Prognostic modelling of breast cancer patients: a benchmark of predictive models with external validation

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores – Sistemas Digitais e Percepcionais pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Interferon gamma increases survival in urine experimental cryptococcosis

Systemic disease by Cryptococcus neoformans (C. neoformans) is a common opportunistic infection in immunodeficient patients. Cellular immunity seems to be the most important determinant of resistance. The aim of this study was to assess the effect of recombinant rat interferon gamma (IFN-gamma) in murine cryptococcosis (Balb/c mice infected by IP route with the Rivas strain of C. neoformans), evaluating survival time, macroscopic and microscopic examination of the organs, and massive seeding of brain homogenate. IFN-gamma treatment, at a daily dose of 10,000 IU, did not modify significantly these variables when mice were challenged with a high inoculum (10(7) yeasts) and treatment was delayed to 5 days after infection (median survival 21 days in control mice vs. 23 days in IFN-treated). Another set of experiments suggested that IFN-gamma treatment, at a dose of 10,000 IU/day, begun at the moment of infection could be useful (it prolonged survival from 20 to 28 days, although the difference did not achieve statistical signification). When used simultaneously with infection by 3.5 x 10(5) yeasts, IFN-gamma at 10,000 IU/day for 15 days significantly prolonged survival of mice (p = 0.004). These results suggest that, depending on the experimental conditions, IFN-gamma can improve survival of mice infected with a lethal dose of C. neoformans.

Double coverage and demand for health care: Evidence from quantile regression

An individual experiences double coverage when he bene ts from more than one health insurance plan at the same time. This paper examines the impact of such supplementary insurance on the demand for health care services. Its novelty is that within the context of count data modelling and without imposing restrictive parametric assumptions, the analysis is carried out for di¤erent points of the conditional distribution, not only for its mean location. Results indicate that moral hazard is present across the whole outcome distribution for both public and private second layers of health insurance coverage but with greater magnitude in the latter group. By looking at di¤erent points we unveil that stronger double coverage e¤ects are smaller for high levels of usage. We use data for Portugal, taking advantage of particular features of the public and private protection schemes on top of the statutory National Health Service. By exploring the last Portuguese Health Survey, we were able to evaluate their impacts on the consumption of doctor visi

Long-Term Survival with Heart Transplantation for Fibrosarcoma of the Heart

Primary sarcoma of the heart is a rare disease that has an ominous prognosis with either medical or surgical therapy. We report a case of a 25-year-old woman with sarcoma of the heart who received a transplant and is clinically well after 7 years. We believe that transplantation must be considered in this kind of pathology for selected cases.

O Valor Prognóstico da Resposta Neutrofílica na Era da Reperfusão Mecânica do Enfarte Agudo do Miocárdico

BACKGROUND: In ST-segment elevation myocardial infarction (STEMI) patients treated with primary angioplasty, neutrophil response and its prognostic significance are not entirely understood. METHODS: We retrospectively studied 305 consecutive and non-selected STEMI patients. They were divided into three groups according to the maximum neutrophil percentage in the first 48 hours. We compared baseline demographic characteristics, coronary disease risk factors, cardiac history, clinical presentation, therapeutics administered and clinical evolution. We then assessed survival in the three groups and determined predictors of 30-day mortality. Group 1 (G1) had a mean age of 57 +/- 14 years and showed mean neutrophilia of 73.3%, Group 2 (G2) 61 +/- 13 years and 79.9%, and Group 3 (G3) 66 +/- 13 years and 84.2%. We compared outcomes and 30-day mortality between the groups. RESULTS: Mean age rose with increased neutrophil response. There were no statistically significant baseline differences between the groups except for more smokers in Groups 1 and 2, and more patients presenting with Killip class > or = 2 and fewer with uncomplicated evolution in Group 3. During 30-day follow-up there were 19 deaths (G1=1, G2=3 and G3=15). In univariate analysis mortality predictors were age > or = 75 years, anterior STEMI, maximum creatinine kinase > or = 2500 UI/L, culprit lesion in proximal anterior descending artery, incomplete revascularization, Killip > or = 2 at presentation, and being in G3. After multivariate regression analysis independent predictors were age > or = 75 years, incomplete revascularization and being in G3. CONCLUSION: In myocardial infarction patients undergoing mechanical revascularization, an intense neutrophil response (routinely, easily and inexpensively assessed) is related to worse short-term prognosis.

Inhibitory effect of deferoxamine on Paracoccidioides brasiliensis survival in human monocytes: reversal by holotransferrin not by apotransferrin

The mechanisms used by Paracoccidioides brasiliensis to survive into phagocytic cells are not clear. Cellular iron metabolism is of critical importance to the growth of several intracellular pathogens whose capacity to multiply in mononuclear phagocytes is dependent on the availability of intracellular iron. Thus, the objective of this paper was to investigate the role of intracellular iron in regulating the capacity of P. brasiliensis yeast cells to survive within human monocytes. Treatment of monocytes with deferoxamine, an iron chelator, suppressed the survival of yeasts in a concentration-dependent manner. The effect of deferoxamine was reversed by iron-saturated transferrin (holotransferrin) but not by nonsaturated transferrin (apotransferrin). These results strongly suggest that P. brasiliensis survival in human monocytes is iron dependent.

Survival of Trypanosoma cruzi in sugar cane used to prepare juice

Chagas disease can be transmitted to man by many different means, including contact with infected triatomine feces, blood transfusion, laboratory accidents, organ transplants, and congenital or oral routes. The latter mode has received considerable attention recently. In this assay, we evaluate the survival of Trypanosoma cruzi contaminating sugar cane used to prepare juice, as well as the viability and capacity for infection by the parasite after recovery. Thirty triatomines were contaminated with T. cruzi Y strain and 45 days later pieces of sugar cane were contaminated with the intestinal contents of the insects. The pieces were ground at different intervals after contamination (time = 0, 1, 4, 6, 12 and 24 hours) and the juice extracted and analyzed. Different methods were used to show T. cruzi in the juice: direct analysis, hematocrit tube centrifugation and QBC, and experimental inoculation in 47 female BALB/c mice (five control mice and seven mice for each interval examined (five inoculated orally and two intraperitoneally). Positive results were found using the direct analysis and QBC methods for juice prepared up to 12 hours after initial contamination. However, by the centrifugation technique, positivity was found only up to four hours after contamination of the sugar cane. Inoculated animals showed parasitemia during a 14 day observation period, demonstrating the high survival rate of T. cruzi in sugar cane.

Predictive factors of mortality in burn patients

Burn mortality statistics may be misleading unless they account properly for the many factors that can influence outcome. Such estimates are useful for patients and others making medical and financial decisions concerning their care. This study aimed to define the clinical, microbiological and laboratorial predictors of mortality with a view to focus on better burn care. Data were collected using independent variables, which were analyzed sequentially and cumulatively, employing univariate statistics and a pooled, cross-sectional, multivariate logistic regression to establish which variables better predict the probability of mortality. Survivors and non-survivors among burn patients were compared to define the predictive factors of mortality. Mortality rate was 5.0%. Higher age, larger burn area, presence of fungi in the wound, shorter length of stay and the presence of multi-resistant bacteria in the wound significantly predicted increased mortality. The authors conclude that those patients who are most apt to die are those with age > 50 years, with limited skin donor sites and those with multi-resistant bacteria and fungi in the wound.

Chronic Allograft Dysfunction - Is There a Treatment?

BACKGROUND: The major causes of renal transplant loss are death and chronic allograft dysfunction (CAD). The aims of this study were to determine the incidence of CAD in our population and the relation between allograft survival and immunosuppressive regimens. METHODS: We studied retrospectively 473 patients who received deceased donor kidney transplants with at least 1 allograft biopsy between January 1990 and May 2007. Clinical data included age, gender, biopsy data, and immunosuppression before and after kidney biopsy. Mean age was 45.4 +/- 12.7 years including 65% males with a mean follow-up of 6.7 +/- 4.5 years. CAD was observed in 177 of 473 biopsies: 48 patients showed interstitial fibrosis (IF); 101 chronic rejection (CR); 16 transplant glomerulopathy (TG); and 12, CR and TG. Mean follow-up since the discovery of the histologic feature was 60.5 +/- 50.5 months for IF; 38.3 +/- 40.8 for CR, and 18.2 +/- 19.2 for TG. RESULTS: CAD, which was more common in younger patients (P = .03), correlated upon univariate and multivariate analysis with CKD stage 5d development (P < .001). Deposition of C4d in peritubular capillaries was more frequent among CAD patients (P = .004), an association with particular relevance to recipients with CR (P = .02) and TG (P < .001). When we analyzed CAD subpopulation, we observed a positive correlation between allograft survival and immunosuppression modification after biopsy. Substitution of sirolimus (40/177) was shown in univariate, multivariate and Cox regression analyses to be a renal protector (P < .002). Allograft survival was also correlated with initial mycophenolate mofetil versus azathioprine, (62/177) immunosuppression (P < .001). CONCLUSION: CAD, a frequent histologic feature, may benefit from sirolimus conversion.

Using neural networks and support vector regression to relate marchetti dilatometer test parameters and maximum shear modulus

In the last two decades, small strain shear modulus became one of the most important geotechnical parameters to characterize soil stiffness. Finite element analysis have shown that in-situ stiffness of soils and rocks is much higher than what was previously thought and that stress-strain behaviour of these materials is non-linear in most cases with small strain levels, especially in the ground around retaining walls, foundations and tunnels, typically in the order of 10−2 to 10−4 of strain. Although the best approach to estimate shear modulus seems to be based in measuring seismic wave velocities, deriving the parameter through correlations with in-situ tests is usually considered very useful for design practice.The use of Neural Networks for modeling systems has been widespread, in particular within areas where the great amount of available data and the complexity of the systems keeps the problem very unfriendly to treat following traditional data analysis methodologies. In this work, the use of Neural Networks and Support Vector Regression is proposed to estimate small strain shear modulus for sedimentary soils from the basic or intermediate parameters derived from Marchetti Dilatometer Test. The results are discussed and compared with some of the most common available methodologies for this evaluation.

Using neural networks and support vector regression to relate marchetti dilatometer test parameters and maximum shear modulus

In the last two decades, small strain shear modulus became one of the most important geotechnical parameters to characterize soil stiffness. Finite element analysis have shown that in-situ stiffness of soils and rocks is much higher than what was previously thought and that stress-strain behaviour of these materials is non-linear in most cases with small strain levels, especially in the ground around retaining walls, foundations and tunnels, typically in the order of 10−2 to 10−4 of strain. Although the best approach to estimate shear modulus seems to be based in measuring seismic wave velocities, deriving the parameter through correlations with in-situ tests is usually considered very useful for design practice.The use of Neural Networks for modeling systems has been widespread, in particular within areas where the great amount of available data and the complexity of the systems keeps the problem very unfriendly to treat following traditional data analysis methodologies. In this work, the use of Neural Networks and Support Vector Regression is proposed to estimate small strain shear modulus for sedimentary soils from the basic or intermediate parameters derived from Marchetti Dilatometer Test. The results are discussed and compared with some of the most common available methodologies for this evaluation.

Clinical Outcome and Morphologic Analysis after Endovascular Aneurysm Repair Using the Excluder Endograft

OBJECTIVE: Long-term follow-up after endovascular aneurysm repair (EVAR) is very scarce, and doubt remains regarding the durability of these procedures. We designed a retrospective cohort study to assess long-term clinical outcome and morphologic changes in patients with abdominal aortic aneurysms (AAAs) treated by EVAR using the Excluder endoprosthesis (W. L. Gore and Associates, Flagstaff, Ariz). METHODS: From 2000 to 2007, 179 patients underwent EVAR in a tertiary institution. Clinical data were retrieved from a prospective database. All patients treated with the Excluder endoprosthesis were included. Computed tomography angiography (CTA) scans were retrospectively analyzed preoperatively, at 30 days, and at the last follow-up using dedicated tridimensional reconstruction software. For patients with complications, all remaining CTAs were also analyzed. The primary end point was clinical success. Secondary end points were freedom from reintervention, sac growth, types I and III endoleak, migration, conversion to open repair, and AAA-related death or rupture. Neck dilatation, renal function, and overall survival were also analyzed. RESULTS: Included were 144 patients (88.2% men; mean age, 71.6 years). Aneurysms were ruptured in 4.9%. American Society of Anesthesiologists classification was III/IV in 61.8%. No patients were lost during a median follow-up of 5.0 years (interquartile range, 3.1-6.4; maximum, 11.2 years). Two patients died of medical complications ≤ 30 days after EVAR. The estimated primary clinical success rates at 5 and 10 years were 63.5% and 41.1%, and secondary clinical success rates were 78.3% and 58.3%, respectively. Sac growth was observed in 37 of 142 patients (26.1%). Cox regression showed type I endoleak during follow-up (hazard ratio, 3.74; P = .008), original design model (hazard ratio, 3.85; P = .001), and preoperative neck diameter (1.27 per mm increase, P = .006) were determinants of sac growth. Secondary interventions were required in 32 patients (22.5%). The estimated 10-year rate of AAA-related death or rupture was 2.1%. Overall life expectancy after AAA repair was 6.8 years. CONCLUSIONS: EVAR using the Excluder endoprosthesis provides a safe and lasting treatment for AAA, despite the need for maintained surveillance and secondary interventions. At up to 11 years, the risk of AAA-related death or postimplantation rupture is remarkably low. The incidences of postimplantation sac growth and secondary intervention were greatly reduced after the introduction of the low-permeability design in 2004.

Orthotopic Liver Transplantation in Familial Amyloidotic Polyneuropathy Is Associated with Long-Term Progression of Renal Disease

Orthotopic liver transplantation has become the treatment of choice for familial amyloidotic polyneuropathy. The aims of this study were to evaluate the renal complications post orthotopic liver transplantation in familial amyloidotic polyneuropathy and their impact. We retrospectively studied 185 recipients who underwent 217 orthotopic liver transplants. Mean age 36.8±9.5 years, 59% males, 14.3% with renal dysfunction pre orthotopic liver transplantation. Mean follow-up 3.6±3.7 years. Thirty-two patients died. Univariate and multivariate analysis were performed, and p<0.05 was considered significant. Acute kidney injury occurred in 57 patients and renal replacement therapy was needed in 16/57. In multivariate analysis, acute kidney injury was correlated with development of chronic kidney disease (p<0.001). Relating to development of chronic kidney disease, 23.5% had progress to stage 3, 6% to stage 4 and 5.1% to stage 5d. According to Spearmen correlation, risk factors for chronic kidney disease development were age (p<0.001), renal dysfunction pre orthotopic liver transplantation (p<0.001) and acute kidney injury post orthotopic liver transplantation (p<0.001). Mortality was correlated with age (p<0.001), retransplantation need (p=0.004), renal dysfunction pre orthotopic liver transplantation (p<0.001), acute kidney injury post orthotopic liver transplantation (p=0.04), and chronic kidney disease stage 5 (p<0.001). Using binary regression, mortality was correlated with chronic kidney disease development (p=0.02). In conclusion, familial amyloidotic polyneuropathy patients are disposed to renal complications that have a negative impact on the survival of these patients.

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.

Biological predictors of survival in limphoma and mechanisms underlying follicular lymphoma transformaion into diffuse large B cell lymphoma (vol I e II)

RESUMO: Os biomarcadores tumorais permitem identificar os doentes com maior risco de recorrência da doença, predizer a resposta tumoral à terapêutica e, finalmente, definir candidatos a novos alvos terapêuticos. Novos biomarcadores são especialmente necessários na abordagem clínica dos linfomas. Actualmente, esses tumores são diagnosticados através de uma combinação de características morfológicas, fenotípicas e moleculares, mas o prognóstico e o planeamento terapêutico estão quase exclusivamente dependentes de características clínicas. Estes factores clínicos são, na maioria dos linfomas, insuficientes numa proporção significativa dos doentes, em particular, aqueles com pior prognóstico. O linfoma folicular (LF) é, globalmente, o segundo subtipo mais comum de linfoma. É tipicamente uma doença indolente com uma sobrevida média entre os 8 e 12 anos, mas é geralmente fatal quando se transforma num linfoma agressivo de alto grau, habitualmente o linfoma difuso de grandes células B (LDGCB). Morfologicamente e funcionalmente, as células do LF recapitulam as células normais do centro germinativo na sua dependência de sobrevivência do microambiente não-tumoral, especialmente das células do sistema imunológico. Biomarcadores preditivos de transformação não existem pelo que um melhor conhecimento da biologia intrínseca de progressão do LF poderá revelar novos candidatos. Nesta tese descrevo duas abordagens distintas para a descoberta de novos biomarcadores. A primeira, o estudo da expressão global de genes ('genomics') obtidos por técnicas de alto rendimento que analisam todo o genoma humano sequenciado, permitindo identificar novas anomalias genéticas que possam representar mecanismos biológicos importantes de transformação. São descritos novos genes e alterações genómicas associados à transformação do LF, sendo especialmente relevantes as relacionadas com os eventos iniciais de transformação em LDGCB. A segunda, baseou-se em várias hipóteses centradas no microambiente do LF, rico em vários tipos de células nãomalignas. Os estudos imunoarquitectural de macrófagos, células T regulatórias e densidade de microvasos efectuado em biopsias de diagnóstico de doentes com LF tratados uniformemente correlacionaram-se significativamente, e independentemente dos critérios clínicos, com a evolução clínica e, mais importante, com o risco de transformação em LDGCB. Nesta tese, foram preferencialmente utilizadas (e optimizadas) técnicas que permitam o uso de amostras fixadas em parafina e formalina (FFPET). Estas são facilmente acessíveis a partir das biopsias de diagnóstico de rotina presentes nos arquivos de todos os departamentos de patologia, facilitando uma transição rápida dos novos marcadores para a prática clínica. Embora o FL fosse o tema principal da tese, os novos achados permitiram estender facilmente hipóteses semelhantes a outros subtipos de linfoma. Assim, são propostos e validados vários biomarcadores promissores e relacionados com o microambiente não tumoral, sobretudo dependentes das células do sistema imunológico, como contribuintes importantes para a biologia dos linfomas. Estes sugerem novas opções para a abordagem clínica destas doenças e, eventualmente, novos alvos terapêuticos.------------- ABSTRACT: Cancer biomarkers provide an opportunity to identify those patients most at risk for disease recurrence, predict which tumours will respond to different therapeutic approaches and ultimately define candidate biomarkers that may serve as targets for personalized therapy. New biomarkers are especially needed in the management of lymphoid cancers. At present, these tumours are diagnosed using a combination of morphologic, phenotypic and molecular features but prognosis and overall survival are mostly dependent on clinical characteristics. In most lymphoma types, these imprecisely assess a significant proportion of patients, in particular, those with very poor outcomes. Follicular lymphoma (FL) is the second most common lymphoma subtype worldwide. It is typically an indolent disease with current median survivals in the range of 8-12 years, but is usually fatal when it transforms into an aggressive high-grade lymphoma, characteristically Diffuse Large B Cell Lymphoma (DLBCL). Morphologically and functionally it recapitulates the normal cells of the germinal center with its survival dependency on non-malignant immune and immunerelated cells. Informative markers of transformation related to the intrinsic biology of FL progression are needed. Within this thesis two separate approaches to biomarker discovery were employed. The first was to study the global expression of genes (‘genomics’) obtained using high-throughput, wholegenome-wide approaches that offered the possibility for discovery of new genetic abnormalities that might represent the important biological mechanisms of transformation. Gene signatures associated with early events of transformation were found. Another approach relied on hypothesis-driven concepts focusing upon the microenvironment, rich in several non-malignant cell types. The immunoarchitectural studies of macrophages, regulatory T cells and microvessel density on diagnostic biopsies of uniformly treated FL patients significantly predicted clinical outcome and, importantly, also informed on the risk of transformation. Techniques that enabled the use of routine formalin fixed paraffin embedded diagnostic specimens from the pathology department archives were preferentially used in this thesis with the goal of fulfilling a rapid bench-to-beside” translation for these new findings. Although FL was the main subject of the thesis the new findings and hypotheses allowed easy transition into other lymphoma types. Several promising biomarkers were proposed and validated including the implication of several non-neoplastic immune cells as important contributors to lymphoma biology, opening new options for better treatment planning and eventually new therapeutic targets and candidate therapeutics.