Strasheela: Design and usage of a music composition environment based on the Oz programming model

Strasheela provides a means for the composer to create a symbolic score by formally describing it in a rule-based way. The environment defines a rich music representation for complex polyphonic scores. Strasheela enables the user to define expressive compositional rules and then to apply them to the score. Compositional rules can restrict many aspects of the music - including the rhythmic structure, the melodic structure and the harmonic structure - by constraining the parameters (e.g. duration or pitch) of musical events according to some numerical or logical relation. Strasheela combines this expressivity with efficient search strategies.

Double potential step chronoamperometry at microdisk electrodes: simulating the case of unequal diffusion coefficients

An efficient approach to the simulation of the double potential step chronoamperometry at a microdisk electrode based on an exponentially expanding time grid and conformal mapping of the space is presented. The dimensionless second potential step flux data are included as a function of the first potential step duration and the ratio of the diffusion coefficients of the reacting species allowing instant analysis of the experimental double potential step chronoamperograms without a need for simulation. The values of the diffusion coefficients are determined for several test systems and found to be in good agreement with existing literature data. (C) 2004 Elsevier B.V. All rights reserved.

Deficiencies of double-strand break repair factors and effects on mutagenesis in directly gamma-irradiated and medium-mediated bystander human lymphoblastoid cells

Using RNA interference techniques to knock down key proteins in two major double-strand break (DSB) repair pathways (DNA-PKcs for nonhomologous end joining, NHEJ, and Rad54 for homologous recombination, HR), we investigated the influence of DSB repair factors on radiation mutagenesis at the autosomal thymidine kinase (TK) locus both in directly irradiated cells and in unirradiated bystander cells. We also examined the role of p53 (TP53) in these processes by using cells of three human lymphoblastoid cell lines from the same donor but with differing p53 status (TK6 is p53 wild-type, NH32 is p53 null, and WTK1 is p53 mutant). Our results indicated that p53 status did not affect either the production of radiation bystander mutagenic signals or the response to these signals. In directly irradiated cells, knockdown of DNA-PKcs led to an increased mutant fraction in WTK1 cells and decreased mutant fractions in TK6 and NH32 cells. In contrast, knockdown of DNA-PKcs led to increased mutagenesis in bystander cells regardless of p53 status. In directly irradiated cells, knockdown of Rad54 led to increased induced mutant fractions in WTK1 and NH32 cells, but the knockdown did not affect mutagenesis in p53 wild-type TK6 cells. In all cell lines, Rad54 knockdown had no effect on the magnitude of bystander mutagenesis. Studies with extracellular catalase confirmed the involvement of H2O2 in bystander signaling. Our results demonstrate that DSB repair factors have different roles in mediating mutagenesis in irradiated and bystander cells. (C) 2008 by Radiation Research Society.

Non-nematode-derived double-stranded RNAs induce profound phenotypic changes in Meloidogyne incognita and Globodera pallida infective juveniles

Nine non-nematode-derived double-stranded RNAs (dsRNAs), designed for use as controls in RNA interference (RNAi) screens of neuropeptide targets, were found to induce aberrant phenotypes and an unexpected inhibitory effect on motility of root knot nematode Meloidogyne incognita J2s following 24 h soaks in 0.1 mg/ml dsRNA; a simple soaking procedure which we have found to elicit profound knockdown of neuronal targets in Globodera pallida J2s. We have established that this inhibitory phenomenon is both time- and concentration-dependent, as shorter 4 h soaks in 0.1 mg/ml dsRNA had no negative impact on M. incognita J2 stage worms, yet a 10-fold increase in concentration to 1 mg/ml for the same 4 h time period had an even greater qualitative and quantitative impact on worm phenotype and motility. Further, a 10-fold increase of J2s soaked in 0.1 mg/ml dsRNA did not significantly alter the observed phenotypic aberration, which suggests that dsRNA uptake of the soaked J2s is not saturated under these conditions. This phenomenon was not initially observed in potato cyst nematode G. pallida J2s, which displayed no aberrant phenotype, or diminution of migratory activity in response to the same 0.1 mg/ml dsRNA 24 h soaks. However, a 10-fold increase in dsRNA to 1 mg/ml was found to elicit comparable irregularity of phenotype and inhibition of motility in G. pallida, to that initially observed in M. incognita following a 24 h soak in 0.1 mg/ml dsRNA. Again, a 10-fold increase in the number of G. pallida J2s soaked in the same volume of 1 mg/ml dsRNA preparation did not significantly affect the observed phenotypic deviation. We do not observe any global impact on transcript abundance in either M. incognita or G. pallida J2s following 0.1 mg/ml dsRNA soaks, as revealed by reverse transcriptase-PCR and quantitative PCR data. This study aims to raise awareness of a phenomenon which we observe consistently and which we believe signifies a more expansive deficiency in our knowledge and understanding of the variables inherent to RNAi-based investigation.

Systematic Usage of Embedded Modelling Languages in Automated Model Transformation Chains

Annotation of programs using embedded Domain-Specific Languages (embedded DSLs), such as the program annotation facility for the Java programming language, is a well-known practice in computer science. In this paper we argue for and propose a specialized approach for the usage of embedded Domain-Specific Modelling Languages (embedded DSMLs) in Model-Driven Engineering (MDE) processes that in particular supports automated many-step model transformation chains. It can happen that information defined at some point, using an embedded DSML, is not required in the next immediate transformation step, but in a later one. We propose a new approach of model annotation enabling flexible many-step transformation chains. The approach utilizes a combination of embedded DSMLs, trace models and a megamodel. We demonstrate our approach based on an example MDE process and an industrial case study.