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Increased accuracy of starch granule type quantification using mixture distributions.

ABSTRACT: The proportion of granule types in wheat starch is an important characteristic that can affect its functionality. It is widely accepted that granule types are either large, disc-shaped A-type granules or small, spherical B-type granules. Additionally, there are some reports of the tiny C-type granules. The differences between these granule types are due to its carbohydrate composition and crystallinity which is highly, but not perfectly, correlated with the granule size. A majority of the studies that have considered granule types analyse them based on a size threshold rather than chemical composition. This is understandable due to the expense of separating starch into different types. While the use of a size threshold to classify granule type is a low-cost measure, this results in misclassification. We present an alternative, statistical method to quantify the proportion of granule types by a fit of the mixture distribution, along with an R package, a web based app and a video tutorial for how to use the web app to enable its straightforward application.Our results show that the reliability of the genotypic effects increase approximately 60% using the proportions of the A-type and B-type granule estimated by the mixture distribution over the standard size-threshold measure. Although there was a marginal drop in reliability for C-type granules. The latter is likely due to the low observed genetic variance for C-type granules.The determination of the proportion of granule types from size-distribution is better achieved by using the mixing probabilities from the fit of the mixture distribution rather than using a size-threshold.

SUBMITTER: Tanaka E

PROVIDER: S-EPMC5718142 | biostudies-other | 2017

REPOSITORIES: biostudies-other

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Increased accuracy of starch granule type quantification using mixture distributions.

Tanaka Emi E Ral Jean-Phillippe F JF Li Sean S Gaire Raj R Cavanagh Colin R CR Cullis Brian R BR Whan Alex A

Plant methods 20171206

<h4>Background</h4>The proportion of granule types in wheat starch is an important characteristic that can affect its functionality. It is widely accepted that granule types are either large, disc-shaped A-type granules or small, spherical B-type granules. Additionally, there are some reports of the tiny C-type granules. The differences between these granule types are due to its carbohydrate composition and crystallinity which is highly, but not perfectly, correlated with the granule size. A maj ...[more]

PMID: 29225662

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Project description:BACKGROUND:Volatile organic compounds (VOC), which include many hazardous chemicals, have been used extensively in personal, commercial and industrial products. Due to the variation in source emissions, differences in the settings and environmental conditions where exposures occur, and measurement issues, distributions of VOC concentrations can have multiple modes, heavy tails, and significant portions of data below the method detection limit (MDL). These issues challenge standard parametric distribution models needed to estimate the exposures, even after log-transformation of the data. METHODS:This paper considers mixture of distributions that can be directly applied to concentration and exposure data. Two types of mixture distributions are considered: the traditional finite mixture of normal distributions, and a semi-parametric Dirichlet process mixture (DPM) of normal distributions. Both methods are implemented for a sample data set obtained from the Relationship between Indoor, Outdoor and Personal Air (RIOPA) study. Performance is assessed based on goodness-of-fit criteria that compare the closeness of the density estimates with the empirical density based on data. The goodness-of-fit for the proposed density estimation methods are evaluated by a comprehensive simulation study. RESULTS:The finite mixture of normals and DPM of normals have superior performance when compared to the single normal distribution fitted to log-transformed exposure data. The advantages of using these mixture distributions are more pronounced when exposure data have heavy tails or a large fraction of data below the MDL. Distributions from the DPM provided slightly better fits than the finite mixture of normals. Additionally, the DPM method avoids certain convergence issues associated with the finite mixture of normals, and adaptively selects the number of components. CONCLUSIONS:Compared to the finite mixture of normals, DPM of normals has advantages by characterizing uncertainty around the number of components, and by providing a formal assessment of uncertainty for all model parameters through the posterior distribution. The method adapts to a spectrum of departures from standard model assumptions and provides robust estimates of the exposure density even under censoring due to MDL.

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Increased accuracy of starch granule type quantification using mixture distributions.

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Increased accuracy of starch granule type quantification using mixture distributions.

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