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.

Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.

Pressing technique and its effect on the quality of Dhaka cheese

Dhaka cheese is a semihard artisanal variety made mainly from bovine milk, using very simple pressing methods. Experimental cheeses were pressed at gauge pressures up to 31 kPa for 12 h at 24 °C and 70% RH. These cheeses were subsequently examined for their compositional, textural and rheological properties plus their microstructures investigated by confocal laser microscopy. The cheese pressed at 15.6 kPa was found to have the best compositional and structural properties.

Cost effectiveness of mitigation measures for water security and water quality in the River Thames catchment: impacts of changing climate, land use and water scarcity

The catchment of the River Thames, the principal river system in southern England, provides the main water supply for London but is highly vulnerable to changes in climate, land use and population. The river is eutrophic with significant algal blooms with phosphorus assumed to be the primary chemical indicator of ecosystem health. In the Thames Basin, phosphorus is available from point sources such as wastewater treatment plants and from diffuse sources such as agriculture. In order to predict vulnerability to future change, the integrated catchments model for phosphorus (INCA-P) has been applied to the river basin and used to assess the cost-effectiveness of a range of mitigation and adaptation strategies. It is shown that scenarios of future climate and land-use change will exacerbate the water quality problems, but a range of mitigation measures can improve the situation. A cost-effectiveness study has been undertaken to compare the economic benefits of each mitigation measure and to assess the phosphorus reductions achieved. The most effective strategy is to reduce fertilizer use by 20% together with the treatment of effluent to a high standard. Such measures will reduce the instream phosphorus concentrations to close to the EU Water Framework Directive target for the Thames.

Evaluating the potential of high pressure high temperature and thermal processing on volatile compounds, nutritional and structural properties of orange and yellow carrots

The present study compares the impact of thermal and high pressure high temperature(HPHT) processing on volatile profile (via a non-targeted headspace fingerprinting) and structural and nutritional quality parameter (via targeted approaches) of orange and yellow carrot purees. The effect of oil enrichment was also considered. Since oil enrichment affects compounds volatility, the effect of oil was not studied when comparing the volatile fraction. For the targeted part, as yellow carrot purees were shown to contain a very low amount of carotenoids, focus was given to orange carrot purees. The results of the non-targeted approach demonstrated HPHT processing exerts a distinct effect on the volatile fractions compared to thermal processing. In addition, different colored carrot varieties are characterized by distinct headspace fingerprints. From a structural point of view, limited or no difference could be observed between orange carrot purees treated with HPHT or HT processes, both for samples without and with oil. From nutritional point of view, only in samples with oil, significant isomerisation of all-trans-β-carotene occurred due to both processing. Overall, for this type of product and for the selected conditions, HPHT processing seems to have a different impact on the volatile profile but rather similar impact on the structural and nutritional attributes compared to thermal processing.

The EU societal awareness of landscape indicator: a review of its meaning, utility and performance across different scales

There is increasing recognition that agricultural landscapes meet multiple societal needs and demands beyond provision of economic and environmental goods and services. Accordingly, there have been significant calls for the inclusion of societal, amenity and cultural values in agri-environmental landscape indicators to assist policy makers in monitoring the wider impacts of land-based policies. However, capturing the amenity and cultural values that rural agrarian areas provide, by use of such indicators, presents significant challenges. The EU social awareness of landscape indicator represents a new class of generalized social indicator using a top-down methodology to capture the social dimensions of landscape without reference to the specific structural and cultural characteristics of individual landscapes. This paper reviews this indicator in the context of existing agri-environmental indicators and their differing design concepts. Using a stakeholder consultation approach in five case study regions, the potential and limitations of the indicator are evaluated, with a particular focus on its perceived meaning, utility and performance in the context of different user groups and at different geographical scales. This analysis supplements previous EU-wide assessments, through regional scale assessment of the limitations and potentialities of the indicator and the need for further data collection. The evaluation finds that the perceived meaning of the indicator does not vary with scale, but in common with all mapped indicators, the usefulness of the indicator, to different user groups, does change with scale of presentation. This indicator is viewed as most useful when presented at the scale of governance at which end users operate. The relevance of the different sub-components of the indicator are also found to vary across regions.

Effect of steeping conditions (sulfur dioxide, lactic acid, and temperature) on starch yield, starch quality, and germ quality from the Intermittent Milling and Dynamic Steeping process (IMDS) for a Brazilian corn hybrid

Effect of lactic acid, SO2, temperature, and their interactions were assessed on the dynamic steeping of a Brazilian dent corn (hybrid XL 606) to determine the ideal relationship among these variables to improve the wet-milling process for starch and corn by-products production. A 2x2x3 factorial experimental design was used with SO2 levels of 0.05 and 0.1% (w/v), lactic acid levels of 0 and 0.5% (v/v), and temperatures of 52, 60, and 68degreesC. Starch yield was used as deciding factor to choose the best treatment. Lactic acid added in the steep solution improved the starch yield by an average of 5.6 percentage points. SO2 was more available to break down the structural protein network at 0.1% than at the 0.05% level. Starch-gluten separation was difficult at 68degreesC. The lactic acid and SO2 concentrations and steeping temperatures for better starch recovery were 0.5, 0.1, and 52degreesC, respectively. The Intermittent Milling and Dynamic Steeping (IMDS) process produced, on average, 1.4% more starch than the conventional 36- hr steeping process. Protein in starch, oil content in germ, and germ damage were used as quality factors. Total steep time can be reduced from 36 hr for conventional wet-milling to 8 hr for the IMDS process.

Electrical conductivity as an indicator of pea seed aging of stored at different temperatures

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural transition on Pb1-xSrxTiO3 produced by chemical method

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Application of wavelets to the evaluation of phantom images for mammography quality control

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

As praças públicas de Natal/RN no âmbito dos problemas socioambientais urbanos

This paper presents the public square as a subsystem of the city for the potential integration of elements 'natural' and built environment. But sometimes the suitability of projects and the social processes involved are not compatible and favorable to their real functions in urban space. The city of Natal, with a population of 803,739 inhabitants has 253 public parks not uniformly distributed in the urban area, but mostly in central areas and their absence in some peripheral neighborhoods. In this sense, the objective of this paper is to analyze the quality and spatiality of the city's public squares within the urban socio-environmental problems. For this, use of simple random sampling to define the sample and the proportional allocation of districts, totaling 168 squares to be raised. We prepared a form to collect data on the field that includes aspects of leisure, infrastructure and environment. For each square sampled was calculated Square Quality Index (PQI), then calculating the average per IQP neighborhood. The rates found were crossed with census data and Municipal Public Administration by neighborhood, using multivariate analysis. We generated maps, charts and tables, considered appropriate to each question format, focused comparison. The public square appears as an indicator of environmental challenges present in intra-urban spaces of the city. Their spatial distribution is not consistent demand population, both by disposition and by how much. In terms of quality are characterized by different levels of inadequacy and degradation aspects of leisure, environmental and infrastructure, often causing disfigurement, abandonment and improper occupation in such spaces. Multivariate analysis point to a central concentration and their problems in certain administrative units, not only as regards the public squares, but also to aspects of education, income, and other violence, perpetuating the problem. The various levels of inadequacy and degradation of public squares have been more blatant in the poorest neighborhoods of the city, pointing to a structural pattern associated with the intrinsic characteristics of the neighborhood and the socioeconomic profile of the local population. These are problems of social and environmental dimensions, threaded in and influenced the political, economic and broader social process of transformation of the city and the urban. Based on an uneven process in which space necessarily reflect the contradictions inherent in the active forces and interests. Thus evidencing the importance of managing the necessary public effectively engaged with the problems that are present there, in order to equate them, without being prioritized certain areas of the city at the expense of others

Breed and season influence on milk quality parameters and in mastitis occurrence

Os objetivos do presente estudo foram avaliar a performance das raças Jersey e Holandesa em diferentes condições de pluviosidade (estações seca e chuvosa) através do monitoramento de aspectos relacionados com a mastite subclínica (contagem de células somáticas, isolamento microbiológico, tipo de patógeno isolado), qualidade do leite (lactose, proteína, gordura e sólidos totais) e produção (media da produção de leite) de ambas as raças. O estudo foi conduzido em propriedade leiteira localizada no estado de São Paulo, Brasil. Oito visitas foram realizadas a propriedade, quatro em período de alta pluviosidade e outro em período de baixa pluviosidade. Amostras de leite foram colhidas de todos os animais para contagem eletrônica de células somáticas e determinação dos principais componentes do leite (proteína, gordura, sólidos totais, lactose). Gordura, proteína, sólidos totais e produção leiteira foram influenciadas tanto pela raça como pela estação, apresentando tendências similares para ambas raças em ambas estações. A contagem de células somáticas (CCS) apresentou resultados similares para ambas as raças. Vacas holandesas com infecção intramamária (IIM) apresentaram um maior aumento na CCS quando comparadas as vacas Jersey (P<0.001). Na estação seca, 53 animais tiveram IIM em pelo menos um mês do estudo. Destes, 32 eram da raça Holandesa e 21 da raça Jersey. Na estação chuvosa, 65 animais possuíram infecção intramamária, dos quais 43 eram da raça Holandesa e 22 da raça Jersey. A frequência de casos de IIM foi maior na estação chuvosa em comparação à estação seca. Vacas Jersey apresentaram uma menor chance de desenvolver sinais e sintomas de IIM em relação às vacas holandesas na estação chuvosa (razão de chances=0.52). O maior numero de casos de IIM na estação chuvosa pode ter contribuído para uma menor taxa de lactose no leite para ambas as raças, sendo que esta pode ser considerada como um indicador do status de IIM. Existiu uma prevalência de patógenos contagiosos durante todo o experimento. O modelo estatístico aplicado mostrou que patógenos ambientais foram mais frequentemente isolados da raça Jersey, independentemente do período do estudo. Aparentemente existem diferenças na resposta imune das raças Jersey e Holandesa.

Storage temperature and quality of red mombin fruits (Spondias purpurea L.)

The aim was to study the effect of different storage temperatures on quality of red mombin fruit. The red mombin fruits were obtained from the Company CEAGESP/São Paulo/Brazil and transported in cool boxes to the laboratory, where they were selected on the base of appearance, maturity lack of physical damage, sanitized in 50 ppm chlorine-free solution and packaged in polystyrene trays wrapped with film of polyvinyl chloride (PVC). The experiment was a completely randomized design with three temperatures (4, 8 and 25 degrees C) and 5 time intervals (0, 2, 4, 6 and 8 days after the experiment installation). In each survey firmness, titratable acidity, soluble solids, ascorbic acid content, the skin color and also the release of CO(2) by the fruit over time were evaluated. It was observed that low temperatures prolong the fruits shelf life and the storage temperature influences the characteristics, the temperature of 8 degrees C was most suitable for the storage of red mombin fruits. Besides, the fruit color was a good indicator of changes in the pulp during storage.

Optical and structural properties of GaAs/GaInP quantum wells grown by Chemical Beam Epitaxy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mineralogical characterization of clays used in the structural ceramic industry in west of S. Paulo State, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)