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• Innovative phenotype-genotype association analysis for categorical genomic data having non-ignorable missing values. • Statistical learning method of random forest is used for variable selection in the analysis. • Weighted logistic ridge regression with EM algorithm is used for missing data imputation in the analysis. • Linear statistical hypothesis testing is used for determining the missingness mechanism in the analysis. • An application to analyzing real data from Australia breast cancer genome-wide association study (GWAS). Genomic data arising from a genome-wide association study (GWAS) are often not only of large-scale, but also incomplete. A specific form of their incompleteness is missing values with non-ignorable missingness mechanism. The intrinsic complications of genomic data present significant challenges in developing an effective and efficient procedure of phenotype-genotype association analysis by a statistical variable selection approach. In this paper we develop a coherent procedure of categorical phenotype-genotype association analysis, in the presence of missing values with non-ignorable missingness mechanism in genomic data. It is developed by integrating the statistical learning methods of random forest for variable selection, joint weighted logistic ridge regression with EM algorithm for missing data imputation, and linear statistical hypothesis testing for determining the missingness mechanism. Two simulated genomic datasets are used to undertake the phenotype-genotype association analysis by the proposed procedure, with the performance validated. The proposed procedure is then applied to analyze a real data set from breast cancer GWAS. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, a two-dimensional control volume finite-element computational model is developed for simulating saltwater intrusion in a heterogeneous coastal alluvial aquifer system at Gooburrum located near Bundaberg in Queensland, Australia. The model consists of a coupled system of two non-linear partial differential equations. The first equation describes the flow of a variable-density fluid, and the second equation describes the transport of dissolved salt via a form of the Fokker–Planck equation. The outcomes of the work demonstrate that transport simulation techniques provide excellent tools for hydraulic investigations even when complex transition zones are involved. [Copyright &y& Elsevier]