SEON: a pyramid of ontologies for software evolution and its applications

The Semantic Web provides a standardized, well-established framework to define and work with ontologies. It is especially apt for machine processing. However, researchers in the field of software evolution have not really taken advantage of that so far. In this paper, we address the potential of representing software evolution knowledge with ontologies and Semantic Web technology, such as Linked Data and automated reasoning. We present Seon, a pyramid of ontologies for software evolution, which describes stakeholders, their activities, artifacts they create, and the relations among all of them. We show the use of evolution-specific ontologies for establishing a shared taxonomy of software analysis services, for defining extensible meta-models, for explicitly describing relationships among artifacts, and for linking data such as code structures, issues (change requests), bugs, and basically any changes made to a system over time. For validation, we discuss three different approaches, which are backed by Seon and enable semantically enriched software evolution analysis. These techniques have been fully implemented as tools and cover software analysis with web services, a natural language query interface for developers, and large-scale software visualization.     

Composite indicator for railway infrastructure management

Railway Engineering Science - The assessment and analysis of railway infrastructure capacity is an essential task in railway infrastructure management carried out to meet the required quality and...     

Josephson effect of a superconducting ferromagnet

A point contact tunneling technique has been used to investigate the existence of superconductivity in a long-range, magnetically ordered phase in the reentrant pseudoternary system (Er_{1 – x}Ho_x)Rh₄B₄ in the vicinity of the lower critical temperature T _{c 2}. In this experiment, Josephson-like current-voltage characteristics could be observed in a Nb-Nb oxide-(Er_0.58Ho_0.42)Rh₄B₄ junction even in a temperature region below T _{c 2} (1.8–1.96 K), that is, in the magnetically ordered phase.This work was carried out while on leave of absence.Sponsored by Suisse National Science Foundation.Work in La Jolla sponsored by the National Science Foundation under contract No. NSF/DMR77-08469.     

Towards Efficient Execution of MPI Applications on the Grid: Porting and Optimization Issues

The message passing interface (MPI) is a standard used by many parallel scientific applications. It offers the advantage of a smoother migration path for porting applications from high performance computing systems to the Grid. In this paper Grid-enabled tools and libraries for developing MPI applications are presented. The first is MARMOT, a tool that checks the adherence of an application to the MPI standard. The second is PACX-MPI, an implementation of the MPI standard optimized for Grid environments. Besides the efficient development of the program, an optimal execution is of paramount importance for most scientific applications. We therefore discuss not only performance on the level of the MPI library, but also several application specific optimizations, e.g., for a sparse, parallel equation solver and an RNA folding code, like latency hiding, prefetching, caching and topology-aware algorithms.     

Are Reviews an Alternative to Pair Programming?

From the first presentation of extreme programming on, pair programming has attracted a wide range of programmers to work together in front of one display. The proposed advantages of pair programming are a faster development cycle and code with higher quality. However, the nearly doubled personnel cost when compared to single developers seems to outweigh these advantages. Instead of showing the superiority of pair programming, we seek an alternative. Can a single developer be assisted by an already known technique with which he produces the quality of pairs with only a fraction of the cost? The answer with some restrictions is: yes, he can. Reviews are a reasonable candidate with respect to code quality and cost.     

Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser

We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.     

Topography simulation of sputtering using an algorithm with second order approximation in space

For the efficient simulation of topography evolution due to, e.g., focused ion beam processes, continuum surface advancement algorithms are commonly used. In this work we present a two-dimensional surface advancement algorithm that uses circular arcs between nodes and allows kinks in the surface. The algorithm is based on the method of characteristics, which yields the motion of the points and the slope of the surface. By the interpolation with circular arcs not only the final result is better represented, but also more accurate simulation is possible after insertion of new points as the surface evolves. Kinks in the surface (shocks) are detected by the generation of loops in the surface string or by a new criterion based on the analysis of infinitesimally separated characteristics. It requires the curvature of the surface, which may readily be determined from the radii of the circular arcs. The proposed algorithm uses a second order approximation in space and therefore requires fewer data points during calculation than first order methods. It is shown to converge with third order as a function of node number. The method is demonstrated by examples of trench formation including the effect of redeposition and of facet formation from a step-like surface.     

Age and individual differences in prospective memory during a "Virtual Week": The roles of working memory, vigilance, task regularity, and cue focality.

Young (ages 18–22 years) and older (ages 61–87 years) adults (N = 106) played the Virtual Week board game, which involves simulating common prospective memory (PM) tasks of everyday life (e.g., taking medication), and performed working memory (WM) and vigilance tasks. The Virtual Week game includes regular (repeated) and irregular (nonrepeated) PM tasks with cues that are either more or less focal to other ongoing activities. Age differences in PM were reduced for repeated tasks, and performance improved over the course of the week, suggesting retrieval was more spontaneous or habitual. Correlations with WM within each age group were reduced for PM tasks that had more regular or focal cues. WM (but not vigilance) ability was a strong predictor of irregular PM tasks with less focal cues. Taken together, these results support the hypothesis that habitual and focally cued PM tasks are less demanding of attentional resources (specifically, WM), whereas tasks that are more demanding of controlled attentional processes produce larger age differences, which may be attributable to individual differences in WM. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Shifting the pH Optima of (R)-Selective Transaminases by Protein Engineering

Amine transaminases (ATAs) are powerful biocatalysts for the stereoselective synthesis of chiral amines. However, wild-type ATAs usually show pH optima at slightly alkaline values and exhibit low catalytic activity under physiological conditions. For efficient asymmetric synthesis ATAs are commonly used in combination with lactate dehydrogenase (LDH, optimal pH: 7.5) and glucose dehydrogenase (GDH, optimal pH: 7.75) to shift the equilibrium towards the synthesis of the target chiral amine and hence their pH optima should fit to each other. Based on a protein structure alignment, variants of (R)-selective transaminases were rationally designed, produced in E. coli, purified and subjected to biochemical characterization. This resulted in the discovery of the variant E49Q of the ATA from Aspergillus fumigatus, for which the pH optimum was successfully shifted from pH 8.5 to 7.5 and this variant furthermore had a two times higher specific activity than the wild-type protein at pH 7.5. A possible mechanism for this shift of the optimal pH is proposed. Asymmetric synthesis of (R)-1-phenylethylamine from acetophenone in combination with LDH and GDH confirmed that the variant E49Q shows superior performance at pH 7.5 compared to the wild-type enzyme.     

CCBE1 Is Essential for Epicardial Function during Myocardium Development

The epicardium is a single cell layer of mesothelial cells that plays a critical role during heart development contributing to different cardiac cell types of the developing heart through epithelial-to-mesenchymal transition (EMT). Moreover, the epicardium is a source of secreted growth factors that promote myocardial growth. CCBE1 is a secreted extracellular matrix protein expressed by epicardial cells that is required for the formation of the primitive coronary plexus. However, the role of CCBE1 during epicardial development was still unknown. Here, using a Ccbe1 knockout (KO) mouse model, we observed that loss of CCBE1 leads to congenital heart defects including thinner and hyper-trabeculated ventricular myocardium. In addition, Ccbe1 mutant hearts displayed reduced proliferation of cardiomyocyte and epicardial cells. Epicardial outgrowth culture assay to assess epicardial-derived cells (EPDC) migration showed reduced invasion of the collagen gel by EPDCs in Ccbe1 KO epicardial explants. Ccbe1 KO hearts also displayed fewer nonmyocyte/nonendothelial cells intramyocardially with a reduced proliferation rate. Additionally, RNA-seq data and experimental validation by qRT-PCR showed a marked deregulation of EMT-related genes in developing Ccbe1 mutant hearts. Together, these findings indicate that the myocardium defects in Ccbe1 KO mice arise from disruption of epicardial development and function.