A novel strategy for building interoperable MPI environment in heterogeneous high performance systems

Breakthrough advances in microprocessor technology and efficient power management have altered the course of development of processors with the emergence of multi-core processor technology, in order to bring higher level of processing. The utilization of many-core technology has boosted computing power provided by cluster of workstations or SMPs, providing large computational power at an affordable cost using solely commodity components. Different implementations of message-passing libraries and system softwares (including Operating Systems) are installed in such cluster and multi-cluster computing systems. In order to guarantee correct execution of message-passing parallel applications in a computing environment other than that originally the parallel application was developed, review of the application code is needed. In this paper, a hybrid communication interfacing strategy is proposed, to execute a parallel application in a group of computing nodes belonging to different clusters or multi-clusters (computing systems may be running different operating systems and MPI implementations), interconnected with public or private IP addresses, and responding interchangeably to user execution requests. Experimental results demonstrate the feasibility of this proposed strategy and its effectiveness, through the execution of benchmarking parallel applications.

SINGULARLY PERTURBED DISCOUNTED MARKOV CONTROL PROCESSES IN A GENERAL STATE SPACE

This paper studies the asymptotic optimality of discrete-time Markov decision processes (MDPs) with general state space and action space and having weak and strong interactions. By using a similar approach as developed by Liu, Zhang, and Yin [Appl. Math. Optim., 44 (2001), pp. 105-129], the idea in this paper is to consider an MDP with general state and action spaces and to reduce the dimension of the state space by considering an averaged model. This formulation is often described by introducing a small parameter epsilon > 0 in the definition of the transition kernel, leading to a singularly perturbed Markov model with two time scales. Our objective is twofold. First it is shown that the value function of the control problem for the perturbed system converges to the value function of a limit averaged control problem as epsilon goes to zero. In the second part of the paper, it is proved that a feedback control policy for the original control problem defined by using an optimal feedback policy for the limit problem is asymptotically optimal. Our work extends existing results of the literature in the following two directions: the underlying MDP is defined on general state and action spaces and we do not impose strong conditions on the recurrence structure of the MDP such as Doeblin's condition.

Chains of Infinite Order, Chains with Memory of Variable Length, and Maps of the Interval

We show how to construct a topological Markov map of the interval whose invariant probability measure is the stationary law of a given stochastic chain of infinite order. In particular we characterize the maps corresponding to stochastic chains with memory of variable length. The problem treated here is the converse of the classical construction of the Gibbs formalism for Markov expanding maps of the interval.

The peculiar isolated neutron star in the Carina Nebula Deep XMM-Newton and ESO-VLT observations of 2XMM J104608.7-594306

While fewer in number than the dominant rotation-powered radio pulsar population, peculiar classes of isolated neutron stars (INSs) which include magnetars, the ROSAT-discovered "Magnificent Seven" (M7), rotating radio transients (RRATs), and central compact objects in supernova remnants (CCOs) - represent a key element in understanding the neutron star phenomenology. We report the results of an observational campaign to study the properties of the source 2XMM J104608.7-594306, a newly discovered thermally emitting INS. The evolutionary state of the neutron star is investigated by means of deep dedicated observations obtained with the XMM-Newton Observatory, the ESO Very Large Telescope, as well as publicly available gamma-ray data from the Fermi Space Telescope and the AGILE Mission. The observations confirm previous expectations and reveal a unique type of object. The source, which is likely within the Carina Nebula (N-H = 2.6x10(21) cm(-2)), has a spectrum that is both thermal and soft, with kT(infinity) = 135 eV. Non-thermal (magnetospheric) emission is not detected down to 1% (3 sigma, 0.1-12 keV) of the source luminosity. Significant deviations (absorption features) from a simple blackbody model are identified in the spectrum of the source around energies 0.6 keV and 1.35 keV. While the former deviation is likely related to a local oxygen overabundance in the Carina Nebula, the latter can only be accounted for by an additional spectral component, which is modelled as a Gaussian line in absorption with EW = 91 eV and sigma = 0.14 keV (1 sigma). Furthermore, the optical counterpart is fainter than m(V) = 27 (2 sigma) and no gamma-ray emission is significantly detected by either the Fermi or AGILE missions. Very interestingly, while these characteristics are remarkably similar to those of the M7 or the only RRAT so far detected in X-rays, which all have spin periods of a few seconds, we found intriguing evidence of very rapid rotation, P = 18.6ms, at the 4 sigma confidence level. We interpret these new results in the light of the observed properties of the currently known neutron star population, in particular those of standard rotation-powered pulsars, recycled objects, and CCOs. We find that none of these scenarios can satisfactorily explain the collective properties of 2XMM J104608.7-594306, although it may be related to the still poorly known class of Galactic anti-magnetars. Future XMM-Newton data, granted for the next cycle of observations (AO11), will help us to improve our current observational interpretation of the source, enabling us to significantly constrain the rate of pulsar spin down.

Complex Transition to Cooperative Behavior in a Structured Population Model

Cooperation plays an important role in the evolution of species and human societies. The understanding of the emergence and persistence of cooperation in those systems is a fascinating and fundamental question. Many mechanisms were extensively studied and proposed as supporting cooperation. The current work addresses the role of migration for the maintenance of cooperation in structured populations. This problem is investigated in an evolutionary perspective through the prisoner's dilemma game paradigm. It is found that migration and structure play an essential role in the evolution of the cooperative behavior. The possible outcomes of the model are extinction of the entire population, dominance of the cooperative strategy and coexistence between cooperators and defectors. The coexistence phase is obtained in the range of large migration rates. It is also verified the existence of a critical level of structuring beyond that cooperation is always likely. In resume, we conclude that the increase in the number of demes as well as in the migration rate favor the fixation of the cooperative behavior.

Mutation Spectrum in the Large GTPase Dynamin 2, and Genotype-Phenotype Correlation in Autosomal Dominant Centronuclear Myopathy

Centronuclear myopathy (CNM) is a genetically heterogeneous disorder associated with general skeletal muscle weakness, type I fiber predominance and atrophy, and abnormally centralized nuclei. Autosomal dominant CNM is due to mutations in the large GTPase dynamin 2 (DNM2), a mechanochemical enzyme regulating cytoskeleton and membrane trafficking in cells. To date, 40 families with CNM-related DNM2 mutations have been described, and here we report 60 additional families encompassing a broad genotypic and phenotypic spectrum. In total, 18 different mutations are reported in 100 families and our cohort harbors nine known and four new mutations, including the first splice-site mutation. Genotype-phenotype correlation hypotheses are drawn from the published and new data, and allow an efficient screening strategy for molecular diagnosis. In addition to CNM, dissimilar DNM2 mutations are associated with Charcot-Marie-Tooth (CMT) peripheral neuropathy (CMTD1B and CMT2M), suggesting a tissue-specific impact of the mutations. In this study, we discuss the possible clinical overlap of CNM and CMT, and the biological significance of the respective mutations based on the known functions of dynamin 2 and its protein structure. Defects in membrane trafficking due to DNM2 mutations potentially represent a common pathological mechanism in CNM and CMT. Hum Mutat 33: 949-959, 2012. (C) 2012 Wiley Periodicals, Inc.

Convergent evolution of [D-Leucine1] microcystin-LR in taxonomically disparate cyanobacteria

Abstract Background Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS secondary metabolic pathway. They are produced by a variety of cyanobacteria and are responsible for the poisoning of humans as well as the deaths of wild and domestic animals around the world. The chemical diversity of the microcystin family is attributed to a number of genetic events that have resulted in the diversification of the pathway for microcystin assembly. Results Here, we show that independent evolutionary events affecting the substrate specificity of the microcystin biosynthetic pathway have resulted in convergence on a rare [D-Leu1] microcystin-LR chemical variant. We detected this rare microcystin variant from strains of the distantly related genera Microcystis, Nostoc, and Phormidium. Phylogenetic analysis performed using sequences of the catalytic domains within the mcy gene cluster demonstrated a clear recombination pattern in the adenylation domain phylogenetic tree. We found evidence for conversion of the gene encoding the McyA2 adenylation domain in strains of the genera Nostoc and Phormidium. However, point mutations affecting the substrate-binding sequence motifs of the McyA2 adenylation domain were associated with the change in substrate specificity in two strains of Microcystis. In addition to the main [D-Leu1] microcystin-LR variant, these two strains produced a new microcystin that was identified as [Met1] microcystin-LR. Conclusions Phylogenetic analysis demonstrated that both point mutations and gene conversion result in functional mcy gene clusters that produce the same rare [D-Leu1] variant of microcystin in strains of the genera Microcystis, Nostoc, and Phormidium. Engineering pathways to produce recombinant non-ribosomal peptides could provide new natural products or increase the activity of known compounds. Our results suggest that the replacement of entire adenylation domains could be a more successful strategy to obtain higher specificity in the modification of the non-ribosomal peptides than point mutations.

Modularity and evolutionary constraints in a baculovirus gene regulatory network

Abstract Background The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. Results We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. Conclusions Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

Science publication workshops as a strategy to improve the visibility of scholarly production: the experience of the University of Sao Paulo (USP) - Brazil

The objective of this work is to present the experience of workshops that have been developed at the University of Sao Paulo by the Integrated Library System in partnership with Research Commission. The poster presents the main results of workshops that were made in 2011, in two knowledge areas: life science and engineering, about science publication processes, and directed to graduates, pos-doctorates, researchers, professors and library staff. The realization of workshops made possible identifies gaps in different aspects of scholarly communication such as research planning, search information strategy, information organization, submission process, identification of journals with high impact, and so on, areas where professors and librarians can help. Besides, workshops reveal that the majority of participants believe in its importance. Despite the ubiquity of digital technology that transversely impacts all academic activities, it is imperative to promote efforts to find a convergence between information and media literacy in higher education and university research activities. This is particularly important when we talk about how science is produced, communicated and preserved for future use. In this scenario, libraries and librarians assume a new, more active and committed role.

Incorporating IT & AT Convergence into Lean Thinking/Six Sigma via the Smarter Operation Transformation (SOT) Methodology

The growing demands for industrial products are imposing an increasingly intense level of competitiveness on the industrial operations. In the meantime, the convergence of information technology (IT) and automation technology (AT) is showing itself to be a tool of great potential for the modernization and improvement of industrial plants. However, for this technology fully to achieve its potential, several obstacles need to be overcome, including the demonstration of the reasoning behind estimations of benefits, investments and risks used to plan the implementation of corporative technology solutions. This article focuses on the evolutionary development of planning and adopting processes of IT & AT convergence. It proposes the incorporation of IT & AT convergence practices into Lean Thinking/Six Sigma, via the method used for planning the convergence of technological activities, known as the Smarter Operation Transformation (SOT) methodology. This article illustrates the SOT methodology through its application in a Brazilian company in the sector of consumer goods. In this application, it is shown that with IT & AT convergence is possible with low investment, in order to reduce the risk of not achieving the goals of key indicators.

Universal behavior of the Shannon mutual information of critical quantum chains

We consider the Shannon mutual information of subsystems of critical quantum chains in their ground states. Our results indicate a universal leading behavior for large subsystem sizes. Moreover, as happens with the entanglement entropy, its finite-size behavior yields the conformal anomaly c of the underlying conformal field theory governing the long-distance physics of the quantum chain. We study analytically a chain of coupled harmonic oscillators and numerically the Q-state Potts models (Q = 2, 3, and 4), the XXZ quantum chain, and the spin-1 Fateev-Zamolodchikov model. The Shannon mutual information is a quantity easily computed, and our results indicate that for relatively small lattice sizes, its finite-size behavior already detects the universality class of quantum critical behavior.