Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Multi-dimensional scaling applied to histogram-based DNA analysis

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

Determination of chitin content in fungal cell wall: an alternative flow cytometric method

The conventional methods used to evaluate chitin content in fungi, such as biochemical assessment of glucosamine release after acid hydrolysis or epifluorescence microscopy, are low throughput, laborious, time-consuming, and cannot evaluate a large number of cells. We developed a flow cytometric assay, efficient, and fast, based on Calcofluor White staining to measure chitin content in yeast cells. A staining index was defined, its value was directly related to chitin amount and taking into consideration the different levels of autofluorecence. Twenty-two Candida spp. and four Cryptococcus neoformans clinical isolates with distinct susceptibility profiles to caspofungin were evaluated. Candida albicans clinical isolate SC5314, and isogenic strains with deletions in chitin synthase 3 (chs3Δ/chs3Δ) and genes encoding predicted Glycosyl Phosphatidyl Inositol (GPI)-anchored proteins (pga31Δ/Δ and pga62Δ/Δ), were used as controls. As expected, the wild-type strain displayed a significant higher chitin content (P < 0.001) than chs3Δ/chs3Δ and pga31Δ/Δ especially in the presence of caspofungin. Ca. parapsilosis, Ca. tropicalis, and Ca. albicans showed higher cell wall chitin content. Although no relationship between chitin content and antifungal drug susceptibility phenotype was found, an association was established between the paradoxical growth effect in the presence of high caspofungin concentrations and the chitin content. This novel flow cytometry protocol revealed to be a simple and reliable assay to estimate cell wall chitin content of fungi.

A web-based intelligent tutoring system on teaching and learning electrical project

The Information and Communication Technology (ICT) provide new strategies for disseminating information and new communication models in order to change attitudes and human behaviour concerning to education. Nowadays the internet is crucial as a means of communication and information sharing. To education or tutorship will be required to use ICT, supported on the internet, to establish the communication of teacher-student and student-student, disseminating the content of the subjects, and as a way of teaching and learning process. This paper presents an intelligent tutor that aims to be a tool to support teaching and learning in the field of the electrical engineering project.

Content adaptation for an adaptive hypermedia system

The aim of this paper is presenting the recommendation module of the Mathematics Collaborative Learning Platform (PCMAT). PCMAT is an Adaptive Educational Hypermedia System (AEHS), with a constructivist approach, which presents contents and activities adapted to the characteristics and learning style of students of mathematics in basic schools. The recommendation module is responsible for choosing different learning resources for the platform, based on the user's characteristics and performance. Since the main purpose of an adaptive system is to provide the user with content and interface adaptation, the recommendation module is integral to PCMAT’s adaptation model.

Personality, emotion, and mood in agent-based group decision making

Group decision making plays an important role in organizations, especially in the present-day economy that demands high-quality, yet quick decisions. Group decision-support systems (GDSSs) are interactive computer-based environments that support concerted, coordinated team efforts toward the completion of joint tasks. The need for collaborative work in organizations has led to the development of a set of general collaborative computer-supported technologies and specific GDSSs that support distributed groups (in time and space) in various domains. However, each person is unique and has different reactions to various arguments. Many times a disagreement arises because of the way we began arguing, not because of the content itself. Nevertheless, emotion, mood, and personality factors have not yet been addressed in GDSSs, despite how strongly they influence results. Our group’s previous work considered the roles that emotion and mood play in decision making. In this article, we reformulate these factors and include personality as well. Thus, this work incorporates personality, emotion, and mood in the negotiation process of an argumentbased group decision-making process. Our main goal in this work is to improve the negotiation process through argumentation using the affective characteristics of the involved participants. Each participant agent represents a group decision member. This representation lets us simulate people with different personalities. The discussion process between group members (agents) is made through the exchange of persuasive arguments. Although our multiagent architecture model4 includes two types of agents—the facilitator and the participant— this article focuses on the emotional, personality, and argumentation components of the participant agent.

A model updating technique based on FRFs for damped structures

Model updating methods often neglect that in fact all physical structures are damped. Such simplification relies on the structural modelling approach, although it compromises the accuracy of the predictions of the structural dynamic behaviour. In the present work, the authors address the problem of finite element (FE) model updating based on measured frequency response functions (FRFs), considering damping. The proposed procedure is based upon the complex experimental data, which contains information related to the damped FE model parameters and presents the advantage of requiring no prior knowledge about the damping matrix structure or its content, only demanding the definition of the damping type. Numerical simulations are performed in order to establish the applicability of the proposed damped FE model updating technique and its results are discussed in terms of the correlation between the simulated experimental complex FRFs and the ones obtained from the updated FE model.

Salt content in bread and dough from northern Portugal: method development and comparison

In the initial stage of this work, two potentiometric methods were used to determine the salt (sodium chloride) content in bread and dough samples from several cities in the north of Portugal. A reference method (potentiometric precipitation titration) and a newly developed ion-selective chloride electrode (ISE) were applied. Both methods determine the sodium chloride content through the quantification of chloride. To evaluate the accuracy of the ISE, bread and respective dough samples were analyzed by both methods. Statistical analysis (0.05 significance level) indicated that the results of these methods did not differ significantly. Therefore the ISE is an adequate alternative for the determination of chloride in the analyzed samples. To compare the results of these chloride-based methods with a sodium-based method, sodium was quantified in the same samples by a reference method (atomic absorption spectrometry). Significant differences between the results were verified. In several cases the sodium chloride content exceeded the legal limit when the chloride-based methods were used, but when the sodium-based method was applied this was not the case. This could lead to the erroneous application of fines and therefore the authorities should supply additional information regarding the analytical procedure for this particular control.

Sistema de recomendação e personalização de televisão

Com a expansão da Televisão Digital e a convergência entre os meios de difusão convencionais e a televisão sobre IP, o número de canais disponíveis tem aumentado de forma gradual colocando o espectador numa situação de difícil escolha quanto ao programa a visionar. Sobrecarregados com uma grande quantidade de programas e informação associada, muitos espectadores desistem sistematicamente de ver um programa e tendem a efectuar zapping entre diversos canais ou a assistir sempre aos mesmos programas ou canais. Diante deste problema de sobrecarga de informação, os sistemas de recomendação apresentam-se como uma solução. Nesta tese pretende estudar-se algumas das soluções existentes dos sistemas de recomendação de televisão e desenvolver uma aplicação que permita a recomendação de um conjunto de programas que representem potencial interesse ao espectador. São abordados os principais conceitos da área dos algoritmos de recomendação e apresentados alguns dos sistemas de recomendação de programas de televisão desenvolvidos até à data. Para realizar as recomendações foram desenvolvidos dois algoritmos baseados respectivamente em técnicas de filtragem colaborativa e de filtragem de conteúdo. Estes algoritmos permitem através do cálculo da similaridade entre itens ou utilizadores realizar a predição da classificação que um utilizador atribuiria a um determinado item (programa de televisão, filme, etc.). Desta forma é possível avaliar o nível de potencial interesse que o utilizador terá em relação ao respectivo item. Os conjuntos de dados que descrevem as características dos programas (título, género, actores, etc.) são armazenados de acordo com a norma TV-Anytime. Esta norma de descrição de conteúdo multimédia apresenta a vantagem de ser especificamente vocacionada para conteúdo audiovisual e está disponível livremente. O conjunto de recomendações obtidas é apresentado ao utilizador através da interacção com uma aplicação Web que permite a integração de todos os componentes do sistema. Para validação do trabalho foi considerado um dataset de teste designado de htrec2011-movielens-2k e cujo conteúdo corresponde a um conjunto de filmes classificados por diversos utilizadores num ambiente real. Este conjunto de filmes possui, para além da classificações atribuídas pelos utilizadores, um conjunto de dados que descrevem o género, directores, realizadores e país de origem. Para validação final do trabalho foram realizados diversos testes dos quais o mais relevante correspondeu à avaliação da distância entre predições e valores reais e cujo objectivo é classificar a capacidade dos algoritmos desenvolvidos preverem com precisão as classificações que os utilizadores atribuiriam aos itens analisados.

Oxidative Leaching of metals from electronic waste with solutions based on quaternary ammonium salts

The treatment of electric and electronic waste (WEEE) is a problem which receives ever more attention. An inadequate treatment results in harmful products ending up in the environment. This project intends to investigate the possibilities of an alternative route for recycling of metals from printed circuit boards (PCBs) obtained from rejected computers. The process is based on aqueous solutions composed of an etchant, either 0.2 M CuCl2.2H2O or 0.2 M FeCl3.6H2O, and a quaternary ammonium salt (quat) such as choline chloride or chlormequat. These solutions are reminiscent of deep eutectic solvents (DES) based on quats. DES are quite similar to ionic liquids (ILs) and are used as well as alternative solvents with a great diversity of physical properties, making them attractive for replacement of hazardous, volatile solvents (e.g. VOCs). A remarkable difference between genuine DES and ILs with the solutions used in this project is the addition of rather large quantities of water. It is shown the presence of water has a lot of advantages on the leaching of metals, while the properties typical for DES still remain. The oxidizing capacities of Cu(II) stem from the existence of a stable Cu(I) component in quat based DES and thus the leaching stems from the activity of the Cu(II)/Cu(I) redox couple. The advantage of Fe(III) in combination with DES is the fact that the Fe(III)/Fe(II) redox couple becomes reversible, which is not true in pure water. This opens perspectives for regeneration of the etching solution. In this project the leaching of copper was studied as a function of gradual increasing water content from 0 - 100w% with the same concentration of copper chloride or iron(III) chloride at room temperature and 80ºC. The solutions were also tested on real PCBs. At room temperature a maximum leaching effect for copper was obtained with 30w% choline chloride with 0.2 M CuCl2.2H2O. The leaching effect is still stronger at 80°C, b ut of course these solutions are more energy consuming. For aluminium, tin, zinc and lead, the leaching was faster at 80ºC. Iron and nickel dissolved easily at room temperature. The solutions were not able to dissolve gold, silver, rhodium and platinum.

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.

A SON Enhanced Algorithm for Observed Time Differences Based Geolocation in Real 3G Networks

Conferência - 16th International Symposium on Wireless Personal Multimedia Communications (WPMC)- Jun 24-27, 2013

Interlimb relation during the double support phase of gait: an electromyographic, mechanical and energy based analysis

The purpose of this study is to analyse the interlimb relation and the influence of mechanical energy on metabolic energy expenditure during gait. In total, 22 subjects were monitored as to electromyographic activity, ground reaction forces and VO2 consumption (metabolic power) during gait. The results demonstrate a moderate negative correlation between the activity of tibialis anterior, biceps femoris and vastus medialis of the trailing limb during the transition between midstance and double support and that of the leading limb during double support for the same muscles, and between these and gastrocnemius medialis and soleus of the trailing limb during double support. Trailing limb soleus during the transition between mid-stance and double support was positively correlated to leading limb tibialis anterior, vastus medialis and biceps femoris during double support. Also, the trailing limb centre of mass mechanical work was strongly influenced by the leading limbs, although only the mechanical power related to forward progression of both limbs was correlated to metabolic power. These findings demonstrate a consistent interlimb relation in terms of electromyographic activity and centre of mass mechanical work, being the relations occurred in the plane of forward progression the more important to gait energy expenditure.

Admittance spectroscopy of Cu2ZnSnS4 based thin film solar cells

In this report, we propose an AC response equivalent circuit model to describe the admittance measurements of Cu2ZnSnS4 thin film solar cell grown by sulphurization of stacked metallic precursors. This circuit describes the contact resistances, the back contact, and the heterojunction with two trap levels. The study of the back contact resistance allowed the estimation of a back contact barrier of 246 meV. The analysis of the trap series with varying temperature revealed defect activation energies of 45 meV and 113 meV. The solar cell’s electrical parameters were obtained from the J-V curve: conversion efficiency, 1.21%; fill factor, 50%; open circuit voltage, 360 mV; and short circuit current density, 6.8 mA/cm2.

Strategic bidding in electricity markets: an agent-based simulator with game theory for scenario analysis

Electricity markets are complex environments, involving a large number of different entities, with specific characteristics and objectives, making their decisions and interacting in a dynamic scene. Game-theory has been widely used to support decisions in competitive environments; therefore its application in electricity markets can prove to be a high potential tool. This paper proposes a new scenario analysis algorithm, which includes the application of game-theory, to evaluate and preview different scenarios and provide players with the ability to strategically react in order to exhibit the behavior that better fits their objectives. This model includes forecasts of competitor players’ actions, to build models of their behavior, in order to define the most probable expected scenarios. Once the scenarios are defined, game theory is applied to support the choice of the action to be performed. Our use of game theory is intended for supporting one specific agent and not for achieving the equilibrium in the market. MASCEM (Multi-Agent System for Competitive Electricity Markets) is a multi-agent electricity market simulator that models market players and simulates their operation in the market. The scenario analysis algorithm has been tested within MASCEM and our experimental findings with a case study based on real data from the Iberian Electricity Market are presented and discussed.