Applying RADIC in Open MPI: the methodology used to implement RADIC over a Message Passing Library

Fault tolerance has become a major issue for computer and software engineers because the occurrence of faults increases the cost of using a parallel computer. RADIC is the fault tolerance architecture for message passing systems which is transparent, decentralized, flexible and scalable. This master thesis presents the methodology used to implement the RADIC architecture over Open MPI, a well-know large-used message passing library. This implementation kept the RADIC architecture characteristics. In order to validate the implementation we have executed a synthetic ping program, besides, to evaluate the implementation performance we have used the NAS Parallel Benchmarks. The results prove that the RADIC architecture performance depends on the communication pattern of the parallel application which is running. Furthermore, our implementation proves that the RADIC architecture could be implemented over an existent message passing library.

Memòria de recerca: paral·lelització dels diccionaris de la Standard Template Library de C++

Estudi elaborat a partir d’una estada a la Universität Karlsruhe entre gener i maig del 2007. Les biblioteques d’estructures de dades defineixen interfícies i implementen algorismes i estructures de dades fonamentals. Un exemple n’és la Satandard Template Library (STL ), que forma part del llenguatge de programació C++. En el marc d’una tesi, s’està treballant per obtenir implementacions més eficients i/o versàtils d’alguns components de la STL. Per a fer-ho s’utilitzen tècniques de la enginyeria d’algorismes. En particular, s’integra el coneixement de la comunitat algorítmica i es té en consideració la tecnologia existent. L’acció durant l’estada s’ha emmarcat en el desenvolupament la Multi Core STL (MCSTL ). La MCSTL és una implementació paral•lela de la STL per a màquines multi-core. Les màquines multi-core són actualment l’únic tipus de màquina disponible al mercat. Per tant, tot i que el paral•lelisme obtingut no sigui òptim, és preferible a tenir els processadors esperant, ja que , la tendència és que el nombre de processadors per computador augmenti.

A stable phage lysin (Cpl-1) dimer with increased antipneumococcal activity and decreased plasma clearance.

Bacteriophages (phages) produce endolysins (lysins) as part of their lytic cycle in order to degrade the peptidoglycan layer of the infected bacteria for subsequent release of phage progeny. Because these enzymes maintain their lytic and lethal activity against Gram-positive bacteria when added extrinsically to the cells, they have been actively exploited as novel anti-infectives, sometimes termed enzybiotics. As with other relatively small peptides, one issue in their clinical development is their rapid inactivation through proteolytic degradation, immunological blockage and renal clearance. The antipneumococcal lysin Cpl-1 was shown to escape both proteolysis and immunological blockage. However, its short plasma half-life (20.5 min in mice) may represent a shortcoming for clinical usefulness. Here we report the construction of a Cpl-1 dimer with a view to increasing both the antipneumococcal specific activity and plasma half-life of Cpl-1. Dimerisation was achieved by introducing specific cysteine residues at the C-terminal end of the enzyme, thus favouring disulphide bonding. Compared with the native monomer, the constructed dimer demonstrated a two-fold increase in specific antipneumococcal activity and a ca. ten-fold decrease in plasma clearance. As several lysins are suspected to dimerise on contact with their cell wall substrate to be fully active, stable pre-dimerised enzymes may represent a more efficient alternative to the native monomer.

Desenvolupament d'un servidor d'informació geogràfica

L'explosió d'aplicacions a Internet basades en oferir serveis de localització, com són portals web de mobilitat o aplicacions de seguiment de vehicles en línia han motivat aquest projecte. Google Maps ens permet afegir mapes fàcilment en un lloc web amb la seva API, però OpenLayers, una llibreria JavaScript lliure ens dóna l'opció de carregar cobertures de mapa i marcadors des de qualsevol font. OpenStreetMap proporciona dades geogràfiques de manera lliure, com per exemple mapes de carrers i carreteres. Un estudi acurat de l'estructura i agrupació de les dades en el format OSM i el desenvolupament d'un servidor basat en el model de tessel·les, són els principals elements de partida per crear la nostra pròpia font de dades cartogràfiques. En aquest projecte s'analitza i processa DXF Drawing eXchange Format passant al format OSM. Un fitxer OSM conté la informació geogràfica necessària per a la base de dades espaial a partir de la qual, entre d'altres aplicacions, es podran visualitzar els mapes propis en una aplicació de seguiment de vehicles o en un portal web.

The p53 gene expression and its developmental regulation in schistosomes

We have studied the gene expression, especially of the oncoproteins, and its regulation in schistosomes. Schistosomes have a complex life cycle with defined dimorphic lifestyle. The parasite are so far unique in biology in expressing oncogene products in their adult stage. In order to characterize the expression and developmental regulation, a lambda gt 11 cDNA library and lambda EMBL4 genomic DNA library of each growth stage of Schistosoma mansoni and S. japonicum was constructed, and was screened with various monoclonal antibodies against ongogene products. One positive plaque reacted to anti-p53 antibody (Ab-2, Oncogene Science, Inc.) was further analyzed. This fusion protein was about 120 KDa in molecular weights, and expressed as 1.4 Kb RNA in the adult stage. P53 gene is well-known as the negative regulator of the cell cicle, and the mutations in the gene are turning out to be the most common genetic alterations in human cancers. The comparison of the gene structure among species and stages were being conducted. Chromosome structures, C-band formation, and the results of in situ hybridization using the phage probe would be discussed.

Sequencing and identification of expressed Schistosoma mansoni genes by random selection of cDNA clones from a directional library

We have initiated a gene discovery program in Schistosoma mansoni based on the technique of Expressed Sequence Tags (ESTs), i.e. partial sequences of cDNAs obtained from single passes in automatic DNA sequencers. ESTs can be used to identify genese onf the basis of their homology whith sequences from other species deposited in DNA or protein databases. Trasncripts with sequences without matches in teh databases may represent novel parasite-specific genes. This approach has shown to be very efficient and in less than two years a broad range of novel genes has already been ascertained, more than doubling the number of known S. mansoni genes.

Television before TV : a transnational history of an experimental medium on display, 1928 - 1939

Dès le milieu des années 1920 et le développement des premiers prototypes fonctionnels, la télévision se fait objet d'exposition. La nouvelle technologie est montrée à des foires industrielles et dans des grands magasins, à des expositions universelles et nationales : exposée, la télévision devient un mass media avant même qu'elle ne diffuse des émissions régulières. En étudiant les présentations publiques de la télévision en Allemagne, en Grande-Bretagne et aux Etats-Unis entre 1928 - date de l'ouverture des premières expositions annuelles dans les trois pays - et 1939 - moment de l'interruption de celles-ci suite à l'éclatement de la Deuxième Guerre mondiale - Television before TV montre que les lieux où le médium rencontre son premier public constituent les mêmes espaces qui, rétrospectivement, permettent de comprendre son avènement. Cette recherche propose ainsi de nouvelles pistes pour l'histoire des médias en interrogeant la définition de la télévision en tant que médium du privé. Elle rappelle l'importance historique de l'espace public pour la « vision à distance » et, dépassant la perspective nationale, reconstitue les différences et similarités techniques, médiatiques et institutionnelles de la télévision allemande, américaine et britannique dans l'entre-deux-guerres. Développée dans un contexte qui est simultanément nationaliste et nourri d'échanges et de compétitions internationales, la télévision sert de comparatif dans les rivalités entre pays, mais stimule également la circulation de savoir-faire et de personnes. Sa forte valeur symbolique comme emblème du progrès scientifique et, dans le cas allemand, comme preuve de la modernité du régime national-socialiste se traduit dans les salles d'expositions par des scénographies souvent innovatrices, dont les photographies et descriptions se propagent au-delà de la presse locale. Au centre d'un réseau discursif et représentationnel, les expositions jouent alors un rôle essentiel pour la construction sociale, politique et culturelle de la télévision. Remplaçant l'analyse de textes audiovisuels par l'étude de la machine exposée, ma recherche reformule la question bazinienne de qu'est-ce que la télévision ? pour demander où le médium se situe-t-il ? Cette prémisse méthodologique permet de contourner une évaluation qualitative de la technologie qui déplorerait ses multiples imperfections, et éclaire d'un nouveau jour des dispositifs télévisuels qui, même sans programme, intègrent un univers voué à la culture de consommation et du loisir.

IPH Response to Dept of Justice and Equality Review of the Code of Practice on the Sale and Display of Alcohol in Mixed Trading Premises

IPH responded to the Department of Justice, Equality and Defence review of the voluntary Code of Practice for the display and sale of alcohol in supermarkets, convenience stores and similar mixed trading outlets. The voluntary Code was introduced in 2008 as an alternative to the statutory rules for structural separation of alcohol products in mixed trading outlets which are set out in section 9 of the Intoxicating Liquor Act 2008. Interested bodies and individuals were invited to submit comments on the Compliance Report for 2011 and on the effectiveness of the voluntary approach to structural separation by 20th December 2011. The Minister said he intended to also seek the views of the Minister for Health and the Joint Oireachtas Committee on Justice, Defence and Equality before reaching any decision on whether to bring the statutory rules in the 2008 Act into operation.

Characterization of constitutive and putative differentially expressed mRNAs by means of expressed sequence tags, differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR from the sand fly vector Lutzomyia longipalpis

Molecular studies of insect disease vectors are of paramount importance for understanding parasite-vector relationship. Advances in this area have led to important findings regarding changes in vectors' physiology upon blood feeding and parasite infection. Mechanisms for interfering with the vectorial capacity of insects responsible for the transmission of diseases such as malaria, Chagas disease and dengue fever are being devised with the ultimate goal of developing transgenic insects. A primary necessity for this goal is information on gene expression and control in the target insect. Our group is investigating molecular aspects of the interaction between Leishmania parasites and Lutzomyia sand flies. As an initial step in our studies we have used random sequencing of cDNA clones from two expression libraries made from head/thorax and abdomen of sugar fed L. longipalpis for the identification of expressed sequence tags (EST). We applied differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR to characterize differentially expressed mRNA from sugar and blood fed insects, and, in one case, from a L. (V.) braziliensis-infected L. longipalpis. We identified 37 cDNAs that have shown homology to known sequences from GeneBank. Of these, 32 cDNAs code for constitutive proteins such as zinc finger protein, glutamine synthetase, G binding protein, ubiquitin conjugating enzyme. Three are putative differentially expressed cDNAs from blood fed and Leishmania-infected midgut, a chitinase, a V-ATPase and a MAP kinase. Finally, two sequences are homologous to Drosophila melanogaster gene products recently discovered through the Drosophila genome initiative.

Forensic examination of ink by high-performance thin layer chromatography - The United States Secret Service Digital Ink Library

Forensic examinations of ink have been performed since the beginning of the 20th century. Since the 1960s, the International Ink Library, maintained by the United States Secret Service, has supported those analyses. Until 2009, the search and identification of inks were essentially performed manually. This paper describes the results of a project designed to improve ink samples' analytical and search processes. The project focused on the development of improved standardization procedures to ensure the best possible reproducibility between analyses run on different HPTLC plates. The successful implementation of this new calibration method enabled the development of mathematical algorithms and of a software package to complement the existing ink library.

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile).

Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

Antimicrobial susceptibility, phage types, and pulsetypes of Salmonella Typhimurium, in São Paulo, Brazil

A total of 283 Salmonella Typhimurium strains isolated from cases of human infections and non human sources, were examined for antimicrobial susceptibilityand the incidence of resistance was 38% and multiple resistance (to three or more antimicrobials) was 15%. All 43 multidrug-resistant strains (MDR) and 13 susceptible ones were characterized by phage typing and pulsed- field gel electrophoresis (PFGE). The strains encompassed 14 definitive phage types (DT), three were untypable (UT), and 18 atypicals or reaction does not conform (RDNC), which belonged to 21 PFGE patterns, A1-A21. The predominant phage types were DT49, DT193, and RDNC and two strains belonging to DT 104 and 104b were also identified. The most commum PFGE patterns were A1 and A8. Analysis by PFGE and phage typing demonstrated that the most of the MDR were multiclonal and association among multiresistance, phage typing, and PFGE patterns was not so significant.