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Food and waterborne protozoan pathogens can cause serious disease in people. Three common species Cryptosporidium parvum, Giardia enterica and Toxoplasma gondii can contaminate diverse shellfish species, including commercial oysters. Current methods of protozoan detection in shellfish are not standardized, and few are able to simultaneously identify multiple species. Here, we present a novel metabarcoding assay targeting the 18S rRNA gene followed by next generation sequencing (NGS) for simultaneous detection of Cryptosporidium spp., Giardia spp. and T. gondii spiked into oyster samples. We further developed a bioinformatic pipeline to process and analyze 18S rRNA data for protozoa classification. The ability of the NGS assay to detect protozoa was later compared with conventional PCR. Results demonstrated that background amplification of oyster and other eukaryotic DNA competed with that of protozoa for obtained sequence reads. Sequences of target protozoans were obtained across all spiking levels; however, low numbers of target sequences in negative controls imply that a threshold for true positives must be defined for assay interpretation. While this study focused on three target parasites, the ability of this approach to detect numerous known and potentially unknown protozoan pathogens make it a promising screening tool for monitoring protozoan contamination in food and water.

A number of sentinel species are regularly sampled from the environment near the Oil Sands Region (OSR) in Alberta, Canada. In particular, trout-perch are sampled as a proxy for the health of the aquatic ecosystem. As the development of the OSR began before the environmental monitoring program was in place, there is currently no established measure for the baseline health of the local ecosystem. A common solution is to calculate normal ranges for fish endpoints. Observations found to be outside the normal range are then flagged, alerting researchers to the potential presence of stressors in the local environment. The quality of the normal ranges is dependent on the accuracy of the estimates used to calculate them. This paper explores the use of neural networks and regularized regression for improving the prediction accuracy of fish endpoints. We also consider the trade-off between the prediction accuracy and interpretability of each model. We find that neural networks can provide increased prediction accuracy, but this improvement in accuracy may not be worth the loss in interpretability in some ecological studies. The elastic net offers both good prediction accuracy and interpretability, making it a safe choice for many ecological applications. A hybridized method combining both the neural network and elastic net offers high prediction accuracy as well as some interpretability, and therefore it is the recommended method for this application. [ABSTRACT FROM AUTHOR]

Mixture of regression model is widely used to cluster subjects from a suspected heterogeneous population due to differential relationships between response and covariates over unobserved subpopulations. In such applications, statistical evidence pertaining to the significance of a hypothesis is important yet missing to substantiate the findings. In this case, one may wish to test hypotheses regarding the effect of a covariate such as its overall significance. If confirmed, a further test of whether its effects are different in different subpopulations might be performed. This paper is motivated by the analysis of Chiroptera dataset, in which, we are interested in knowing how forearm length development of bat species is influenced by precipitation within their habitats and living regions using finite Gaussian mixture regression (GMR) model. Since precipitation may have different effects on the evolutionary development of the forearm across the underlying subpopulations among bat species worldwide, we propose several testing procedures for hypotheses regarding the effect of precipitation on forearm length under finite GMR models. In addition to the real analysis of Chiroptera data, through simulation studies, we examine the performances of these testing procedures on their type I error rate, power, and consequently, the accuracy of clustering analysis. [ABSTRACT FROM AUTHOR]

Abstract Background It is desirable in genomic studies to select biomarkers that differentiate between normal and diseased populations based on related data sets from different platforms, including microarray expression and proteomic data. Most recently developed integration methods focus on correlation analyses between gene and protein expression profiles. The correlation methods select biomarkers with concordant behavior across two platforms but do not directly select differentially expressed biomarkers. Other integration methods have been proposed to combine statistical evidence in terms of ranks and p-values, but they do not account for the dependency relationships among the data across platforms. Results In this paper, we propose an integration method to perform hypothesis testing and biomarkers selection based on multi-platform data sets observed from normal and diseased populations. The types of test statistics can vary across the platforms and their marginal distributions can be different. The observed test statistics are aggregated across different data platforms in a weighted scheme, where the weights take into account different variabilities possessed by test statistics. The overall decision is based on the empirical distribution of the aggregated statistic obtained through random permutations. Conclusion In both simulation studies and real biological data analyses, our proposed method of multi-platform integration has better control over false discovery rates and higher positive selection rates than the uncombined method. The proposed method is also shown to be more powerful than rank aggregation method.