Rice seed quality development and temperature during late development and maturation

The potential longevity of japonica rice (Oryza sativa L. subsp. japonica) seed is particularly sensitive to high temperature – and thus climate change – during development and maturation. Cultivar Taipei 309 was grown at 28/208C (12 h/12 h) and then from 19 DAA (days after 50% anthesis), when seeds were just over half filled, at 28/208C, 30/228C, 32/248C or 34/268C (12 h/12 h). Whereas ability to germinate ex planta had been achieved in almost all seeds by 24 DAA, only half the population were desiccation tolerant. Desiccation tolerance continued to increase over the subsequent 28 d, similarly at all four temperatures. Subsequent longevity, assessed by p50 (period in days to reduce viability to 50% in hermetic storage at 408C with c. 15% moisture content), increased progressively at 28/208C until 38 DAA, and remained constant until the final harvest (52 DAA). The three warmer temperature regimes provided similar longevity to 28/208C at any one harvest, except at 38 DAA where the warmest (34/268C) was poorer. That temperature regime also provided greater seed-to-seed variability within each survival curve. The results confirm that appreciable improvement in seed quality occurs during seed development and also subsequent maturation in japonica rice, but that increase in temperature from 28/208C to 34/268C during late seed filling onwards has comparatively little effect thereon. Comparison with previous investigations suggests that seed quality development may be less sensitive to high temperatures during late development and maturation than during the early seed development that precedes it.

Novel on-line sensor technology for continuous monitoring of milk coagulation and whey separation in cheese making

The cheese industry has continually sought a robust method to monitor milk coagulation. Measurement of whey separation is also critical to control cheese moisture content, which affects quality. The objective of this study was to demonstrate that an online optical sensor detecting light backscatter in a vat could be applied to monitor both coagulation and syneresis during cheesemaking. A prototype sensor having a large field of view (LFV) relative to curd particle size was constructed. Temperature, cutting time, and calcium chloride addition were varied to evaluate the response of the sensor over a wide range of coagulation and syneresis rates. The LFV sensor response was related to casein micelle aggregation and curd firming during coagulation and to changes in curd moisture and whey fat contents during syneresis. The LFV sensor has potential as an online, continuous sensor technology for monitoring both coagulation and syneresis during cheesemaking.

Improving aircraft maintenance, repair, and overhaul: A novel text mining approach

Aircraft Maintenance, Repair and Overhaul (MRO) feedback commonly includes an engineer’s complex text-based inspection report. Capturing and normalizing the content of these textual descriptions is vital to cost and quality benchmarking, and provides information to facilitate continuous improvement of MRO process and analytics. As data analysis and mining tools requires highly normalized data, raw textual data is inadequate. This paper offers a textual-mining solution to efficiently analyse bulk textual feedback data. Despite replacement of the same parts and/or sub-parts, the actual service cost for the same repair is often distinctly different from similar previously jobs. Regular expression algorithms were incorporated with an aircraft MRO glossary dictionary in order to help provide additional information concerning the reason for cost variation. Professional terms and conventions were included within the dictionary to avoid ambiguity and improve the outcome of the result. Testing results show that most descriptive inspection reports can be appropriately interpreted, allowing extraction of highly normalized data. This additional normalized data strongly supports data analysis and data mining, whilst also increasing the accuracy of future quotation costing. This solution has been effectively used by a large aircraft MRO agency with positive results.

Distributed multimedia quality: the user perspective

Distributed multimedia supports a symbiotic infotainment duality, i.e. the ability to transfer information to the user, yet also provide the user with a level of satisfaction. As multimedia is ultimately produced for the education and / or enjoyment of viewers, the user’s-perspective concerning the presentation quality is surely of equal importance as objective Quality of Service (QoS) technical parameters, to defining distributed multimedia quality. In order to extensively measure the user-perspective of multimedia video quality, we introduce an extended model of distributed multimedia quality that segregates quality into three discrete levels: the network-level, the media-level and content-level, using two distinct quality perspectives: the user-perspective and the technical-perspective. Since experimental questionnaires do not provide continuous monitoring of user attention, eye tracking was used in our study in order to provide a better understanding of the role that the human element plays in the reception, analysis and synthesis of multimedia data. Results showed that video content adaptation, results in disparity in user video eye-paths when: i) no single / obvious point of focus exists; or ii) when the point of attention changes dramatically. Accordingly, appropriate technical- and user-perspective parameter adaptation is implemented, for all quality abstractions of our model, i.e. network-level (via simulated delay and jitter), media-level (via a technical- and user-perspective manipulated region-of-interest attentive display) and content-level (via display-type and video clip-type). Our work has shown that user perception of distributed multimedia quality cannot be achieved by means of purely technical-perspective QoS parameter adaptation.

Improving sequence-based fold recognition by using 3D model quality assessment

Motivation: The ability of a simple method (MODCHECK) to determine the sequence–structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-likemodels. Results: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile–profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information.

Improvement of the GenTHREADER method for genomic fold recognition

Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Managing Water Quality in Agricultural Catchments

Until recently, pollution control in rural drainage basins of the UK consisted solely of water treatment at the point of abstraction. However, prevention of agricultural pollution at source is now a realistic option given the possibility of financing the necessary changes in land use through modification of the Common Agricultural Policy. This paper uses a nutrient export coefficient model to examine the cost of land-use change in relation to improvement of water quality. Catchment-wide schemes and local protection measures are considered. Modelling results underline the need for integrated management of entire drainage basins. A wide range of benefits may accrue from land-use change, including enhanced habitats for wildlife as well as better drinking water.

Avoiding a bad apple: insect pollination enhances fruit quality and economic value

Insect pollination is important for food production globally and apples are one of the major fruit crops which are reliant on this ecosystem service. It is fundamentally important that the full range of benefits of insect pollination to crop production are understood, if the costs of interventions aiming to enhance pollination are to be compared against the costs of the interventions themselves. Most previous studies have simply assessed the benefits of pollination to crop yield and ignored quality benefits and how these translate through to economic values. In the present study we examine the influence of insect pollination services on farmgate output of two important UK apple varieties; Gala and Cox. Using field experiments, we quantify the influence of insect pollination on yield and importantly quality and whether either may be limited by sub-optimal insect pollination. Using an expanded bioeconomic model we value insect pollination to UK apple production and establish the potential for improvement through pollination service management. We show that insects are essential in the production of both varieties of apple in the UK and contribute a total of £36.7 million per annum, over £6 million more than the value calculated using more conventional dependence ratio methods. Insect pollination not only affects the quantity of production but can also have marked impacts on the quality of apples, influencing size, shape and effecting their classification for market. These effects are variety specific however. Due to the influence of pollination on both yield and quality in Gala, there is potential for insect pollination services to improve UK output by up to £5.7 million per annum. Our research shows that continued pollinator decline could have serious financial implications for the apple industry but there is considerable scope through management of wild pollinators or using managed pollinator augmentation, to improve the quality of production. Furthermore, we show that it is critically important to consider all production parameters including quality, varietal differences and management costs when valuing the pollination service of any crop so investment in pollinator management can be proportional to its contribution.

Using high-frequency water quality data to assess sampling strategies for the EU Water Framework Directive

The EU Water Framework Directive (WFD) requires that the ecological and chemical status of water bodies in Europe should be assessed, and action taken where possible to ensure that at least "good" quality is attained in each case by 2015. This paper is concerned with the accuracy and precision with which chemical status in rivers can be measured given certain sampling strategies, and how this can be improved. High-frequency (hourly) chemical data from four rivers in southern England were subsampled to simulate different sampling strategies for four parameters used for WFD classification: dissolved phosphorus, dissolved oxygen, pH and water temperature. These data sub-sets were then used to calculate the WFD classification for each site. Monthly sampling was less precise than weekly sampling, but the effect on WFD classification depended on the closeness of the range of concentrations to the class boundaries. In some cases, monthly sampling for a year could result in the same water body being assigned to three or four of the WFD classes with 95% confidence, due to random sampling effects, whereas with weekly sampling this was one or two classes for the same cases. In the most extreme case, the same water body could have been assigned to any of the five WFD quality classes. Weekly sampling considerably reduces the uncertainties compared to monthly sampling. The width of the weekly sampled confidence intervals was about 33% that of the monthly for P species and pH, about 50% for dissolved oxygen, and about 67% for water temperature. For water temperature, which is assessed as the 98th percentile in the UK, monthly sampling biases the mean downwards by about 1 °C compared to the true value, due to problems of assessing high percentiles with limited data. Low-frequency measurements will generally be unsuitable for assessing standards expressed as high percentiles. Confining sampling to the working week compared to all 7 days made little difference, but a modest improvement in precision could be obtained by sampling at the same time of day within a 3 h time window, and this is recommended. For parameters with a strong diel variation, such as dissolved oxygen, the value obtained, and thus possibly the WFD classification, can depend markedly on when in the cycle the sample was taken. Specifying this in the sampling regime would be a straightforward way to improve precision, but there needs to be agreement about how best to characterise risk in different types of river. These results suggest that in some cases it will be difficult to assign accurate WFD chemical classes or to detect likely trends using current sampling regimes, even for these largely groundwater-fed rivers. A more critical approach to sampling is needed to ensure that management actions are appropriate and supported by data.

Developments in the quality of treated greywater supplies for buildings, and associated user perception and acceptance

A manufactured aeration and nanofiltration MBR greywater system was tested during continuous operation at the University of Reading, to demonstrate reliability in delivery of high quality treated greywater. Its treatment performance was evaluated against British Standard criteria [BSI (Greywater Systems—Part 1 Code of Practice: BS8525-1:2010. BS Press, 2010); (Greywater Systems—Part 2 Domestic Greywater Treatment, Requirements and Methods: BS 8525-2:2011. BS Press, 2011)]. The low carbon greywater recycling technology produced excellent analytical results as well as consistency in performance. User acceptance of such reliably treated greywater was then evaluated through user perception studies. The results inform the potential supply of treated greywater to student accommodation. Out of 135 questionnaire replies, 95% demonstrated a lack of aversion in one or more attributes, to using treated, recycled greywater.

Dietary Quality and Associated Factors among Factory Workers in the Metropolitan Region of Sao Paulo, Brazil

The workplace is a manageable community-based setting for ensuring proper nutrition. This study aimed to evaluate dietary quality and associated factors among adult workers at a cosmetics factory in the metropolitan area of Sao Paulo, Brazil. This factory was actively participating in the Brazilian Workers` Meal Program, which was created to ensure workers` nutritional health. In this cross-sectional study, data on 202 adult workers were assessed using questionnaires (sociodemographic, anthropometric, and lifestyle characteristics) administered during August and September 2006. Dietary intake, measured by 24-hour dietary recall, was used to calculate the modified Healthy Eating Index (HEI). A repeated administration of the 24-hour dietary recall was applied in a random subsample to calculate the modified HEI adjusted for the within-person variation in intake. Mean adjusted modified HEI scores were analyzed using multiple linear regression adjusted for energy. The mean adjusted modified HEI score was 72.3 +/- 8.0. The lowest adjusted modified HEI components scores were ""milk and dairy products"" (4.4 +/- 3.2) and ""sodium"" (3.7 +/- 3.1). Two percent of workers had ""poor diet"" (adjusted modified HEI score <51 points) and the majority (87%) had ""diet that needs modification"" (adjusted modified HEI score between 51 and 80), despite their participation in the meal program. Adjusted modified HEI scores were considerably higher for men (74.7 +/- 7.0) than for women (66.9 +/- 8.2) and for normal body mass index (calculated as kg/m(2)) (73.3 +/- 7.8) than for overweight/obese (70.9 +/- 8.1). Based on these results, the vast majority of workers were found to have diets that needed improvement. Individuals with higher-quality diets were more likely to have lower body mass index and to be male. J Am Diet Assoc. 2010;110:786-790.

Dietary Quality Index and Associated Factors among Adolescents of the State of Sao Paulo, Brazil

Objective To assess dietary quality and associated factors in adolescents. Study design We conducted a population-based cross-sectional study in a sample of 1584 adolescents living in areas of the state of Sao Paulo, Brazil. Dietary intake was measured with the 24-hour recall method, and dietary quality was assessed by means of the Health Eating Index (HEI), adapted to fit to the local requirements. Linear regression analyses were performed to assess the association between the HEI and demographic, socioeconomic, and lifestyle variables. Results A total of 97.1% of the adolescents studied had an inadequate diet or a diet that needed improvement. The mean overall HEI score was 59.7. Lower mean HEI scores were found for fruits, dairy products, and vegetables. Male adolescents who were physically active and lived in a house or apartment had higher HEI scores. The multiple regression analyses showed that the quality of the diet improved as age decreased. Adolescents who lived in houses or apartments had higher HEI scores than adolescents living in shacks or slums, regardless of age and energy intake. Conclusions Dietary quality is associated with income and age. A better understanding of the factors associated can provide input to the formulation of policies and development of nutritional actions. (J Pediatr 2010; 156:456-60).

Dietary omega-3 fatty acid and omega-3: omega-6 fatty acid ratio predict improvement in glucose disturbances in Japanese Brazilians

Objective: We investigated whether lifestyle-induced changes in dietary fat quality are related to Improvements on glucose metabolism disturbances in Japanese Brazilians at high risk of type 2 diabetes Methods: One hundred forty-eight first- and second-generation subjects with impaired glucose tolerance or impaired fasting glycemia who attended a lifestyle intervention program for 12 mo were studied in the city of Bauru. State of Sao Paulo, Brazil Dietary fatty acid intakes at baseline and after 12 mo were estimated using three 24-h recalls. The effect of dietary fat intake on glucose metabolism was investigated by multiple logistic regression models Results: At baseline, mean standard deviation age and body mass index were 60 II y and 25 5 4.2 kg/m2, respectively After 12 mo. 92 subjects had normal plasma glucose levels and 56 remained in prediabetic conditions. Using logistic regression models adjusted for age, gender, generation, basal intake of explanatory nutrient, energy intake, physical activity, and waist circumference, the odds ratios (95% confidence intervals) for reversion to normoglycemia were 3 14 (1 22-8 10) in the second wrote of total w-3 fatty acid, 4 26 (1.34-13 57) in the second tunic of eicosapentaenoic acid, and 280 (1 10-7.10) in the second tertile of linolenic acid. Similarly. subjects in the highest wrote of w-3.w-6 fatty acid ratio showed a higher chance of improving glucose disturbances (2 51, 1.01-6.37) Conclusions: Our findings support the evidence of an independent protective effect of omega-3 fatty acid and of a higher omega-3:omega-6 fatty acid ratio on the glucose metabolism of high-risk individuals (C) 2010 Elsevier Inc All rights reserved.

Diet quality of persons living with HIV/AIDS on highly active antiretroviral therapy

Background This study sought to assess the diet quality of individuals living with HIV/AIDS who were receiving antiretroviral therapy in Sao Paulo Brazil,. Methods This cross-sectional study involved 56 HIV-infected adults. Demographic and anthropometric data were collected, and diet quality was measured using the Healthy Eating Index (HEI), modified for Brazilians, which included ten components: adequacy of intake of six different food groups, total fat, cholesterol, dietary fibre and dietary variety. Results Among the individuals assessed, 64.3% of the participants had a diet needing improvement, while 8.7% had a poor diet. The overall HEI score was 68.3 points (SD = 14.9). Mean scores were low for fruits, vegetables, dairy products and dietary fibre; and high for meats and eggs, total fat and cholesterol. The overall HEI score was higher among individuals who were not overweight (P = 0.003), who were also more likely to achieve dietary goals for dairy products (P = 0.039) and grains (P = 0.005). Conclusion Most of these adults living with HIV/AIDS had diets that required improvement, and being overweight was associated with poorer diet quality. Nutritional interventions aimed at maintaining healthy body weight and diet should be taken into account in caring for HIV-infected people.