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Coming dissertations at Uppsala university

Please note that the date and time given on these pages is the time of electronic publication, and not the date of the public defense. To find the time and venue of the public defense, please follow the link to DiVA of the thesis in question.
  • Hip Revision Surgery : Identification of Genetic Markers and Evaluation of Novel Treatment Strategies

    Author: Anders Brüggemann
    Publication date: 2020-02-07 09:34

    Total hip arthroplasty (THA) is, despite its overall good outcome, for some patients followed by hip revision surgery. This seems in parts to be because of genetic susceptibility to revision surgery. The most common reason for revision surgery is aseptic loosening followed by periprosthetic joint infection and dislocation. Cups made of porous tantalum (TM cups) were thought to be favorable in revision surgery to address aseptic loosening, but they seem to confer an increased risk of dislocation. The effectiveness and biocompatibility in vivo of TM cups have not been researched. Dual mobility cups (DMCs) with two articulating surfaces are proposed to prevent dislocation to a higher degree than standard polyethylene liners.

    Our hypotheses were that TM cups are superior to their historical treatment alternative in terms of re-revision rates; that the combination of DMC cemented into TM cups would decrease the risk for dislocation after revision surgery; that tantalum ion liberation is marginal after the use of TM cups; and that certain risk genes are associated with an increased risk for revision surgery after total joint arthroplasty.

    Studies I&II were register-based cohort studies comparing the implant survival of TM cups and conventional acetabular reinforcement rings (study I), and the combination of TM cups/DMC with TM cups/standard polyethylene liners (study II). We found that TM cups perform equally well as reinforcement rings, but that the two implants differ in their failure mechanisms. Cementing a DMC into TM cups adequately addressed the issue of recurrent dislocation. In study III we investigated whether tantalum ion liberation does occur after implantation of a TM cups and how this affects patients’ immunological response by comparison of three groups: primary non-tantalum THA, primary tantalum THA and revision tantalum THA. We found the highest concentration of tantalum ions in the revision cases, yet tantalum ions were not associated with an immunological response, and we found no signs of alteration in the investigated lymphocyte subsets. Study IV aimed to identify possible risk genes for revision surgery after total hip or knee replacement by a genome wide association study. We found six significant risk genes for the endpoint revision surgery for any reason, and three for the endpoint revision due to aseptic loosening. We found a variety of suggestive risk genes within the region coding for the ABO-system.

    In conclusion, the novel treatment options TM cups and DMC show good results in hip revision surgery, but longer follow-up is warranted. The use of porous tantalum seems not to be associated with the immunological activation that can be observed in metallosis. The risk for revision surgery is associated with certain risk genes.

  • Aiming at Moving Targets : Applying Cognitive Work Analysis to Work Domains in Transition

    Author: Ida Löscher
    Publication date: 2020-02-06 10:44

    The design of IT systems for complex work environments is essential for workers to be able to operate more effectively and efficiently. To design a system that supports the workers' specific tasks we need to understand the work demands and the context in which the system operates. However, this is a difficult task because of the dynamic nature of complex systems. The thesis investigates how the cognitive work analysis (CWA) framework (Vicente, 1999) can be applied to understand a domain under transformation by (1) developing methods to manage challenges associated with applying CWA to real-world complex systems and (2) investigating how models from the CWA framework can be used to contend with the moving target for development. The studies are carried out within two quite different application domains: long-haul driving and health care. An activity prioritization method was suggested as a useful technique to focus the analyzing efforts during the analysis of tasks and strategies. However, adaption to practical constraints has to be done thoughtfully in order not to lose the value of the analysis. Moreover, workshops were proposed as a means to bridge the gap between the analysis and design by finding design metaphors and possible future work strategies from the domain knowledge of the drivers. Third, a study was done using the abstraction hierarchy (AH) to learn about digitization in health care, which is an example of ongoing change in a work domain. The AH was also adapted to model health IT systems as a means to provide an overview and consistent vision of strategic decisions. Using the AH as an overview of sub-systems that were developed by different organizations or organizational units would make it possible to identify collaboration needs or a lack of connectivity and integration between systems. The AH can therefore be applied to support the development of an IT system that is to be part of a transforming work domain.

  • Induction of Mast Cell Apoptosis via Granule Permeabilization : A Novel Approach to Target Mast Cells

    Author: Aida Paivandy
    Publication date: 2020-02-06 09:23

    Mast cells are densely granulated tissue-resident immune cells that play an important role in orchestrating inflammatory responses. Dysregulated increases in the numbers and activation status of mast cells can have deleterious consequences for the body in various inflammatory diseases. Mast cells are best-known for their detrimental roles in allergic diseases, e.g., asthma. Thus, strategies that target mast cells and their harmful activities in such pathological conditions are potentially attractive therapeutic options. An efficient strategy to accomplish a full blockade of the harmful events mediated by various mast cell mediators is to locally eliminate mast cell populations altogether by inducing their apoptosis.

    Using in vitro-cultured mast cells, we identified that mefloquine, an antimalarial drug with lysosomotropic activity, causes permeabilization of secretory granules, increased production of reactive oxygen species (ROS), release of granule-localized proteases into the cytosol and apoptotic cell death (Paper I). Moreover, intraperitoneal injections of mefloquine in mice resulted in a reduced peritoneal mast cell population in vivo.

    To evaluate the possibility of using lysosomotropic agents for selectively depleting human lung mast cells by induction of apoptosis, human lung specimens were used. Exposure of either intact human lung tissue, purified lung mast cells or mixed populations of lung cells to mefloquine revealed that human lung mast cells are highly susceptible to ROS-induced apoptosis in this setting. In contrast, other cell populations of the lung were largely refractory (Paper II).

    Lastly, in an attempt to gain a deeper insight into the mechanism underlying ROS production and the downstream events in response to lysosomotropic challenge, we identified that the mast cell secretory granules comprise major subcellular compartments for ROS production in response to mefloquine (Paper III). Lysosomal iron, granzyme B and the ERK1/2 MAP kinase signaling pathway were found to contribute to production of ROS in response to mefloquine. Furthermore, granule acidification was shown to be essential for mefloquine-mediated effects in mast cells, i.e., granule permeabilization, ROS production and cell death. Collectively, the present thesis introduces the possibility of inducing selective mast cell apoptosis via granule permeabilization as a novel strategy to target mast cells. Thus, this strategy has a potential to be used therapeutically to ameliorate mast cell-mediated detrimental effects in inflammatory diseases, such as asthma.

  • Solid-state nanopores : fabrication and applications

    Author: Shuangshuang Zeng
    Publication date: 2020-01-31 10:13

    Nanopores are of great interest in study of DNA sequencing, protein profiling and power generation. Among them, solid-state nanopores show obvious advantages over their biological counterparts in terms of high chemical stability and reusability as well as compatibility with the existing CMOS fabrication techniques. Nanopore sensing is most frequently based on measuring ionic current through a nanopore while applying a voltage across it. When an analyte passes through the pore, the ionic current temporarily changes, providing information of the analyte such as its size, shape and surface charge. Although many magnificent reports on using solid-state nanopores have appeared in the literature, several challenges still remain for their wider applications, which include improvement of fabrication reproducibility for mass production of ultra-small nanopores and minimization of measurement instability as well as control of translocation speed and reduction of background noise. This thesis work explores different techniques to achieve robust and high throughput fabrication of sub-10 nm nanopores for different applications.

    The thesis starts with presenting various fabrication techniques explored during my PhD studies. Focused ion beam method was firstly employed to drill nanopores in free-standing SiNx membranes. Sub-10 nm nanopores could be obtained with a focused helium ion beam. But the fabrication throughput was limited with this technique. A new fabrication process combing electron beam lithography (EBL) with reactive ion etching/ion beam etching, which is compatible with the existing CMOS fabrication technology, was developed to realize a high throughput, mass production of nanopores in free-standing SiNx membranes. However, the smallest size that could be controllably achieved with this process was around 40 nm, which is still far from sub-10 nm in size required for, e.g., DNA sequencing. Finally, by using anisotropic etching of single-crystal silicon in KOH solution, sub-5 nm truncated pyramidal nanopores were mass produced with good process controllability in a silicon-on-insulator (SOI) substrate. In addition, nanopore arrays were also successfully fabricated using a modified EBL based fabrication process.

    Then, several sensing application examples using either single nanopores or nanopore arrays were investigated. Translocation of nanoparticles, DNA and proteins were demonstrated using the fabricated single nanopores or nanopore arrays in a single freestanding membrane. Moreover, the kinetics and mechanism of the lipid bilayer formation in nanopore array, aiming to prevent non-specific adsorption, were studied using ionic current measurements. In addition, individual addressability of a solid-state nanopore array on separated freestanding membranes was realized by integrating microfluidics and a customized multiplexer.

  • Too close for comfort : The role of Contact-Dependent growth Inhibition (CDI) in interbacterial competition and cooperation

    Author: Marcus Wäneskog
    Publication date: 2020-01-31 06:21

    Contact-Dependent growth inhibition (CDI) was discovered in 2005 in the E. coli isolate EC93. Since then our knowledge of CDI systems and their impact on bacterial communities have increased exponentially. Yet many biological aspects of CDI systems are still unknown and their impact on complex microbial communities have only just begun to be studied. CDI systems require the function of three proteins; CdiBAI. The outer-membrane transport protein, CdiB, allows for the transportation of the toxin delivery protein CdiA to the cell surface of an inhibitor cell. Through a contact- and receptor-dependent interaction with a target cell the toxic C-terminal domain of CdiA is cleaved off and delivered into the target cell were it mediates a growth arrest. Different CdiA-CT domains encodes for diverse toxic activities, such as nucleases and membrane ionophore toxins. Each unique CdiA-CT toxin has a cognate immunity protein (CdiI) that binds and neutralize against its toxic activity, thus preventing a possible self-inhibition.

    In this thesis I have studied the effect of CDI system(s) on both single cell and population level, within both intra- and interspecies bacterial communities. The findings presented here shows that multiple class I cdiBAI loci within a cell can function in a synergetic manner and act as versatile interbacterial warfare systems able to inhibit the growth of rival bacteria, even when CdiA expression is low. We also show that class II CdiA receptor-binding domains can mediate broad-range cross-species toxin delivery and growth inhibition, even when a non-optimal target cell receptor is expressed at a low level. Additionally, we show that the cdiA gene supports the expression of two separate proteins. The full-length CdiA protein, able to mediate an extracellular toxin delivery, but also the discrete CdiA-CT toxin domain. This stand-alone CdiA-CT expression was stress-dependent and together with its cognate CdiI immunity protein functioned as a selfish-genetic element. Moreover, we show that CDI systems can increase bacterial stress tolerance via an extracellular toxin delivery between kin-cells. This stress tolerance phenotype only occurred under conditions when we also observed a selective degradation of the CdiI immunity protein. Therefore, we suggest that a selective CdiI degradation allows for a sub-population of cells to self-intoxicate, thereby becoming transiently dormant, which confers an increase in stress tolerance. The findings presented in this thesis collectively suggest that CDI systems could function as a pseudo-quorum sensing system able to mediate behavioral changes and stress tolerance within a sub-population of cells in a bacterial community.

  • Characterizing the spectrum of somatic alterations in canine and human cancers

    Author: Sharadha Sakthikumar
    Publication date: 2020-01-31 06:18

    Cancers arise as a result of deleterious somatic alterations accumulating in the genome during the process of cell division. These alterations arise either via exposure to mutagens or due to errors occurring during DNA replication. In this thesis, a systematic exploration, from discovery to analyses of somatic alterations in three diverse cancers that affect dogs and humans, was undertaken.

    In Studies I and II, whole-exome sequencing of dogs affected by the cancers of osteosarcoma and hemangiosarcoma were done to delineate coding mutations that can contribute to their carcinogenesis. Besides, as these cancers mirror the corresponding human disease in clinical manifestation and histological features, a secondary objective was to confirm the molecular drivers found in the canines were also influencing factors in the human cancer(s).

    In the osteosarcoma investigations with three breeds, we found that tumors show a high frequency of somatic copy-number alterations, affecting key cancer genes. TP53 was the most frequently altered gene, akin to human osteosarcoma. The second most mutated gene, histone methyltransferase SETD2, has known epigenetic roles in multiple cancers but not in osteosarcoma. Our study highlights the strong genetic similarities between human and dog osteosarcoma, suggesting that canine disease may serve as an excellent model for developing treatment strategies in both species.

    In the hemangiosarcoma study in golden retrievers, putative driver alterations were identified in the tumor suppressor TP53 and in genes involved in the cell cycle regulating PI3K pathway, including PIK3CA and PIK3R1. Furthermore, we find several somatic alterations between the dog hemangiosarcoma and human angiosarcoma overlap, indicating we can use the canine model to apprise the infrequently occurring human disease.

    In Study III, we implemented whole-genome sequencing methodologies to define both coding and non-coding alterations in the glioblastoma cancer genome. We find the coding somatic alterations recapitulate what has been previously seen for the cancer, including driver alterations in the genes of EGFR, PTEN, and TP53. Significantly though, using the concept of evolutionary constraint, we find an enrichment of non-coding mutations in regulatory regions, around GBM-implicated genes. The mutated regions include splice sites, promoters, and transcription factor binding sites, suggesting the importance of regulatory mutations for the pathogenesis of glioblastoma.

    Overall, the insights garnered from the above exome- and genome-wide surveys provide novel insights into unraveling some of the complexities associated with somatic genomic alterations in cancer genomes. It also convincingly underscores the benefits of using sequencing technologies to comprehend complex biological diseases.

  • Tissue Factor regulation, signaling and functions beyond coagulation with a focus on diabetes

    Author: Desirée Edén
    Publication date: 2020-01-30 09:49

    Background: Tissue factor (TF) is a 47 kDa transmembrane glycoprotein best known for initiating the coagulation cascade upon binding of its ligand FVIIa. Apart from its physiological role in coagulation, TF and TF/FVIIa signaling has proved to be involved in diseases such as diabetes, cancer and cardiovascular diseases. Biological functions coupled to TF/FVIIa signaling include diet-induced obesity, apoptosis, angiogenesis and migration.

    Aim: The aim of this thesis was to investigate the role of TF/FVIIa in cells of importance in diabetes, to further investigate the mechanism behind TF/FVIIa anti-apoptotic signaling in cancer cells and lastly to examine the regulation of TF expression in monocytes by micro RNAs (miRNA).

    Results: In paper I we found that TF/FVIIa signaling augments cytokine-induced beta cell death and impairs glucose stimulated insulin secretion from human pancreatic islets. In paper II the relevance of TF/FVIIa in isolated human primary adipocytes was investigated. Adipocytes are a target cell for insulin and diabetics typically have increased lipolysis and impaired glucose uptake. No evidence was found for a role of TF/FVIIa in lipolysis or glucose uptake in adipocytes. However, adipocytes were found to express TF and FVII. The FVII produced was sufficient to initiate coagulation in the adipocytes. In paper III an anti-apoptotic TF/FVIIa induced signaling pathway in prostate and breast cancer cells was investigated in depth. Previous research has shown that TF/FVIIa signaling results in transactivation of insulin-like growth factor 1 receptor (IGF-1R) leading to subsequent protection from apoptosis induced by TNF-related apoptosis inducing ligand (TRAIL). The current results propose a mechanism where IGF-1R transactivation by TF/FVIIa is dependent on integrin β1 (ITGβ1) signaling. TF/FVIIa/ ITGβ1 signaling was found to result in phosphorylation of src and subsequent phosphorylation of caveolin 1 (Cav1). Once phosphorylated, the inhibitory effect of Cav1 on IGF-1R is cancelled, resulting in IGF-1R activation. In paper IV the role of miRNA regulation of TF expression in monocytic cells was investigated. The miRNA miR-223-3p was identified to be differentially expressed in U937 cells undergoing differentiation to a more monocyte-like phenotype and an anti-parallel correlation between TF and miR-223-3p expression in monocytes was proved. Hence, miR-223-3p regulates the inducible expression of TF in monocytes.

    Conclusions: The work in this thesis furthers the knowledge of molecular mechanisms behind TF regulation and TF/FVIIa signaling and some functional consequences as well as their biological relevance in diabetes. 

  • Fiber Floer cohomology and conormal stops

    Author: Johan Asplund
    Publication date: 2020-01-30 09:10
  • Guiding Concepts : Essays on Normative Concepts, Knowledge, and Deliberation

    Author: Olle Risberg
    Publication date: 2020-01-29 12:35

    This thesis addresses a range of questions about normativity, broadly understood. Recurring themes include (i) the idea of normative ‘action-guidance’, and the connection between normativity and motivational states, (ii) the possibility of normative knowledge and its role in deliberation, and (iii) the question of whether (and if so, how) normative concepts can themselves be evaluated.

    The first two papers, ‘The Entanglement Problem and Idealization in Moral Philosophy’ and ‘Weighting Surprise Parties: Some Problems for Schroeder’, critically examine various versions of the view that what we ought to do depends on some (actual or hypothetical) motivational states, such as desires. It is suggested that such views are, for different but interrelated reasons, extensionally inadequate.

    The third paper, ‘From Evolutionary Theory to Moral Skepticism, via Disagreement’ (co- authored with Folke Tersman), proposes that two arguments for moral skepticism can be combined in a mutually supportive way. A central role is played by the principle that a subject S knows that p only if S adherently believes that p, where this roughly means that S could not easily have failed to believe that p unless her epistemic position were worse or p were false. It is suggested that evolutionary considerations and facts about moral disagreement together indicate that moral beliefs violate this principle.

    The fourth paper, ‘Ethics and the Question of What to Do’, offers an account of the so- called ‘central deliberative question’ that is highlighted by several kinds of choice situations, including those that involve normative uncertainty and normative conflicts. It is proposed that this question is not best understood as the question of what one ought to do, not even in an ‘all things considered’ sense, but as the question of what to do. A meta-normative view that involves elements of both cognitivism and non-cognitivism is put forward as the best explanation of this fact.

    The fifth paper, ‘Meta-Skepticism’, develops a novel skeptical challenge to beliefs about the external world, the central idea being that even if beliefs about the external world can constitute knowledge, there are various other knowledge-like concepts that they cannot satisfy even if they are true. This raises the question of whether some of these concepts are epistemically more important than the others, and, in particular, the further question of how the relevant notion of ‘epistemic importance’ should be understood. Several answers to this question are considered and found wanting.

  • In Vivo Accuracy and Precision in Prosthodontics

    Author: Robert Nedelcu
    Publication date: 2020-01-24 13:49

    Background: There has been a dramatic increase in commercially available intraoral scanners (IOS) in the last decade, offering to replace indirect digitization of models (MOD) fabricated from impressions (IMPR). IOS has benefits of less patient discomfort and a faster workflow to fabricate fixed dental prosthesis (FDP), and implant-supported prostheses (IFD). However, in vivo evidence is lacking not only for IOS, but also for MOD, FDP and IFD fit.

    Aims: Paper I: to evaluate in vitro finish line distinction and accuracy in seven IOS and one MOD. To assess parameters of resolution, tessellation, topography, and color. Paper II: to evaluate a method of acquiring an in vivo reference measurement in dentate subjects and analyse accuracy and precision of IOS and MOD. Paper III: to evaluate an in vivo reference-measurement method in fully edentulous maxillae with full-arch implant treatments and to analyse accuracy of MOD and fit of existing IFD. Paper IV: to analyse precision and accuracy of IOS using different acquisition protocols compared to the reference-measurement in Paper III.

    Material and Methods: Paper I: A model with a crown preparation was reference-scanned with an industrial scanner, (ATOS), scanned with seven IOS and the MOD of an IMPR was digitized. Best-fit Alignment and 3D Compare Analysis was followed by descriptive analysis. Paper II: A reference-scan was acquired with ATOS. Subjects were scanned with IOS and one MOD of an IMPR was digitized. Accuracy and precision were evaluated after Best-Fit Alignment and 3D Compare Analysis. Paper III: A reference-measurement of implant positions was acquired with ATOS. MOD from IMPR was digitized and IFD scanned. Datum and Relative Point System Alignment was followed by accuracy and precision analysis. Paper IV: Subjects in Paper III were scanned with IOS using three different protocols, followed by accuracy and precision analysis.

    Results: Paper I: There were considerable differences between IOS depiction of finish line and finish line accuracy. Paper II: IOS presented varying results for impressions in up to ten units. No differences were found for MOD. Paper III: IFD was significantly less accurate than MOD. Paper IV: Differences were found between scanning protocols. Compared to Paper III, IFD was less accurate. No differences were found for MOD.

    Conclusion: There are relevant differences between IOS when scanning subgingival preparations. Some IOS are better suited for long-span scans. Some IOS can be used for full-arch impressions for IFD in the maxilla, however, adequate soft-tissue management is crucial.