Bayesian estimation of group sizes for a coastal cetacean using aerial survey data

Many small cetacean, sirenian, and pinniped species aggregate in groups of large or variable size. Accurate estimation of group sizes is essential for estimating the abundance and distribution of these species, but is challenging as individuals are highly mobile and only partially visible. We developed a Bayesian approach for estimating group sizes using wide‐angle aerial photographic or video imagery. Our approach accounts for both availability and perception bias, including a new method (analogous to distance sampling) for estimating perception bias due to small image size in wide‐angle images. We demonstrate our approach through an application to aerial survey data for an endangered population of beluga whales (Delphinapterus leucas) in Cook Inlet, Alaska. Our results strengthen understanding of variation in group size estimates and allow for probabilistic statements about the size of detected groups. Aerial surveys are a standard tool for estimating the abundance and distribution of various marine mammal species. The role of aerial photographic and video data in wildlife assessment is expected to increase substantially with the widespread uptake of unmanned aerial vehicle technology. Key aspects of our approach are relevant to group size estimation for a broad range of marine mammal, seabird, other waterfowl, and terrestrial ungulate species.     

Yeast Spontaneous Mutation Rate and Spectrum Vary with Environment

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Imputation approaches for estimating diagnostic accuracy for multiple tests from partially verified designs

Interest often focuses on estimating sensitivity and specificity of a group of raters or a set of new diagnostic tests in situations in which gold standard evaluation is expensive or invasive. Various authors have proposed semilatent class modeling approaches for estimating diagnostic accuracy in this situation. This article presents imputation approaches for this problem. I show how imputation provides a simpler way of performing diagnostic accuracy and prevalence estimation than the use of semilatent modeling. Furthermore, the imputation approach is more robust to modeling assumptions and, in general, there is only a moderate efficiency loss relative to a correctly specified semilatent class model. I apply imputation to a study designed to estimate the diagnostic accuracy of digital radiography for gastric cancer. The feasibility and robustness of imputation is illustrated with analysis, asymptotic results, and simulations.     

Human oncogene tissue-specific expression level significantly correlates with sequence compositional features

To explore whether there exist correlations between human gene expressions and corresponding sequence features, the expression levels for 81 oncogenes in 24 human tissues were collected and correlated with 159 sequence features. It was found that there do exist significant correlations between them, some of which are of significance to understanding translational selection on sequence features of human genes and some have important implications for diagnosing cancers.     

Early childhood stress and adult age mortality--a study of dental enamel hypoplasia in the medieval Danish village of Tirup

This study explores how linear enamel hypoplasia (LEH) affects mortality in the village of Tirup (A.D. 1150-1350), Denmark. Data consist of information on 583 skeletons aged 1 year or more. Three partly overlapping subsamples were defined. (1) 104 skeletons of young children aged 1-6 years and 120 skeletons of adults giving information on LEH. (2) 458 skeletons aged 6 years or more. (3) 109 adult skeletons (aged 20 years or more) that provided transition analysis age estimates, sex assessments, and LEH information. Of the 109 skeletons in Subsample 3, 60 had no and 49 had at least one LEH. In Subsample 1, it was found that the case fatality rate for episodes potentially leading to LEH dropped from over 0.5 in 1-year olds to around 0.1 in 3-5-year olds. Only models with heterogeneity of frailty could describe late childhood and adolescent mortality. Further, it was shown that only a model with continuously varying frailty preserved heterogeneity to adulthood. Among young adult females and males in all adult ages, people with LEH experienced a higher mortality than people without it. Among males, the mortality rate ratio (MRR) was 2.28. The analyses indicate that the MRR gives an unbiased estimate for the extra risk of dying for adult males with LEH. The values of the case fatality rates for young children might be slightly biased upward because of a higher than average number of older children and adolescents dying with LEH.     

The effects of differential gene expression on coding sequence features: analysis by one-way ANOVA

It is well-established that non-random patterns in coding DNA sequence (CDS) features can be partially explained by translational selection. Recent extensions of microarray and proteomic expression data have stimulated many genome-wide investigations of the relationships between gene expression and various CDS features. However, only modest correlations have been found. Here we introduced the one-way ANOVA, a more powerful extension of previous grouping methods, to re-examine these relationships at the whole genome scale for Saccharomyces cerevisiae, where genome-wide protein abundance has been recently quantified. Our results clarify that coding sequence features are inappropriate for use as genome-wide estimators for protein expression levels. This analysis also demonstrates that one-way ANOVA is a powerful and simple method to explore the influence of gene expression on CDS features.     

Uniform amplification of multiple DNAs by emulsion PCR

When several DNAs are amplified by PCR in one PCR tube, biased amplification is known to occur because amplification efficiency differs from one DNA to another. Therefore, we conducted PCR in the water in oil-emulsion (W/O emulsion) to examine whether the procedure allows the uniform amplification of several DNAs. In the amplification of a model library consisting of two clones, the emulsification of the PCR mixture successfully reduced the difference in its amplification efficiency to approximately one-seventh the value obtained without emulsification. Furthermore, we conducted repeated PCR to amplify a model library consisting of ten short hairpin RNA (shRNA) expression vectors as a model experiment for gene discovery using an shRNA expression library. Consequently, the emulsification of the PCR mixture successfully reduced PCR bias. Our results indicate that emulsion PCR is capable of uniformly amplifying libraries of shRNA, ribozyme, cDNA, and others, and is useful also for gene discovery using these libraries.