João Correia Lopes

High Performance Computing for Computational Science - VECPAR 2006

1: Grid Computing.- An Opportunistic Algorithm for Scheduling Workflows on Grids.- A Service Oriented System for on Demand Dynamic Structural Analysis over Computational Grids.- Scalable Desktop Grid System.- Analyzing Overheads and Scalability Characteristics of OpenMP Applications.- Parallel Fuzzy c-Means Cluster Analysis.- Peer-to-Peer Models for Resource Discovery in Large-Scale Grids: A Scalable Architecture.- 2: Cluster Computing.- JaceV: A Programming and Execution Environment for Asynchronous Iterative Computations on Volatile Nodes.- Aspect Oriented Pluggable Support for Parallel Computing.- Model for Simulation of Heterogeneous High-Performance Computing Environments.- On Evaluating Decentralized Parallel I/O Scheduling Strategies for Parallel File Systems.- Distributed Security Constrained Optimal Power Flow Integrated to a DSM Based Energy Management System for Real Time Power Systems Security Control.- Metaserver Locality and Scalability in a Distributed NFS.- Top-k Query Processing in the APPA P2P System.- Posterior Task Scheduling Algorithms for Heterogeneous Computing Systems.- Design and Implementation of an Environment for Component-Based Parallel Programming.- Anahy: A Programming Environment for Cluster Computing.- DWMiner: A Tool for Mining Frequent Item Sets Efficiently in Data Warehouses.- A Parallel Implementation of the K Nearest Neighbours Classifier in Three Levels: Threads, MPI Processes and the Grid.- On the Use of the MMC Language to Utilize SIMD Instruction Set.- A Versatile Pipelined Hardware Implementation for Encryption and Decryption Using Advanced Encryption Standard.- 3: Numerical Methods.- Combinatorial Scientific Computing: The Enabling Power of Discrete Algorithms in Computational Science.- Improving the Numerical Simulation of an Airflow Problem with the BlockCGSI Algorithm.- EdgePack: A Parallel Vertex and Node Reordering Package for Optimizing Edge-Based Computations in Unstructured Grids.- Parallel Processing of Matrix Multiplication in a CPU and GPU Heterogeneous Environment.- Robust Two-Level Lower-Order Preconditioners for a Higher-Order Stokes Discretization with Highly Discontinuous Viscosities.- The Impact of Parallel Programming Models on the Performance of Iterative Linear Solvers for Finite Element Applications.- Efficient Parallel Algorithm for Constructing a Unit Triangular Matrix with Prescribed Singular Values.- A Rewriting System for the Vectorization of Signal Transforms.- High Order Fourier-Spectral Solutions to Self Adjoint Elliptic Equations.- Multiresolution Simulations Using Particles.- Evaluation of Several Variants of Explicitly Restarted Lanczos Eigensolvers and Their Parallel Implementations.- PyACTS: A High-Level Framework for Fast Development of High Performance Applications.- Sequential and Parallel Resolution of the Two-Group Transient Neutron Diffusion Equation Using Second-Degree Iterative Methods.- Enhancing the Performance of Multigrid Smoothers in Simultaneous Multithreading Architectures.- Block Iterative Algorithms for the Solution of Parabolic Optimal Control Problems.- Evaluation of Linear Solvers for Astrophysics Transfer Problems.- 4: Large Scale Simulations in Physics.- Scalable Cosmological Simulations on Parallel Machines.- Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems.- Numerical Simulation of Three-Phase Flow in Heterogeneous Porous Media.- Simulation of Laser Propagation in a Plasma with a Frequency Wave Equation.- A Particle Gradient Evolutionary Algorithm Based on Statistical Mechanics and Convergence Analysis.- 5: Computing in Biosciences.- A Computational Framework for Cardiac Modeling Based on Distributed Computing and Web Applications.- Triangular Clique Based Multilevel Approaches to Identify Protein Functional Modules.- BioPortal: A Portal for Deployment of Bioinformatics Applications on Cluster and Grid Environments.- Workshop 1: Computational Grids and Clusters.- Adaptive Distributed Metamodeling.- Distributed General Logging Architecture for Grid Environments.- Interoperability Between UNICORE and ITBL.- Using Failure Injection Mechanisms to Experiment and Evaluate a Grid Failure Detector.- Semantic-Based Service Trading: Application to Linear Algebra.- Management of Services Based on a Semantic Description Within the GRID-TLSE Project.- Extending the Services and Sites of Production Grids by the Support of Advanced Portals.- Workshop 2: High-Performance Data Management in Grid Environments.- PSO-Grid Data Replication Service.- Execution Management of Scientific Models on Computational Grids.- Replica Refresh Strategies in a Database Cluster.- A Practical Evaluation of a Data Consistency Protocol for Efficient Visualization in Grid Applications.- Experiencing Data Grids.

MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393).

Reliable, quick and low-cost methods are needed for the early detection of multidrug-resistant and highly virulent high-risk B2 and D Escherichia coli clones or clonal complexes (HiRCC). Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) seems to have a good discriminatory potential at different subspecies levels, but it was never evaluated for the discrimination of E. coli clones. We assessed the potential of MALDI-TOF MS coupled to multivariate data analysis to discriminate representative E. coli B2 and D HiRCC. Seventy-three E. coli isolates from B2 (including ST131 and B2 non-ST131 clones) and D (ST69, ST393, ST405) with variable pulsed-field gel electrophoresis (PFGE) patterns, origins and dates (1980–2010) were tested. MS spectra were acquired from independent extracts obtained from different plate cultures in two different Microflex LT MALDI-TOF devices (Bruker) after a standard extraction procedure. MALDI-TOF MS fingerprinting analysis revealed a good discriminatory ability between the four HiRCC analysed (ST131, ST69, ST405, ST393) and between B2 ST131 and other B2 non-ST131 isolates. Clusters defined by MALDI-TOF MS were consistent with the clonal complexes assigned by multilocus sequence typing (MLST), although differences were detected regarding the composition of clusters obtained by the comparison of PFGE profiles. We demonstrate, for the first time, that characteristic mass fingerprints of different E. coli HiRCC are sufficiently discriminatory and robust to enable their differentiation by MALDI-TOF MS, which might represent a promising tool for the optimisation of infection control, individual patient management and large-scale epidemiological studies of public health relevance. The good correlation between phenotypic and genotypic features further corroborates phylogenetic relationships delineated by MLST.

Identification of carbapenem-resistant Acinetobacter baumannii clones using infrared spectroscopy.

In this work we assessed the discriminatory ability of Fourier-transform Infrared Spectroscopy (FTIR) in 22 representative isolates from a collection of 318 carbapenem-hydrolyzing class D β -lactamases (CHDL)-producing Acinetobacter spp. (5 hospitals; 2001-2008) previously characterized by DNA-based typing methods. FTIR spectra were acquired with a Bruker spectrometer and analyzed with support of several chemometric tools. The results showed that FTIR spectroscopy was able to distinguish the main CHDL-producing Acinetobacter baumannii lineages causing infection in Portugal, the ST103 carrying blaOXA-58 , ST98 carrying blaOXA-24/40 and ST92 carrying blaOXA-23 . Moreover, this study revealed distinctive phenotypic features of A. baumannii lineages causing infections that might justify different epidemic potential. Spectroscopy may arise as a low cost and easily to perform alternative for typing A. baumannii isolates.

Differentiation of Bacillus pumilus and Bacillus safensis using MALDI-TOF-MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.

Adding Space and Senses to Mobile World Exploration

This chapter focuses on adding spatial and sensory information to mobile technologies to augment the affordability of mobile world exploration by primary school children. It starts by analyzing the significance of space and senses in childrens literacy and mobile learning applications. The opportunities and constraints associated with the use of mobile technologies for the exploration of senses and space within primary school learning activities are explored. The experience of the SchoolSenses@Internet project that designed a mobile application for creating georeferenced multisensory messages within a classroom collaborative environmental activity is described, highlighting the goals, development, and implementation processes. A study carried out over an academic year to investigate how children use GPS-equipped mobile phones to explore, create, and share multisensory geographic information is presented and analyzed to evaluate the use of mobile technology in environmental education and to assess learning achievements. The design and implementation process of the application is outlined, and the lessons learned are identified and summarized in the chapter.

Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy

We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from B2(n = 9) and D(n = 13) phylogenetic groups. Eighty-eight E. coli isolates belonging to phylogenetic groups B2(n = 39) and D(n = 49), including particularly widespread high risk clones or clonal complexes (HiRCC) ST131, ST69, ST393 and ST405 were studied. Spectra were analysed by unsupervised (hierarchical cluster analysis-HCA) and supervised methods (soft independent modelling of class analogy-SIMCA and partial least square discriminant analysis-PLSDA). B2-ST131 isolates were discriminated from B2 non-ST131 and D phylogroup isolates (ST69, ST393, ST405) by HCA, SIMCA and PLSDA. D-ST69, D-ST393 and D-ST405 isolates were also distinguished from each other and from other STs from phylogroup D by the three methods. We demonstrate that FTIR-ATR coupled with chemometrics is a reliable and alternative method to accurately discriminate particular E. coli clones. Its validation towards an application at a routine basis could revolutionize high-throughput bacterial typing.

Dendro: Collaborative Research Data Management Built on Linked Open Data

Research datasets in the so-called “long-tail of science” are easily lost after their primary use. Support for preservation, if available, is hard to fit in the research agenda. Our previous work has provided evidence that dataset creators are motivated to spend time on data description, especially if this also facilitates data exchange within a group or a project. This activity should take place early in the data generation process, when it can be regarded as an actual part of data creation. We present the first prototype of the Dendro platform, designed to help researchers use concepts from domain-specific ontologies to collaboratively describe and share datasets within their groups. Unlike existing solutions, ontologies are used at the core of the data storage and querying layer, enabling users to establish meaningful domain-specific links between data, for any domain. The platform is currently being tested with research groups from the University of Porto.

Ontology-based multi-domain metadata for research data management using triple stores

Most current research data management solutions rely on a fixed set of descriptors (e.g. Dublin Core Terms) for the description of the resources that they manage. These are easy to understand and use, but their semantics are limited to general concepts, leaving out domain-specific metadata. The textual values for descriptors are easily indexed through free-text indexes, but faceted search and dataset interlinking becomes limited. From the point of view of the relational database schema modeler, designing a more flexible metadata model represents a non-trivial challenge because it means representing entities with attributes unknown at the time of modeling and that can change in time. Those traits, combined with the presence of hierarchies among the entities, can make the relational schema quite complex. This work demonstrates the approaches followed by current open-source platforms and proposes a graph-based model for achieving modular, ontology-based metadata for interlinked data assets in the Semantic Web. The proposed model was implemented in a collaborative research data management platform currently under development at the University of Porto.

Using a mobile phone and a geobrowser to create multisensory geographic information

This document describes how we are using mobile phones together with Google Earth to allow children to create multisensory geographic information in learning and participatory contexts.

M-GIS: Mobile and interoperable access to geographic information

This paper describes an architecture which can be used to access geographic information from mobile devices with limited display and processing characteristics, such as Personal Digital Assistants (PDA) or Mobile Phones. The information may come from different sources leading to an interoperable solution.