Single operation multiple data - paralelismo de dados ao nível da sub-rotina

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples

Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10% non-buffered or 10% buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10% non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.

Testing Nelder-Mead Based Repulsion Algorithms for Multiple Roots of Nonlinear Systems via a Two-Level Factorial Design of Experiments

This paper addresses the challenging task of computing multiple roots of a system of nonlinear equations. A repulsion algorithm that invokes the Nelder-Mead (N-M) local search method and uses a penalty-type merit function based on the error function, known as 'erf', is presented. In the N-M algorithm context, different strategies are proposed to enhance the quality of the solutions and improve the overall efficiency. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm.

Analysis of Natural and Artificial Phenomena Using Signal Processing and Fractional Calculus

In this paper we study several natural and man-made complex phenomena in the perspective of dynamical systems. For each class of phenomena, the system outputs are time-series records obtained in identical conditions. The time-series are viewed as manifestations of the system behavior and are processed for analyzing the system dynamics. First, we use the Fourier transform to process the data and we approximate the amplitude spectra by means of power law functions. We interpret the power law parameters as a phenomenological signature of the system dynamics. Second, we adopt the techniques of non-hierarchical clustering and multidimensional scaling to visualize hidden relationships between the complex phenomena. Third, we propose a vector field based analogy to interpret the patterns unveiled by the PL parameters.

Waste collection routing-limited multiple landfills and heterogeneous fleet

This article deals with a real-life waste collection routing problem. To efficiently plan waste collection, large municipalities may be partitioned into convenient sectors and only then can routing problems be solved in each sector. Three diverse situations are described, resulting in three different new models. In the first situation, there is a single point of waste disposal from where the vehicles depart and to where they return. The vehicle fleet comprises three types of collection vehicles. In the second, the garage does not match any of the points of disposal. The vehicle is unique and the points of disposal (landfills or transfer stations) may have limitations in terms of the number of visits per day. In the third situation, disposal points are multiple (they do not coincide with the garage), they are limited in the number of visits, and the fleet is composed of two types of vehicles. Computational results based not only on instances adapted from the literature but also on real cases are presented and analyzed. In particular, the results also show the effectiveness of combining sectorization and routing to solve waste collection problems.

High diagnostic efficiency of IgM-ELISA with the use of multiple antigen peptides (MAP1) from T. gondii ESA (SAG-1, GRA-1 and GRA-7), in acute toxoplasmosis

The main serological marker for the diagnosis of recent toxoplasmosis is the specific IgM antibody, along with IgG antibodies of low avidity. However, in some patients these antibodies may persist long after the acute/recent phase, contributing to misdiagnosis in suspected cases of toxoplasmosis. In the present study, the diagnostic efficiency of ELISA was evaluated, with the use of peptides derived from T. gondii ESA antigens, named SAG-1, GRA-1 and GRA-7. In the assay referred to, we studied each of these peptides individually, as well as in four different combinations, as Multiple Antigen Peptides (MAP), aiming to establish a reliable profile for the acute/recent toxoplasmosis with only one patient serum sample. The diagnostic performance of the assay using MAP1, with the combination of SAG-1, GRA-1 and GRA-7 peptides, demonstrated better discrimination of the acute/recent phase from non acute/recent phase of toxoplasmosis. Our results show that IgM antibodies to MAP1 may be useful as a serological marker, enhancing the diagnostic efficiency of the assay for acute/recent phase of toxoplasmosis.

Analyzing Multiple Outcomes: Is it Really Worth the use of Multivariate Linear Regression?

In health related research it is common to have multiple outcomes of interest in a single study. These outcomes are often analysed separately, ignoring the correlation between them. One would expect that a multivariate approach would be a more efficient alternative to individual analyses of each outcome. Surprisingly, this is not always the case. In this article we discuss different settings of linear models and compare the multivariate and univariate approaches. We show that for linear regression models, the estimates of the regression parameters associated with covariates that are shared across the outcomes are the same for the multivariate and univariate models while for outcome-specific covariates the multivariate model performs better in terms of efficiency.

Analysis of the Out-Of-Plane Seismic Behavior of Unreinforced Masonry: A Literature Review

Although the issue of the out-of-plane response of unreinforced masonry structures under earthquake excitation is well known with consensus among the research community, this issue is simultaneously one of the more complex and most neglected areas on the seismic assessment of existing buildings. Nonetheless, its characterization should be found on the solid knowledge of the phenomenon and on the complete understanding of methodologies currently used to describe it. Based on this assumption, this article presents a general framework on the issue of the out-of-plane performance of unreinforced masonry structures, beginning with a brief introduction to the topic, followed by a compact state of art in which the principal methodologies proposed to assess the out-of-plane behavior of unreinforced masonry structures are presented. Different analytical approaches are presented, namely force and displacement-based, complemented with the presentation of existing numerical tools for the purpose presented above. Moreover, the most relevant experimental campaigns carried out in order to reproduce the phenomenon are reviewed and briefly discussed.

Development and implementation of strategies for the incorporation of reinforcing elements in aluminium alloys by solid state processing

Dissertação para obtenção do Grau de Mestre em Engenharia Mecânica

A Multiple Criteria Utility-based Approa h for the Unit Commitment with Wind Power and Pumped Storage Hydro

The integration of wind power in eletricity generation brings new challenges to unit commitment due to the random nature of wind speed. For this particular optimisation problem, wind uncertainty has been handled in practice by means of conservative stochastic scenario-based optimisation models, or through additional operating reserve settings. However, generation companies may have different attitudes towards operating costs, load curtailment, or waste of wind energy, when considering the risk caused by wind power variability. Therefore, alternative and possibly more adequate approaches should be explored. This work is divided in two main parts. Firstly we survey the main formulations presented in the literature for the integration of wind power in the unit commitment problem (UCP) and present an alternative model for the wind-thermal unit commitment. We make use of the utility theory concepts to develop a multi-criteria stochastic model. The objectives considered are the minimisation of costs, load curtailment and waste of wind energy. Those are represented by individual utility functions and aggregated in a single additive utility function. This last function is adequately linearised leading to a mixed-integer linear program (MILP) model that can be tackled by general-purpose solvers in order to find the most preferred solution. In the second part we discuss the integration of pumped-storage hydro (PSH) units in the UCP with large wind penetration. Those units can provide extra flexibility by using wind energy to pump and store water in the form of potential energy that can be generated after during peak load periods. PSH units are added to the first model, yielding a MILP model with wind-hydro-thermal coordination. Results showed that the proposed methodology is able to reflect the risk profiles of decision makers for both models. By including PSH units, the results are significantly improved.

Oral Contraceptive Use and Clinical Outcomes in Patients with Multiple Sclerosis

Experimental and clinical data suggest a role of sex steroids in the pathogenesis of multiple sclerosis (MS). Scant information is available about the potential effect of oral contraceptive (OC) use on the prognosis of the disease. We aimed to evaluate this. The study population consisted of 132 women with relapsing-remitting MS before receiving disease modifying treatment and a mean disease duration 6.2 (SD 5.1) years. Three groups of patients were distinguished according to their OC behavior: [1] never-users, patients who never used OC [2] past-users, patients who stopped OC use before disease onset, and [3] after-users, those who used these drugs after disease onset. Multiple linear and logistic regression models were used to analyze the association between oral contraceptive use and annualized relapse rates, disability accumulation and severity of the disease. After-user patients had lower Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Severity Score (MSSS) values than never users (p<0.001 and p=0.002, respectively) and past users (p=0.010 and p=0.002, respectively). These patients were also more likely to have a benign disease course (MSSS<2.5) than never and past users together (OR: 4.52, 95%CI: 2.13-9.56, p<0.001). This effect remained significant after adjustment for confounders, including smoking and childbirths (OR: 2.97, 95%CI: 1.24, 6.54, p=0.011 and for MSSS β: -1.04; 95% C.I. -1.78, -0.30, p=0.006). These results suggest that OC use in women with relapsing-remitting MS is possible associated with a milder disabling disease course.

Long-term biosignals visualization and processing

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

Desenvolvimento e Controlo de um Veículo Autónomo Aéreo Quadrotor

A crescente necessidade de meios de inspecção e recolha de informação de infraestruturas e do meio ambiente natural, origina o recurso a meios tecnológicos cada vez mais evoluídos. Neste contexto, os robôs móveis autónomos aéreos surgem como uma ferramenta importante. Em particular, os veículos aéreos de asa móvel, pela sua manobrabilidade e controlo podem-se utilizar eficazmente em meios complexos como cenários interiores onde o ambiente é parcialmente controlado. A sua utilização em coordenação com outros veículos robóticos móveis e em particular com a crescente autonomia de decisão, permitem uma eficiência elevada, por exemplo, em tarefas de recolha automática de informação, vigilância, apoio a comunicações, etc. A inexistência de um veículo autónomo de asa móvel no cenário multi-robótico desenvolvido pelo Laboratório de Sistemas Autónomos do Instituto Superior de Engenharia do Porto, aliada às suas aplicações referidas, criou a necessidade do desenvolvimento de um veículo desta gama. Identificou-se, pois, o desenvolvimento de um veículo autónomo aéreo do tipo quadrotor com capacidade de vôo base estabilizado como o problema a resolver. Foi efectuado um levantamento de requisitos do sistema, a caracterização de um veículo autónomo aéreo Vertical Take-off and Landing - VTOL, e efectuado um trabalho de pesquisa a fim de possibilitar o conhecimento das técnicas e tecnologias envolvidas. Tendo em vista o objectivo de controlo e estabilização do veículo, foi efectuada a modelização do sistema que serviu não só para a melhor compreensão da sua dinâmica mas também para o desenvolvimento de um simulador que possibilitou a validação de estratégias de controlo e avaliação de comportamentos do veículo para diferentes cenários. A inexistência de controladores de motores brushless adequada (frequência de controlo), originou o desenvolvimento de um controlador dedicado para motores brushless, motores esses utilizados para a propulsão do veículo. Este controlador permite uma taxa de controlo a uma frequência de 20KHz, possui múltiplas interfaces de comunicação (CAN, RS232, Ethernet, SPI e JTAG), é de reduzido peso e dimensões e modular, visto ter sido implementado em dois módulos, i.e., permite a sua utilização com diferentes interfaces de potência. Projectou-se um veículo autónomo aéreo em termos físicos com a definição da sua arquitectura de hardware e software bem como o sistema de controlo de vôo. O sistema de estabilização de vôo compreende o processamento de informação fornecida por um sistema de navegação inercial, um sonar e o envio de referências de velocidade para cada um dos nós de controlo ligados a um barramento CAN instalado no veículo. A implementação do veículo foi alcançada nas suas vertentes mecânica, de hardware e software. O UAV foi equipado com um sistema computacional dotando-o de capacidades para o desempenho de tarefas previamente analisadas. No presente trabalho, são também tiradas algumas conclusões sobre o desenvolvimento do sistema e sua implementação bem como perspectivada a sua evolução futura no contexto de missões coordenadas de múltiplos veículos robóticos.

Histoplasmosis presenting with multiple pulmonary nodules. A case mimicking radiological features of pulmonary metastasis

We present a case of histoplasmosis with multiple pulmonary nodules in a patient with a history of melanoma. This case closely simulated malignancy, including the presence of feeding vessel sign, which occurs in pulmonary metastasis. We emphasize the need to be aware of this infection in areas where histoplasmosis is endemic.