Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Carcinoma Oculto da Mama com Metástases Axilares. A Propósito de Dois Casos Clínicos

INTRODUÇÃO: O carcinoma oculto é uma entidade pouco frequente, que se define como a presença de metástases com tumor primário indetetável na altura da apresentação. O prognóstico da maioria dos casos de tumor oculto é reservado, no entanto, o desenvolvimento de técnicas imunohistoquímicas que permitem a caracterização do tumor, tornaram alguns subgrupos de tumor oculto potencialmente curáveis. A presença de adenopatias axilares é a forma de apresentação do cancro da mama em 0,3-1% das mulheres, sendo a origem mais provável a mama ipsilateral. CASO CLÍNICO: Os autores relatam dois casos clínicos de tumor oculto da mama: Caso 1: Doente de 57 anos, com antecedentes familiares de primeiro e segundo grau de cancro da mama, com estudo genético negativo. Recorreu à consulta por adenopatia axilar direita.Exame objetivo (EO), mamografia + ecografia mamária normais. Microbiópsia (MB) ganglionar:metástase de carcinoma compatível com origem na mama, recetores de estrogénios (RE) +, HER2 +, CK7 +, Ca125 +, CK20 (-). RMN mamária e PET não identificaram tumor primário. Procedeu-se a dissecção axilar: 10 gânglios sem metástases. Realizou terapêutica adjuvante com quimioterapia (QT) e imunoterapia (IT). Manteve follow-up regular com EO, RMN e mamografia alternadas até aos 4 anos sem alterações. Aos 4,5 anos detetou-se ao E.O. nódulo palpável na mama direita e nódulo axilar. Mamografia + ecografia: lesão sólida suspeita (R5) cuja caracterização histológicademonstrouCDIG3, recetores hormonais (-) (RH), HER2 3+, Ki67 >30%. A TC TAP e a cintigrafia óssea não revelaram alterações. Em reunião multidisciplinar de decisão terapêutica (RMDT) decidiu-serealizar mastectomia total direita + mastectomia profilática contralateral com reconstrução. Exame histológico:CDI G3 com 22mm,confirmando-se a caracterização imunohistoquímica, com invasão vascular e presença de 3 gânglios com metástase e extensão extracapsular (T2 N2). Realizou terapêutica adjuvante com QT + IT+ Radioterapia (RT) da parede torácica e ganglionar. Um ano após a mastectomia, a doente mantém-se em follow-up sem sinais de recidiva. Caso 2: Doente de 50 anos, com antecedentes familiares de primeiro grau de cancro da mama. Recorreu à consulta por nódulo da axila esquerda e nódulo da mama direita com 2 meses de evolução. EO: nódulo palpável da mama direita e duas adenopatias axilares à esquerda. Mamografia + eco: microcalcificações atípicas da mama esquerda (R5) ealterações benignas da mama direita (R2). Realizaram-se microbiópsia por estereotaxia e biópsia assistida por vácuo da mama esquerda e citologia aspirativa de agulha fina (CAAF) de nódulo da mama direita:sem alterações neoplásicas. A biópsia de adenopatia axilar revelou metástase ganglionar de carcinoma compatível com origem na mama, RH (-), GCDFP15 (-),HER2 3+ e CK7 +.A RM mamária revelou apenas lesões benignas. TC TAP, ecografia abdominal e cintigrafia óssea normais. PET: lesão localizada na axila esquerda, nos três níveis axilares. Por recusa da doente em realizar microbiópsias adicionais ou mastectomia radical modificada, optou-se por realizar dissecção axilar esquerda. Exame histológico: 7 em 14 gânglios com metástases, morfologia e estudo imunohistoquímico concordantes com o anterior. Em RMDT foi decidida terapêuticaadjuvante com RT, QT e IT que a doente se encontra no momento a realizar. DIAGNÓSTICOS DIFERENCIAIS/ DISCUSSÃO A presença de adenopatias axilares relaciona-se na maioria dos casos com processos benignos, mas naqueles em que se diagnostica uma neoplasia maligna, mais de 50% correspondem a carcinoma da mama. Outras neoplasias que se podem apresentar com metástases axilares são: linfoma, melanoma, sarcoma, tiróide, pulmão, estômago, ovário, útero. A avaliação diagnóstica deve incluir além do exame físico, a biópsia ganglionar (para exame histológico e caracterização imunohistoquímica), mamografia, ecografia mamária e ressonância magnética mamária, eventual TC toraco-abdominal, cintigrafia óssea nas mulheres sintomáticas, existindo controvérsia sobre autilidade da PET. CONCLUSÕES O tumor oculto representa um problema diagnóstico e um desafio terapêutico. O carcinoma da mama apresentando-se sob a forma de metástase axilar sem tumor primário identificável e sem doença à distância, considera-se um dos casos potencialmente curáveis, se for tratado de acordo com as guidelines para o estadio II do cancro da mama. A abordagem recomendada inclui dissecção axilar, de importância crucial pela informação prognóstica que guiará o restante tratamento e por ajudar no controlo local da doença. A terapêutica adequada da mama ipsilateral é controversa, e pode passar pela mastectomia radical modificada ou RT. Não existem até à data estudos randomizados comparando a mastectomia versus RT mamária e os estudos retrospetivos disponíveis não apresentam resultados consensuais. A decisão de RT da parede torácica pós-mastectomia e de terapêutica adjuvante deverá ser tomada tendo em conta as guidelines publicadas. BIBLIOGRAFIA 1- www.uptodate.com; Kaklamani, V., et al; “Axillary node metastases with occult primary breast cancer”; Mar 2012 2- Wang, J., et al; “Occult breast cancer presenting as metastatic adenocarcinoma of unknown primary: clinical presentation, immunohistochemistry, and molecular analysis”; Case Rep Oncol 2012;5:9-16 3- Takabatake, D.; “Two cases of occult breast cancer in which PET-CT was helpful in identifying primary tumors”; Breast Cancer (2008) 15:181-184 4- Kinoshita, S., et al.; “Metachronous secondary primary occult breast cancer initially presenting with metastases to the contralateral axillary lymph nodes: report of a case”; Breast Cancer (2010) 17:71-74 5- Bresser, J., et al; “Breast MRI in clinically and mammographically occult breast cancer presenting with an axillary metastasis: a systematic review”; EJSO 36 (2010) 114-119 6- Sharon, W., et al.; “Benefit of ultrasonography in the detection of clinically and mammographically occult breast cancer”; World J Surg (2008) 32:2593-2598 7- Masinghe, S.P., et al.; “Breast radiotherapy for occult breast cancer with axillary nodal metastases – does it reduce the local recurrence rate and increase overall survival?”; Clinical Oncology 23 (2011) 95-100 8- Altan, E., et al.; “Clinical and pathological characteristics of occult breast cancer and review of the literature”; J Buon 2011 Jul-Sep;16(3):434-6

Automated segmentation, tracking and evaluation of bacteria in microscopy images

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Predição de Pré-Eclâmpsia no Primeiro Trimestre em Gravidezes de Baixo Risco: Determinação do Cut-Off numa Amostra da População Portuguesa

Objective:We aimed to identify the cut-off for risk of pre-eclampsia (PE) in Portuguese population by applying the first trimester prediction model from Fetal Medicine Foundation (FMF) in a prospective enrolled cohort of low risk pregnant women. Population and methods: A prospective cohort of low risk singleton pregnancies underwent routine first-trimester scree - ning from 2011 through 2013. Maternal characteristics, blood pressure, uterine artery Doppler, levels of pregnancy-associated plasma protein-A (PAPP-A) and free b-human chorionic gonadotropin were evaluated. The prediction of PE in first trimester was calculated through software Astraia, the outcome obtained from medical records and the cutoff value was subse quently calculated. Results:Of the 273 enrolled patients, 7 (2.6%) developed PE. In first trimester women who developed PE presented higher uterine arteries resistance, represented by higher values of lowest and mean uterine pulsatility index, p <0.005. There was no statistical significance among the remaining maternal characteristics, body mass index, blood pressure and PAPP-A. Using the FMF first trimester PE algorithm, an ideal cut-off of 0.045 (1/22) would correctly detect 71% women who developed PE for a 12% false positive rate and a likelihood ratio of 12.98 (area under the curve: 0.69; confidence interval 95%: 0.39-0.99). By applying the reported cutoff to our cohort, we would obtain 71.4% true positives, 88.3% true negatives, 11.4% false positives and 28.6% false negatives. Conclusion: By applying a first trimester PE prediction model to low risk pregnancies derived from a Portuguese population, a significant proportion of patients would have been predicted as high risk. New larger studies are required to confirm the present findings.

The impact of sizeof the firm and exchange rate in the export propensity of domestic and foreign owned firms in a developing country: A study of the Brazilian exporters

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Rate of reversion of hepatosplenic schistosomiasis after specific therapy

Seventy patients with hepatosplenic schistosomiasis were treated with oxamniquine. The patients lived iti an endemic area and were evaluated 6, 18 and 24 months after treatment, during which time transmission in the area was interrupted. After treatment, clinical improvement occurred in 49 (70%) of the patients, as seen by reduction in visceromegaly and reversion of liver nodules. Reversion of hepatosplenic disease occurred in 28 (40%) patients and in liver nodularity in 26 (47.3%)patients after 24 months. Reversion of hepatosplenic disease was seen in 12 (21%) patients and liver nodules disappeared in 4 (8.5%) as early as 6 months after treatment. In general, hepatosplenomegaly reverses earlier than liver nodularity. Itis notable that reversion of hepatosplenic disease occurred in many individuals with a history ofprevious treatment and also in some with advanced age. In four cases this clinical form of the disease had existed for 20 years. Therefore, there must exist factors other than age and duration of the condition which determine the reversibility of this clinical form. Ourresults reinforce the concept that, in patients with hepatosplenic disease without esophageal hemorrhages, specific treatment shouldpreceed surgical intervention even in those with a history of previous treatment. At least 18 months should be allowed for the ejfects of treatment to be manifest.

Rate of action of schistosomicides in mice infected with Schistosoma mansoni

Mice infected with adult Schistosoma mansoni were dosed with a single oral dose of 125 or 250 mg/kg oltipraz, 50 or 100 mg/kg oxamniquine, or 200 or 400 mg/kg praziquantel. The mortality rate of worms and oogram changes were determined between 1 and 16 weeks after dosing. The time required between dosing and postmortem to obtain maximum effectiveness was 1 week for praziquantel, 2 weeks for oxamniquine and 8 weeks for oltipraz. Changes in oograms persisted throughout most of the experiment, although relapse has been observed at the 4th week on.

Chagas' disease: an algorithm for donor screening and positive donor counseling

Classical serological screening assays for Chagas' disease are time consuming and subjective. The objective of the present work is to evaluate the enzyme immuno-assay (ELISA) methodology and to propose an algorithm for blood banks to be applied to Chagas' disease. Seven thousand, nine hundred and ninety nine blood donor samples were screened by both reverse passive hemagglutination (RPHA) and indirect immunofluorescence assay (IFA). Samples reactive on RPHA and/or IFA were submitted to supplementary RPHA, IFA and complement fixation (CFA) tests. This strategy allowed us to create a panel of 60 samples to evaluate the ELISA methodology from 3 different manufacturers. The sensitivity of the screening by IFA and the 3 different ELISA's was 100%. The specificity was better on ELISA methodology. For Chagas disease, ELISA seems to be the best test for blood donor screening, because it showed high sensitivity and specificity, it is not subjective and can be automated. Therefore, it was possible to propose an algorithm to screen samples and confirm donor results at the blood bank.

Maintaining the correctness of transactional memory programs

Dissertação para obtenção do Grau de Doutor em Engenharia Informática

Serial heart rate changes in rats inoculated by conjunctival instillation of Trypanosoma cruzi obtained from bug faeces

The cardiac effects of experimentally induced myocarditis, when the parasite is obtained from mouse blood, are well known. However, the consequences of the infection when the parasites are obtained from bug faeces are less well defined. In the present investigation, we have used the "Y" strain of Trypanosoma cruzi, which was maintained in Rhodnius prolixus by repeated passages in mice. The faeces of 30 infected bugs were collected, the number of parasites counted and 4,000 parasites inoculated by the conjunctival route in 60 rats. Twenty-nine other rats received faeces from noninfected bugs (sham-inoculated controls) and 40 were used as normal controls. The heart rate of the three groups of animals was recorded under general anesthesia with ether. The heart rate, at day 0 pre-inoculation, was similar in the three groups of animals (Controls: 379 ± 27 beats/min Mean ± SD; Sham-inoculated: 366 ± 31; Infected: 351 ± 29) (p> 0.05). In the infected animals, the mean heart rate began to increase significantly by day 12 following infection (375 ± 31), reaching the highest values between days 18 (390 ± 33) and 21 (403 ± 33) and returned to baseline by day 30 (359 ± 28) (p< 0.05). The heart rate changes were statistically different from those observed in the sham-inoculated controls and in the control animals. Therefore, these heart rate changes were provoked by the Trypanosoma cruzi-induced infection. Thus, it appears that irrespective of the source of the parasite and route of inoculation Trypanosoma cruziacute infection provokes a transient sinus tachycardia.

Analysis of urban land use and land cover changes: a case of study in Bahir Dar, Ethiopia

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies

Acredita Portugal: How to improve the implementation rate of entrepreneurial projects?

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Rastreio combinado do 1º trimestre e doenças autoimunes : Impacto das variaveis pré-analíticas na avaliação do risco

RESUMO: Contexto: As anomalias congénitas, com particular destaque para as neuploidias , afectam aproximadamente 2% dos recém-nascidos, constituindo causas frequentes de morbilidade e mortalidade. Actualmente, a avaliação do grau de risco para as aneuploidias mais prevalentes (T21, T13, T18) é efectuada através do “Rastreio Combinado do 1º Trimestre”, devendo as grávidas com risco acrescido ser sujeitas a exames invasivos (ex.biópsia das vilosidades coriónicas,amniocentese). Quanto mais qualidade existir num rastreio, menos falsos positivos existirão e menor o número de exames diagnósticos invasivos desnecessários. As doenças autoimunes são doenças inflamatórias crónicas em cuja fisiopatologia se encontram distúrbios da imunidade humoral e celular, dependentes de factores genéticos, hormonais,psicológicos e ambientais. Atingem mais o sexo feminino e durante a idade fértil,podendo influenciar o outcome da gravidez e a saúde neonatal causando significativa morbilidade e mortalidade. O lúpus eritematoso sistémico para além de potencialmente afectado pelas alterações imunoendócrinas fisiológicas da gravidez, associa-se frequentemente a problemas de fertilidade. Recentemente, foi sugerido que as anormalidades ocorridas durante a invasão precoce do sinciciotrofoblasto, resultando em deficiente diferenciação, deficiente maturação e diminuição na produção de hCG, poderão ser o mecanismo fisiopatológico primário para as perdas fetais no primeiro trimestre, nos doentes com SLE. A ocorrência de níveis elevados de hCG total e ß-hCG livre no rastreio para despiste de síndrome de Down do segundo e do primeiro trimestre foi assinalada em grávidas portadoras de lúpus, mas a escassez de estudos comprovativos e a pequena dimensão das amostras estudadas constituiu uma limitação significativa na fidedignidade dos resultados obtidos. Objectivos: O estudo teve como objectivos i. estabelecer valores normativos Portugueses e de distribuição para as MoM’s dos parâmetros séricos do primeiro trimestre, por semana de gestação:(PAPP-A e ß-hCG livre), ii. avaliar a influência que as doenças autoimunes têm sobre as MoM’s individuais dos parâmetros bioquímicos PAPP-A e/ou ß-hCG livre, utilizados no rastreio pré-natal combinado do 1º trimestre, e iii. saber se as doenças autoimunes podem condicionar um aumento da taxa de resultados falsos positivos, com consequente aumento do número de amniocenteses. Metodologia: Estudo longitudinal prospectivo, consistindo num rastreio pré-natal combinado de 1º trimestre para pesquisa de aneuploidias, em duas amostras provenientes do Reino Unido (n= 45,854) e de Portugal (n=3122). Foram avaliados parâmetros socio-demográficos, ecográficos, laboratoriais, e calculados os indicadores de desempenho do rastreio combinado. A execução analítica dos testes bioquímicos séricos (PAPP-A e ß-hCG livre) foi realizada no autoanalisador Brahms Kryptor e no autoanalizador 6000 Delfia Xpress. Compararam-se os grupos autoimune e não autoimune das amostras. Resultados: Relativamente às características populacionais, o grupo auto imune tinha valores significativamente superiores nas variáveis idade materna e idade gestacional. Comparando os grupos com e sem doença autoimune, constatou-se a existência de uma elevação das MoM’s da ß-hCG livre nas grávidas com doença autoimune, nomeadamente nos casos de lúpus eritematoso sistémico. Conclusões: os resultado obtidos reforçam a indicação do rastreio combinado do 1º trimestre certificado pela FMF nas grávidas com doenças autoimunes, nomeadamente para as doentes com LES; no entanto, devem ser calculados e introduzidos factores de correcção no algoritmo de risco, de modo a evitar a subida no número de resultados falso-positivos, e consequentemente a sobre- utilização de métodos invasivos.------------ ABSTRACT: Context: Congenital anomalies, with particular reference to aneuploidias, affect approximately 2% of newborns, and are frequent causes of morbidity and mortality. Currently, the risk evaluation for the most prevalent aneuploidias (T21, T13, T18) is carried out through the “combined first trimester screening”, and pregnant women with increased risk are subjected to invasive tests (e.g. villus biopsy done, amniocentesis). The more quality exists in a screening, less false positives exists and fewer unnecessary invasive diagnostic exams. Autoimmune diseases are chronic inflammatory diseases in whose pathophysiology are immune humoral and cellular disorders, dependent on genetic factors, hormonal, psychological and environmental factors. The disease is more prevalent among females, during the child-bearing age, and may influence the outcome of pregnancy and neonatal health causing significant morbidity and mortality. Lupus Erythematosus in addition to potentially affected by immunoendocrine physiological changes of pregnancy, is often associated with fertility problems. Recently, it has been suggested that the abnormalities that occurred during the early invasion of the syncytiotrophoblast, resulting in insufficient differentiation, deficient maturation and decrease in production of hCG may be the primary pathophysiological mechanism for fetal losses in the first quarter, in patients with SLE. The occurrence of elevated levels of total hCG and free ß-hCG in screening for Down’s syndrome of the second and first trimester was reported in pregnant women with lupus, but the paucity of supporting studies and the small size of the samples studied constituted a significant limitation on the trustworthiness of the results obtained. Objectives: this study aims to i. establish normative values for the serum parameters MoM’s (PAPP-A and free β-hCG) and it’s distribution, in the first trimester, by week of pregnancy; ii. assess the influence that the autoimmune diseases have on the MoM’s of individual biochemical PAPP-A and/or β-hCG, used in antenatal screening combined for the first trimester, and iii. whether the autoimmune diseases may make an increased rate of false positives, with consequent increase in the number of amniocenteses.Methodology: Prospective longitudinal study, consisting of a combined first trimester antenatal screening for aneuploidies lookup in two samples from the United Kingdom (n=45.854) and Portugal (n= 3.122). Socio-demographic, echographic and laboratory parameters were evaluated, and combined screening performance indicators were calculated. The analytical run of serum biochemical tests (PAPP-A and ß-hCG) was held at the Brahms Kryptor and in Delfia Xpress 6000. Comparisons between autoimmune group and non-autoimmune group were made. Results: Relating to population characteristics, the autoimmune group had significantly diferente values in the variables maternal age and gestational age. Comparing the groups with and without autoimmune disease, it was noted that there is an elevation of the MoM’s of free ß-hCG levels in pregnant women with autoimmune disease, particularly in cases of systemic lupus erythematosus. Conclusions: The results obtained reinforce the indication of FMF certified combined screening in pregnant women with autoimmune diseases, notably to the patients with SLE; However, correction factors should be calculated and entered in the risk algorithm, in order to avoid the rise in the number of false positive results, and consequently the over-use of invasive methods.

Machine learning Gaussian short rate

Dissertação para obtenção do Grau de Doutor em Estatística e Gestão do Risco

Microscopy image segmentation by active contour models

In this thesis a semi-automated cell analysis system is described through image processing. To achieve this, an image processing algorithm was studied in order to segment cells in a semi-automatic way. The main goal of this analysis is to increase the performance of cell image segmentation process, without affecting the results in a significant way. Even though, a totally manual system has the ability of producing the best results, it has the disadvantage of taking too long and being repetitive, when a large number of images need to be processed. An active contour algorithm was tested in a sequence of images taken by a microscope. This algorithm, more commonly known as snakes, allowed the user to define an initial region in which the cell was incorporated. Then, the algorithm would run several times, making the initial region contours to converge to the cell boundaries. With the final contour, it was possible to extract region properties and produce statistical data. This data allowed to say that this algorithm produces similar results to a purely manual system but at a faster rate. On the other hand, it is slower than a purely automatic way but it allows the user to adjust the contour, making it more versatile and tolerant to image variations.