07341 Abstracts Collection -- Code Instrumentation and Modeling for Parallel Performance Analysis

From 20th to 24th August 2007, the Dagstuhl Seminar 07341 ``Code Instrumentation and Modeling for Parallel Performance Analysis\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Holistic Hardware Counter Performance Analysis of Parallel Programs

The KOJAK toolkit has been augmented with refined hardware performance counter support, including more convenient measurement specification, additional metric derivations and hierarchical structuring, and an extended algebra for integrating multiple experiments. Comprehensive automated analysis of a hybrid OpenMP/MPI parallel program, the ASC Purple sPPM benchmark, is demonstrated with performance experiments on equisized POWER4-II-based IBM Regatta p690+ cluster, Opteron-based Cray XD1 cluster and UltraSPARC-IV-based Sun Fire E25000 systems. Automatically assessed communication and synchronisation performance properties, combined with a rich set of measured and derived counter metrics, provide a holistic analysis context and facilitate multi-platform comparison

10181 Executive Summary -- Program Development for Extreme-Scale Computing

From May 2nd to May 7th, 2010, the Dagstuhl Seminar 10181 ``Program Development for Extreme-Scale Computing \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. This paper provides an executive summary of the seminar

10181 Abstracts Collection -- Program Development for Extreme-Scale Computing

From May 2nd to May 7th, 2010, the Dagstuhl Seminar 10181 ``Program Development for Extreme-Scale Computing \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. Links to extended abstracts or full papers are provided, if available

Formation problems of consolidated budget income in the Russian Federation in terms of Tomsk region

The article highlights the problems of increasing pressure on budgets in the territorial entity of the Russian Federation and therefore, the ability to mobilize financial resources to regional budgets of executive authorities. Industrial analysis of revenues got from the territory of Tomsk region is carried out, as well as the dynamics of income distribution due to the budget levels is examined. It is obvious that most of the revenues incoming from Tomsk Region, are credited to the federal budget. It can be explained by the development of oil and gas industry and high level of tax liabilities at such enterprises. The paper analyzes the structure of consolidated budget in Tomsk region to identify the basic sources of income. Furthermore, the dependence of revenues of regional and local budgets from the implemented federal fiscal policy is examined, the examples of the decisions that led to the falling revenues of the regional and local budgets are given

Особенности моделирования прогнозных оценок экономических объектов

Теория и практика экономических исследований свидетельствует о том, что моделирование прогнозных оценок будущего состояния экономических объектов является наиболее успешным только в тех случаях, когда модель в полной мере отражает как природу процесса управления, так и специфику деловой среды, то есть речь идет, по сути, об адекватности используемой модели

The Mont-Blanc Project: First Phase Successfully Finished

Running from October 2011 to June 2015, the aim of the European project Mont-Blanc has been to develop an approach to Exascale computing based on embedded power-efficient technology. The main goals of the project were to i) build an HPC prototype using currently available energy-efficient embedded technology, ii) design a Next Generation system to overcome the limitations of the built prototype and iii) port a set of representative Exascale applications to the system. This article summarises the contributions from the Leibniz Supercomputing Centre (LRZ) and the Juelich Supercomputing Centre (JSC), Germany, to the Mont-Blanc project.Comment: 5 pages, 3 figure

Single chain Fab (scFab) fragment

BACKGROUND: The connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. RESULTS: Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised. CONCLUSION: A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera for detection

Details Matter in Structure-based Drug Design

Successful structure-based drug design (SBDD) requires the optimization of interactions with the target protein and the minimization of ligand strain. Both factors are often modulated by small changes in the chemical structure which can lead to profound changes in the preferred conformation and interaction preferences of the ligand. We draw from examples of a Roche project targeting phosphodiesterase 10 to highlight that details matter in SBDD. Data mining in crystal structure databases can help to identify these sometimes subtle effects, but it is also a great resource to learn about molecular recognition in general and can be used as part of molecular design tools. We illustrate the use of the Cambridge Structural Database for identifying preferred structural motifs for intramolecular hydrogen bonding and of the Protein Data Bank for deriving propensities for protein-ligand interactions

Fetal RHD Screening in RH1 Negative Pregnant Women: Experience in Switzerland.

RH1 incompatibility between mother and fetus can cause hemolytic disease of the fetus and newborn. In Switzerland, fetal RHD genotyping from maternal blood has been recommended from gestational age 18 onwards since the year 2020. This facilitates tailored administration of RH immunoglobulin (RHIG) only to RH1 negative women carrying a RH1 positive fetus. Data from 30 months of noninvasive fetal RHD screening is presented. Cell-free DNA was extracted from 7192 plasma samples using a commercial kit, followed by an in-house qPCR to detect RHD exons 5 and 7, in addition to an amplification control. Valid results were obtained from 7072 samples, with 4515 (64%) fetuses typed RHD positive and 2556 (36%) fetuses being RHD negative. A total of 120 samples led to inconclusive results due to the presence of maternal or fetal RHD variants (46%), followed by women being serologically RH1 positive (37%), and technical issues (17%). One sample was typed false positive, possibly due to contamination. No false negative results were observed. We show that unnecessary administration of RHIG can be avoided for more than one third of RH1 negative pregnant women in Switzerland. This reduces the risks of exposure to a blood-derived product and conserves this limited resource to women in actual need