The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Evaluation of Variability Concepts for Simulink in the Automotive Domain

Modeling variability in Matlab/Simulink becomes more and more important. We took the two variability modeling concepts already included in Matlab/Simulink and our own one and evaluated them to find out which one is suited best for modeling variability in the automotive domain. We conducted a controlled experiment with developers at Volkswagen AG to decide which concept is preferred by developers and if their preference aligns with measurable performance factors. We found out that all existing concepts are viable approaches and that the delta approach is both the preferred concept as well as the objectively most efficient one, which makes Delta-Simulink a good solution to model variability in the automotive domain.Comment: 10 pages, 7 figures, 6 tables, Proceedings of 48th Hawaii International Conference on System Sciences (HICSS), pp. 5373-5382, Kauai, Hawaii, USA, IEEE Computer Society, 201

Darwinian Data Structure Selection

Data structure selection and tuning is laborious but can vastly improve an application's performance and memory footprint. Some data structures share a common interface and enjoy multiple implementations. We call them Darwinian Data Structures (DDS), since we can subject their implementations to survival of the fittest. We introduce ARTEMIS a multi-objective, cloud-based search-based optimisation framework that automatically finds optimal, tuned DDS modulo a test suite, then changes an application to use that DDS. ARTEMIS achieves substantial performance improvements for \emph{every} project in $5$ Java projects from DaCapo benchmark, $8$ popular projects and $30$ uniformly sampled projects from GitHub. For execution time, CPU usage, and memory consumption, ARTEMIS finds at least one solution that improves \emph{all} measures for $86\%$ ($37/43$) of the projects. The median improvement across the best solutions is $4.8\%$, $10.1\%$, $5.1\%$ for runtime, memory and CPU usage. These aggregate results understate ARTEMIS's potential impact. Some of the benchmarks it improves are libraries or utility functions. Two examples are gson, a ubiquitous Java serialization framework, and xalan, Apache's XML transformation tool. ARTEMIS improves gson by $16.5$\%, $1\%$ and $2.2\%$ for memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by $23.5$\%. \emph{Every} client of these projects will benefit from these performance improvements.Comment: 11 page

Modeling and Testing for Joint Association Using a Genetic Random Field Model

Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by the joint effect of a large number of genetic variants instead of a single variant. The joint analysis of multiple genetic variants considering linkage disequilibrium (LD) and potential interactions can further enhance the discovery process, leading to the identification of new disease-susceptibility genetic variants. Motivated by the recent development in spatial statistics, we propose a new statistical model based on the random field theory, referred to as a genetic random field model (GenRF), for joint association analysis with the consideration of possible gene-gene interactions and LD. Using a pseudo-likelihood approach, a GenRF test for the joint association of multiple genetic variants is developed, which has the following advantages: 1. considering complex interactions for improved performance; 2. natural dimension reduction; 3. boosting power in the presence of LD; 4. computationally efficient. Simulation studies are conducted under various scenarios. Compared with a commonly adopted kernel machine approach, SKAT, GenRF shows overall comparable performance and better performance in the presence of complex interactions. The method is further illustrated by an application to the Dallas Heart Study.Comment: 17 pages, 4 tables, the paper has been published on Biometric

Artificial table testing dynamically adaptive systems

Dynamically Adaptive Systems (DAS) are systems that modify their behavior and structure in response to changes in their surrounding environment. Critical mission systems increasingly incorporate adaptation and response to the environment; examples include disaster relief and space exploration systems. These systems can be decomposed in two parts: the adaptation policy that specifies how the system must react according to the environmental changes and the set of possible variants to reconfigure the system. A major challenge for testing these systems is the combinatorial explosions of variants and envi-ronment conditions to which the system must react. In this paper we focus on testing the adaption policy and propose a strategy for the selection of envi-ronmental variations that can reveal faults in the policy. Artificial Shaking Table Testing (ASTT) is a strategy inspired by shaking table testing (STT), a technique widely used in civil engineering to evaluate building's structural re-sistance to seismic events. ASTT makes use of artificial earthquakes that simu-late violent changes in the environmental conditions and stresses the system adaptation capability. We model the generation of artificial earthquakes as a search problem in which the goal is to optimize different types of envi-ronmental variations