A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems

Heterogeneous systems are becoming more common on High Performance Computing (HPC) systems. Even using tools like CUDA and OpenCL it is a non-trivial task to obtain optimal performance on the GPU. Approaches to simplifying this task include Merge (a library based framework for heterogeneous multi-core systems), Zippy (a framework for parallel execution of codes on multiple GPUs), BSGP (a new programming language for general purpose computation on the GPU) and CUDA-lite (an enhancement to CUDA that transforms code based on annotations). In addition, efforts are underway to improve compiler tools for automatic parallelization and optimization of affine loop nests for GPUs and for automatic translation of OpenMP parallelized codes to CUDA. In this paper we present an alternative approach: a new computational framework for the development of massively data parallel scientific codes applications suitable for use on such petascale/exascale hybrid systems built upon the highly scalable Cactus framework. As the first non-trivial demonstration of its usefulness, we successfully developed a new 3D CFD code that achieves improved performance.Comment: Parallel Computing 2011 (ParCo2011), 30 August -- 2 September 2011, Ghent, Belgiu

A Universal Point Set for 2-Outerplanar Graphs

A point set $S \subseteq \mathbb{R}^2$ is universal for a class $\cal G$ if every graph of ${\cal G}$ has a planar straight-line embedding on $S$. It is well-known that the integer grid is a quadratic-size universal point set for planar graphs, while the existence of a sub-quadratic universal point set for them is one of the most fascinating open problems in Graph Drawing. Motivated by the fact that outerplanarity is a key property for the existence of small universal point sets, we study 2-outerplanar graphs and provide for them a universal point set of size $O(n \log n)$.Comment: 23 pages, 11 figures, conference version at GD 201

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures

BACKGROUND: There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characterized on a sequence level and three structures of its members (1gz0, 1ipa, and 1k3r) have been solved. However, none of these structures include the cofactor or the substrate. Due to the strong evolutionary divergence and the paucity of experimental information, no confident predictions of protein-ligand and protein-substrate interactions could be made, which hampered the study of sequence-structure-function relationships in the SPOUT superfamily. RESULTS: We used the computational docking program AutoDock to identify the AdoMet-binding site on the surface of three MTase structures. We analyzed the sequence divergence in two distinct lineages of the SPOUT superfamily in the context of surface features and preferred cofactor binding mode to propose specific function for the conserved residues. CONCLUSION: Our docking analysis has confidently predicted the common AdoMet-binding site in three remotely related proteins structures. In the vicinity of the cofactor-binding site, subfamily-conserved grooves were identified on the protein surface, suggesting location of the target-binding/catalytic site. Functionally important residues were inferred and a general reaction mechanism, involving conformational change of a glycine-rich loop, was proposed

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

BACKGROUND: Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe(2+ )oxygenase superfamily. RESULTS: In this article, we report identification and sequence analysis of five human members of the (2OG-Fe(2+)) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. CONCLUSIONS: We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes

Superpatterns and Universal Point Sets

An old open problem in graph drawing asks for the size of a universal point set, a set of points that can be used as vertices for straight-line drawings of all n-vertex planar graphs. We connect this problem to the theory of permutation patterns, where another open problem concerns the size of superpatterns, permutations that contain all patterns of a given size. We generalize superpatterns to classes of permutations determined by forbidden patterns, and we construct superpatterns of size n^2/4 + Theta(n) for the 213-avoiding permutations, half the size of known superpatterns for unconstrained permutations. We use our superpatterns to construct universal point sets of size n^2/4 - Theta(n), smaller than the previous bound by a 9/16 factor. We prove that every proper subclass of the 213-avoiding permutations has superpatterns of size O(n log^O(1) n), which we use to prove that the planar graphs of bounded pathwidth have near-linear universal point sets.Comment: GD 2013 special issue of JGA

Increased Responsiveness to Toll-Like Receptor 4 Stimulation in Peripheral Blood Mononuclear Cells from Patients with Recent Onset Rheumatoid Arthritis

Background. Cell signaling via Toll-like receptors (TLRs) leads to synovial inflammation in rheumatoid arthritis (RA). We aimed to assess effects of TLR2 and TLR4 stimulation on proinflammatory cytokine production by peripheral blood mononuclear cells (PBMCs) from patients with recent-onset RA, osteoarthrosis (OA), and healthy control (HC). Methods. PBMCs were stimulated with LPS, biglycan and cytokine mix. Cytokines were analyzed in supernatants with ELISA. Expression of toll-like receptors mRNA in leukocytes was analyzed using real-time qPCR. Results. PBMCs from RA patients spontaneously produced less IL-6 and TNFα than cells from OA and HC subjects. LPS increased cytokines' production in all groups. In RA patients increase was dramatic (30 to 48-fold and 17 to 31-fold, for respective cytokines) compared to moderate (2 to 8-fold) in other groups. LPS induced 15-HETE generation in PBMCs from RA (mean 251%) and OA patients (mean 43%), although only in OA group, the increase was significant. TLR2 and TLR4 gene expressions decreased in response to cytokine mix, while LPS enhanced TLR2 expression in HC and depressed TLR4 expression in OA patients. Conclusion. PBMCs from recent-onset RA patients are overresponsive to stimulation with bacterial lipopolysaccharide. TLR expression is differentially regulated in healthy and arthritic subjects

The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation, but whether post-transcriptional mechanisms can regulate this process is unknown. Here, we identify that an RNA methyltransferase (Misu/Nsun2) is required to balance stem cell self-renewal and differentiation in skin. In the epidermis, this methyltransferase is found in a defined sub-population of hair follicle stem cells poised to undergo lineage commitment, and its depletion results in enhanced quiescence and aberrant stem cell differentiation. Our results reveal that post-transcriptional RNA methylation can play a previously unappreciated role in controlling stem cell fate

Model Checking for Formal Verification of Space Systems

The goal of the presented activity is to integrate an existing model checking engine – SPIN1 – with the TASTE2 MBSE environment. For this purpose, the modelling languages used in TASTE – ASN.1, AADL and SDL need to be translated into PROMELA, a language for modelling and verification of concurrent systems. This paper describes the current achievements of the activity – proposal of a TASTE model checking workflow, formalization of requirement specification and established PROMELA translation patterns. Finally, the development of SDL models for validation of the tools and exploration of their utility in the design of space systems is discussed

The self-care of diabetics : the role of a nurse

Chorzy na cukrzycę powinni stać się samowystarczalni w zakresie kontroli stężenia glukozy we krwi oraz wstrzyknięć insuliny do tkanki podskórnej. Posiadanie tych umiejętności nie uzależnia ich od innych osób. Stawiają się w komfortowej sytuacji, jaką jest zdolność do samoopieki. Wychodząc naprzeciw tej tezie autorzy omawiają korzystanie ze strzykawki do wstrzyknięć insuliny, charakteryzują obsługę automatycznych wstrzykiwaczy ( PEN-ów). Przedstawiają także nowoczesne rozwiązania techniczne stosowane w leczeniu chorych na cukrzycę insulinozależną.Diabetics should become self-sufficient as far as controlling their glucose level and injecting insulin to the subcutaneous tissue are concerned. Having these skill makes them independent from the help of others. It puts them in a convenient position of being capable of self-care. With the intention of exploring this matter, the authors discuss using the syringe to inject insulin and characterize the use of automatic injectors (pens). They also present modern technological solutions used for treating the insulin-dependent diabetics