Parallel run-time for CO-OPN

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Avaliação do comportamento e reforço da Ponte de Maçaínhas sob a ação do tráfego ferroviário

A presente dissertação tem como principal objetivo a avaliação do estado de conservação de uma ponte ferroviária metálica centenária para posteriormente se efetuar o reforço desta. O objeto de estudo foi a Ponte de Maçaínhas, uma ponte metálica treliçada que se situa na linha da Beira Baixa permitindo a ligação entre a Guarda e a Covilhã. Este trabalho envolveu um estudo profundo de vários conteúdos normativos relativos a ações em pontes ferroviárias e ações ambientais. Este estudo estende-se ainda ao campo das verificações regulamentares e critérios de segurança estrutural adequadas ao presente contexto. A operação de reforço começou numa rigorosa análise dos componentes estruturais da ponte, através do estudo de plantas e de um extenso registo fotográfico, para posteriormente se conceber um modelo numérico que traduzisse a situação real. Ao modelo concebido foram aplicadas as cargas regulamentares adequadas por forma a entender o comportamento que a ponte apresenta perante estas e se as suas secções transversais apresentam capacidade resistente suficiente. Caso estas não apresentem capacidade resistente suficiente teriam de ser intervencionadas. Concluído o processo de avaliação estrutural e de reforço, procedeu-se à verificação do comportamento da estrutura reforçada perante as ações de projeto. Com isto pretende-se avaliar se os esforços se distribuem da mesma maneira ou se a operação de reforço teve algum efeito na distribuição destes. Por último, para avaliar o comportamento da estrutura perante a passagem de tráfego real, realizaram-se análises dinâmicas que tiveram por base um grupo de veículos que habitualmente circulam na linha da Beira Baixa e um comboio de alta velocidade. Estas análises foram realizadas tanto para a situação pré reforço como pós reforço. Desta forma conseguiu-se fazer um paralelo entre ambas as condições e perceber se a operação de reforço foi bem-sucedida.

Multicore Scheduling of Real-Time Irregular Parallel Algorithms in Linux

Face à estagnação da tecnologia uniprocessador registada na passada década, aos principais fabricantes de microprocessadores encontraram na tecnologia multi-core a resposta `as crescentes necessidades de processamento do mercado. Durante anos, os desenvolvedores de software viram as suas aplicações acompanhar os ganhos de performance conferidos por cada nova geração de processadores sequenciais, mas `a medida que a capacidade de processamento escala em função do número de processadores, a computação sequencial tem de ser decomposta em várias partes concorrentes que possam executar em paralelo, para que possam utilizar as unidades de processamento adicionais e completar mais rapidamente. A programação paralela implica um paradigma completamente distinto da programação sequencial. Ao contrário dos computadores sequenciais tipificados no modelo de Von Neumann, a heterogeneidade de arquiteturas paralelas requer modelos de programação paralela que abstraiam os programadores dos detalhes da arquitectura e simplifiquem o desenvolvimento de aplicações concorrentes. Os modelos de programação paralela mais populares incitam os programadores a identificar instruções concorrentes na sua lógica de programação, e a especificá-las sob a forma de tarefas que possam ser atribuídas a processadores distintos para executarem em simultâneo. Estas tarefas são tipicamente lançadas durante a execução, e atribuídas aos processadores pelo motor de execução subjacente. Como os requisitos de processamento costumam ser variáveis, e não são conhecidos a priori, o mapeamento de tarefas para processadores tem de ser determinado dinamicamente, em resposta a alterações imprevisíveis dos requisitos de execução. `A medida que o volume da computação cresce, torna-se cada vez menos viável garantir as suas restrições temporais em plataformas uniprocessador. Enquanto os sistemas de tempo real se começam a adaptar ao paradigma de computação paralela, há uma crescente aposta em integrar execuções de tempo real com aplicações interativas no mesmo hardware, num mundo em que a tecnologia se torna cada vez mais pequena, leve, ubíqua, e portável. Esta integração requer soluções de escalonamento que simultaneamente garantam os requisitos temporais das tarefas de tempo real e mantenham um nível aceitável de QoS para as restantes execuções. Para tal, torna-se imperativo que as aplicações de tempo real paralelizem, de forma a minimizar os seus tempos de resposta e maximizar a utilização dos recursos de processamento. Isto introduz uma nova dimensão ao problema do escalonamento, que tem de responder de forma correcta a novos requisitos de execução imprevisíveis e rapidamente conjeturar o mapeamento de tarefas que melhor beneficie os critérios de performance do sistema. A técnica de escalonamento baseado em servidores permite reservar uma fração da capacidade de processamento para a execução de tarefas de tempo real, e assegurar que os efeitos de latência na sua execução não afectam as reservas estipuladas para outras execuções. No caso de tarefas escalonadas pelo tempo de execução máximo, ou tarefas com tempos de execução variáveis, torna-se provável que a largura de banda estipulada não seja consumida por completo. Para melhorar a utilização do sistema, os algoritmos de partilha de largura de banda (capacity-sharing) doam a capacidade não utilizada para a execução de outras tarefas, mantendo as garantias de isolamento entre servidores. Com eficiência comprovada em termos de espaço, tempo, e comunicação, o mecanismo de work-stealing tem vindo a ganhar popularidade como metodologia para o escalonamento de tarefas com paralelismo dinâmico e irregular. O algoritmo p-CSWS combina escalonamento baseado em servidores com capacity-sharing e work-stealing para cobrir as necessidades de escalonamento dos sistemas abertos de tempo real. Enquanto o escalonamento em servidores permite partilhar os recursos de processamento sem interferências a nível dos atrasos, uma nova política de work-stealing que opera sobre o mecanismo de capacity-sharing aplica uma exploração de paralelismo que melhora os tempos de resposta das aplicações e melhora a utilização do sistema. Esta tese propõe uma implementação do algoritmo p-CSWS para o Linux. Em concordância com a estrutura modular do escalonador do Linux, ´e definida uma nova classe de escalonamento que visa avaliar a aplicabilidade da heurística p-CSWS em circunstâncias reais. Ultrapassados os obstáculos intrínsecos `a programação da kernel do Linux, os extensos testes experimentais provam que o p-CSWS ´e mais do que um conceito teórico atrativo, e que a exploração heurística de paralelismo proposta pelo algoritmo beneficia os tempos de resposta das aplicações de tempo real, bem como a performance e eficiência da plataforma multiprocessador.

Locally Advanced and Metastatic Prostate Cancer Treated with Intermittent Androgen Monotherapy or Maximal Androgen Blockade: Results from a Randomised Phase 3 Study by the South European Uroncological Group

BACKGROUND: Few randomised studies have compared antiandrogen intermittent hormonal therapy (IHT) with continuous maximal androgen blockade (MAB) therapy for advanced prostate cancer (PCa). OBJECTIVE: To determine whether overall survival (OS) on IHT (cyproterone acetate; CPA) is noninferior to OS on continuous MAB. DESIGN, SETTING, AND PARTICIPANTS: This phase 3 randomised trial compared IHT and continuous MAB in patients with locally advanced or metastatic PCa. INTERVENTION: During induction, patients received CPA 200 mg/d for 2 wk and then monthly depot injections of a luteinising hormone-releasing hormone (LHRH; triptoreline 11.25 mg) analogue plus CPA 200 mg/d. Patients whose prostate-specific antigen (PSA) was <4 ng/ml after 3 mo of induction treatment were randomised to the IHT arm (stopped treatment and restarted on CPA 300 mg/d monotherapy if PSA rose to ≥20 ng/ml or they were symptomatic) or the continuous arm (CPA 200 mg/d plus monthly LHRH analogue). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Primary outcome measurement was OS. Secondary outcomes included cause-specific survival, time to subjective or objective progression, and quality of life. Time off therapy in the intermittent arm was recorded. RESULTS AND LIMITATIONS: We recruited 1045 patients, of which 918 responded to induction therapy and were randomised (462 to IHT and 456 to continuous MAB). OS was similar between groups (p=0.25), and noninferiority of IHT was demonstrated (hazard ratio [HR]: 0.90; 95% confidence interval [CI], 0.76-1.07). There was a trend for an interaction between PSA and treatment (p=0.05), favouring IHT over continuous therapy in patients with PSA ≤1 ng/ml (HR: 0.79; 95% CI, 0.61-1.02). Men treated with IHT reported better sexual function. Among the 462 patients on IHT, 50% and 28% of patients were off therapy for ≥2.5 yr or >5 yr, respectively, after randomisation. The main limitation is that the length of time for the trial to mature means that other therapies are now available. A second limitation is that T3 patients may now profit from watchful waiting instead of androgen-deprivation therapy. CONCLUSIONS: Noninferiority of IHT in terms of survival and its association with better sexual activity than continuous therapy suggest that IHT should be considered for use in routine clinical practice.

Intravenous Busulfan for Autologous Stem Cell Transplantation in Adult Patients with Acute Myeloid Leukemia: a Survey of 952 Patients on Behalf of the Acute Leukemia Working Party of the European Group for Blood and Marrow Transplantation

Oral busulfan is the historical backbone of the busulfan+cyclophosphamide regimen for autologous stem cell transplantation. However intravenous busulfan has more predictable pharmacokinetics and less toxicity than oral busulfan; we, therefore, retrospectively analyzed data from 952 patients with acute myeloid leukemia who received intravenous busulfan for autologous stem cell transplantation. Most patients were male (n=531, 56%), and the median age at transplantation was 50.5 years. Two-year overall survival, leukemia-free survival, and relapse incidence were 67±2%, 53±2%, and 40±2%, respectively. The non-relapse mortality rate at 2 years was 7±1%. Five patients died from veno-occlusive disease. Overall leukemia-free survival and relapse incidence at 2 years did not differ significantly between the 815 patients transplanted in first complete remission (52±2% and 40±2%, respectively) and the 137 patients transplanted in second complete remission (58±5% and 35±5%, respectively). Cytogenetic risk classification and age were significant prognostic factors: the 2-year leukemia-free survival was 63±4% in patients with good risk cytogenetics, 52±3% in those with intermediate risk cytogenetics, and 37 ± 10% in those with poor risk cytogenetics (P=0.01); patients ≤50 years old had better overall survival (77±2% versus 56±3%; P<0.001), leukemia-free survival (61±3% versus 45±3%; P<0.001), relapse incidence (35±2% versus 45±3%; P<0.005), and non-relapse mortality (4±1% versus 10±2%; P<0.001) than older patients. The combination of intravenous busulfan and high-dose melphalan was associated with the best overall survival (75±4%). Our results suggest that the use of intravenous busulfan simplifies the autograft procedure and confirm the usefulness of autologous stem cell transplantation in acute myeloid leukemia. As in allogeneic transplantation, veno-occlusive disease is an uncommon complication after an autograft using intravenous busulfan.

Internationalization strategy: Dom Pedro Hotel Group - São Paulo

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

International Airlines Group: Equity Investment Report

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

Atherogenesis and atherosclerosis in primary antiphospholipid syndrome

ABSTRACT: In the late seventies the term “Haematological Stress Syndrome” defined some haematological abnormalities appearing in the course of acute and chronic disorders, such as raised plasma levels of fibrinogen (FNG) and factor VIII, reduced fibrinolytic activity and hyperviscosity. In the early nineties the “Membrane stress syndrome hypothesis” proposed the unification of the concepts of haematological stress syndrome with those of oxidation, inflammation and immune activation to explain the pathogenesis of the antiphospholipid syndrome (APS) Antiphospholipid antibodies, coagulation, fibrinolysis and thrombosis. This chapter investigated the occurrence of the “Haematological Stress Syndrome” and thrombosis in 144 participants positive for aPL detected by clotting and immune tests. Among the clotting assays for the detection of lupus anticoagulant, dilute Russell's viper venom time better correlated with a history of venous thrombosis than activated partial thromboplastin time (p<0.0002 vs p<0.009) and was the only test correlated with a history of arterial thrombosis (p<0.01). By regression analysis, serum levels of IgG anticardiolipin antibodies (aCL) associated with the number of venous occlusions (p<0.001). With regards to FNG and von Willebrand factor (vWF), the former rose by 36% (95% CI; 21%, 53%) and the latter by 50% (95% CI; 29%, 75%) at the first venous occlusion and remained unchanged after subsequent occlusions. At variance FNG rose by 45% (95% CI; 31%, 60%) per arterial occlusion and vWF by 27% (95% CI; 10%, 47%) per arterial occlusion throughout. The coagulation/fibrinolytic balance was cross-sectionally evaluated on 18 thrombotic PAPS patients, 18 subjects with persistence of idiopathic aPL and in healthy controls. Markers of thrombin generation prothrombin fragment 1+2 (F1+2), thrombin-antithrombin complex (TAT) and of fibrin turnover D-Dimer (D-D) were higher in thrombotic (p=0.006)and non-thrombotic subjects (p=0.0001) than in controls as were those of D-D (p<0.0001 and p=0.003 respectively). TAT levels did not differ. Gender analysed data revealed blunted tPA release (hence a negative venous occlusion test) in thrombotic females but neither in thrombotic males (p=0.01) nor in asymptomatic subjects of either sex. Also, in both patient groups females had higher mean PAI than males (p<0.0002) and control females (p<0.02). The activity of factor XIII (FXIIIa) was evaluated was evaluated in 29 patients with PAPS, 14 persistent carriers of aPL without thrombosis, 24 thrombotic patients with inherited thrombophilia, 28 healthy controls and 32 patients with mitral and aortic valve prosthesis as controls for FXIII only. FXIIIa was highest in PAPS (p=0.001), particularly in patients with multiple (n=12) than single occlusion (p=0.02) and in correlation with PAI (p=0.003) and FNG (p=0.005). Moreover FXIIIa was strongly associated with IgG aCL and IgG anti-2GPI (p=0.005 for both) in the PAPS group and to a lesser degree in the aPL group (FXIIIa with IgG aCL, p=0.02, with IgG anti-2GPI, p=0.04). Altogether these results indicate: 1) a differential relationship of aPL, vWF and FNG with venous and arterial thrombosis; 2) heightened thrombin generation, accelerated fibrin turnover and fibrinolysis abnormalities also in asymptomatic carriers of aPLs; 3) enhanced FXIIIa that may contribute to atherothrombosis via increased fibrin/fibrinogen cross-linking. Lipid profile, lipid peroxidation and anti-lipoprotein antibodies in thrombotic primary antiphospholipid syndrome. Given the atherogenic lipid profile of SLE, the same possibility was explored in PAPS by comparing high-density lipoprotein (HDL), low-density lipoprotein (LDL), total cholesterol (CHO), apolipoprotein AI (ApoAI), apolipoprotein B (ApoB), triglycerides (TG), anti-lipoprotein antibodies, beta-2-glycoprotein I complexed to oxidized low-density lipoprotein (oxLDL-2GPI) and C-reactive protein (CRP) in 34 thrombotic PAPS patients compared to 36 thrombotic patients with inherited thrombophilia (IT), to 18 subjects persistently positive for antiphospholipid antibodies (aPL) with no underlying autoimmune or non-autoimmune disorders and to 28 healthy controls. Average concentrations of HDL (p<0.0001), LDL (p<0.0001), CHO (p=0.0002), ApoAI (p=0.002) were lower in PAPS whereas average TRY was higher (p=0.01) than other groups. Moreover PAPS showed higher IgG anti-HDL (p=0.01) and IgG anti-ApoAI (p<0.0001) as well as greater average oxLDL-2GPI (p=0.001) and CRP (p=0.003). Within PAPS, IgG anti-HDL correlated negatively to HDL (p=0.004) and was an independent predictor of oxLDL-2GPI (p=0.009). HDL and ApoAI correlated negatively with CRP (p=0.001 and p=0.007, respectively). IgG anti-HDL may hamper the antioxidant and anti-inflammatory effect of HDL favouring low-grade inflammation and enhanced oxidation in thrombotic PAPS. Indeed plasma 8-epi-prostaglandin F2α (a very specific marker of lipid peroxidation) was significantly higher in 10 patients with PAPS than 10 age and sex matched healthy subjects (p=0.0002) and strongly related to the titre of plasma IgG aCL (r=0.89, p=0.0004). Hence oxidative stress, a major player in atherogenesis, also characterises PAPS. Nitric oxide and nitrative stress in thrombotic primary antiphosholipid syndrome. Oxidative stress goes hand in hand with nitrative stress and to address the latter plasma nitrotyrosine (NT, marker of nitrative stress), nitrite (NO2-) and nitrate (NO3-) were measured in 46 thrombotic PAPS patients, 21 asymptomatic but persistent carriers of antiphospholipid antibodies (PCaPL), 38 patients with inherited thrombophilia (IT), 33 patients with systemic lupus erythematosus (SLE) and 29 healthy controls (CTR). Average crude NT was higher in PAPS and SLE (p=0.01) whereas average plasma NO2- was lower in PAPS and average NO3- highest in SLE (p<0.0001). In PAPS, IgG aCL titer and number of vascular occlusions negatively predicted NO2-, (p=0.03 and p=0.001, respectively) whereas arterial occlusions and smoking positively predicted NO3- (p=0.05 and p=0.005). Moreover CRP (an inflammatory marker) positively predicted NT (p=0.004). Nitric oxide metabolites relates to type and number of vascular occlusions and to aPL titers, whereas nitrative stress relates to low grade marker) positively predicted NT (p=0.004). Nitric oxide metabolites relates to type and number of vascular occlusions and to aPL titers, whereas nitrative stress relates to low grade inflammation and both phenomena may have implications for thrombosis and atherosclerosis in PAPS Inflammation and immune activation in thrombotic primary antiphospholipid syndrome. To investigate inflammation and immune activation in thrombotic PAPS high-sensitivity CRP (hs-CRP), serum amyloid A (SAA), oxLDL-2GPI, CRP bound to oxLDL-2GPI (CRP-oxLDL-2GPI) (as inflammatory markers) neopterin (NPT) and soluble CD14 (sCD14) (as immune activation markers) were measured by ELISA in 41 PAPS patients, in 44 patients with inherited thrombophilia (IT) and 39 controls (CTR). Compared to other groups, PAPS presented with higher plasma concentrations of inflammatory, hs-CRP (p=0.0004), SAA (p<0.01), CRP-oxLDL-2GPI (p=0.0004) and immune activation markers, NPT (p<0.0001) and sCD14 (p=0.007). By regression analysis SAA independently predicted thrombosis number (p=0.003) and NPT independently predicted thrombosis type (arterial, p=0.03) and number (p=0.04). These data confirm that low-grade inflammation and immune activation occur and relate to vascular features of PAPS. Antiphosholipid antibodies, haemostatic variables and atherosclerosis in thrombotic primary antiphospholipid syndrome To evaluate whether IgG aCL titre, haemostatic variables and the lipid profile bore any relationship to the intima media thickness (IMT) of carotid arteries high-resolution sonography was applied to the common carotid (CC), carotid bifurcation (CB) and internal carotid (IC) of 42 aPL subjects, 29 with primary thrombotic antiphospholipid syndrome and 13 with persistence of aPL in the absence of any underlying disorder. The following were measured: plasma FNG, vWF, PAI, homocysteine (HC), CHO, TG, HDL, LDL, platelet numbers and aCL of IgG and IgM isotype. By multiple regression analysis, IgG aCL titre independently predicted IMT at all carotid segments examined (p always <0.005). Plasma FNG and HC independently predicted IMT at the CB (p=0.001 and p<0.0001, respectively) and IC (p=0.03 and p<0.0001, respectively). These data strongly support an atherogenic role for IgG aCL in patients with aPL in addition to traditional risk factors. The atherosclerosis hypothesis was investigated in an age and sex-matched case-double-control study including 49 thrombotic PAPS patients (18 M, 31 F, mean age 37 ± 11), 49 thrombotic patients for IT and 49 healthy subjects. Average IMT was always greater in PAPS than control patients (CC: p=0.004, CB: p=0.013, IC: p=0.001). By dividing participants into age tertiles the IMT was greater in the second (CC: p=0.003, CB: p=0.023, IC: p=0.003) and third tertiles (CC: p=0.03, CB: p=0.004, IC: p=0.007). Conclusion: Coagulation activation, fibrinolysis depression, hightened fibrin turnover, oxidative and nitrative stress in parallel with low grade inflammation and immune activation characterise thrombotic PAPS: all these are early atherogenic processes and contribute to the demonstrated premature atherosclerosis that should be considered a clinical feature of PAPS.

Vodacom Group: Equity research

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

Duffy blood group genotypes among malaria patients in Rondônia, Western Brazilian Amazon

We have compared Duffy blood group genotype distribution, as determined by polymerase chain reaction with allele-specific primers, in 68 Plasmodium vivax-infected patients and 59 non-vivax malaria controls from Rondônia, Brazil. Homozygosity for the allele Fy, which abolishes Duffy antigen expression on erythrocytes, was observed in 12% non-vivax controls but in no P. vivax patient. However, no significant association was found between Fy heterozygosity and protection against P. vivax. The Fy x allele, which has recently been associated with very weak erythrocyte expression of Duffy antigen, was not found in local P. vivax patients.

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia Informática