Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

Using Modern Tools to Explain the Use of the Smith Chart

The concept of explaining the use of an old tool like the Smith chart, using modern tools like MATLAB [1] scripts in combination with e-learning facilities, is exemplified by two MATLAB scripts. These display, step by step, the graphical procedure that must be used to solve the double-stub impedance-matching problem. These two scripts correspond to two different possible ways to analyze this matching problem, and they are important for students to learn by themselves.

Planeamento e optimização em redes celulares móveis auto-geridas assentes em LTE

O objectivo deste trabalho consiste em avaliar os benefícios das Self Organizing Networks (SON), no que concerne ao planeamento e optimização de redes Long Term Evolution (LTE), não só através do seu estudo, como também através do desenvolvimento e teste de algoritmos, que permitem avaliar o funcionamento de algumas das suas principais funções. O estudo efectuado sobre as SON permitiu identificar um conjunto de funções, tais como a atribuição automática de Physical Cell Id (PCI), o Automatic Neighbour Relation (ANR) e a optimização automática de parâmetros de handover, que permitem facilitar ou mesmo substituir algumas das tarefas mais comuns em planeamento e optimização de redes móveis celulares, em particular, redes LTE. Recorrendo a um simulador LTE destinado à investigação académica, em código aberto e desenvolvido em Matlab®, foi desenvolvido um conjunto de algoritmos que permitiram a implementação das funções em questão. Para além das funções implementadas, foram também introduzidas alterações que conferem a este simulador a capacidade de representar e simular redes reais, permitindo uma análise mais coerente dos algoritmos desenvolvidos. Os resultados obtidos, para além de evidenciarem claramente o benefício dos algoritmos desenvolvidos, foram ainda comparados com os obtidos pela ferramenta profissional de planeamento e optimização Atoll®, tendo-se verificado a franca proximidade de desempenho em algumas das funções. Finalmente, foi desenvolvida uma interface gráfica que permite o desenho, configuração e simulação de cenários, bem como a análise de resultados.

Mapping atmospheric pollutants emissions in European countries

In this paper we present a methodology which enables the graphical representation, in a bi-dimensional Euclidean space, of atmospheric pollutants emissions in European countries. This approach relies on the use of Multidimensional Unfolding (MDU), an exploratory multivariate data analysis technique. This technique illustrates both the relationships between the emitted gases and the gases and their geographical origins. The main contribution of this work concerns the evaluation of MDU solutions. We use simulated data to define thresholds for the model fitting measures, allowing the MDU output quality evaluation. The quality assessment of the model adjustment is thus carried out as a step before interpretation of the gas types and geographical origins results. The MDU maps analysis generates useful insights, with an immediate substantive result and enables the formulation of hypotheses for further analysis and modeling.

An ultrasound based computer-aided diagnosis tool for steatosis detection

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. In this paper, a new computer-aided diagnosis (CAD) system for steatosis classification, in a local and global basis, is presented. Bayes factor is computed from objective ultrasound textural features extracted from the liver parenchyma. The goal is to develop a CAD screening tool, to help in the steatosis detection. Results showed an accuracy of 93.33%, with a sensitivity of 94.59% and specificity of 92.11%, using the Bayes classifier. The proposed CAD system is a suitable graphical display for steatosis classification.

Global and local detection of liver steatosis from ultrasound

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. Steatosis is usually a diffuse liver disease, since it is globally affected. However, steatosis can also be focal affecting only some foci difficult to discriminate. In both cases, steatosis is detected by laboratorial analysis and visual inspection of ultrasound images of the hepatic parenchyma. Liver biopsy is the most accurate diagnostic method but its invasive nature suggest the use of other non-invasive methods, while visual inspection of the ultrasound images is subjective and prone to error. In this paper a new Computer Aided Diagnosis (CAD) system for steatosis classification and analysis is presented, where the Bayes Factor, obatined from objective intensity and textural features extracted from US images of the liver, is computed in a local or global basis. The main goal is to provide the physician with an application to make it faster and accurate the diagnosis and quantification of steatosis, namely in a screening approach. The results showed an overall accuracy of 93.54% with a sensibility of 95.83% and 85.71% for normal and steatosis class, respectively. The proposed CAD system seemed suitable as a graphical display for steatosis classification and comparison with some of the most recent works in the literature is also presented.

Embedded platform for ECG biometric recognition

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações

Reputação e recomendação como serviços para transportes públicos

Projecto Final de Mestrado para obtenção do grau de Mestre em Engenharia Informática e de Computadores

Análise prospetiva de modelos de transporte e usos do solo

Dissertação para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

Automatic synthesis of VHDL Hardware Components from IOPT Petri Net models

Conferência: 39th Annual Conference of the IEEE Industrial-Electronics-Society (IECON), Vienna, Austria, Nov 10-14, 2013

Automatic diagnosis of liver steatosis by ultrasound using autoregressive tissue characterization

Liver steatosis is mainly a textural abnormality of the hepatic parenchyma due to fat accumulation on the hepatic vesicles. Today, the assessment is subjectively performed by visual inspection. Here a classifier based on features extracted from ultrasound (US) images is described for the automatic diagnostic of this phatology. The proposed algorithm estimates the original ultrasound radio-frequency (RF) envelope signal from which the noiseless anatomic information and the textural information encoded in the speckle noise is extracted. The features characterizing the textural information are the coefficients of the first order autoregressive model that describes the speckle field. A binary Bayesian classifier was implemented and the Bayes factor was calculated. The classification has revealed an overall accuracy of 100%. The Bayes factor could be helpful in the graphical display of the quantitative results for diagnosis purposes.

Observação e controlo da segurança estrutural de barragens de betão: utilização integrada de modelos numéricos e de modelos de separação de efeitos

Dissertação de Natureza Científica elabora da no âmbito do protocolo de cooperação entre o ISEL e o LNEC para obtenção do grau de Mestre em Engenharia Civil

Um site, um conteúdo e incontáveis dispositivos: as estratégias de design utilizadas para ambientes multiplataformas

Dissertação apresentada à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Audiovisual e Multimédia.

Sistema de visão para aterragem automática de UAV

Dissertação para obtenção do grau de Mestre em Engenharia Electrotécnica Ramo de Automação e Electrónica Industrial

Multifunctional controller architecture for sold-state marx modulator based on FPGA

This paper proposes a multifunctional architecture to implement field-programmable gate array (FPGA) controllers for power converters and presents a prototype for a pulsed power generator based on a solid-state Marx topology. The massively parallel nature of reconfigurable hardware platforms provides very high processing power and fast response times allowing the implementation of many subsystems in the same device. The prototype includes the controller, a failure detection system, an interface with a safety/emergency subsystem, a graphical user interface, and a virtual oscilloscope to visualize the generated pulse waveforms, using a single FPGA. The proposed architecture employs a modular design that can be easily adapted to other power converter topologies.