Variational Ensemble Kalman Filtering in Hydrology

The current thesis manuscript studies the suitability of a recent data assimilation method, the Variational Ensemble Kalman Filter (VEnKF), to real-life fluid dynamic problems in hydrology. VEnKF combines a variational formulation of the data assimilation problem based on minimizing an energy functional with an Ensemble Kalman filter approximation to the Hessian matrix that also serves as an approximation to the inverse of the error covariance matrix. One of the significant features of VEnKF is the very frequent re-sampling of the ensemble: resampling is done at every observation step. This unusual feature is further exacerbated by observation interpolation that is seen beneficial for numerical stability. In this case the ensemble is resampled every time step of the numerical model. VEnKF is implemented in several configurations to data from a real laboratory-scale dam break problem modelled with the shallow water equations. It is also tried in a two-layer Quasi- Geostrophic atmospheric flow problem. In both cases VEnKF proves to be an efficient and accurate data assimilation method that renders the analysis more realistic than the numerical model alone. It also proves to be robust against filter instability by its adaptive nature.

Kalman filter for computational market dynamics

Kalman filter is a recursive mathematical power tool that plays an increasingly vital role in innumerable fields of study. The filter has been put to service in a multitude of studies involving both time series modelling and financial time series modelling. Modelling time series data in Computational Market Dynamics (CMD) can be accomplished using the Jablonska-Capasso-Morale (JCM) model. Maximum likelihood approach has always been utilised to estimate the parameters of the JCM model. The purpose of this study is to discover if the Kalman filter can be effectively utilized in CMD. Ensemble Kalman filter (EnKF), with 50 ensemble members, applied to US sugar prices spanning the period of January, 1960 to February, 2012 was employed for this work. The real data and Kalman filter trajectories showed no significant discrepancies, hence indicating satisfactory performance of the technique. Since only US sugar prices were utilized, it would be interesting to discover the nature of results if other data sets are employed.

On Variational Ensemble Kalman Filtering

The Extended Kalman Filter (EKF) and four dimensional assimilation variational method (4D-VAR) are both advanced data assimilation methods. The EKF is impractical in large scale problems and 4D-VAR needs much effort in building the adjoint model. In this work we have formulated a data assimilation method that will tackle the above difficulties. The method will be later called the Variational Ensemble Kalman Filter (VEnKF). The method has been tested with the Lorenz95 model. Data has been simulated from the solution of the Lorenz95 equation with normally distributed noise. Two experiments have been conducted, first with full observations and the other one with partial observations. In each experiment we assimilate data with three-hour and six-hour time windows. Different ensemble sizes have been tested to examine the method. There is no strong difference between the results shown by the two time windows in either experiment. Experiment I gave similar results for all ensemble sizes tested while in experiment II, higher ensembles produce better results. In experiment I, a small ensemble size was enough to produce nice results while in experiment II the size had to be larger. Computational speed is not as good as we would want. The use of the Limited memory BFGS method instead of the current BFGS method might improve this. The method has proven succesful. Even if, it is unable to match the quality of analyses of EKF, it attains significant skill in forecasts ensuing from the analysis it has produced. It has two advantages over EKF; VEnKF does not require an adjoint model and it can be easily parallelized.

The Regulation of Skeletal and Cardiac Muscle Blood Flow in Humans. Studies by positron emission tomography with special reference to exercise, adenosine and nitric oxide

Virtually every cell and organ in the human body is dependent on a proper oxygen supply. This is taken care of by the cardiovascular system that supplies tissues with oxygen precisely according to their metabolic needs. Physical exercise is one of the most demanding challenges the human circulatory system can face. During exercise skeletal muscle blood flow can easily increase some 20-fold and its proper distribution to and within muscles is of importance for optimal oxygen delivery. The local regulation of skeletal muscle blood flow during exercise remains little understood, but adenosine and nitric oxide may take part in this process. In addition to acute exercise, long-term vigorous physical conditioning also induces changes in the cardiovasculature, which leads to improved maximal physical performance. The changes are largely central, such as structural and functional changes in the heart. The function and reserve of the heart’s own vasculature can be studied by adenosine infusion, which according to animal studies evokes vasodilation via it’s a_2A receptors. This has, however, never been addressed in humans in vivo and also studies in endurance athletes have shown inconsistent results regarding the effects of sport training on myocardial blood flow. This study was performed on healthy young adults and endurance athletes and local skeletal and cardiac muscle blod flow was measured by positron emission tomography. In the heart, myocardial blood flow reserve and adenosine A_2A receptor density, and in skeletal muscle, oxygen extraction and consumption was also measured. The role of adenosine in the control of skeletal muscle blood flow during exercise, and its vasodilator effects, were addressed by infusing competitive inhibitors and adenosine into the femoral artery. The formation of skeletal muscle nitric oxide was also inhibited by a drug, with and without prostanoid blockade. As a result and conclusion, it can be said that skeletal muscle blood flow heterogeneity decreases with increasing exercise intensity most likely due to increased vascular unit recruitment, but exercise hyperemia is a very complex phenomenon that cannot be mimicked by pharmacological infusions, and no single regulator factor (e.g. adenosine or nitric oxide) accounts for a significant part of exercise-induced muscle hyperemia. However, in the present study it was observed for the first time in humans that nitric oxide is not only important regulator of the basal level of muscle blood flow, but also oxygen consumption, and together with prostanoids affects muscle blood flow and oxygen consumption during exercise. Finally, even vigorous endurance training does not seem to lead to supranormal myocardial blood flow reserve, and also other receptors than A_2A mediate the vasodilator effects of adenosine. In respect to cardiac work, atheletes heart seems to be luxuriously perfused at rest, which may result from reduced oxygen extraction or impaired efficiency due to pronouncedly enhanced myocardial mass developed to excel in strenuous exercise.

Transcriptional Profiling of Organ‐Specific Autoimmunity in Human

Our understanding of the pathogenesis of organ‐specific autoinflammation has been restricted by limited access to the target organs. Peripheral blood, however, as a preferred transportation route for immune cells, provides a window to assess the entire immune system throughout the body. Transcriptional profiling with RNA stabilizing blood collection tubes reflects in vivo expression profiles at the time the blood is drawn, allowing detection of the disease activity in different samples or within the same sample over time. The main objective of this Ph.D. study was to apply gene‐expression microarrays in the characterization of peripheral blood transcriptional profiles in patients with autoimmune diseases. To achieve this goal a custom cDNA microarray targeted for gene‐expression profiling of human immune system was designed and produced. Sample collection and preparation was then optimized to allow gene‐expression profiling from whole‐blood samples. To overcome challenges resulting from minute amounts of sample material, RNA amplification was successfully applied to study pregnancy related immunosuppression in patients with multiple sclerosis (MS). Furthermore, similar sample preparation was applied to characterize longitudinal genome‐wide expression profiles in children with type 1 diabetes (T1D) associated autoantibodies and eventually clinical T1D. Blood transcriptome analyses, using both the ImmunoChip cDNA microarray with targeted probe selection and genome‐wide Affymetrix U133 Plus 2.0 oligonucleotide array, enabled monitoring of autoimmune activity. Novel disease related genes and general autoimmune signatures were identified. Notably, down‐regulation of the HLA class Ib molecules in peripheral blood was associated with disease activity in both MS and T1D. Taken together, these studies demonstrate the potential of peripheral blood transcriptional profiling in biomedical research and diagnostics. Imbalances in peripheral blood transcriptional activity may reveal dynamic changes that are relevant for the disease but might be completely missed in conventional cross‐sectional studies.

The Peace and Security Council of the African Union : its relationship with the United Nations, African Union and sub-regional mechanisms

Avhandlingen undersöker den Afrikanska Unionens freds- och säkerhetsråd och dess roll i framhävandet och upprätthållandet av fred, säkerhet och stabilitet i Afrika. Detta freds- och säkerhetsråd etablerades formellt 2004 och opererar under den Afrikanska Unionen (AU) som å sin sida upprättades 2002. Den Afrikanska Unionens freds- och säkerhetsråds roll i framhävandet av fred, säkerhet och stabilitet gör rådet till en hörnsten inom ramen för konfliktförebyggande och -hantering, samt konfliktlösning på den afrikanska kontinenten. Den Afrikanska Unionens freds- och säkerhetsråd spelar också en högst viktig roll i implementeringen av ansvaret att beskydda civilbefolkningen i konfliktsituationer. För uppfyllandet av sitt mandat att framhäva och upprätthålla fred, säkerhet och stabilitet i Afrika krävs det att freds- och säkerhetsrådet samarbetar med andra institutioner och mekanismer som handhar internationella och regionala freds- och säkerhetsärenden. Avhandlingen analyserar tre dimensioner av denna typ av relationer som freds- och säkerhetsrådet bör etablera med dessa organ och mekanismer för att kunna utföra sitt mandat effektivt. Först analyseras relationen mellan Afrikanska Unionens freds- och säkerhetsråd och Förenta Nationernas säkerhetsråd som också beskrivs i artikel 17 (1) i protokollet som förde till etablerandet av AU:s freds- och säkerhetsråd. Analysen understryker FN:s säkerhetsråd som det organ som bär det primära ansvaret i förhållande till fred och säkerhet, medan AU:s freds- och säkerhetsråd fungerar som en kompletterande komponent i sin roll som ett regionalt organ. Avhandlingen fortsätter med att analysera förhållandet mellan AU:s freds- och säkerhetsråd och andra organ inom AU, samt andra relevanta institutioner som framgår av artikel 10, 18 (1), 19 och 20 i protokollet för rådets etablerande. Avhandlingen diskuterar i detalj hur samarbetet mellan AU:s freds- och säkerhetsråd och dessa institutioner och organ kunde förstärkas till fördel för effektivt framhävande och upprätthållande av fred och säkerhet i Afrika. Slutligen analyserar avhandlingen samarbetet mellan AU:s freds- och säkerhetsråd och sub-regionala mekanismer etablerade under regionala ekonomiska gemenskaper som beskrivs i artikel 16 i protokollet för etablerandet av rådet. Avhandlingen diskuterar i detalj rollen för de sub-regionala mekanismerna i den afrikanska freds- och säkerhetsarkitekturen. Avhandlingen diskuterar vidare förhållandet mellan de sub-regionala mekanismerna och den afrikanska stand-by styrkan ASF och förutsättningarna för detta arrangemang att bemöta afrikanska konflikter. Avhandlingen fokuserar också på en harmoniserings- och samarbetsprocess i förhållande till de sub-regionala mekanismerna, de regionala ekonomiska gemenskaperna och den Afrikanska Unionens freds- och säkerhetsråd. Kort sagt beskriver avhandlingen hur förhållandet mellan AU:s freds- och säkerhetsråd och de ovan nämnda organ och mekanismer har en faktisk och potentiell möjlighet att effektivt bidra till fred, säkerhet och stabilitet i Afrika. Avhandlingen identifierar utmaningarna kring att göra detta till ett fungerande förhållande samtidigt som den genererar både generella och specifika rekommendationer om hur dessa utmaningar bäst kan bemötas. Några av dessa utmaningar utgörs av följande aspekter: konflikten mellan AU:s och FN:s reglemang i bemötandet av freds- och säkerhetsutmaningar; de olika metoderna i FN och AU vid implementeringen av principen av universell jurisdiktion; konflikten mellan de olika mandaten som AU:s freds- och säkerhetsråd och FN:s säkerhetsråd har i förhållande till implementeringen av principen om intervention; och konflikten mellan lagarna och metoderna i förhållande till AU:s freds- och säkerhetsråd och de regionala mekanismerna. En av de huvudsakliga rekommendationerna i avhandlingen i bemötandet av de ovan nämnda utmaningarna är att harmonisera de olika systemen för att försäkra att det föreligger ett samordnat bemötande av konflikter i Afrika. Efter att ha identifierat luckorna i AU:s freds- och säkerhetsprotokoll med speciell fokus på förhållandet mellan rådet och de relevanta organen och mekanismerna rekommenderar avhandlingen ett antal tillägg och modifieringar till instrumentet ifråga för att effektivera, stärka och upprätthålla detta förhållande. Avhandlingen föreslår att dessa tillägg och modifieringar skulle företas under 2014 då detta år markerar 10 år efter att AU:s freds- och säkerhetsråd etablerades. Idén bakom detta företagandet ligger i att 10 år torde vara en tillfredställande tidsperiod för att mäta hur freds- och säkerhetsrådet har fungerat och hur dess förhållande med de relevanta institutionerna och mekanismerna kunde förbättras. Avhandlingen representerar den bredaste och nyaste studien inom ramen för artikel 16, 17, 18, 19 och 20 i protokollet för AU:s freds- och säkerhetsråd och introducerar ett innovativt bemötande av utmaningar till fred, säkerhet och stabilitet på den afrikanska kontinenten. Avhandlingen bidrar till teorin och praxisen i AU:s freds- och säkerhetsråd vilket kan vara av intresse för både forskare och praktiker i folkrätt såväl som i internationella freds- och säkerhetsstudier, speciellt i Afrika.

On Glucose Metabolism in Patients with the m.3243A>G Mutation

Background: The m.3243A>G mutation in mitochondrial DNA is the most common cause for mitochondrial diabetes. In addition, unexpected deaths related to the m.3243A>G associate with encephalopathy and cardiomyopathy. Failing mitochondrial respiratory chain in neurons, myocytes and beta cells is considered to underlie the multiorgan manifestations of the m.3243A>G. Aims: The primary aim of the study was to characterize the organ-specific glucose metabolism in patients with m.3243A>G and secondly, to study patients with or without signs of diabetes, cardiomyopathy or encephalopathy. The insulin-stimulated glucose metabolism in brain, heart, skeletal muscle, adipose tissue and liver were measured with 2-deoxy-2-[18F]fluoro-α-D-glucose in 15 patients and 14 controls. Brain oxygen metabolism was assessed with [15O]oxygen and insulin secretion was modelled based on oral glucose tolerance test. Results: The glucose oxidation in brain was globally decreased in patients with or without clinical encephalopathy. The insulin-stimulated glucose influx to skeletal muscle and adipose tissue was decreased in patients with or without diabetes as the hepatic glucose metabolism was normal. Impaired beta cell function and myocardial glucose uptake were associated with the high m.3243A>G heteroplasmy. Conclusions: This cross-sectional study suggests that: 1) The ability of insulin to stimulate glucose metabolism in skeletal muscle and adipose tissue is weakened before the beta cell failure results in mitochondrial diabetes. 2) Glucose oxidation defect is detected in otherwise unaffected cerebral regions in patients with the m.3243A>G, thus it likely precedes the clinical encephalopathy. 3) Uneconomical glucose hypometabolism during hyperinsulinemia contributes to the cardiac vulnerability in patients with high m.3243A>G heteroplasmy