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- Axelsson, Anton, 1981-
(författare)
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Knowledge elicitation as abstraction of purposive behaviour
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Researchers use knowledge elicitation methods to document expert knowledge for the primary purpose of understanding cognitive processes and with this understanding, technical solutions to resolve human factors issues can be produced. This dissertation offers a novel perspective on knowledge elicitation as an abstraction process. Such a theoretical framework has emerged by consolidating the ecological approach of Brunswikian psychology with the ideas of tacit and personal knowledge of Polanyian epistemology. Traditionally, knowledge elicitation has been considered an extraction process in which knowledge can be readily transferred from one individual to another. Here, this traditional position is rejected in favour of Polanyi’s premise that much of the knowledge individuals possess is tacit in nature, which implies that it cannot be documented easily, expressed in explicit form or explained. In this dissertation, knowledge is characterised as a personal process of knowing, highlighting context as a subjective knowledge structure of personal experiences that is formulated implicitly and indirectly over time through a dynamic interaction with the environment. Therefore, tacit knowledge cannot be articulated or shared; however, learners can be inspired by observing other individuals' purposive (i.e., goal-directed) behaviours and thus shape their own tacit knowledge once they practise the observed skills and develop conceptual understanding through reasoning about the learning process. Knowledge elicitation thereby makes use of observations, questions, or more structured process tracing methods in environments familiar to the observed individuals to elicit purposive behaviour from them. Accordingly, functional descriptions can be produced in this process that further conceptual understanding of a particular domain. Knowledge elicitation procedures are a powerful set of methods for reaching such functional descriptions. Moreover, by understanding the resulting knowledge elicitation data as an abstraction derived from multiple collection points in the same environment, the focus shifts from purely subjective mental constructs to the impact of environmental constraints.
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| 2. |
- Karlsson Tiselius, Andreas, 1977-
(författare)
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Island biogeography of young land uplift islands - viewed through the lens of bryophytes in a northern Swedish archipelago
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Increasing habitat fragmentation and rapid global warming is changing the conditions for species populations and ecological communities around the world. This presents challenges for the maintenance of biodiversity and a dominant paradigm for conservation in fragmented habitats is given by island biogeography and metapopulation (or metacommunity) ecology.In this thesis I approach key concepts (area, connectivity and community assembly) in island biogeography and metacommunity ecology within the context of a dynamic land uplift archipelago. The presented work consists of two interwoven themes: (i) A methodological theme in which statistical approaches are developed to deal with the complexities of multispecies dynamic systems, and (ii) an applied theme dealing with community assembly and island biogeography of bryophytes on young land uplift islands.To describe island connectivity for entire species assemblages, an approach using functional principal component analysis (fPCA) on patch connectivity functions (the connectivity of an island as a continuous function of a variable representing the spatial scale of species dispersal capacities) was developed. In addition, a new statistical method, functional co-inertia analysis (fCoIA), for analyzing co-variation between multivariate species data and continuous functions was developed and applied to the relation between bryophyte species incidences and the island age/area-dynamics.Primarily asexual bryophyte species are dispersal limited and presence probabilities are related to island connectivity. No such patterns were found for species, at least occasionally, producing spores. Our results suggest that bryophyte dispersal is regulated by the contribution of spores to a regional spore rain and that bryophyte species with low spore output at the landscape level may be extra vulnerable under habitat fragmentation and loss. Having specialized asexual propagules increases the presence probabilities on islands, partly compensating for the dispersal limitation in asexual species. This suggests a trade-off between dispersal and establishment capacity, but also points to the importance of local dispersal for maintaining populations under the succession driven spatial turnover of microsites on the islands. Bryophyte colonization is strongly limited by habitat availability when a given habitats is rare, but there seems to exist a threshold over which other processes (e.g. dispersal limitation) become more important. Species with more vagile life history strategies appear to be stronger affected by the area of available habitats than many perennial species
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| 3. |
- Nguyen, Van Dang, 1985-
(författare)
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High Performance Finite Element Methods with Application to Simulation of Vertical Axis Wind Turbines and Diffusion MRI
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Finite element methods have been developed over decades, and together with the growth of computer power, they become more and more important in dealing with large-scale simulations in science and industry.The objective of this thesis is to develop high-performance finite element methods, with two concrete applications: computational fluid dynamics (CFD) with simulation of turbulent flow past a vertical axis wind turbine (VAWT), and computational diffusion magnetic resonance imaging (CDMRI). The thesis presents contributions in the form of both new numerical methods for high-performance computing frameworks and efficient, tested software, published open source as part of the FEniCS/FEniCS-HPC platform. More specifically, we have four main contributions through the thesis work.First, we develop a DFS-ALE method which combines the Direct finite element simulation method (DFS) with the Arbitrary Lagrangian-Eulerian method (ALE) to solve the Navier-Stokes equations for a rotating turbine. This method is enhanced with dual-based a posteriori error control and automated mesh adaptation. Turbulent boundary layers are modeled by a slip boundary condition to avoid a full resolution which is impossible even with the most powerful computers available today. The method is validated against experimental data with a good agreement.Second, we propose a partition of unity finite element method to tackle interface problems. In CFD, it allows for imposing slip velocity boundary conditions on conforming internal interfaces for a fluid-structure interaction model. In CDMRI, it helps to overcome the difficulties that the standard approaches have when imposing the microscopic heterogeneity of the biological tissues and allows for efficient solutions of the Bloch-Torrey equation in heterogeneous domains. The method facilitates a straightforward implementation on the FEniCS/ FEniCS-HPC platform. The method is validated against reference solutions, and the implementation shows a strong parallel scalability.Third, we propose a finite element discretization on manifolds in order to efficiently simulate the diffusion MRI signal in domains that have a thin layer or a thin tube geometrical structure. The method helps to significantly reduce the required simulation time, computer memory, and difficulties associated with mesh generation, while maintaining the accuracy. Thus, it opens the possibility to simulate complicated structures at a low cost, for a better understanding of diffusion MRI in the brain.Finally, we propose an efficient portable simulation framework that integrates recent advanced techniques in both mathematics and computer science to enable the users to perform simulations with the Cloud computing technology. The simulation framework consists of Python, IPython and C++ solvers working either on a web browser with Google Colaboratory notebooks or on the Google Cloud Platform with MPI parallelization.
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| 4. |
- Røyne, Frida, 1985-
(författare)
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Exploring the relevance of uncertainty in the life cycle assessment of forest products
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The role of forest biomass as a replacement for fossil fuels and products is becoming increasingly prominent as a means to mitigate climate change. To guide a sustainable transition towards a forest-based bio-economy, it is important that advantages and disadvantages of forest products are assessed, to ensure that the products deliver environmental impact reduction. Life Cycle Assessment (LCA) has become heavily relied upon for assessing the environmental impact of bio-based products. However, LCAs of similar product systems can lead to results that differ considerably, and the method is, thus, associated with uncertainties. It is, therefore, necessary to explore the relevance of uncertainties, to build knowledge about enablers and challenges in using LCA for assessing forest products.Three important challenges in the context of uncertainty in LCA are the focus of this thesis: 1) system boundaries, 2) climate impact assessment practice, and 3) allocation. More specifically, the relevance of a) including and excluding life cycle phases, b) potentially important climate aspects, and c) applying different allocation methods, was assessed. Case studies involved a chemical industry cluster, a biorefinery, and single product value chains for a plastic box, a fuel, and a building.In summary, the thesis demonstrates that:A major share of the environmental impact related to the production of an industry cluster can occur outside the cluster gates, so when strategies involving a transition to forest biomass feedstock are developed and evaluated, a life cycle perspective reveals the full environmental impact reduction potential.For bio-based products differing in functional properties from the fossil products they are meant to replace, material deterioration in the use phase can contribute substantially to overall environmental performance. This is acknowledged if all life cycle phases are regarded.As climate aspects commonly not assessed in forest product LCAs could influence results greatly, and even affect the outcome of comparisons between forest and non-forest products, the climate impact of forest products is uncertain. It is, therefore, important that this uncertainty is acknowledged and communicated, and that appropriate methods and guidelines are developed.The choice of allocation method in the LCA of biorefinery products can have a major influence on results, especially for physically non-dominant products and in consequential studies. In these cases, scenario analysis is especially valuable to show the possible range of results.LCA provides useful guidance for forest product development and production as the life cycle approach reveals causes of environmental impact throughout the product value chain. Proper identification, estimation, and management of uncertainties strengthen the provision of reliable decision support.
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| 5. |
- Gustafsson Bragde, Hanna, 1979-
(författare)
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Biomarkers of Inflammation and Intestinal Mucosa Pathology in Celiac Disease
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Celiac disease (CD) is a chronic small intestinal immune-mediated enteropathy triggered by gluten. The only currently available treatment is complying with a lifelong gluten-free diet, which should not be commenced before a CD diagnosis has been established by diagnostic test results (including histopathologic assessment of small intestinal biopsies and CD-specific antibody levels). This makes diagnostic swiftness and accuracy important. In cases with low CD-specific antibody levels and/or low-grade intestinal injuries the diagnosis can be difficult to establish. The main objective of this thesis was to complement and improve CD diagnostics by identifying and implementing new biomarkers, mainly based on gene expression, in small intestinal biopsies and blood. In paper I, genes were selected to reflect villous height, crypt elongation, immune response, and epithelial integrity. The results showed that a subset of those genes could discriminate active CD mucosa from mucosa without CD-related changes and grade the intestinal injury. In paper III, an unbiased investigation of gene expression in CD mucosa was performed using transcriptome analysis. Active CD and non-CD mucosa showed differential expression in a subset of genes, and some were differentially expressed in CD mucosa before histopathologic assessment could confirm intestinal alterations compatible with a CD diagnosis. Gene set analysis revealed that there are many biological processes affected in CD mucosa, including those associated with immune response, microbial infection, phagocytosis, intestinal barrier function, metabolism, and transportation.In parallel, gene expression was investigated in stabilised whole blood. Blood is a more accessible sampling material than intestinal biopsies, and stabilised blood is suitable for routine diagnostics since transcript levels are preserved at sampling. In paper II, expressions from a selection of genes were quantified in stabilised whole blood (RNA) and/or plasma (protein). Three genes with differential expression in CD were identified. Compared to the CD-specific autoantibodies against tissue transglutaminase (anti-TG2) alone, the addition of the information from the new potential markers resulted in a nonsignificant contribution to the diagnostic capacity of anti-TG2. An unbiased investigation using transcriptome analysis (paper IV) showed that gene level expression differences in stabilised whole blood were small between CD and non-CD. However, expression differences on a gene set level could potentially be used in CD diagnostics. CD-associated biological processes suggested by the results included a pro-inflammatory response, negative regulation of viral replication, proliferation, differentiation, cell migration, cell survival, translation, and haemostasis.Expression analysis using real-time polymerase chain reaction (PCR) is easy to perform, with instrumentation available at most clinical laboratories. Although select solitary biomarkers could be very useful in the diagnosis of CD, basing gene expression profiles on pathway information instead of single genes might also disclose disease heterogeneity between patients and add stability to a diagnostic method based on gene expressions. In conclusion, the results of this work demonstrate that analysing the expression of a few small intestinal genes can complement CD diagnostics. The application of gene expression analysis in cases with minor small intestine histopathological changes shows promising results, but needs further investigations. Additionally, gene expressions in other inflammatory diseases of the small intestine need to be investigated and compared with CD to complete the picture. Moreover, the findings from this work give clues about the biological contexts in which CD resides, and the potential of gene expression in blood at a gene set level is of interest for further investigations.
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