Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Scaling up question-answering to linked data

Linked Data semantic sources, in particular DBpedia, can be used to answer many user queries. PowerAqua is an open multi-ontology Question Answering (QA) system for the Semantic Web (SW). However, the emergence of Linked Data, characterized by its openness, heterogeneity and scale, introduces a new dimension to the Semantic Web scenario, in which exploiting the relevant information to extract answers for Natural Language (NL) user queries is a major challenge. In this paper we discuss the issues and lessons learned from our experience of integrating PowerAqua as a front-end for DBpedia and a subset of Linked Data sources. As such, we go one step beyond the state of the art on end-users interfaces for Linked Data by introducing mapping and fusion techniques needed to translate a user query by means of multiple sources. Our first informal experiments probe whether, in fact, it is feasible to obtain answers to user queries by composing information across semantic sources and Linked Data, even in its current form, where the strength of Linked Data is more a by-product of its size than its quality. We believe our experiences can be extrapolated to a variety of end-user applications that wish to scale, open up, exploit and re-use what possibly is the greatest wealth of data about everything in the history of Artificial Intelligence. © 2010 Springer-Verlag.

PIP-DB:the protein isoelectric point database

A protein's isoelectric point or pI corresponds to the solution pH at which its net surface charge is zero. Since the early days of solution biochemistry, the pI has been recorded and reported, and thus literature reports of pI abound. The Protein Isoelectric Point database (PIP-DB) has collected and collated these data to provide an increasingly comprehensive database for comparison and benchmarking purposes. A web application has been developed to warehouse this database and provide public access to this unique resource. PIP-DB is a web-enabled SQL database with an HTML GUI front-end. PIP-DB is fully searchable across a range of properties.

Experience with the use of Acrobat in the CAJUN publishing project

Adobe's Acrobat software, released in June 1993, is based around a new Portable Document Format (PDF) which offers the possibility of being able to view and exchange electronic documents, independent of the originating software, across a wide variety of supported hardware platforms (PC, Macintosh, Sun UNIX etc.). The fact that Acrobat's imageable objects are rendered with full use of Level 2 PostScript means that the most demanding requirements can be met in terms of high-quality typography and device-independent colour. These qualities will be very desirable components in future multimedia and hypermedia systems. The current capabilities of Acrobat and PDF are described; in particular the presence of hypertext links, bookmarks, and yellow sticker annotations (in release 1.0) together with article threads and multi-media plugins in version 2.0, This article also describes the CAJUN project (CD-ROM Acrobat Journals Using Networks) which has been investigating the automated placement of PDF hypertextual features from various front-end text processing systems. CAJUN has also been experimenting with the dissemination of PDF over e-mail, via World Wide Web and on CDROM.

Online MBPeT dashboard : enabling performance testing as a service in the cloud

In this thesis, tool support is addressed for the combined disciplines of Model-based testing and performance testing. Model-based testing (MBT) utilizes abstract behavioral models to automate test generation, thus decreasing time and cost of test creation. MBT is a functional testing technique, thereby focusing on output, behavior, and functionality. Performance testing, however, is non-functional and is concerned with responsiveness and stability under various load conditions. MBPeT (Model-Based Performance evaluation Tool) is one such tool which utilizes probabilistic models, representing dynamic real-world user behavior patterns, to generate synthetic workload against a System Under Test and in turn carry out performance analysis based on key performance indicators (KPI). Developed at Åbo Akademi University, the MBPeT tool is currently comprised of a downloadable command-line based tool as well as a graphical user interface. The goal of this thesis project is two-fold: 1) to extend the existing MBPeT tool by deploying it as a web-based application, thereby removing the requirement of local installation, and 2) to design a user interface for this web application which will add new user interaction paradigms to the existing feature set of the tool. All phases of the MBPeT process will be realized via this single web deployment location including probabilistic model creation, test configurations, test session execution against a SUT with real-time monitoring of user configurable metric, and final test report generation and display. This web application (MBPeT Dashboard) is implemented with the Java programming language on top of the Vaadin framework for rich internet application development. The Vaadin framework handles the complicated web communications processes and front-end technologies, freeing developers to implement the business logic as well as the user interface in pure Java. A number of experiments are run in a case study environment to validate the functionality of the newly developed Dashboard application as well as the scalability of the solution implemented in handling multiple concurrent users. The results support a successful solution with regards to the functional and performance criteria defined, while improvements and optimizations are suggested to increase both of these factors.

Numerical encoding to tame SQL injection attacks.

Recent years have seen an astronomical rise in SQL Injection Attacks (SQLIAs) used to compromise the confidentiality, authentication and integrity of organisations’ databases. Intruders becoming smarter in obfuscating web requests to evade detection combined with increasing volumes of web traffic from the Internet of Things (IoT), cloud-hosted and on-premise business applications have made it evident that the existing approaches of mostly static signature lack the ability to cope with novel signatures. A SQLIA detection and prevention solution can be achieved through exploring an alternative bio-inspired supervised learning approach that uses input of labelled dataset of numerical attributes in classifying true positives and negatives. We present in this paper a Numerical Encoding to Tame SQLIA (NETSQLIA) that implements a proof of concept for scalable numerical encoding of features to a dataset attributes with labelled class obtained from deep web traffic analysis. In the numerical attributes encoding: the model leverages proxy in the interception and decryption of web traffic. The intercepted web requests are then assembled for front-end SQL parsing and pattern matching by applying traditional Non-Deterministic Finite Automaton (NFA). This paper is intended for a technique of numerical attributes extraction of any size primed as an input dataset to an Artificial Neural Network (ANN) and statistical Machine Learning (ML) algorithms implemented using Two-Class Averaged Perceptron (TCAP) and Two-Class Logistic Regression (TCLR) respectively. This methodology then forms the subject of the empirical evaluation of the suitability of this model in the accurate classification of both legitimate web requests and SQLIA payloads.

Low-power 6-bit 1-GS/s two-channel pipeline ADC with open-loop amplification using amplifiers with local-feedback

IEEE International Symposium on Circuits and Systems, pp. 2258 – 2261, Seattle, EUA

New low-power 1.5-bit time-interleaved MDAC based on MOS capacitor amplification

15th IEEE International Conference on Electronics, Circuits and Systems, Malta

Sistema de televisão interactiva para o mercado hoteleiro

A Nonius Software é uma empresa nacional de engenharia na área de telecomunicações, que se dedica ao desenvolvimento de soluções para a gestão de sistemas informáticos e de entretenimento, tendo como finalidade o mercado mundial hoteleiro e hospitalar. A solução de TV interactiva da Nonius oferece uma experiência única ao hóspede, ao disponibilizar várias opções de entretenimento e acesso a conteúdos de elevada qualidade e interesse. O hóspede tem acesso a canais de TV, aluguer de filmes, Internet, jogos, informações, promoções e compras na TV. O objectivo principal desta dissertação foi implementar alguns serviços de entretenimento numa televisão LG Pro: Centric. Este equipamento tem como principal vantagem o facto de conter a set-top-box inserida dentro da própria televisão. Em termos arquitectónicos, o sistema Nonius TV tem dois elementos fundamentais: o backend, responsável pelo processamento e tratamento da informação centralizada e o frontend instalado nos dispositivos com os quais o hóspede contacta directamente. Uma parte significativa do trabalho desenvolvido centrou-se na implementação de funcionalidades no backend. Foram, no entanto, também desenvolvidas algumas funcionalidades nos serviços de frontend. Para o cumprimento dos objectivos estabelecidos, foi utilizada a tecnologia FLASH, tendo como linguagem de programação a segunda versão do ActionScript. Relativamente ao desenvolvimento de backend são utilizados o PHP e o JavaScript.

Transimpedance amplifier for early detection of breast cancer

Breast cancer is the most common type of cancer worldwide. The effectiveness of its treatment depends on early stage detection, as well as on the accuracy of its diagnosis. Recently, diagnosis techniques have been submitted to relevant breakthroughs with the upcoming of Magnetic Resonance Imaging, Ultrasound Sonograms and Positron Emission Tomography (PET) scans, among others. The work presented here is focused on studying the application of a PET system to a Positron Emission Mammography (PEM) system. A PET/PEM system works under the principle that a scintillating crystal will detect a gamma-ray pulse, originated at the cancerous cells, converting it into a correspondent visible light pulse. The latter must then be converted into an electrical current pulse by means of a Photo- -Sensitive Device (PSD). After the PSD there must be a Transimpedance Amplifier (TIA) in order to convert the current pulse into a suitable output voltage, in a time period lower than 40 ns. In this Thesis, the PSD considered is a Silicon Photo-Multiplier (SiPM). The usage of this recently developed type of PSD is impracticable with the conventional TIA topologies, as it will be proven. Therefore, the usage of the Regulated Common-Gate (RCG) topology will be studied in the design of the amplifier. There will be also presented two RCG variations, comprising a noise response improvement and differential operation of the circuit. The mentioned topology will also be tested in a Radio-Frequency front-end, showing the versatility of the RCG. A study comprising a low-voltage self-biasing feedback TIA will also be shown. The proposed circuits will be simulated with standard CMOS technology (UMC 130 nm), using a 1.2 V power supply. A power consumption of 0.34 mW with a signal-to-noise ratio of 43 dB was achieved.

Design of a low-voltage CMOS RF receiver for energy harvesting sensor node

In this thesis a CMOS low-power and low-voltage RF receiver front-end is presented. The main objective is to design this RF receiver so that it can be powered by a piezoelectric energy harvesting power source, included in a Wireless Sensor Node application. For this type of applications the major requirements are: the low-power and low-voltage operation, the reduced area and cost and the simplicity of the architecture. The system key blocks are the LNA and the mixer, which are studied and optimized with greater detail, achieving a good linearity, a wideband operation and a reduced introduction of noise. A wideband balun LNA with noise and distortion cancelling is designed to work at a 0.6 V supply voltage, in conjunction with a double-balanced passive mixer and subsequent TIA block. The passive mixer operates in current mode, allowing a minimal introduction of voltage noise and a good linearity. The receiver analog front-end has a total voltage conversion gain of 31.5 dB, a 0.1 - 4.3 GHz bandwidth, an IIP3 value of -1.35 dBm, and a noise figure lower than 9 dB. The total power consumption is 1.9 mW and the die area is 305x134.5 m2, using a standard 130 nm CMOS technology.

A novel concept of unidirectional bridgeless combined boost-buck converter for EV battery chargers

This paper presents a novel concept of unidirectional bridgeless combined boost-buck converter for electric vehicles (EVs) battery chargers. The proposed converter is composed by two power stages: an ac-dc front-end converter used to interface the power grid and the dc-link, and a dc-dc back-end converter used to interface the dc-link and the batteries. The ac-dc converter is a bridgeless boost-type converter and the dc-dc converter is an interleaved buck-type converter. The proposed converter operates with sinusoidal grid current and unitary power factor for all operating power levels. Along the paper is described in detail the proposed converter for EV battery chargers: the circuit topology, the different stages describing the principle of operation, the power control theory, and the current control strategy, for both converters. Along the paper are presented several simulation results for a maximum power of 3.5 kW.

The role of deviant-letter position in cognate word processing

Dissertação de mestrado integrado em Psicologia

Diseño e implementación de un receptor GNSS multifrecuencia y multiconstelación

Este proyecto presenta el diseño, test y validación de una cabecera de recepción multiconstelación y multifrecuencia para Sistemas de Navegación Global por Satélite (GNSS). El receptor presentado ha sido diseñado para adquirir las bandas E5/L5 y E1/L1 de los sistemas Galileo y NAVSTAR-GPS. Para trasladar en frecuencia las dos bandas a la vez, se implementa un receptor con arquitectura superheterodina basado en un mezclador de rechazo a frecuencia imagen (IRM). Medidas de ambos sistemas han sido realizadas validando el correcto funcionamiento del receptor en la banda E1/L1. Para ello no sólo se han adquirido los satélites de la constelación GPS, sino que además se han adquirido con éxito los satélites GIOVE-A/B utilizados en la fase de validación en órbita del sistema europeo Galileo.

Monitorització d'alt nivell per a el computing de l'experiment ATLAS (LHC)

Aquest projecte descriu la fusió de les necessitats diaries de monitorització del experiment ATLAS des del punt de vista del cloud. La idea principal es desenvolupar un conjunt de col·lectors que recullin informació de la distribució i processat de les dades i dels test de wlcg (Service Availability Monitoring), emmagatzemant-la en BBDD específiques per tal de mostrar els resultats en una sola pàgina HLM (High Level Monitoring). Un cop aconseguit, l’aplicació ha de permetre investigar més enllà via interacció amb el front-end, el qual estarà alimentat per les estadístiques emmagatzemades a la BBDD.