Dataset Information

Linear-In-The-Parameters Oblique Least Squares (LOLS) Provides More Accurate Estimates of Density-Dependent Survival.

ABSTRACT: Survival is a fundamental demographic component and the importance of its accurate estimation goes beyond the traditional estimation of life expectancy. The evolutionary stability of isomorphic biphasic life-cycles and the occurrence of its different ploidy phases at uneven abundances are hypothesized to be driven by differences in survival rates between haploids and diploids. We monitored Gracilaria chilensis, a commercially exploited red alga with an isomorphic biphasic life-cycle, having found density-dependent survival with competition and Allee effects. While estimating the linear-in-the-parameters survival function, all model I regression methods (i.e, vertical least squares) provided biased line-fits rendering them inappropriate for studies about ecology, evolution or population management. Hence, we developed an iterative two-step non-linear model II regression (i.e, oblique least squares), which provided improved line-fits and estimates of survival function parameters, while robust to the data aspects that usually turn the regression methods numerically unstable.

SUBMITTER: Vieira VM

PROVIDER: S-EPMC5147871 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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Linear-In-The-Parameters Oblique Least Squares (LOLS) Provides More Accurate Estimates of Density-Dependent Survival.

Vieira Vasco M N C S VM Engelen Aschwin H AH Huanel Oscar R OR Guillemin Marie-Laure ML

PloS one 20161209 12

Survival is a fundamental demographic component and the importance of its accurate estimation goes beyond the traditional estimation of life expectancy. The evolutionary stability of isomorphic biphasic life-cycles and the occurrence of its different ploidy phases at uneven abundances are hypothesized to be driven by differences in survival rates between haploids and diploids. We monitored Gracilaria chilensis, a commercially exploited red alga with an isomorphic biphasic life-cycle, having foun ...[more]

PMID: 27936048

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Project description:By convention, slices in a tomosynthesis reconstruction are created on planes parallel to the detector. It has not yet been demonstrated that slices can be generated along oblique directions through the same volume, analogous to multiplanar reconstructions in computed tomography (CT). The purpose of this work is to give a proof-of-principle justification for oblique reconstructions in tomosynthesis, which acquires projection images over a smaller angular range than CT.To investigate the visibility of individual frequencies in an oblique reconstruction, a theoretical framework is developed in which the reconstruction of a sinusoidal input is calculated. The test frequency is pitched at an angle in a 2D parallel-beam acquisition geometry. Reconstructions are evaluated along the pitch of the object. The modulation transfer function (MTF) is calculated from the relative signal at various test frequencies. The MTF determines whether modulation is within detectable limits in oblique reconstructions. In the previous linear systems (LS) model [B. Zhao and W. Zhao, "Three-dimensional linear system analysis for breast tomosynthesis," Med. Phys. 35(12), 5219-5232 (2008)], the MTF was calculated only in reconstructed slices parallel to the detector. This paper generalizes the MTF calculation to reconstructed slices at all possible pitches. Unlike the previous LS model, this paper also analyzes the effect of object thickness on the MTF. A second test object that is considered is a rod whose long axis is pitched similar to the sinusoidal input. The rod is used to assess whether the length of an object can be correctly estimated in oblique reconstructions.To simulate the conventional display of the reconstruction, slices are first created along a 0° pitch. This direction is perpendicular to the rays of the central projection. The authors show that the input frequency of a pitched sinusoidal object cannot be determined using these slices. By changing the pitch of the slice to match the object, it is shown that the input frequency is properly resolved. To prove that modulation is preserved in pitched slices, the MTF is also calculated. Modulation is within detectable limits over a broad range of pitches if the object is thin, but is detectable over a narrower range of pitches if the object is thick. Turning next to the second test object, it is shown that the length of a pitched rod can be correctly determined in oblique reconstructions. Concordant with the behavior of the MTF, the length estimate is accurate over a broad range of pitches if the object is thin, but is correct over a narrower range of pitches if the object is thick.This work justifies the feasibility of oblique reconstructions in tomosynthesis. It is demonstrated that pitched test objects are most easily visualized with oblique reconstructions instead of conventional reconstructions. In order to achieve high image quality over a broad range of pitches, the object must be thin. By analyzing the effect of reconstruction pitch and object thickness on image quality, this paper generalizes the previous LS model for tomosynthesis.

Project description:BACKGROUND: Mortality due to cannibalism in laying hens is a difficult trait to improve genetically, because censoring is high (animals still alive at the end of the testing period) and it may depend on both the individual itself and the behaviour of its group members, so-called associative effects (social interactions). To analyse survival data, survival analysis can be used. However, it is not possible to include associative effects in the current software for survival analysis. A solution could be to combine survival analysis and a linear animal model including associative effects. This paper presents a two-step approach (2STEP), combining survival analysis and a linear animal model including associative effects (LAM). METHODS: Data of three purebred White Leghorn layer lines from Institut de Sélection Animale B.V., a Hendrix Genetics company, were used in this study. For the statistical analysis, survival data on 16,780 hens kept in four-bird cages with intact beaks were used. Genetic parameters for direct and associative effects on survival time were estimated using 2STEP. Cross validation was used to compare 2STEP with LAM. LAM was applied directly to estimate genetic parameters for social effects on observed survival days. RESULTS: Using 2STEP, total heritable variance, including both direct and associative genetic effects, expressed as the proportion of phenotypic variance, ranged from 32% to 64%. These results were substantially larger than when using LAM. However, cross validation showed that 2STEP gave approximately the same survival curves and rank correlations as LAM. Furthermore, cross validation showed that selection based on both direct and associative genetic effects, using either 2STEP or LAM, gave the best prediction of survival time. CONCLUSION: It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens.

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Linear-In-The-Parameters Oblique Least Squares (LOLS) Provides More Accurate Estimates of Density-Dependent Survival.

Publications

Linear-In-The-Parameters Oblique Least Squares (LOLS) Provides More Accurate Estimates of Density-Dependent Survival.

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