Algorithm-oriented design of efficient many-core architectures applied to dense matrix multiplication

Recent integrated circuit technologies have opened the possibility to design parallel architectures with hundreds of cores on a single chip. The design space of these parallel architectures is huge with many architectural options. Exploring the design space gets even more difficult if, beyond performance and area, we also consider extra metrics like performance and area efficiency, where the designer tries to design the architecture with the best performance per chip area and the best sustainable performance. In this paper we present an algorithm-oriented approach to design a many-core architecture. Instead of doing the design space exploration of the many core architecture based on the experimental execution results of a particular benchmark of algorithms, our approach is to make a formal analysis of the algorithms considering the main architectural aspects and to determine how each particular architectural aspect is related to the performance of the architecture when running an algorithm or set of algorithms. The architectural aspects considered include the number of cores, the local memory available in each core, the communication bandwidth between the many-core architecture and the external memory and the memory hierarchy. To exemplify the approach we did a theoretical analysis of a dense matrix multiplication algorithm and determined an equation that relates the number of execution cycles with the architectural parameters. Based on this equation a many-core architecture has been designed. The results obtained indicate that a 100 mm(2) integrated circuit design of the proposed architecture, using a 65 nm technology, is able to achieve 464 GFLOPs (double precision floating-point) for a memory bandwidth of 16 GB/s. This corresponds to a performance efficiency of 71 %. Considering a 45 nm technology, a 100 mm(2) chip attains 833 GFLOPs which corresponds to 84 % of peak performance These figures are better than those obtained by previous many-core architectures, except for the area efficiency which is limited by the lower memory bandwidth considered. The results achieved are also better than those of previous state-of-the-art many-cores architectures designed specifically to achieve high performance for matrix multiplication.

Ostracoda: database for the Neogene of Portugal

The "Ostracoda: database for the Neogene of Portugal", prepared under the Project "POCTl/36531/PAL/2000 - Studies on Portuguese Palaeontology / Post-Paleozoic", is presented. It provides information about 158 especies that have been recognized in sections and boreholes concerning Neogene units in Portugal.

Service-oriented mobility of java code in web services-based architectures

Dissertação apresentada na Faculdade de Ciências e Tecnologias da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Multy-dimensional composition by objectives in aspect-oriented requirements analysis

Thesis submitted to Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa in partial fulfilment of the requirements for the degree of Master in Computer Science

A middleware for service oriented computing in dynamic environments

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Geospatial database generation from digital newspapers: use case for risk and disaster domains.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Analysis of early synthetic dyes with HPLC-DAD-MS: an important database for analysis of colorants used in cultural heritage

Presented thesis at Faculdade de Ciências e Tecnologias, Universidade de Lisboa, to obtain the Master Degree in Conservation and Restoration of Textiles

A calculus for modeling and analyzing conversations in service-oriented computing

Dissertação apresentada para a obtenção do Grau de Doutor em Informática pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Database repairs with answer set programming

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Disposable immunosensor using a simple method for oriented antibody immobilization for label-free real-time detection of an oxidative stress biomarker implicated in cancer diseases

This work proposes a novel approach for a suitable orientation of antibodies (Ab) on an immunosensing platform, applied here to the determination of 8-hydroxy-2′-deoxyguanosine (8OHdG), a biomarker of oxidative stress that has been associated to chronic diseases, such as cancer. The anti-8OHdG was bound to an amine modified gold support through its Fc region after activation of its carboxylic functions. Non-oriented approaches of Ab binding to the platform were tested in parallel, in order to show that the presented methodology favored Ab/Ag affinity and immunodetection of the antigen. The immunosensor design was evaluated by quartz-crystal microbalance with dissipation, atomic force microscopy, electrochemical impedance spectroscopy (EIS) and square-wave voltammetry. EIS was also a suitable technique to follow the analytical behavior of the device against 8OHdG. The affinity binding between 8OHdG and the antibody immobilized in the gold modified platform increased the charge transfer resistance across the electrochemical set-up. The observed behavior was linear from 0.02 to 7.0 ng/mL of 8OHdG concentrations. The interference from glucose, urea and creatinine was found negligible. An attempt of application to synthetic samples was also successfully conducted. Overall, the presented approach enabled the production of suitably oriented Abs over a gold platform by means of a much simpler process than other oriented-Ab binding approaches described in the literature, as far as we know, and was successful in terms of analytical features and sample application.

Oriented Tailoring of Plastic Antibodies for Prostate Specific Antigen and Application of the Imprinted Material as Ionophore in Potentiometric Detection

Prostate Specific Antigen (PSA) is the biomarker of choice for screening prostate cancer throughout the population, with PSA values above 10 ng/mL pointing out a high probability of associated cancer1. According to the most recent World Health Organization (WHO) data, prostate cancer is the commonest form of cancer in men in Europe2. Early detection of prostate cancer is thus very important and is currently made by screening PSA in men over 45 years old, combined with other alterations in serum and urine parameters. PSA is a glycoprotein with a molecular mass of approximately 32 kDa consisting of one polypeptide chain, which is produced by the secretory epithelium of human prostate. Currently, the standard methods available for PSA screening are immunoassays like Enzyme-Linked Immunoabsorbent Assay (ELISA). These methods are highly sensitive and specific for the detection of PSA, but they require expensive laboratory facilities and high qualify personal resources. Other highly sensitive and specific methods for the detection of PSA have also become available and are in its majority immunobiosensors1,3-5, relying on antibodies. Less expensive methods producing quicker responses are thus needed, which may be achieved by synthesizing artificial antibodies by means of molecular imprinting techniques. These should also be coupled to simple and low cost devices, such as those of the potentiometric kind, one approach that has been proven successful6. Potentiometric sensors offer the advantage of selectivity and portability for use in point-of-care and have been widely recognized as potential analytical tools in this field. The inherent method is simple, precise, accurate and inexpensive regarding reagent consumption and equipment involved. Thus, this work proposes a new plastic antibody for PSA, designed over the surface of graphene layers extracted from graphite. Charged monomers were used to enable an oriented tailoring of the PSA rebinding sites. Uncharged monomers were used as control. These materials were used as ionophores in conventional solid-contact graphite electrodes. The obtained results showed that the imprinted materials displayed a selective response to PSA. The electrodes with charged monomers showed a more stable and sensitive response, with an average slope of -44.2 mV/decade and a detection limit of 5.8X10-11 mol/L (2 ng/mL). The corresponding non-imprinted sensors showed smaller sensitivity, with average slopes of -24.8 mV/decade. The best sensors were successfully applied to the analysis of serum samples, with percentage recoveries of 106.5% and relatives errors of 6.5%.

Label-free human chorionic gonadotropin detection at picogram levels using oriented antibodies bound to graphene screen-printed electrodes

Human chorionic gonadotropin (hCG) is a key diagnostic marker of pregnancy and an important biomarker for cancers in the prostate, ovaries and bladder and therefore of great importance in diagnosis. For this purpose, a new immunosensor of screen-printed electrodes (SPEs) is presented here. The device was fabricated by introducing a polyaniline (PANI) conductive layer, via in situ electropolymerization of aniline, onto a screen-printed graphene support. The PANI-coated graphene acts as the working electrode of a three terminal electrochemical sensor. The working electrode is functionalised with anti-hCG, by means of a simple process that enabled oriented antibody binding to the PANI layer. The antibody was attached to PANI following activation of the –COOH group at the Fc terminal. Functionalisation of the electrode was analysed and optimized using Electrochemical Impedance Spectroscopy (EIS). Chemical modification of the surface was characterised using Fourier transform infrared, and Raman spectroscopy with confocal microscopy. The graphene–SPE–PANI devices displayed linear responses to hCG in EIS assays from 0.001 to 50 ng mL−1 in real urine, with a detection limit of 0.286 pg mL−1. High selectivity was observed with respect to the presence of the constituent components of urine (urea, creatinine, magnesium chloride, calcium chloride, sodium dihydrogen phosphate, ammonium chloride, potassium sulphate and sodium chloride) at their normal levels, with a negligible sensor response to these chemicals. Successful detection of hCG was also achieved in spiked samples of real urine from a pregnant woman. The immunosensor developed is a promising tool for point-of-care detection of hCG, due to its excellent detection capability, simplicity of fabrication, low-cost, high sensitivity and selectivity.

Co-Authorship of scientists in the energy field: an exploratory study of the ETDE World Energy Database (ETDEWEB) using Social Network Analysis

Paper presented at the 5th European Conference Economics and Management of Energy in Industry, Vilamoura, Algarve. Apr. 14-17, 2009, 11p. URL: http:// www.cenertec.pt/ecemei/

Co-Authorship of scientists in the energy field: a study of the ETDE World Energy Database (ETDEWEB) using social network analysis

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Gestão de Informação

Message-oriented middleware for smart grids

In order to increase the efficiency in the use of energy resources, the electrical grid is slowly evolving into a smart(er) grid that allows users' production and storage of energy, automatic and remote control of appliances, energy exchange between users, and in general optimizations over how the energy is managed and consumed. One of the main innovations of the smart grid is its organization over an energy plane that involves the actual exchange of energy, and a data plane that regards the Information and Communication Technology (ICT) infrastructure used for the management of the grid's data. In the particular case of the data plane, the exchange of large quantities of data can be facilitated by a middleware based on a messaging bus. Existing messaging buses follow different data management paradigms (e.g.: request/response, publish/subscribe, data-oriented messaging) and thus satisfy smart grids' communication requirements at different extents. This work contributes to the state of the art by identifying, in existing standards and architectures, common requirements that impact in the messaging system of a data plane for the smart grid. The paper analyzes existing messaging bus paradigms that can be used as a basis for the ICT infrastructure of a smart grid and discusses how these can satisfy smart grids' requirements.