Enabling efficient analysis of biobank-scale data with genotype representation graphs.

Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. However, encoding genetic data in existing tabular data structures and file formats has become costly and unsustainable. Here we introduce the genotype representation graph (GRG), a fully connected hierarchical data structure that losslessly encodes phased whole-genome polymorphisms.

Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data.

Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. Current practice is to store large-scale genetic polymorphism data using tabular data structures and file formats, where rows and columns represent samples and genetic variants. However, encoding genetic data in such formats has become unsustainable.

Effect of geomembrane liner on landfill stability under long-term loading: interfacial shear test and numerical simulation.

Clay liners have been widely used in landfill engineering. However, large-scale clay excavation causes secondary environmental damage. This study investigates the feasibility of replacing clay liners with high-density polyethylene (HDPE) geomembranes with different specifications and parameters.

Three-phase flow displacement dynamics and Haines jumps in a hydrophobic porous medium.

We use synchrotron X-ray micro-tomography to investigate the displacement dynamics during three-phase-oil, water and gas-flow in a hydrophobic porous medium. We observe a distinct gas invasion pattern, where gas progresses through the pore space in the form of disconnected clusters mediated by double and multiple displacement events. Gas advances in a process we name three-phase Haines jumps, during which gas re-arranges its configuration in the pore space, retracting from some regions to enable the rapid filling of multiple pores.

Population genomics of East Asian ethnic groups.

East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups.

Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection.

Background: Adenosine-to-inosine (A-to-I) RNA editing plays important roles in diversifying the transcriptome and preventing MDA5 sensing of endogenous dsRNA as nonself. To date, few studies have investigated the population genomic signatures of A-to-I editing due to the lack of editing sites overlapping with SNPs.

Results: In this study, we applied a pipeline to robustly identify SNP editing sites from population transcriptomic data and combined functional genomics, GWAS, and population genomics approaches to study the function and evolution of A-to-I editing.

Product Quality Research Institute evaluation of cascade impactor profiles of pharmaceutical aerosols. Part 3. Final report on a statistical procedure for determining equivalence.

The purpose of this article is to report final results of the evaluation of a chi-square ratio test proposed by the US Food and Drug Administration (FDA) for demonstrating equivalence of aerodynamic particle size distribution (APSD) profiles of nasal and orally inhaled drug products. A working group of the Product Quality Research Institute previously published results demonstrating some limitations of the proposed test. In an effort to overcome the test's limited discrimination, the group proposed a supplemental test, a population bioequivalence (PBE) test for impactor-sized mass (ISM).

Product Quality Research Institute evaluation of cascade impactor profiles of pharmaceutical aerosols: part 2--evaluation of a method for determining equivalence.

The purpose of this article is to present the thought process, methods, and interim results of a PQRI Working Group, which was charged with evaluating the chi-square ratio test as a potential method for determining in vitro equivalence of aerodynamic particle size distribution (APSD) profiles obtained from cascade impactor measurements. Because this test was designed with the intention of being used as a tool in regulatory review of drug applications, the capability of the test to detect differences in APSD profiles correctly and consistently was evaluated in a systematic way across a designed space of possible profiles. To establish a "base line," properties of the test in the simplest case of pairs of identical profiles were studied.

Product Quality Research Institute evaluation of cascade impactor profiles of pharmaceutical aerosols, part 1: background for a statistical method.

The purpose of this article is 2-fold: (1) to document in the public domain the considerations that led to the development of a regulatory statistical test for comparison of aerodynamic particle size distribution (APSD) of aerosolized drug formulations, which was proposed in a US Food and Drug Administration (FDA) draft guidance for industry; and (2) to explain the background and process for evaluation of that test through a working group involving scientists from the FDA, industry, academia, and the US Pharmacopeia, under the umbrella of the Product Quality Research Institute (PQRI). The article and the referenced additional statistical information posted on the PQRI Web site explain the reasoning and methods used in the development of the APSD test, which is one of the key tests required for demonstrating in vitro equivalence of orally inhaled and nasal aerosol drug products. The article also describes the process by which stakeholders with different perspectives have worked collaboratively to evaluate properties of the test by drawing on statistical models, historical and practical information, and scientific reasoning.