Program Understanding: A Reengineering Case for the Transformation Tool Contest

In Software Reengineering, one of the central artifacts is the source code of the legacy system in question. In fact, in most cases it is the only definitive artifact, because over the time the code has diverged from the original architecture and design documents. The first task of any reengineering project is to gather an understanding of the system's architecture. Therefore, a common approach is to use parsers to translate the source code into a model conforming to the abstract syntax of the programming language the system is implemented in which can then be subject to querying. Despite querying, transformations can be used to generate more abstract views on the system's architecture. This transformation case deals with the creation of a state machine model out of a Java syntax graph. It is derived from a task that originates from a real reengineering project.Comment: In Proceedings TTC 2011, arXiv:1111.440

The sequence spectrum of frameshift reversions obtained with a novel adaptive mutation assay in Saccharomyces cerevisiae

Research on the mechanisms of adaptive mutagenesis in resting, i.e. non-replicating cells relies on appropriate mutation assays. Here we provide a novel procedure for the detection of frameshift-reverting mutations in yeast. Proliferation of non-reverted cells in this assay is suppressed by the lack of a fermentable carbon source. The test allele was constructed in a way that the reversions mimic microsatellite instability, a condition often found in cancer cells. We show the cell numbers during these starvation conditions and provide a DNA sequence spectrum of a representative set of revertants. The data in this article support the publication "Glucose starvation as a selective tool for the study of adaptive mutations in Saccharomyces cerevisiae" (Heidenreich and Steinboeck, 2016) [1]

Non-homologous end joining as an important mutagenic process in cell cycle-arrested cells

Resting cells experience mutations without apparent external mutagenic influences. Such DNA replication-independent mutations are suspected to be a consequence of processing of spontaneous DNA lesions. Using experimental systems based on reversions of frameshift alleles in Saccharomyces cerevisiae, we evaluated the impact of defects in DNA double-strand break (DSB) repair on the frequency of replication-independent mutations. The deletion of the genes coding for Ku70 or DNA ligase IV, which are both obligatory constituents of the non-homologous end joining (NHEJ) pathway, each resulted in a 50% reduction of replication-independent mutation frequency in haploid cells. Sequencing indicated that typical NHEJ-dependent reversion events are small deletions within mononucleotide repeats, with a remarkable resemblance to DNA polymerase slippage errors. Experiments with diploid and RAD52- or RAD54-deficient strains confirmed that among DSB repair pathways only NHEJ accounts for a considerable fraction of replication-independent frameshift mutations in haploid and diploid NHEJ non-repressed cells. Thus our results provide evidence that G(0) cells with unrepressed NHEJ capacity pay for a large-scale chromosomal stability with an increased frequency of small-scale mutations, a finding of potential relevance for carcinogenesis

Siponimod versus placebo in secondary progressive multiple sclerosis (EXPAND): a double-blind, randomised, phase 3 study

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