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Model reduction is a powerful and ubiquitous tool used to reduce the complexity of a dynamical system while preserving the input-output behavior. It has been applied throughout many different disciplines, including controls, fluid and structural dynamics. Model reduction via proper orthogonal decomposition (POD) is utilized for of control of partial differential equations. In this thesis, the analytical expressions of POD modes are derived for the heat equation. The autocorrelation function of the latter is viewed as the kernel of a self adjoint compact operator, and the POD modes and corresponding eigenvalues are computed by solving homogeneous integral equations of the second kind. The computed POD modes are compared to the modes obtained from snapshots for both the one-dimensional and two-dimensional heat equation. Boundary feedback control is obtained through reduced-order POD models of the heat equation and the effectiveness of reduced-order control is compared to the full-order control. Moreover, the explicit computation of the POD modes and eigenvalues are shown to allow the computation of different n-widths approximations for the heat equation, including the linear, Kolmogorov, Gelfand, and Bernstein n-widths.

Aerodynamic parameter estimation from closed loop data has been developed as another research area since control and stability augmentation systems have been mandatory for aircrafts. This thesis focuses on aerodynamic parameter estimation of an air to ground missile from closed loop data using separate surface excitations. A design procedure is proposed for designing separate surface excitations. The effect of excitations signals to the system is also analyzed by examining autopilot disturbance rejection performance. Aerodynamic parameters are estimated using two different estimation techniques which are ordinary least squares and complex linear regression. The results are compared with each other and with the aerodynamic database. An application of the studied techniques to a real system is also given to validate that they are directly applicable to real life.

Aerodynamic parameter estimation from closed loop data has been developed as another research area since control and stability augmentation systems have been mandatory for aircrafts. This thesis focuses on aerodynamic parameter estimation of an air to ground missile from closed loop data using separate surface excitations. A design procedure is proposed for designing separate surface excitations. The effect of excitations signals to the system is also analyzed by examining autopilot disturbance rejection performance. Aerodynamic parameters are estimated using two different estimation techniques which are ordinary least squares and complex linear regression. The results are compared with each other and with the aerodynamic database. An application of the studied techniques to a real system is also given to validate that they are directly applicable to real life.

The aim of this Master thesis was to examine news journalism covering expressions of mourning related to violent or unexpected deaths. What rituals for mourning are brought out in media and do media present guidance to how mourners should behave?   The questions examined were: What characterised news events that leaded to texts on expressions of mourning? How was grief framed? Which narrative patterns were there in the texts? How was the deceased represented? How were the mourners represented?   165 texts, from Swedish daily newspapers, covering 93 different news events were analysed. The methods were mainly discourse analysis with focus on identities and relations, but also semiotic analysis with focus on staging and symbols and narrative analysis with focus on patterns for storytelling.   The result showed that a news story about ordinary people expressing their feelings of grief has elements of melodrama. The news story is based on the myth of the victim, and formed as a typical story where equilibrium is disturbed when the inconceivable happens and the mourners can by their actions restore equilibrium. The paradigms behind are the opposites life – death and good – evil.    The deceased is represented as a victim in a mythic sense. The most important qualities of a victim are youth, innocence and goodness. The victim is framed as a person we could sympathise and identify with. The mourners in the texts praise the victim and sanctify the place where the victim died with candles, roses and notes. The mourners are essential to the story; they create identification and an identity that include us as readers in a community and a discourse of mourning and mourners. The ordinary people who appear as mourners in the texts are relatives and close friends of the victim, but also mourning tourists, media chosen friends and anonymous women who are represented, in a stereotypical way, as the professional female mourner who weep over the deceased. In some texts celebrities appear as mourners of ordinary people, and they personalize how the distinction between public and private is erased in popular journalism. They also might give a kind of legitimacy to the way media frame the story about ordinary people mourning the innocent victim.   Some texts had a partly diverging story. If the victim, in some aspect, could not be framed as innocent the paradigm good – evil became problematic. When victims or mourners had foreign origin the contrast us – them was added.  In some texts the ethical code for Swedish journalists was disregarded, mainly by publishing information on ethnicity or by interviewing children and people in shock

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Species of Argulus are macro-, ecto-parasites known to infect a wide variety of fish, but in the UK mainly cause problems in rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta). Argulus foliaceus is estimated to have caused problems in over 25% of stillwater trout fisheries in the UK. While A. foliaceus does not usually cause high levels of mortality, the parasite affects fish welfare, and also makes fish harder to catch due to morbidity and reduced appetite. This can cause severe economic problems for the fishery, resulting in reduced angler attendance due to poor capture rates and the reduced aesthetic appearance of fish; in the worst-case scenario this can result in the closure of the fishery. Current methods of control include chemical treatment with chemotherapeutant emamectin benzoate (Slice), physical intervention with egg-laying boards which are removed periodically and cleaned in order to reduce the number of parasites hatching into the environment, and the complete draining and liming of the lake to remove all free-living and egg stages of the parasite. While these treatments have all been shown to reduce parasite numbers, none are known to have resulted in permament eradication of the parasite. There is evidence to suggest that A. foliaceus will eventually develop resistance to Slice - the only currently available chemical treatment against the infection - and egg-laying boards and the draining and liming of the lake are both time- and labour-intensive. Previous studies have shown that slow fish turnover is a risk factor with respect to A. foliaceus infections, and with a wide variety of stocking practices occurring in the UK one of the first aims of this project was to determine their impact on the host-parasite dynamics. Mathematical models provide a cost-effective way of examining the impact of such practices, and after a literature review (chapter one), in chapter two a three-compartment mathematical model was adapted for use in the A. foliaceus-trout system. Four generalised stocking methods were then incorporated and analysed, and a minimum threshold host density was found to be necessary to sustain the parasite. Including a function which reduced the capture rate as the parasite burden increased allowed the parasite to survive at a lower host density, as susceptible fish were removed from the water at a slower rate, and attached parasites also remained in the water for longer. This resulted in hysteresis in the model, as the invasion threshold for the parasite remained the same, but once established the parasite became harder to eradicate, requiring significant reductions in the host density. In chapter three the model was further developed in order to improve its biological real- ism. Several features were added and these included: natural host mortalities, a separate compartment for the parasite egg population, and parasite survival after the natural or parasite-induced mortality of its host. In chapter four seasonality was added by incorporating temperature-dependent egg-laying rates and an over-wintering period during which the parasite was unable to reproduce. The model was then fit to the available data, and estimates for the rate of parasite-induced host mortalities and the parasite’s rate of attachment to a host were found. In chapter five we returned to stocking methods, this time looking at the frequency and timing of stocking events and the impact of imposing a rod limit (whereby anglers are only permitted to capture four fish per visit); it was concluded that while current guidelines suggest that very frequent trickle stocking is recommended when dealing with Argulus spp. infections, monthly stocking does not appear to worsen the infection, and if the fish capture rate is high then less-frequent stocking may also be permissable - particularly if stocking occurs towards the end of the year when the parasite is no longer active. This practice may, however, be detrimental to the fishery due to low fish densities in the summer months. In chapter six treatment with Slice was included in the model, and it was demonstrated that with constant treatment, and in the absence of reservoir hosts and a withdrawal period from the drug prior to stocking treated fish into the fishery, the parasite was eradicated. Under current veterinary cascade guidelines, however, trout are required to undergo a withdrawal period of 500 degree days prior to being made available for human consumption. When this was included in the model the drug still decreased parasite abundance, but did not eradicate it - this is in agreement with results reported by communications with fishery managers currently treating fish with Slice. A reduction in the withdrawal period of 25% was shown to further decrease parasite abundance, but still did not result in parasite extinction. As constant treatment with Slice is not advisable due to the potential for resistance build-up, we then sought to find time at which to apply a single treatment of Slice, and found that this was in August when the temperature was highest and the parasite was reproducing and attaching to hosts quickly. Egg-laying boards were also incorporated into the model and similarly to findings by Fenton et al. [11] the success of this treatment was mostly dependent on the proportion of eggs being laid on the boards (as opposed to natural substrates). In contrast with the A. coregoni system, however, the boards would have to be cleaned and replaced more frequently that once per year, as several cohorts of A. foliaceus emerge during a single year.

To understand how the components of a complex system like the biological cell interact and regulate each other, we need to collect data for how the components respond to system perturbations. Such data can then be used to solve the inverse problem of inferring a network that describes how the pieces influence each other. The work in this thesis deals with modelling the cell regulatory system, often represented as a network, with tools and concepts derived from systems biology. The first investigation focuses on network sparsity and algorithmic biases introduced by penalised network inference procedures. Many contemporary network inference methods rely on a sparsity parameter such as the L1 penalty term used in the LASSO. However, a poor choice of the sparsity parameter can give highly incorrect network estimates. In order to avoid such poor choices, we devised a method to optimise the sparsity parameter, which maximises the accuracy of the inferred network. We showed that it is effective on in silico data sets with a reasonable level of informativeness and demonstrated that accurate prediction of network sparsity is key to elucidate the correct network parameters. The second investigation focuses on how knowledge from association networks can be transferred to regulatory network inference procedures. It is common that the quality of expression data is inadequate for reliable gene regulatory network inference. Therefore, we constructed an algorithm to incorporate prior knowledge and demonstrated that it increases the accuracy of network inference when the quality of the data is low. The third investigation aimed to understand the influence of system and data properties on network inference accuracy. L1 regularisation methods commonly produce poor network estimates when the data used for inference is ill-conditioned, even when the signal to noise ratio is so high that all links in the network can be proven to exist for the given significance. In this study we elucidated some general principles for under what conditions we expect strongly degraded accuracy. Moreover, it allowed us to estimate expected accuracy from conditions of simulated data, which was used to predict the performance of inference algorithms on biological data. Finally, we built a software package GeneSPIDER for solving problems encountered during previous investigations. The software package supports highly controllable network and data generation as well as data analysis and exploration in the context of network inference. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p><p> </p>

Although inductively coupled plasma mass spectrometry (ICP-MS) is generally considered a reliable analytical technique, increasing demands on its capabilities require continued research and improvements. ICP-MS is susceptible to both matrix effects and drift, leading to a decline in accuracy and precision. A number of techniques are routinely used to compensate for these issues. Internal standardization is one such solution that requires relatively simple sample preparation and yet offers the possibility of improving both accuracy and precision. In order to be effective, an optimal analyte/internal standard pair must be chosen. Traditionally, analyte/internal standard pairs are chosen based on similarities in mass and/or ionization potential. The present studies sought to develop a program that determined standards based on the minimization of analytical error. 102 masses were monitored over 27 perturbations, i.e., changes to sample matrix and operating parameters. The standard deviations of the analyte/internal standard ratios were then used as a measure of internal standard performance. A thorough statistical analysis was conducted to determine trends between a good analyte/internal standard pair and similarities in chemical property. Similarities in mass offered the strongest relationship to a good internal standard choice, although many exceptions existed. The program was then tested over time and multiple instrument optimizations as well as on a completely different ICP-MS instrument. Results of these tests suggest that the data originally collected for the prediction program is not instrument-specific and thus provided a broader base of useful applications. Due to its unmatched sensitivity and multielement capabilities, ICP-MS is frequently utilized for biological samples. A more recent application, however, seeks to use ICPMS for the purpose of determining specific associations between metals and proteins. Such speciation requires a high resolution and reproducible separation prior to ICPMS analysis. Gel electrophoresis offers good separation and is well matched with the scanning properties of laser ablation sample introduction. The present study utilized native gel electrophoresis coupled with a uniquely modified electroblot system to improve sensitivity and to elucidate additional information. Chemically modified quartz fiber filters were successfully used as the transfer membrane to improve protein and metal capture efficiency. / text

Type 2 diabetes is a global disease which affects an increasing number of peopleevery year. At the heart of the disease lies insulin resistance in the target tissues,primarily fat and muscle. The insulin resistance is caused by the failure of a complexsignalling network, and several mechanistic hypotheses for this failure havebeen proposed. Herein, we evaluate a hypothesis that revolves around the proteinmammalian target of rapamycin (mTOR) and its feedback signals to insulin receptorsubstrate-1 (IRS1). In particular, we have re-examined this hypothesis andrelevant biological data using a mathematical modelling approach. During the course of modelling we gained several important insights. For instance,the model was unable to reproduce the relation between the EC50-valuesin the dose-response curves for IRS1 and its serine residue 312 (Ser-312). Thisimplies that the presented hypothesis, where the phosphorylation of Ser-312 liesdownstream of the tyrosine phosphorylation of IRS1, is inconsistent with the provideddata, and that the hypothesis or the data might be incorrect. Similarly, wealso realized that in order to fully account for the information in the dose-responsedata, time curves needed to be incorporated into the model. A preliminary model is presented, which explains most of the data-sets, butstill is unable to describe all the details in the data. The originally proposed hypothesisas an explanation to the given data has been revised, and our analysisserves to exemplify that an evaluation of a mechanistic hypothesis by mere biochemicalreasoning often misses out on important details, and/or leads to incorrectconclusions. A model-based approach, on the other hand, can efficiently pin-pointsuch weaknesses, and if combined with a comprehensive understanding of biologicalvariation and generation of experimental data, mathematical modelling canprove to be a method of great potential in the search for mechanistic explanationsto the cause of insulin resistance in type 2 diabetics.