Diversity of Vibrionaceae bacteria isolated from the haemolymph of the spider crab Maja brachydactyla

Aims: The aim of this study was to characterise and identify vibrios isolated from the haemolymph of apparently healthy adult spider crabs (Maja brachydactyla) wild-caught in the Spanish localities of Galician coast and in the Canary Islands and also from captive animals held at IRTA’s facilities in the Ebro Delta of Catalonia, north-west Spanish Mediterranean coast. Methods and Results: A total of 277 bacterial isolates were obtained, and of these, 171 were characterised with rep-PCR, resulting electrophoretic bands were analysed and clusters formed. Identification of representative strains of each cluster was made by sequencing the 16S rRNA. Samples from animals caught in Galicia and captive at IRTA (around 15–18 C) rendered mostly species belonging to the Splendidus clade (72Æ2 and 76Æ6% respectively), commonly found in cold waters (below 20 C). Higher species diversity was found in the haemolymph of the captive animals. In the warmer Canary Islands waters (around 21 C), the diversity of vibrios is dominated by three clades, Harveyi (Vibrio core group, 39Æ3%), Orientalis (23Æ2%) and Splendidus (21Æ4%) with a species diversity that equals that of the colder captive animals. Conclusions: Differences in the vibrios populations were found in the haemolymph extracted from animals collected from the three localities. Potential new species were found, and their description is under way. Significance and Impact of Study: As with other invertebrates, spider crabs also contain a diverse population of vibrios. These findings should help researchers to diagnose when a crab is infected.

Parallelization of whole genome alignment

With the advent of High performance computing, it is now possible to achieve orders of magnitude performance and computation e ciency gains over conventional computer architectures. This thesis explores the potential of using high performance computing to accelerate whole genome alignment. A parallel technique is applied to an algorithm for whole genome alignment, this technique is explained and some experiments were carried out to test it. This technique is based in a fair usage of the available resource to execute genome alignment and how this can be used in HPC clusters. This work is a rst approximation to whole genome alignment and it shows the advantages of parallelism and some of the drawbacks that our technique has. This work describes the resource limitations of current WGA applications when dealing with large quantities of sequences. It proposes a parallel heuristic to distribute the load and to assure that alignment quality is mantained.

Comparación de datos de expresión génica del servidor local con datos de una base de datos remota

En la presente memoria se detalla con precisión las diversas fases del trabajo para construir una aplicación web en el servidor http://revolutionresearch.uab.es que permite enriquecer los clusters de la microarray del usuario con información biomédica de una base de datos remota. Los clusters de origen estadístico (o no) de la microarray del usuario se enriquecen a partir de cruzar sus genes marcadores con la base de datos de genes marcadores de microarrays (base de datos remota) con clusters basados en información biomédica. La base de datos de genes marcadores de microarrays ha sido obtenida a partir de la base de datos de GEO Profiles del NCBI.

Integración de Hadoop con planificadores batch

Cada vez es mayor el número de aplicaciones desarrolladas en el ámbito científico, como en la Bioinformática o en las Geociencias, escritas bajo el modelo MapReduce, empleando herramientas de código abierto como Apache Hadoop. De la necesidad de integrar Hadoop en entornos HPC, para posibilitar la ejecutar aplicaciones desarrolladas bajo el paradigma MapReduce, nace el presente proyecto. Se analizan dos frameworks diseñados para facilitar dicha integración a los desarrolladores: HoD y myHadoop. En este proyecto se analiza, tanto las posibilidades en cuanto a entornos que ofrecen dichos frameworks para la ejecución de aplicaciones MapReduce, como el rendimiento de los clúster Hadoop generados con HoD o myHadoop respecto a un clúster Hadoop físico.

Search for dark matter using VHE gamma-ray telescopes

One of the unresolved questions of modern physics is the nature of Dark Matter. Strong experimental evidences suggest that the presence of this elusive component in the energy budget of the Universe is quite significant, without, however, being able to provide conclusive information about its nature. The most plausible scenario is that of weakly interacting massive particles (WIMPs), that includes a large class of non-baryonic Dark Matter candidates with a mass typically between few tens of GeV and few TeVs, and a cross section of the order of weak interactions. Search for Dark Matter particles using very high energy gamma-ray Cherenkov telescopes is based on the model that WIMPs can self-annihilate, leading to production of detectable species, like photons. These photons are very energetic, and since unreflected by the Universe's magnetic fields, they can be traced straight to the source of their creation. The downside of the approach is a great amount of background radiation, coming from the conventional astrophysical objects, that usually hides clear signals of the Dark Matter particle interactions. That is why good choice of the observational candidates is the crucial factor in search for Dark Matter. With MAGIC (Major Atmospheric Gamma-ray Imaging Cherenkov Telescopes), a two-telescope ground-based system located in La Palma, Canary Islands, we choose objects like dwarf spheroidal satellite galaxies of the Milky Way and galaxy clusters for our search. Our idea is to increase chances for WIMPs detection by pointing to objects that are relatively close, with great amount of Dark Matter and with as-little-as-possible pollution from the stars. At the moment, several observation projects are ongoing and analyses are being performed.

Identificació de paisatges funcionals mitjançant anàlisi cluster

El terme paisatge i les seves aplicacions són cada dia més utilitzats per les administracions i altres entitats com a eina de gestió del territori. Aprofitant la gran quantitat de dades en bases compatibles amb SIG (Sistemes d’Informació Geogràfica) existents a Catalunya s’ha desenvolupat una síntesi cartogràfica on s’identifiquen els Paisatges Funcionals (PF) de Catalunya, concepte que fa referència al comportament fisico-ecològic del terreny a partir de variables topogràfiques i climàtiques convenientment transformades i agregades. S’ha utilitzat un mètode semiautomàtic i iteratiu de classificació no supervisada (clustering) que permet la creació d’una llegenda jeràrquica o nivells de generalització. S’ha obtingut com a resultat el Mapa de Paisatges Funcionals de Catalunya (MPFC) amb una llegenda de 26 categories de paisatges i 5 nivells de generalització amb una resolució espacial de 180 m. Paral·lelament, s’han realitzat validacions indirectes sobre el mapa obtingut a partir dels coneixements naturalistes i la cartografia existent, així com també d’un mapa d’incertesa (aplicant lògica difusa) que aporten informació de la fiabilitat de la classificació realitzada. Els Paisatges Funcionals obtinguts permeten relacionar zones de condicions topo-climàtiques homogènies i dividir el territori en zones caracteritzades ambientalment i no políticament amb la intenció que sigui d’utilitat a l’hora de millorar la gestió dels recursos naturals i la planificació d’actuacions humanes.

Clustering algorithms for anti-money laundering using graph theory and social network analysis

HEMOLIA (a project under European community’s 7th framework programme) is a new generation Anti-Money Laundering (AML) intelligent multi-agent alert and investigation system which in addition to the traditional financial data makes extensive use of modern society’s huge telecom data source, thereby opening up a new dimension of capabilities to all Money Laundering fighters (FIUs, LEAs) and Financial Institutes (Banks, Insurance Companies, etc.). This Master-Thesis project is done at AIA, one of the partners for the HEMOLIA project in Barcelona. The objective of this thesis is to find the clusters in a network drawn by using the financial data. An extensive literature survey has been carried out and several standard algorithms related to networks have been studied and implemented. The clustering problem is a NP-hard problem and several algorithms like K-Means and Hierarchical clustering are being implemented for studying several problems relating to sociology, evolution, anthropology etc. However, these algorithms have certain drawbacks which make them very difficult to implement. The thesis suggests (a) a possible improvement to the K-Means algorithm, (b) a novel approach to the clustering problem using the Genetic Algorithms and (c) a new algorithm for finding the cluster of a node using the Genetic Algorithm.

Counterpoise-corrected geometries and harmonic frequencies of N-body clusters: application to (HF)n (n=3,4)

A study was conducted on the methods of basis set superposition error (BSSE)-free geometry optimization and frequency calculations in clusters larger than a dimer. In particular, three different counterpoise schemes were critically examined. It was shown that the counterpoise-corrected supermolecule energy can be easily obtained in all the cases by using the many-body partitioning of energy

Porting and performance analysis of EC-Earth System on the BSC-MareNostrum Supercomputer

Earth System Models (ESM) have been successfuly developed over past few years, and are currently beeing used for simulating present day-climate, seasonal to interanual predictions of climate change. The supercomputer performance plays an important role in climate modeling since one of the challenging issues for climate modellers is to efficiently and accurately couple earth System components on present day computers architectures. At the Barcelona Supercomputing Center (BSC), we work with the EC- Earth System Model. The EC- Earth is an ESM, which currently consists of an atmosphere (IFS) and an ocean (NEMO) model that communicate with each other through the OASIS coupler. Additional modules (e.g. for chemistry and vegetation ) are under development. The EC-Earth ESM has been ported successfully over diferent high performance computin platforms (e.g, IBM P6 AIX, CRAY XT-5, Intelbased Linux Clusters, SGI Altix) at diferent sites in Europ (e.g., KNMI, ICHEC, ECMWF). The objective of the first phase of the project was to identify and document the issues related with the portability and performance of EC-Earth on the MareNostrum supercomputer, a System based on IBM PowerPC 970MP processors and run under a Linux Suse Distribution. EC-Earth was successfully ported to MareNostrum, and a compilation incompatibilty was solved by a two step compilation approach using XLF version 10.1 and 12.1 compilers. In addition, the EC-Earth performance was analyzed with respect to escalability and trace analysis with the Paravear software. This analysis showed that EC-Earth with a larger number of IFS CPUs (<128) is not feasible at the moment since some issues exists with the IFS-NEMO balance and MPI Communications.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount of “unannotated transcription.” We use a number of disparate features to classify the 6988 novel TARs—array expression profiles across cell lines and conditions, sequence composition, phylogenetic profiles (presence/absence of syntenic conservation across 17 species), and locations relative to genes. In the classification, we first filter out TARs with unusual sequence composition and those likely resulting from cross-hybridization. We then associate some of those remaining with proximal exons having correlated expression profiles. Finally, we cluster unclassified TARs into putative novel loci, based on similar expression and phylogenetic profiles. To encapsulate our classification, we construct a Database of Active Regions and Tools (DART.gersteinlab.org). DART has special facilities for rapidly handling and comparing many sets of TARs and their heterogeneous features, synchronizing across builds, and interfacing with other resources. Overall, we find that ∼14% of the novel TARs can be associated with known genes, while ∼21% can be clustered into ∼200 novel loci. We observe that TARs associated with genes are enriched in the potential to form structural RNAs and many novel TAR clusters are associated with nearby promoters. To benchmark our classification, we design a set of experiments for testing the connectivity of novel TARs. Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously.

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

BACKGROUND: The trithorax group (trxG) and Polycomb group (PcG) proteins are responsible for the maintenance of stable transcriptional patterns of many developmental regulators. They bind to specific regions of DNA and direct the post-translational modifications of histones, playing a role in the dynamics of chromatin structure. RESULTS: We have performed genome-wide expression studies of trx and ash2 mutants in Drosophila melanogaster. Using computational analysis of our microarray data, we have identified 25 clusters of genes potentially regulated by TRX. Most of these clusters consist of genes that encode structural proteins involved in cuticle formation. This organization appears to be a distinctive feature of the regulatory networks of TRX and other chromatin regulators, since we have observed the same arrangement in clusters after experiments performed with ASH2, as well as in experiments performed by others with NURF, dMyc, and ASH1. We have also found many of these clusters to be significantly conserved in D. simulans, D. yakuba, D. pseudoobscura and partially in Anopheles gambiae. CONCLUSION: The analysis of genes governed by chromatin regulators has led to the identification of clusters of functionally related genes conserved in other insect species, suggesting this chromosomal organization is biologically important. Moreover, our results indicate that TRX and other chromatin regulators may act globally on chromatin domains that contain transcriptionally co-regulated genes.

A simple permutation test for clusteredness

Hierarchical clustering is a popular method for finding structure in multivariate data,resulting in a binary tree constructed on the particular objects of the study, usually samplingunits. The user faces the decision where to cut the binary tree in order to determine the numberof clusters to interpret and there are various ad hoc rules for arriving at a decision. A simplepermutation test is presented that diagnoses whether non-random levels of clustering are presentin the set of objects and, if so, indicates the specific level at which the tree can be cut. The test isvalidated against random matrices to verify the type I error probability and a power study isperformed on data sets with known clusteredness to study the type II error.

Testing for convergence clubs in income per-capita: A predictive density approach

The paper proposes a technique to jointly test for groupings of unknown size in the cross sectional dimension of a panel and estimates the parameters of each group, and applies it to identifying convergence clubs in income per-capita. The approach uses the predictive density of the data, conditional on the parameters of the model. The steady state distribution of European regional data clusters around four poles of attraction with different economic features. The distribution of incomeper-capita of OECD countries has two poles of attraction and each grouphas clearly identifiable economic characteristics.

The ethics of creative accounting

The term 'creative accounting' can be defined in a number ofways. Initially we will offer this definition: 'a processwhereby accountants use their knowledge of accounting rulesto manipulate the figures reported in the accounts of abusiness'.To investigate the ethical issues raised by creativeaccounting we will:- Explore some definitions of creative accounting.- Consider the various ways in which creative accounting can be undertaken.- Explore the range of reasons for a company's directors to engage in creative accounting.- Review the ethical issues that arise in creative accounting.- Report on surveys of auditors' perceptions of creative accounting in the UK, Spain and New Zealand.

Creative accounting: Some ethical issues of macro- and micro-manipulation

This paper examines two principal categories of manipulative behaviour. The term'macro-manipulation' is used to describe the lobbying of regulators to persuadethem to produce regulation that is more favourable to the interests of preparers.'Micro-manipulation' describes the management of accounting figures to produce abiased view at the entity level. Both categories of manipulation can be viewed asattempts at creativity by financial statement preparers. The paper analyses twocases of manipulation which are considered in an ethical context. The paperconcludes that the manipulations described in it can be regarded as morallyreprehensible. They are not fair to users, they involve an unjust exercise ofpower, and they tend to weaken the authority of accounting regulators.