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  • Nucleic acid structure, Computational Methods  (4)
  • Beverages  (3)
  • Oxford University Press  (7)
  • Wiley
  • 2015-2019
  • 2010-2014  (7)
  • 1980-1984
  • 1960-1964
  • 1925-1929
  • 2012  (7)
  • 1981
  • 1926
  • 1
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    Global or local? Predicting secondary structure and accessibility in mRNAs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-28
    Description: Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis -regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding was more accurate than the classic global approach. We investigated how the locality parameters, maximum base pair span and window size, influenced the prediction performance. A span of 150 provided a reasonable balance between maximizing the number of accurately predicted base pairs, while minimizing effects of incorrect long-range predictions. We characterized the error at artificial sequence ends, which we reduced by setting the window size sufficiently greater than the maximum span. Our method, LocalFold, diminished all border effects and produced the most robust performance.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Statistical evaluation of improvement in RNA secondary structure prediction (2012)
    Oxford University Press
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    Publication Date: 2012-02-28
    Description: With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorithms are compared against each other and one is selected as best without statistical testing to determine whether the improvement is significant. In this work, it is demonstrated that the prediction accuracies of methods correlate with each other over sets of sequences. One possible reason for this correlation is that many algorithms use the same underlying principles. A set of benchmarks published previously for programs that predict a structure common to three or more sequences is statistically analyzed as an example to show that it can be rigorously evaluated using paired two-sample t -tests. Finally, a pipeline of statistical analyses is proposed to guide the choice of data set size and performance assessment for benchmarks of structure prediction. The pipeline is applied using 5S rRNA sequences as an example.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics (2012)
    Oxford University Press
    Details
    Publication Date: 2012-02-17
    Description: The GeoPCA package is the first tool developed for multivariate analysis of dihedral angles based on principal component geodesics. Principal component geodesic analysis provides a natural generalization of principal component analysis for data distributed in non-Euclidean space, as in the case of angular data. GeoPCA presents projection of angular data on a sphere composed of the first two principal component geodesics, allowing clustering based on dihedral angles as opposed to Cartesian coordinates. It also provides a measure of the similarity between input structures based on only dihedral angles, in analogy to the root-mean-square deviation of atoms based on Cartesian coordinates. The principal component geodesic approach is shown herein to reproduce clusters of nucleotides observed in an – plot. GeoPCA can be accessed via http://pca.limlab.ibms.sinica.edu.tw .
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Stop or go? How is the UK food industry responding to front-of-pack nutrition labels? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-30
    Description: The adoption of voluntary front-of-pack (FOP) nutrition labels by UK food retailers and manufacturers is explored. These labels highlight key nutrients, facilitating product comparisons. Information for 2,201 products launched between 2007 and 2009 was analysed. Binary and multinomial logistic regression models explore drivers of FOP label use. Products introduced more recently by retailers and certain food categories were more likely to carry FOP labels. Increasing the content of sodium and sugar decreased odds of FOP use in some categories, but with limited significance. Discussion includes policy options to optimise firm response and implications for evolving mandatory FOP labelling proposals.
    Keywords: L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 5
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    R-CHIE: a web server and R package for visualizing RNA secondary structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-28
    Description: Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R- chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Functional foods as differentiated products: the Italian yogurt market (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: In spite of the growing consumers' interest for functional foods, the knowledge regarding the demand for these products and their profitability is limited. Adapting the LA/AIDS (Linear Approximated–Almost Ideal Demand System) model by means of Pinkse, Slade and Brett's distance metric method (2002), this article studies demand, substitution pattern, and profitability of conventional and functional alternatives inside the yogurt category in Italy. Results indicate that, in the yogurt market, functional alternatives' demand is often less elastic than that of their conventional counterparts, that brand loyalty plays a key role, and that the profitability of the functional alternatives is, on average, larger than that of conventional ones.
    Keywords: L11 - Production, Pricing, and Market Structure ; Size Distribution of Firms, L13 - Oligopoly and Other Imperfect Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 7
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    Network externalities in supermarket retailing (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: Supermarkets face a two-sided demand for shelf space: consumers demand variety and suppliers demand shelf space. We exploit the asymmetric ability of consumers and suppliers to internalise network effects to derive a novel test of network effects in multi-product retail markets. Because consumers fully internalise network effects but suppliers cannot, retail margins rise and wholesale margins fall as variety increases. We test this hypothesis using retail scanner data for a ‘shopping basket’ of items from competing retailers using a structural model of retail variety and vertical pricing. Our results support the existence of positive, two-sided network effects in supermarket retailing.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, L11 - Production, Pricing, and Market Structure ; Size Distribution of Firms, L13 - Oligopoly and Other Imperfect Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, L81 - Retail and Wholesale Trade ; e-Commerce
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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