Portable Node-Level Parallelism for the PGAS Model

The Partitioned Global Address Space (PGAS) programming model brings intuitive shared memory semantics to distributed memory systems. Even with an abstract and unifying virtual global address space it is, however, challenging to use the full potential of different systems. Without explicit support by the implementation node-local operations have to be optimized manually for each architecture. A goal of this work is to offer a user-friendly programming model that provides portable performance across systems. In this paper we present an approach to integrate node-level programming abstractions with the PGAS programming model. We describe the hierarchical data distribution with local patterns and our implementation, MEPHISTO, in C++ using two existing projects. The evaluation of MEPHISTO shows that our approach achieves portable performance while requiring only minimal changes to port it from a CPU-based system to a GPU-based one using a CUDA or HIP back-end.

     

The Pristionchus pacificus mab-5 gene is involved in the regulation of ventral epidermal cell fates

One system that can be used to study the evolution of gene function is the nematode vulva. In Caenorhabditis elegans, the vulva is formed from three of the six multipotent precursors P(3-8).p. Comparison of vulval development between C. elegans and Pristionchus pacificus has revealed that, during evolution, there have been changes in the specification of cell fate for certain vulval cells. For example, the cell P8.p is a vulval precursor cell (VPC) in C. elegans, but is incompetent to adopt vulval fate in P. pacificus We have fate specification and have isolated P. pacificus mutants with a second vulva-like structure in the posterior region resulting from the ectopic differentiation of P8.p Genetic and molecular analysis indicated that point mutations in the Hox-cluster gene mab-5 of P. pacificus cause this multivulval phenotype. Further cell ablation studies revealed that the differentiation of P8.p is independent of gonadal signaling. In C. elegans, mab-5 also acts in P8.p specification, but mab-5 mutant animals do not develop differs between species, indicating that alterations in the intrinsic properties of P8.p and corresponding changes in the functional specificity of mab-5 have occurred during evolution.     

The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool for mass finger-printing of peptide mixtures obtained after enzymatic ingel digestion of proteins separated by two-dimensional electrophoresis (2-DE). In the course of a proteome analysis of mycobacteria using mass spectrometric identification, it was found that 94% of the most intense MALDI-MS peaks denote peptides bearing arginine at the C-terminal end. The effect was demonstrated to be equally prominent using an equimolar mixture of the synthetic peptides known to be present in the tryptic digest of the mycobacterial 35 kDa antigen ("synthetic mass map"). In addition, several binary mixtures of synthetic peptides differing exclusively at the C terminus (Arg or Lys) were examined to rationalize the higher sensitivity toward arginine-containing peptides. The extent of the effect described depends on the matrix used and may facilitate a more reliable assignment of mass fingerprint data to protein sequences in databases.     

Behavioral adaptation of information systems through goal models

Customizing software to perfectly fit individual needs is becoming increasingly important in information systems engineering. Users want to be able to customize software behavior through reference to terms familiar to their diverse needs and experience. We present a requirements-driven approach to behavioral customization of software systems. Goal models are constructed to represent alternative behaviors that users can exhibit to achieve their goals. Customization information is then added to restrict the space of possibilities to those that fit specific users, contexts, or situations. Meanwhile, elements of the goal models are mapped to units of source code. This way, customization preferences posed at the requirements level are directly translated into system customizations. Our approach, which we apply to an on-line shopping cart system and an automated teller machine simulator, does not assume adoption of a particular development methodology, platform, or variability implementation technique and keeps the reasoning computation overhead from interfering with the execution of the configured application.     

Surface analysis of the electropolishing layer on Si(111) in ammonium fluoride solution

The influence of potential and pH on the thickness and composition of the anodic films formed on n-Si(111) in dilute ammonium fluoride solutions is investigated by photoelectron spectroscopy. A combined electrochemistry/surface analysis system with very low contamination levels is used for the investigation of the oxidic layers. XPS data show that the film thicknesses increase with decreasing pH reaching 25 Å at pH 3. A potential dependence measured at lower coverage at a pH of 4.9 reveals changes in thickness and composition by increasing the potential from flatband to +5 V. Fluorine is incorporated into these films in substantial amounts which otherwise consist predominantly of silicon oxide. Silicon fluoride and silicon oxyfluoride are found. We define a current transmissivity, T_c, of the layers which shows strong variations with potential and pH. For a pH of 3, T_c is about 5×10² larger than for pH 4.9. The potential dependence shows a variation of T_c by a factor of three and an increase for thicknesses exceeding 5 Å. These observations are explained by a structural transition from a high density pseudomorphic interfacial layer to a more open structure at larger thicknesses (up to 25 Å). The analysis of the UP-spectra shows only little changes of the electron affinity χ with coverage. We obtain χ4.15±0.1 eV. A distinct band bending is not detected. From HeII spectra, we determine the valence band offset ΔE_v between Si and the oxidic layer to be 5.2 eV.