and 77% to 99% at the food group level. Agreement at the nutrient level was highest for alcohol (97%) and lowest for percent energy from polyunsaturated fatty acids (77%). Crude unadjusted correlations for nutrients ranged between .43 and .86. Agreement at the food group level was highest for “other fruits” (eg, apples, pears, oranges) and lowest for “cakes, pastries, and buns”. For food groups, correlations ranged between .41 and .90. Conclusions: The results demonstrate that the online Food4Me FFQ has good agreement with the validated printed EPIC-Norfolk FFQ for assessing both nutrient and food group intakes, rendering it a useful tool for ranking individuals based on nutrient and food group intakes.

A novel combined biomarker including plasma carotenoids, vitamin C, and ferric reducing antioxidant power is more strongly associated with fruit and vegetable intake than the individual components

BACKGROUND: Monitoring of fruit and vegetable (F&V) intake is fraught with difficulties. Available dietary assessment methods are associated with considerable error, and the use of biomarkers offers an attractive alternative. Few studies to date have examined the use of plasma biomarkers to monitor or predict the F&V intake of volunteers consuming a wide range of intakes from both habitual F&V and manipulated diets. OBJECTIVE: This study tested the hypothesis that an integrated biomarker calculated from a combination of plasma vitamin C, cholesterol-adjusted carotenoid concentration and Ferric Reducing Antioxidant Power (FRAP) had more power to predict F&V intake than each individual biomarker. METHODS: Data from a randomized controlled dietary intervention study [FLAVURS (Flavonoids University of Reading Study); n = 154] in which the test groups observed sequential increases of 2.3, 3.2, and 4.2 portions of F&Vs every 6 wk across an 18-wk period were used in this study. RESULTS: An integrated plasma biomarker was devised that included plasma vitamin C, total cholesterol-adjusted carotenoids, and FRAP values, which better correlated with F&V intake (r = 0.47, P < 0.001) than the individual biomarkers (r = 0.33, P < 0.01; r = 0.37, P < 0.001; and r = 0.14, respectively; P = 0.099). Inclusion of urinary potassium concentration did not significantly improve the correlation. The integrated plasma biomarker predicted F&V intake more accurately than did plasma total cholesterol-adjusted carotenoid concentration, with the difference being significant at visit 2 (P < 0.001) and with a tendency to be significant at visit 1 (P = 0.07). CONCLUSION: Either plasma total cholesterol-adjusted carotenoid concentration or the integrated biomarker could be used to distinguish between high- and moderate-F&V consumers. This trial was registered at www.controlled-trials.com as ISRCTN47748735.

Optimising mirid control on cocoa farms through complementary monitoring systems

Mirids (Sahlbergella singularis and Distantiella theobroma) are the most important insect pests affecting cocoa production across West Africa. Understanding the population dynamics of mirids is key to their management, however, the current recommended hand-height assessment method is labour intensive. The objective of the study was to compare recently developed mirid sex pheromone trapping and visual hand-height assessment methods as monitoring tools on cocoa farms and to consider implications for a decision support system. Ten farms from the Eastern and Ashanti regions of Ghana were used for the study. Mirid numbers and damage were assessed fortnightly on twenty trees per farm, using both methods, from January 2012 to April 2013. The mirid population increased rapidly in June, reached a peak in September and began to decline in October. There was a significant linear relationship between numbers of mirids sampled to hand-height and mirid damage. High numbers of male mirids were recorded in pheromone traps between January and April 2012 after which there was a gradual decline. There was a significant inverse relationship between numbers of trapped adult mirids and mirids sampled to hand-height (predominantly nymphs). Higher temperatures and lower relative humidities in the first half of the year were associated with fewer mirids at hand-height but larger numbers of adult males were caught in pheromone traps. The study showed that relying solely on one method is not sufficient to provide accurate information on mirid population dynamics and a combination of the two methods is necessary.

Deconstruction plan assessment using multi-criteria decision-making methods

The purpose of this paper is to present two multi-criteria decision-making models, including an Analytic Hierarchy Process (AHP) model and an Analytic Network Process (ANP) model for the assessment of deconstruction plans and to make a comparison between the two models with an experimental case study. Deconstruction planning is under pressure to reduce operation costs, adverse environmental impacts and duration, in the meanwhile to improve productivity and safety in accordance with structure characteristics, site conditions and past experiences. To achieve these targets in deconstruction projects, there is an impending need to develop a formal procedure for contractors to select a most appropriate deconstruction plan. Because numbers of factors influence the selection of deconstruction techniques, engineers definitely need effective tools to conduct the selection process. In this regard, multi-criteria decision-making methods such as AHP have been adopted to effectively support deconstruction technique selection in previous researches. in which it has been proved that AHP method can help decision-makers to make informed decisions on deconstruction technique selection based on a sound technical framework. In this paper, the authors present the application and comparison of two decision-making models including the AHP model and the ANP model for deconstruction plan assessment. The paper concludes that both AHP and ANP are viable and capable tools for deconstruction plan assessment under the same set of evaluation criteria. However, although the ANP can measure relationship among selection criteria and their sub-criteria, which is normally ignored in the AHP, the authors also indicate that whether the ANP model can provide a more accurate result should be examined in further research.

Assessment of intercalibration methods for satellite microwave humidity sounders

Three methods for intercalibrating humidity sounding channels are compared to assess their merits and demerits. The methods use the following: (1) natural targets (Antarctica and tropical oceans), (2) zonal average brightness temperatures, and (3) simultaneous nadir overpasses (SNOs). Advanced Microwave Sounding Unit-B instruments onboard the polar-orbiting NOAA 15 and NOAA 16 satellites are used as examples. Antarctica is shown to be useful for identifying some of the instrument problems but less promising for intercalibrating humidity sounders due to the large diurnal variations there. Owing to smaller diurnal cycles over tropical oceans, these are found to be a good target for estimating intersatellite biases. Estimated biases are more resistant to diurnal differences when data from ascending and descending passes are combined. Biases estimated from zonal-averaged brightness temperatures show large seasonal and latitude dependence which could have resulted from diurnal cycle aliasing and scene-radiance dependence of the biases. This method may not be the best for channels with significant surface contributions. We have also tested the impact of clouds on the estimated biases and found that it is not significant, at least for tropical ocean estimates. Biases estimated from SNOs are the least influenced by diurnal cycle aliasing and cloud impacts. However, SNOs cover only relatively small part of the dynamic range of observed brightness temperatures.

Comparison of ammonium lactate, sodium bicarbonate and double calcium lactate methods for extraction of phosphorus from wetland peat soils

Procedures for routine analysis of soil phosphorus (P) have been used for assessment of P status, distribution and P losses from cultivated mineral soils. No similar studies have been carried out on wetland peat soils. The objective was to compare extraction efficiency of ammonium lactate (PAL), sodium bicarbonate (P-Olsen), and double calcium lactate (P-DCaL) and P distribution in the soil profile of wetland peat soils. For this purpose, 34 samples of the 0-30, 30-60 and 60-90 cm layers were collected from peat soils in Germany, Israel, Poland, Slovenia, Sweden and the United Kingdom and analysed for P. Mean soil pH (CaCl2, 0.01 M) was 5.84, 5.51 and 5.47 in the 0-30, 30-60 and 60-90 cm layers, respectively. The P-DCaL was consistently about half the magnitude of either P-AL or P-Olsen. The efficiency of P extraction increased in the order P-DCaL < P-AL &LE; P-Olsen, with corresponding means (mg kg(-1)) for all soils (34 samples) of 15.32, 33.49 and 34.27 in 0-30 cm; 8.87, 17.30 and 21.46 in 30-60 cm; and 5.69, 14.00 and 21.40 in 60-90 cm. The means decreased with depth. When examining soils for each country separately, P-Olsen was relatively evenly distributed in the German, UK and Slovenian soils. P-Olsen was linearly correlated (r = 0.594, P = 0.0002) with pH, whereas the three P tests (except P-Olsen vs P-DCaL) significantly correlated with each other (P = 0.017850.0001). The strongest correlation (r = 0.617, P = 0.0001) was recorded for P-AL vs P-DCaL) and the two methods were inter-convertible using a regression equation: P-AL = -22.593 + 5.353 pH + 1.423 P-DCaL, R-2 = 0.550.

Coronary heart disease risk screening: the community pharmacy Healthy Heart Assessment Service

Objectives We examined the characteristics and CHD risks of people who accessed the free Healthy Heart Assessment (HHA) service operated by a large UK pharmacy chain from August 2004 to April 2006. Methods Associations between participants’ gender, age, and socioeconomics were explored in relation to calculated 10-year CHD risks by cross-tabulation of the data. Specific associations were tested by forming contingency tables and using Pearson chi-square (χ2). Results Data from 8,287 records were analysable; 5,377 were at low and 2,910 at moderate-to-high CHD risk. The likelihood of moderate-to-high risk for a male versus female participant was significantly higher with a relative risk ratio (RRR) 1.72 (P < 0.001). A higher percentage of those in socioeconomic categories ‘constrained by circumstances’ (RRR 1.15; P < 0.05) and ‘blue collar communities’ (RRR 1.13; P < 0.05) were assessed with moderate-to-high risk compared to those in ‘prospering suburbs’. Conclusions People from ‘hard-to-reach’ sectors of the population, men and people from less advantaged communities, accessed the HHA service and were more likely to return moderate-to-high CHD risk. Pharmacists prioritised provision of lifestyle information above the sale of a product. Our study supports the notion that pharmacies can serve as suitable environments for the delivery of similar screening services.

Uptake of a free coronary heart disease risk screening programme in community pharmacy: the Healthy Heart Assessment service

Introduction Health promotion (HP) aims to enhance good health while preventing ill-health at three levels of activity; primary (preventative), secondary (diagnostic) and tertiary (management).1 It can range from simple provision of health education to ongoing support, but the effectiveness of HP is ultimately dependent on its ability to influence change. HP as part of the Community Pharmacy Contract (CPC) aims to increase public knowledge and target ‘hard-to-reach’ individuals by focusing mainly on primary and tertiary HP. The CPC does not include screening programmes (secondary HP) as a service. Coronary heart disease (CHD) is a significant cause of morbidity and mortality in the UK. While there is evidence to support the effectiveness of some community pharmacy HP strategies in CHD, there is paucity of research in relation to screening services.2 Against this background, Alliance Pharmacy introduced a free CHD risk screening programme to provide tailored HP advice as part of a participant–pharmacist consultation. The aim of this study is to report on the CHD risk levels of participants and to provide a qualitative indication of consultation outcomes. Methods Case records for 12 733 people who accessed a free CHD risk screening service between August 2004 and April 2006 offered at 217 community pharmacies were obtained. The service involved initial self-completion of the Healthy Heart Assessment (HHA) form and measurement of height, weight, body mass index, blood pressure, total cholesterol and highdensity lipoprotein levels by pharmacists to calculate CHD risk.3 Action taken by pharmacists (lifestyle advice, statin recommendation or general practitioner (GP) referral) and qualitative statements of advice were recorded, and a copy provided to the participants. The service did not include follow-up of participants. All participants consented to taking part in evaluations of the service. Ethical committee scrutiny was not required for this service development evaluation. Results Case records for 10 035 participants (3658 male) were evaluable; 5730 (57%) were at low CHD risk (<15%); 3636 (36%) at moderate-to-high CHD risk (≥15%); and 669 (7%) had existing heart disease. A significantly higher proportion of male (48% versus 30% female) participants were at moderate- to-high risk of CHD (chi-square test; P < 0.005). A range of outcomes resulted from consultations. Lifestyle advice was provided irrespective of participants’ CHD risk or existing disease. In the moderate-to-high-risk group, of which 52% received prescribed medication, lifestyle advice was recorded for 62%, 16% were referred and 34% were advised to have a re-assessment. Statin recommendations were made in 1% of all cases. There was evidence of supportive and motivational statements in the advice recorded. Discussion Pharmacists were able to identify individuals’ level of CHD risk and provide them with bespoke advice. Identification of at-risk participants did not automatically result in referrals or statin recommendation. One-third of those accessing the screening service had moderate-to-high risk of CHD, a significantly higher proportion of whom were men. It is not known whether these individuals had been previously exposed to HP but presumably by accessing this service they may have contemplated change. As effectiveness of HP advice will depend among other factors on ability to influence change, future consultations may need to explore patients’ attitude towards change in relation to the Trans Theoretical Model4 to better tailor HP advice. The high uptake of the service by those at moderate-to-high CHD risk indicates a need for this type of screening programme in community pharmacy, perhaps specifically to reach men who access medical services less.

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions.

The use of life cycle assessment to compare the environmental impact of production and feeding of conventional and genetically modified maize for broiler production in Argentina

The paper presents the methods and results of a life-cycle assessment (LCA) applied to the production of maize grain from a conventional variety compared with maize grain from a variety genetically modified to be herbicide tolerant and insect protected and to contain an enhanced oil and lysine content, and its impact when fed to broiler chickens. The findings show that there are both environmental and human health benefits of growing GM maize including lower impacts on global warming, ozone depletion, freshwater ecotoxicity and human toxicity. However, when considered in terms of the use of maize as a feed input to broiler chicken production, the benefits of the GM alternative become negligible compared to the use of conventional maize.

ALARM: Assessing large-scale environment risks for biodiversity with tested methods

The EU-funded research project ALARM will develop and test methods and protocols for the assessment of large-scale environmental risks in order to minimise negative human impacts. Research focuses on the assessment and forecast of changes in biodiversity and in the structure, function, and dynamics of ecosystems. This includes the relationships between society, the economy and biodiversity.

A critical assessment of a desk study comparing crop production systems: The example of the 'system of rice intensification' versus 'best management practice'

When assessing hypotheses, the possibility and consequences of false-positive conclusions should be considered along with the avoidance of false-negative ones. A recent assessment of the system of rice intensification (SRI) by McDonald et al. [McDonald, A.J., Hobbs, P.R., Riha, S.J., 2006. Does the system of rice intensification outperform conventional best management? A synopsis of the empirical record. Field Crops Res. 96, 31-36] provides a good example where this was not done as it was preoccupied with avoiding false-positives only. It concluded, based on a desk study using secondary data assembled selectively from diverse sources and with a 95% level of confidence, that 'best management practices' (BMPs) on average produce 11% higher rice yields than SRI methods, and that, therefore, SRI has little to offer beyond what is already known by scientists.