Can power laws help us understand gene and proteome information?

Proteins are biochemical entities consisting of one or more blocks typically folded in a 3D pattern. Each block (a polypeptide) is a single linear sequence of amino acids that are biochemically bonded together. The amino acid sequence in a protein is defined by the sequence of a gene or several genes encoded in the DNA-based genetic code. This genetic code typically uses twenty amino acids, but in certain organisms the genetic code can also include two other amino acids. After linking the amino acids during protein synthesis, each amino acid becomes a residue in a protein, which is then chemically modified, ultimately changing and defining the protein function. In this study, the authors analyze the amino acid sequence using alignment-free methods, aiming to identify structural patterns in sets of proteins and in the proteome, without any other previous assumptions. The paper starts by analyzing amino acid sequence data by means of histograms using fixed length amino acid words (tuples). After creating the initial relative frequency histograms, they are transformed and processed in order to generate quantitative results for information extraction and graphical visualization. Selected samples from two reference datasets are used, and results reveal that the proposed method is able to generate relevant outputs in accordance with current scientific knowledge in domains like protein sequence/proteome analysis.

Desenvolvimento do sistema de protecção, monitorização e gestão de baterias de iões de lítio do tipo LiFePO4 para aplicação em veículos eléctricos

A mobilidade é considerada um dos factores chave na sustentabilidade e desenvolvimento de qualquer economia. Em Portugal essa realidade não é diferente. Em 2011 verifica-se que 41% do consumo global de combustíveis pertence ao sector rodoviário [1] o que evidencia a sua relevância na economia do país. No que concerne aos veículos de tracção eléctrica, começaram a surgir nos finais do séc. XIX, e no início do séc. XX nos Estados Unidos da América representavam 38% dos veículos [2]. Diversos factores económicos e tecnológicos conduziram a um crescente desinteresse por parte da indústria em investir na produção deste tipo de veículos. Contudo com a introdução de baterias de iões de lítio em veículos de tracção eléctrica, torna-os viáveis e competitivos. Neste trabalho é proposto o desenvolvimento de um sistema de gestão de baterias de iões de lítio do tipo LiFePO4 para aplicação em veículos eléctricos. O sistema deverá assegurar a protecção das baterias e indicar o estado de carga das mesmas. Este sistema permitirá uma optimização no uso deste género de baterias, proporcionará uma melhor utilização, aumentando a sua vida útil. O sistema irá ser aplicado e testado experimentalmente no veículo eléctrico ecológico (Veeco). No âmbito do projecto Veeco foi projectado e construído um banco de ensaios utilizado na análise do comportamento das baterias, e determinar quais os requisitos necessários para o sistema de gestão desenvolvido. Foi também projectado e realizado um sistema de aquisição e processamento de dados que permite obter informações acerca da bateria, dados que estarão disponíveis no interface Homem-máquina do Veeco.

Processing XML with Java – a performance benchmark

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as Java, it becomes necessary to use effective mechanisms, e.g. APIs, which allow reading and processing of large documents in appropriated manners. This paper presents a performance study of the main existing Java APIs that deal with XML documents, in order to identify the most suitable one for processing large XML files

Performance analysis of Java APIS for XML processing

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as Java, it becomes necessary to use effective mechanisms, e.g. APIs, which allow reading and processing of large documents in appropriated manners. This paper presents a performance study of the main existing Java APIs that deal with XML documents, in order to identify the most suitable one for processing large XML files.

Validação de um método de cromatografia líquida de alta resolução (HPLC) para doseamento da vitamina D em géneros alimentícios: aplicação do método em diferentes matrizes alimentares

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Unveiling the Biometric Potential of Finger-Based ECG Signals

The ECG signal has been shown to contain relevant information for human identification. Even though results validate the potential of these signals, data acquisition methods and apparatus explored so far compromise user acceptability, requiring the acquisition of ECG at the chest. In this paper, we propose a finger-based ECG biometric system, that uses signals collected at the fingers, through a minimally intrusive 1-lead ECG setup recurring to Ag/AgCl electrodes without gel as interface with the skin. The collected signal is significantly more noisy than the ECG acquired at the chest, motivating the application of feature extraction and signal processing techniques to the problem. Time domain ECG signal processing is performed, which comprises the usual steps of filtering, peak detection, heartbeat waveform segmentation, and amplitude normalization, plus an additional step of time normalization. Through a simple minimum distance criterion between the test patterns and the enrollment database, results have revealed this to be a promising technique for biometric applications.

Contribution of traffic and tobacco smoke in the distribution of polycyclic aromatic hydrocarbons on outdoor and indoor PM2.5

Traffic emissions and tobacco smoke are considered two main sources of polycyclic aromatic hydrocarbons (PAHs) in indoor and outdoor air. In this study, the impact of these sources on the level of fine particulate matter (PM2.5) and on the distribution of 15 PAHs regarded as priority pollutants by the US-EPA on PM2.5 were evaluated and compared. Outdoor and indoor PM2.5 samples were collected during winter 2008 in Oporto city in Portugal, for sampling periods of 12 and 24 hours, respectively. The outdoor PM2.5 were sampled at one site directly influenced by traffic emissions and the indoor PM2.5 samples were collected at one home directly influenced by tobacco smoke and another one without smoke. A methodology based on microwave-assisted extraction and liquid chromatography with fluorescence detection was applied for the efficient PAHs determination in indoor and outdoor PM2.5. PAHs in indoor PM2.5 concentrations were significantly influenced by the presence of traffic and tobacco smoking emissions. The mean of ΣPAHs in the outdoor traffic PM2.5 was not significantly different from the value attained in the indoor without smoking site. The tobacco smoke increased significantly PAHs concentrations on average about 1000 times more, when compared with the outdoor profile samples suggesting that tobacco smoking may be the most important source of indoor PAHs pollution.

Copper and lead removal by peanut hulls: equilibrium and kinetic studies

This research work aims to study the use of peanut hulls, an agricultural and food industry waste, for copper and lead removal through equilibrium and kinetic parameters evaluation. Equilibrium batch studies were performed in a batch adsorber. The influence of initial pH was evaluated (3–5) and it was selected between 4.0 and 4.5. The maximum sorption capacities obtained for the Langmuir model were 0.21 ± 0.03 and 0.18 ± 0.02 mmol/g, respectively for copper and lead. In bi-component systems, competitive sorption of copper and lead was verified, the total amount adsorbed being around 0.21 mmol of metal per gram of material in both mono and bi-component systems. In the kinetic studies equilibrium was reached after 200 min contact time using a 400 rpm stirring rate, achieving 78% and 58% removal, in mono-component system, for copper and lead respectively. Their removal follows a pseudo-second-order kinetics. These studies show that most of the metals removal occurred in the first 20 min of contact, which shows a good uptake rate in all systems.

Determination of ametryn in soils via microwave-assisted solvent extraction coupled to anodic stripping voltammetry with a gold ultramicroelectrode

An extraction-anodic adsorptive stripping voltammetric procedure using microwave-assisted solvent extraction and a gold ultramicroelectrode was developed for determining the pesticide ametryn in soil samples. The method is based on the use of acetonitrile as extraction solvent and on controlled adsorptive accumulation of the herbicide at the potential of 0.50 V (vs. Ag/AgCl) in the presence of Britton-Robinson buffer (pH 3.3). Soil sample extracts were analysed directly after drying and redissolution with the supporting electrolyte but without other pre-treatment. The limit of detection obtained for a 10 s collection time was 0.021 µg g-1. Recovery experiments for the global procedure, at the 0.500 µg g-1 level, gave satisfactory mean and standard deviation results which were comparable to those obtained by HPLC with UV detection.

Screening of grapes and wine for azoxystrobin, kresoxim-methyl and trifloxystrobin fungicides by HPLC with diode array detection

The Quinone outside Inhibitors (QoI) are one of the most important and recent fungicide groups used in viticulture and also allowed by Integrated Pest Management. Azoxystrobin, kresoxim-methyl and trifloxystrobin are the main active ingredients for treating downy and powdery mildews that can be present in grapes and wines. In this paper, a method is reported for the analysis of these three QoI-fungicides in grapes and wine. After liquid–liquid extraction and a clean-up on commercial silica cartridges, analysis was by isocratic HPLC with diode array detection (DAD) with a run time of 13 min. Confirmation was by solid-phase micro-extraction (SPME), followed by GC/MS determination. The main validation parameters for the three compounds in grapes and wine were a limit of detection up to 0.073mg kg-1, a precision not exceeding 10.0% and an average recovery of 93% ±38.

Development of biocompatible and “smart” porous structures using CO2-assisted processes

Dissertação apresentada para a obtenção do grau de Doutor em Engenharia Química, especialidade Engenharia da Reacção Química, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Analysis and recognition of similar environmental sounds

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

Business micro-location: factors, preferences and indicators to assess the influence factors

The paper presents a study on business micro-location behaviour as well as corresponding factors of influence, conducted in two metropolitan areas, Bucharest-Ilfov (Romania) and Greater Porto (Portugal). By business micro-location we refer to a specific site such as a building or facility, accommodating a business within a small, compact geographical area (e.g. metropolitan area). At this geographical scale, the macroeconomic layer factors were excluded, applicable when discern between regions or countries. The factors derived from location theory and previous empirical studies were surveyed, completing a cross-sectional analysis in order to find out the specific weights of the location factors and preferences, by region and by industry. Based on already established firms’ feedback on location, the specific weights were granted by each industry to the main location factors, types of areas, and types of accommodation facilities. The authors also suggested a model to integrate these results into a Geographical Information System (GIS).

Parallel hyperspectral unmixing method via split augmented lagrangian on GPU

One of the main problems of hyperspectral data analysis is the presence of mixed pixels due to the low spatial resolution of such images. Linear spectral unmixing aims at inferring pure spectral signatures and their fractions at each pixel of the scene. The huge data volumes acquired by hyperspectral sensors put stringent requirements on processing and unmixing methods. This letter proposes an efficient implementation of the method called simplex identification via split augmented Lagrangian (SISAL) which exploits the graphics processing unit (GPU) architecture at low level using Compute Unified Device Architecture. SISAL aims to identify the endmembers of a scene, i.e., is able to unmix hyperspectral data sets in which the pure pixel assumption is violated. The proposed implementation is performed in a pixel-by-pixel fashion using coalesced accesses to memory and exploiting shared memory to store temporary data. Furthermore, the kernels have been optimized to minimize the threads divergence, therefore achieving high GPU occupancy. The experimental results obtained for the simulated and real hyperspectral data sets reveal speedups up to 49 times, which demonstrates that the GPU implementation can significantly accelerate the method's execution over big data sets while maintaining the methods accuracy.

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.