Automated Code Generation for Industrial-Strength Systems

Model-driven engineering proposes to develop software systems by first creating an executable model of the system design and then transforming this model into an implementation. This paper discusses the design of an automatic code generation system that transforms such models into product implementations for highly reliable, industrial-strength systems. It provides insights, practical considerations, and lessons learned when developing code generators for applications that must conform to the constraints imposed by real-world, high-performance systems. Automatic code generation has played a large part in dramatically increasing both the quality and the reliability of software for these systems

Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii

BACKGROUND: Next generation sequencing is helping to overcome limitations in organisms less accessible to classical or reverse genetic methods by facilitating whole genome mutational analysis studies. One traditionally intractable group, the Apicomplexa, contains several important pathogenic protozoan parasites, including the Plasmodium species that cause malaria. Here we apply whole genome analysis methods to the relatively accessible model apicomplexan, Toxoplasma gondii, to optimize forward genetic methods for chemical mutagenesis using N-ethyl-N-nitrosourea (ENU) and ethylmethane sulfonate (EMS) at varying dosages. RESULTS: By comparing three different lab-strains we show that spontaneously generated mutations reflect genome composition, without nucleotide bias. However, the single nucleotide variations (SNVs) are not distributed randomly over the genome; most of these mutations reside either in non-coding sequence or are silent with respect to protein coding. This is in contrast to the random genomic distribution of mutations induced by chemical mutagenesis. Additionally, we report a genome wide transition vs transversion ratio (ti/tv) of 0.91 for spontaneous mutations in Toxoplasma, with a slightly higher rate of 1.20 and 1.06 for variants induced by ENU and EMS respectively. We also show that in the Toxoplasma system, surprisingly, both ENU and EMS have a proclivity for inducing mutations at A/T base pairs (78.6% and 69.6%, respectively). CONCLUSIONS: The number of SNVs between related laboratory strains is relatively low and managed by purifying selection away from changes to amino acid sequence. From an experimental mutagenesis point of view, both ENU (24.7%) and EMS (29.1%) are more likely to generate variation within exons than would naturally accumulate over time in culture (19.1%), demonstrating the utility of these approaches for yielding proportionally greater changes to the amino acid sequence. These results will not only direct the methods of future chemical mutagenesis in Toxoplasma, but also aid in designing forward genetic approaches in less accessible pathogenic protozoa as well. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-354) contains supplementary material, which is available to authorized users

A Copper-Mediated Conjugate Addition Approach to Analogues of Aconitine-Type Diterpenoid Alkaloids.

A copper-mediated conjugate addition of electron-rich aryl groups into a complex vinyl nitrile using arylmagnesium bromides is reported. The conjugate addition adducts were advanced toward the synthesis of designed aconitine-type analogues. The variation in oxygenation patterns on the arene coupling partner, introduced through the current conjugate addition approach, may ultimately provide insight into structure-activity relationships of the diterpenoid alkaloids

Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

Several recent studies have focused on the evolution of recently duplicated genes in Drosophila. Currently, however, little is known about the evolutionary forces acting upon duplications that are segregating in natural populations. We used a high-throughput, paired-end sequencing platform (Illumina) to identify structural variants in a population sample of African D. melanogaster. Polymerase chain reaction and sequencing confirmation of duplications detected by multiple, independent paired-ends showed that paired-end sequencing reliably uncovered the break points of structural rearrangements and allowed us to identify a number of tandem duplications segregating within a natural population. Our confirmation experiments show that rates of confirmation are very high, even at modest coverage. Our results also compare well with previous studies using microarrays (Emerson J, Cardoso-Moreira M, Borevitz JO, Long M. 2008. Natural selection shapes genome wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 320:1629–1631. and Dopman EB, Hartl DL. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104:19920–19925.), which both gives us confidence in the results of this study as well as confirms previous microarray results

Immune function biomarkers in children exposed to lead and organochlorine compounds: a cross-sectional study

BACKGROUND: Different organochlorines and lead (Pb) have been shown to have immunomodulating properties. Children are at greater risk for exposure to these environmental toxicants, but very little data exist on simultaneous exposures to these substances. METHODS: We investigated whether the organochlorine compounds (OC) dichlorodiphenylethylene (DDE), hexachlorobenzene (HCB), hexachlorocyclohexane (γ-HCH), the sum of polychlorinated biphenyls (ΣPCBs) and Pb were associated with immune markers such as immunoglobulin (Ig) levels, white blood cell (WBC), counts of lymphocytes; eosinophils and their eosinophilic granula as well as IgE count on basophils. The investigation was part of a cross-sectional environmental study in Hesse, Germany. In 1995, exposure to OC and Pb were determined, questionnaire data collected and immune markers quantified in 331 children. For the analyses, exposure (OC and Pb) concentrations were grouped in quartiles (γ-HCH into tertiles). Using linear regression, controlling for age, gender, passive smoking, serum lipids, and infections in the previous 12 months, we assessed the association between exposures and immune markers. Adjusted geometric means are provided for the different exposure levels. RESULTS: Geometric means were: DDE 0.32 μg/L, ΣPCBs 0.50 μg/L, HCB 0.22 μg/L, γ-HCH 0.02 μg/L and Pb 26.8 μg/L. The ΣPCBs was significantly associated with increased IgM levels, whereas HCB was inversely related to IgM. There was a higher number of NK cells (CD56+) with increased γ-HCH concentrations. At higher lead concentrations we saw increased IgE levels. DDE showed the most associations with significant increases in WBC count, in IgE count on basophils, IgE, IgG, and IgA levels. DDE was also found to significantly decrease eosinophilic granula content. CONCLUSION: Low-level exposures to OC and lead (Pb) in children may have immunomodulating effects. The increased IgE levels, IgE count on basophils, and the reduction of eosinophilic granula at higher DDE concentrations showed a most consistent pattern, which could be of clinical importance in the etiology of allergic diseases

THE EUML-ARC PROGRAMMING MODEL

The EUML-ARC programming model shows that the increasing parallelism available on multi-core processors requires evolutionary (not revolutionary) changes in software design. The EUML-ARC programming model combines and extends software technology available even before the introduction of multi-core processors to provide software engineers with the ability to specify software systems that expose abstract platform-independent parallelism. The EUML-ARC programming model is a synthesis of Executable UML, the Actor model, role-based modeling, split objects, and aspect-based coordination. Computation in the EUML-ARC programming model is structured in terms of semantic entities composed of actor-based agents whose behaviors are expressed in hierarchical state machines. An entity is composed of a base intrinsic agent and multiple extrinsic role agents, all with dedicated conceptual threads of control. Entities interact through their role agents in the context of featureoriented collaborations orchestrated by coordinator agents. The conceptual threads of control associated with the agents in a software system expose both intra-entity and inter-entity parallelism that is mapped by the EUML-ARC model compiler to the hardware threads available on the target multi-core processor. The hardware and software e ciency achieved with representative benchmark systems show that the EUML-ARC programming model and its compiler can exploit multi-core parallelism while providing a productive model-driven approach to software development.Ph.D. in Computer Science, July 201

Actor-eUML for Concurrent Programming

Abstract. The advent of multi-core processors offers an opportunity to increase the usage of Executable UML. Researchers are advocating the division of software systems into a productivity layer and an efficiency layer to shield mainstream programmers from the complexities of parallelism. Such separation of application and platform concerns is the foundation of Executable UML. To leverage this opportunity, an approach to Executable UML must address the complexity of the UML standard and provide a formal model of concurrency. In this paper, we introduce the Actor-eUML model and formalize the mapping between actors in the Actor model and Executable UML agents (active objects) by unifying the semantics of actor behavior and the hierarchical state machine (HSM) semantics of Executable UML agents. The UML treatment of concurrency is simplified, and the Actor model is extended to enable a set of actor behaviors to specify the HSM for an Executable UML active class

A Copper-Mediated Conjugate Addition Approach to Analogues of Aconitine-Type Diterpenoid Alkaloids.

A copper-mediated conjugate addition of electron-rich aryl groups into a complex vinyl nitrile using arylmagnesium bromides is reported. The conjugate addition adducts were advanced toward the synthesis of designed aconitine-type analogues. The variation in oxygenation patterns on the arene coupling partner, introduced through the current conjugate addition approach, may ultimately provide insight into structure-activity relationships of the diterpenoid alkaloids