Modern techniques for constraint solving the CASPER experience

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Informática, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Using data mining techniques to support breast cancer diagnosis

More than ever, there is an increase of the number of decision support methods and computer aided diagnostic systems applied to various areas of medicine. In breast cancer research, many works have been done in order to reduce false-positives when used as a double reading method. In this study, we aimed to present a set of data mining techniques that were applied to approach a decision support system in the area of breast cancer diagnosis. This method is geared to assist clinical practice in identifying mammographic findings such as microcalcifications, masses and even normal tissues, in order to avoid misdiagnosis. In this work a reliable database was used, with 410 images from about 115 patients, containing previous reviews performed by radiologists as microcalcifications, masses and also normal tissue findings. Throughout this work, two feature extraction techniques were used: the gray level co-occurrence matrix and the gray level run length matrix. For classification purposes, we considered various scenarios according to different distinct patterns of injuries and several classifiers in order to distinguish the best performance in each case described. The many classifiers used were Naïve Bayes, Support Vector Machines, k-nearest Neighbors and Decision Trees (J48 and Random Forests). The results in distinguishing mammographic findings revealed great percentages of PPV and very good accuracy values. Furthermore, it also presented other related results of classification of breast density and BI-RADS® scale. The best predictive method found for all tested groups was the Random Forest classifier, and the best performance has been achieved through the distinction of microcalcifications. The conclusions based on the several tested scenarios represent a new perspective in breast cancer diagnosis using data mining techniques.

Detection of mycoplasmas in urethral swabs from HIV-1 infected patients and control individuals using culture techniques and polymerase chain reaction

The objective of the present study was to determine the prevalence of certain mycoplasma species, i.e., Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma penetrans, in urethral swabs from HIV-1 infected patients compared to swabs from a control group. Mycoplasmas were detected by routine culture techniques and by the Polymerase Chain Reaction (PCR) technique, using 16SrRNA generic primers of conserved region and Mycoplasma penetrans specific primers. The positivity rates obtained with the two methods were comparable. Nevertheless, PCR was more sensitive, while the culture techniques allowed the quantification of the isolates. The results showed no significant difference (p < 0.05) in positivity rates between the methods used for mycoplasma detection.

PALEOPARASITOLOGY: PERSPECTIVES WITH NEW TECHNIQUES

Paleoparasitology is the study of parasites found in archaeological material. The development of this field of research began with histological identification of helminth eggs in mummy tissues, analysis of coprolites, and recently through molecular biology. An approach to the history of paleoparasitology is reviewed in this paper, with special reference to the studies of ancient DNA identified in archaeological material.

Tolerância a falhas em sistemas de tempo-real distribuídos e embebidos

Este documento descreve um modelo de tolerância a falhas para sistemas de tempo-real distribuídos. A sugestão deste modelo tem como propósito a apresentação de uma solu-ção fiável, flexível e adaptável às necessidades dos sistemas de tempo-real distribuídos. A tolerância a falhas é um aspeto extremamente importante na construção de sistemas de tempo-real e a sua aplicação traz inúmeros benefícios. Um design orientado para a to-lerância a falhas contribui para um melhor desempenho do sistema através do melhora-mento de aspetos chave como a segurança, a confiabilidade e a disponibilidade dos sis-temas. O trabalho desenvolvido centra-se na prevenção, deteção e tolerância a falhas de tipo ló-gicas (software) e físicas (hardware) e assenta numa arquitetura maioritariamente basea-da no tempo, conjugada com técnicas de redundância. O modelo preocupa-se com a efi-ciência e os custos de execução. Para isso utilizam-se também técnicas tradicionais de to-lerância a falhas, como a redundância e a migração, no sentido de não prejudicar o tempo de execução do serviço, ou seja, diminuindo o tempo de recuperação das réplicas, em ca-so de ocorrência de falhas. Neste trabalho são propostas heurísticas de baixa complexida-de para tempo-de-execução, a fim de se determinar para onde replicar os componentes que constituem o software de tempo-real e de negociá-los num mecanismo de coordena-ção por licitações. Este trabalho adapta e estende alguns algoritmos que fornecem solu-ções ainda que interrompidos. Estes algoritmos são referidos em trabalhos de investiga-ção relacionados, e são utilizados para formação de coligações entre nós coadjuvantes. O modelo proposto colmata as falhas através de técnicas de replicação ativa, tanto virtual como física, com blocos de execução concorrentes. Tenta-se melhorar ou manter a sua qualidade produzida, praticamente sem introduzir overhead de informação significativo no sistema. O modelo certifica-se que as máquinas escolhidas, para as quais os agentes migrarão, melhoram iterativamente os níveis de qualidade de serviço fornecida aos com-ponentes, em função das disponibilidades das respetivas máquinas. Caso a nova configu-ração de qualidade seja rentável para a qualidade geral do serviço, é feito um esforço no sentido de receber novos componentes em detrimento da qualidade dos já hospedados localmente. Os nós que cooperam na coligação maximizam o número de execuções para-lelas entre componentes paralelos que compõem o serviço, com o intuito de reduzir atra-sos de execução. O desenvolvimento desta tese conduziu ao modelo proposto e aos resultados apresenta-dos e foi genuinamente suportado por levantamentos bibliográficos de trabalhos de in-vestigação e desenvolvimento, literaturas e preliminares matemáticos. O trabalho tem também como base uma lista de referências bibliográficas.

Archaeological roman glasses: comparative characterisation by non-destructive analytical techniques

Dissertation presented in fulfilment of the requirements for the Master’s degree in Conservation and Restoration

Measurement of lead concentration in biological tissues by atomic spectroscopy techniques

Dissertation for the degree of Doctor of Philosophy in Physics

Immunoprecipitation techniques and Elisa in the detection of anti-Fonsecaea pedrosoi antibodies in chromoblastomycosis

Chromoblastomycosis (CBM) is a chronic subcutaneous infection caused by several dematiaceous fungi. The most commonly etiological agent found in Brazil is Fonsecaea pedrosoi, which appears as thick walled, brownish colored cells with transverse and longitudinal division in the lesions, called "muriform cells". This disease is found worldwide but countries like Madagascar and Brazil have highest incidence. Diagnosis is made by clinical, direct and histopathologic examination and culture of specimens. Serological tests have been used to identify specific antibodies against Fonsecaea pedrosoi antigens, as well as immunotechniques have been used for CBM serological identification and diagnosis. In the present study double immunodiffusion (DID), counterimmunoelectrophoresis (CIE) and immunoenzymatic test (ELISA) have been used to evaluate humoral immune response in patients with CBM caused by F. pedrosoi. Metabolic antigen was used for immunoprecipitation tests (DID and CIE) while somatic antigen for ELISA. Our results demonstrated 53% sensitivity and 96% specificity for DID, while CIE presented 68% sensitivity and 90.5% specificity. ELISA demonstrated 78% sensibility and 83% specificity. Serological tests can be a useful tool to study different aspects of CBM, such as helping differential diagnosis, when culture of the pathogenic agent is impossible.

Comparison between immunomagnetic separation, coupled with immunofluorescence, and the techniques of Faust et al. and of Lutz for the diagnosis of Giardia lamblia cysts in human feces

In the present study, the performance of Immunomagnetic Separation technique, coupled with Immunofluorescence (IMS-IFA), was compared with the FAUST et al. and Lutz parasitological techniques for the detection of Giardia lamblia cysts in human feces. One hundred and twenty-seven samples were evaluated by the three techniques at the same time showing a rate of cyst detection of 27.5% by IMS-IFA and 15.7% by both Faust et al. and Lutz techniques. Data analysis showed a higher sensitivity of IMS-IFA for the detection of G. lamblia cysts in comparison with the techniques of FAUST et al. and Lutz. The use of this methodology as a routine procedure enables the processing of many samples simultaneously, in order to increase recovery rate of G. lamblia cysts and reduce the time of sample storage.

A Review of Operational Matrices and Spectral Techniques for Fractional Calculus

Recently, operational matrices were adapted for solving several kinds of fractional differential equations (FDEs). The use of numerical techniques in conjunction with operational matrices of some orthogonal polynomials, for the solution of FDEs on finite and infinite intervals, produced highly accurate solutions for such equations. This article discusses spectral techniques based on operational matrices of fractional derivatives and integrals for solving several kinds of linear and nonlinear FDEs. More precisely, we present the operational matrices of fractional derivatives and integrals, for several polynomials on bounded domains, such as the Legendre, Chebyshev, Jacobi and Bernstein polynomials, and we use them with different spectral techniques for solving the aforementioned equations on bounded domains. The operational matrices of fractional derivatives and integrals are also presented for orthogonal Laguerre and modified generalized Laguerre polynomials, and their use with numerical techniques for solving FDEs on a semi-infinite interval is discussed. Several examples are presented to illustrate the numerical and theoretical properties of various spectral techniques for solving FDEs on finite and semi-infinite intervals.

Active cycle breathing techniques como técnica de higiene brônquica na asma: estudo piloto

RESUMO: Relevância e Objectivos: O objectivo deste estudo consistiu em verificar a eficácia e segurança de uma técnica de higiene brônquica – Active Cycle breathing technique (ACBT), na remoção de secreções e desinsuflação em crianças asmáticas. É uma técnica recente, que ainda não foi estudada nesta população. Metodologia: A amostra foi constituída por um total de 14 crianças, com idades compreendidas entre os 6 e 18 anos, com o diagnóstico de asma. Foi dividida em dois grupos: grupo de controlo, constituído por asmáticos estáveis e grupo experimental constituído por asmáticos pós-crise. Ambos receberam o mesmo tratamento, que consistiu numa única sessão de ACBT. Realizaram um exame da função respiratória (variáveis FEV1, PEF, MEF75%, RV e FRC) antes e após a aplicação da técnica. Mediu-se a Saturação de O2 antes, a meio e no fim da aplicação da técnica. Por último, pesaram-se as secreções recolhidas durante a sessão de tratamento. Resultados: Como resultados, quando omparamos o antes e após aplicação do ACBT, obtivemos diferenças significativas no RV (p <0,05) e FRC (p <0,05); muito significativa na Sa02 (p <0,01) e peso de secreções, nos asmáticos pós crise. Ocorreu uma melhoria significativa da saturação (p <0,05) em asmáticos estáveis, não havendo secreções. Não houve efeitos adversos nem broncoespasmo em ambos os grupos.Conclusão: O ACBT é uma técnica que promove a remoção de secreções e diminuição da insuflação na população de asmáticos.--------------------ABSTRACT:Relevance and Goals: the goal of this study was to verify the efficiency and security of a bronchial hygienic technique - Active Cycle Breathing Technique (ACBT) – in the obstruction and insufflation of asthmatic children. This is a new technique that has not yet been studied in this population. Procedures: The subjects were 14 children aged between 6 and 18 years old with asthma diagnosis. They were divided in two groups: the control group with stable asthmatics and the experimental group with post-crisis asthmatics. Both received the same treatment that was a single session of ACBT. They made a lung function test before and after the application of the technique (variables FEV1, PEF, MEF75%, RV and FRC). The level of O2 saturation was measured before, during and after the procedure. In the end, the secretions collected during the treatment were weighted. Results: We observed a significant difference on RV (p ˂0,05), FRC (p ˂0,05), Sa02 (p ˂0,01) and in the weight of the secretions in the post-crisis asthmatics after ACBT. There was a significant improvement of saturation (p ˂0,05) only in the stable asthmatics. There were no adverse effects or bronchospasm in both groups.

Optimization of random amplified polymorphic DNA techniques for use in genetic studies of Cuban triatominae

Random amplified polymorphic DNA (RAPD) technique is a simple and reliable method to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of assay. In this study, we analyzed the effect of changing the concentration of primer, magnesium chloride, template DNA and Taq DNA polymerase with the objective of determining their optimum concentration for the standardization of RAPD technique for genetic studies of Cuban Triatominae. Reproducible amplification patterns were obtained using 5 pmoL of primer, 2.5 mM of MgCl2, 25 ng of template DNA and 2 U of Taq DNA polymerase in 25 µL of the reaction. A panel of five random primers was used to evaluate the genetic variability of T. flavida. Three of these (OPA-1, OPA-2 and OPA-4) generated reproducible and distinguishable fingerprinting patterns of Triatominae. Numerical analysis of 52 RAPD amplified bands generated for all five primers was carried out with unweighted pair group method analysis (UPGMA). Jaccard's Similarity Coefficient data were used to construct a dendrogram. Two groups could be distinguished by RAPD data and these groups coincided with geographic origin, i.e. the populations captured in areas from east and west of Guanahacabibes, Pinar del Río. T. flavida present low interpopulation variability that could result in greater susceptibility to pesticides in control programs. The RAPD protocol and the selected primers are useful for molecular characterization of Cuban Triatominae.