Hybrid systems biology: application to Escherichia coli

Dissertation presented to obtain a Master degree in Biotechnology

Perfomance do transverso do abdómen : recurso à ecografia como informação de retorno extrínseca

RESUMO: Desenho do estudo: Estudo quantitativo, experimental prospectivo de factor único, desenho pré-teste, pós-teste. Objectivos: Determinar a efectividade da ecografia em tempo real, como Informação de Retorno Extrínseca Visual Ecográfica (IRE-VE) na performance do transverso do abdómen (TrA), em sujeitos saudáveis; analisar eventuais diferenças entre a IRE-VE e a Informação de Retorno Extrínseca Verbal Clínica (IRE-VC); medir a performance da musculatura abdominal, através das diferenças na espessura dos músculos TrA e oblíquo interno (OI) e deslizamento do TrA, em repouso e em contracção. Enquadramento: A maioria dos indivíduos não tem conhecimentos nem consciência do contributo de uma boa performance do TrA para a estabilidade da coluna lombar. Vários estudos recentes se têm dedicado a este assunto, tendo sido mostrado o importante contributo da ecografia como Informação de Retorno Extrínseca (IRE). Uma vez que o TrA e o OI contribuem para a estabilidade lombo pélvica, e que a aprendizagem do seu controlo motor é essencial para a recuperação da função, torna-se relevante clarificar o contributo da informação de retorno na primeira fase da aprendizagem da performance desses músculos, bem como encontrar as melhores estratégias para a sua realização. A ecografia foi o instrumento escolhido para servir esse objectivo. Métodos: Participaram no estudo 75 sujeitos, sem queixas lombares, com idades compreendidas entre os 18 e os 38 anos com um valor médio de 21,9 anos (±4,03), divididos aleatoriamente em três grupos com uma tarefa comum: a “Manobra do Transverso”, em que um grupo não recebeu IRE (GC), outro recebeu IRE verbal clínica e palpatória (GIRE-VC) e ooutro recebeu IRE visual ecográfica (GIRE-VE). Para efeitos de análise da contracção da musculatura abdominal, foram estudadas a espessura dos músculos TrA e OI e o deslizamento do TrA, visualizados em imagens ecográficas em tempo real, e congeladas para medição em diferido. Estes procedimentos foram apurados num estudo piloto de fidedignidade das medições em causa. Quanto à abordagem estatística das variáveis de performance muscular foi realizada uma análise da variância simples paramétrica para amostras independentes e um teste para a diferença de médias para amostras emparelhadas. Resultados: Observamos que no GC, a ausência de IRE cursou com uma performance idêntica nos dois momentos de avaliação e que nos dois grupos com IRE, das variáveis de performance, é significativamente diferente a contracção do TrA, para uma diferença de 1,95 mm no GIRE-VE (p=0,000) e de 0,84 mm no GIRE-VC (p=0,000). Ao comparar os grupos entre si houve diferenças no limiar da significância (p=0,056) para uma melhor contracção do TrA no GIRE-VE. As outras variáveis, contracção do OI e deslizamento do TrA, não revelaram efeito relacionado com a IRE em nenhum dos grupos. Conclusão: Dos resultados obtidos, podemos concluir que a IRE-VE, quando usada isoladamente, na Manobra do Transverso provoca um maior aumento na espessura do TrA, quando comparada com a IRE-VC . O uso da ecografia mostrou ser efectivo na facilitação da performance da Manobra do Transverso em sujeitos saudáveis.---------------------ABSTRACT: Study Design: Single Factor Experimental Design: Pre-Test Post-test Control Group Design. Objectives: To measure the contribution of different types of biofeedack on Transversus Abdominis (TrA) and Internal Oblique (IO) performance through changes in thickness and lateral slide of TrA anterior fascia during abdominal hollowing exercise (AHE). Background: Increasingly clinicians are using real-time ultrasound imaging as a form of supplementing feedback when teaching trunk stabilization exercises to patients; however, there has been no evidence of its effectiveness when used alone. Material and Methods: Seventy-five healthy subjects were divided randomly into 3 groups that received: group 1, no feedback; group 2, verbal and palpatory feedback, and group 3, realtime ultrasound feedback. The TrA and IO performance of each subject was twice assessed (before and after receiving feedback) when performing the AHE in a supine hook-lying position. Analysis of variance and T-test were used for the independent and paired samples, respectively, to determine significant changes in the performance of TrA and IO, based on intra and inter group analysis. Results: Group 1 had no differences between moments; group 2 had significant differences concerning TrA thickness (p=0,000) to a 0,84 mm thickness difference; group 3 had significant differences concerning TrA thickness (p=0,000) to a 1,94 mm difference; The ability to perform the AHE differed only among group 3 and group 1 (p=0.056), and only for changes in thickness of TrA muscle. No differences among groups were found neither for the lateral slide of TrA anterior fascia, nor for the internal oblique thickness. Conclusion: From the results of this study we conclude that real-time ultrasound feedback, when used alone during an AHE, can have a larger increase in TrA thickness when compared to verbal and palpatory feedback. The use of real time ultrasound showed to be effective as a feedback tool to facilitate the performance of the AHE in a supine hook-lying position in healthy subjects.

Monte Carlo simulations for dosimetric verification in photon and electron beam radiotherapy

Dissertação para obtenção do Grau de Doutor em Engenharia Biomédica

New strategies to detect and understand genotype-by-environment interactions and QTL-by-environment interactions

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

Parallelization of web processing services on cloud computing: A case study of Geostatistical Methods

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

Analysing and visualising areal crime data. A case study of residential burglary in San Francisco, USA

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

From the portolan chart of the mediterranean to the latitude chart of the atlantic

Thesis submitted to the Instituto Superior de Estatística e Gestão de Informação da Universidade Nova de Lisboa in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Information Management – Geographic Information Systems

Understanding the internet banking adoption by Portuguese customers - a unified theory of acceptance and use of technology and perceived risk application.

Trabalho de Projeto apresentado como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Strategic Noise Mapping with GIS for the Universitat Jaume I Smart Campus: best methodology practices

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

Effects of Spatial Pattern of GreenSpace on Land Surface Temperature: A case study on Oasis City Aksu, northwest China

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

Numerical methods and tangible interfaces for pollutant dispersion simulation

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

Intraday volatility

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

Hospital costs and random demand

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

Validation of NASA rotor 67 with openFOAM's transonic density-based solver

Dissertação para obtenção do Grau de Mestre em Engenharia Mecânica

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.