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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.
  • Near Surface High Resolution Seismic Imaging of Glacial Deposits in Sweden at the Heby and Marsta Sites

    Author: Ruixue Sun
    Publication date: 2020-09-14 07:44

    Near surface seismic methods have the potential for mapping theoverburden and bedrock in the Nordic environment. They can provideeffective information about shallow glacial deposits and groundwaterresources in Sweden. We analysed seismic data from the Heby andMarsta sites with the aim of improving the imaging resolution andunderstanding the substructures better, developing systematicstrategies to deal with the detection of aquifers and the delineation ofsome significant boundaries. The general scheme for every case studyis composed of processing, inversion and forward modelling.Processing strategies for the Heby and Marsta have different keypoints, because of the different acquisition equipment and systems.The Heby data were acquired by dynamite and collected withconventional geophones, while the Marsta data were acquired by asledge hammer source and a 3C data landstreamer with MEMSsensors. Inversion can be used for enhancing image quality,particularly in velocity model building. Strongly undulatedsubstructures in the Heby profile cause ambiguities and conflictingdips in the stacked section. By employing the tomographic inversionresult as a starting point to implement prestack depth migration(PSDM) the final image shows better continuity at the top of bedrockand shallow layers are resolved clearer. At Marsta, vertical and radialcomponent data were used to obtain PP and PS information,respectively, to delineate the bedrock surface. Common conversionPoint (CCP) binning of the radial component identifies the surface inbetter resolution, even a 2m variation in the depth of the bedrock canbe seen. PSDM radial component data supports and complements theresult from the CCP binning. In both the Heby and Marsta cases,forward modelling was applied for testing processing workflows forthe field data using models that mimick the real substructures.Acoustic modelling was used for understanding the P-wave responsein the Heby single component data, while elastic wave modelling wasperformed to simulate the multicomponent data at Marsta. The resultsdemonstrate that a comprehensive application of seismic methods inthe near surface (shallower than 100m) can provide adequateresolution. Noteworthy is that an accurate velocity estimation plays asignificant role in the whole scheme for seismic imaging. Thestrategies for building the velocity are also meaningful in thisresearch.

  • Modelling short and long term consequences of changes in diagnostic activity and treatment

    Author: Marcus Westerberg
    Publication date: 2020-09-09 13:37

    Since the late 90’s the diagnostic activity for prostate cancer has increased in Sweden, primarily due to increased use of PSA testing, and this has led to a large increase in diagnoses. Simultaneously, there have been changes in treatment strategies, and more effective treatments have been introduced. This thesis aims to increase the understanding of short and long term consequences of these changes by use of high quality data on virtually all men diagnosed with prostate cancer in Sweden.

    In paper I, the survival of men with metastatic prostate cancer at diagnosis was investigatedby use of survival models, including Kaplan-Meier analyses and Cox proportional hazards regression.The median survival from diagnosis increased with 6 months when comparing mendiagnosed 1998-2001 with men diagnosed 2010-2015, and the risk of death decreased with 13%, while median levels of prostate specific antigen at diagnosis dropped with up to 50%.

    In paper II, the interplay between diagnostic activity, incidence and risk of death by prostate cancer was modelled using a discrete time model. Data on diagnostic activity, e.g. in termsof testing frequencies, was not available and therefore a proxy for the diagnostic activity wasused. The hazards were estimated within the framework of generalized additive models. Two simulations were performed, assuming low and high diagnostic activity respectively, to compare incidence and mortality from 2017-2060. Higher diagnostic activity, compared to lower, led to more men being diagnosed, primarily with lower risk prostate cancer, but in the long run it led to fewer men diagnosed with metastatic disease and fewer prostate cancer deaths.

  • Demand Side Response : Exploring How and Why Users Respond to Signals Aimed at Incentivizing a Shift of Electricity Use in Time

    Author: Isak Öhrlund
    Publication date: 2020-09-04 09:33

    With increased weather-dependent electricity production and electrification at the heart of the ongoing transition away from fossil fuels, peaks in electricity demand are set to increase and become increasingly difficult to meet, which threatens the functioning of the electric power systems that our society depends on. Time-varying electricity rates, which aim to incentivize electricity users to shift their electricity use in time, have been proposed as a key instrument in alleviating grid imbalances and bottlenecks. Previous research has found that users respond to such rates by shifting their electricity use in time, but there is great variability in the observed response between studies that remains unexplained. In other words, it is unclear how and why users respond to time-varying rates, and thus how these so called demand side response policies should be designed to provide the best results.

    This thesis aims to improve our understanding of how and why (not) time-varying rates work by exploring how users respond to both price and non-price signals that aim to incentivize a shift of electricity use in time, and what motivates, discourages, enables and hinders them to respond. This is done through four separate studies that are carried out in contexts where users have been involuntarily subjected to interventions that aim to incentivize demand side response. Using several novel methods, research designs and understudied empirical contexts, the studies also illustrate how biases that are commonly observed in the literature can be avoided and how intervention effects that often remain overlooked can be captured.

    The results suggest that users may hold different motives to respond to signals that aim to incentivize a shift of electricity use in time, including non-financial motives such as a care for the environment and a will to meet the expectations of others. The rhythms and schedules of people’s everyday lives are identified as the most important hindrances for people to engage in demand side response. Notably, there is no evident relationship between how much money users may save by responding to a signal and their actual response. Many users do hold expectations of saving money and claim to engage in demand side response as a result of those expectations, but the fact that users are rarely (if ever) informed of whether their expectations are met or not suggests that many users may actually be willing to engage in demand side response with little or no financial reward. However, there is a risk that users who expect to save money may refrain from or stop engaging in demand side response if their expectations are not met, which poses a potential threat to the long-run effectiveness of conventional price-based demand response programs. There is also a risk that users who primarily hold non-financial motives may be discouraged to engage in demand side response if monetary savings is the key selling point of demand response programs. Policymakers, professionals and researchers should explore these risks and alternative policies that address them, particularly policies that may be more appealing to users that hold non-financial motives to engage in demand side response. Doing so will be key to ensure that current and future demand side response policies are cost-efficient and effective, both today and tomorrow.

  • Epicardial ablation - a study evaluating thoracoscopic and surgical ablation procedures for patients with intractable atrial fibrillation

    Author: Johan Probst
    Publication date: 2020-09-04 08:26

    Atrial fibrillation (AF) is a common condition, increasing in prevalence with age. Symptoms can be severe and quality of life is affected in patients suffering from AF. Treatment regimes aim to alleviate symptoms through rate or rhythm control. Rhythm control can be achieved effectively in early stages of AF with catheter ablation aiming for pulmonary vein isolation (PVI) however, in more advanced stages of the disease a surgical ablation is warranted if rhythm control is the goal.

    The aim of this thesis was to evaluate the thoracoscopic epicardial left atrial surgical procedure for AF (TELA-AF) in patients suffering from highly symptomatic, mainly longstanding persistent AF (LPAF). The hypothesis was that TELA-AF would be effective in treating LPAF and that quality of life (QoL) would increase accordingly.

    This thesis second hypothesis was that restoration of sinus rhythm would improve QoL in patients with permanent AF undergoing concomitant mitral valve surgery (MVS) and left atrial cryoablation compared to MVS alone.

    The TELA-AF surgical technique included pulmonary vein isolation, left atrial "box-lesion" and partial vagal denervation. Patients were followed with clinical evaluation, seven-day Holter electrocardiogram, symptom severity questionnaire (SSQ)and a short form QoL questionnaire (SF-36), six and 12 months after surgery and again after ten years.

    The concomitant MVS study was a sub-study of the randomized double-blinded SWEDMAF trial. Patients in permanent AF, accepted for MVS were randomized to MVS or MVS and cryo-ablation of the left atria. Patients self-reported QoL before and one year after surgery in the SF-36 questionnaire.

    Twelve months after the TELA-AF procedure freedom from AF was 83 % although 12 % suffered from an iatrogenic atrial tachycardia post-surgery. The SSQ scores improved significantly from baseline. The SF-36 scores were similar to patients suffering from severe chronic disease at baseline but were not significantly different from an age-matched normal population at follow-up.

    Ten years after surgery freedom from AF was 22 %, a significant reduction. Quality of life scores were however significantly better than baseline.

    Patients randomized to concomitant surgery experienced a significant increase in QoL one year after surgery, but there was no difference in QoL scores compared to the MVS-alone group.

    In conclusion, severe symptoms in AF patients translate to QoL scores as low as those observed in patients with severe chronic diseases. The TELA-AF procedure can alleviate AF related symptoms and improve QoL to the same level as a normal population in the short term. In the long term QoL can be maintained at a high level although displaying AF recurrence according to guidelines, challenging the concept of 30 seconds arrhythmia as a valid endpoint.

    We could not show any benefit in a concomitant surgery for patients in permanent AF accepted for MVS. It is therefore important to balance the benefits and side effects in both short- and long-term perspective in order to justify the addition of a surgical AF ablation during MVS.

  • Moments on a City Bus : Micro-sociology of Non-verbal Interaction in Urban Bus-riding

    Author: Magdalena Vieira
    Publication date: 2020-09-03 13:01

    This thesis seeks to contribute to research on social interaction in public (and semi-public) places in general, and research on non-verbal mundane interaction in these places in particular. By paying empirical attention to the non-verbal interaction that takes place in the context of riding a city bus – which is a contained and time-limited form of social activity – this thesis explores the theoretically rich source of information about mundane interaction that this specific social activity offers. By systematically applying a Goffmanian-informed conceptual framework to the analysis of data collected through participant observation, this thesis examines what this framework can offer to micro-sociological understandings of mundane non-verbal interaction. Moreover, this thesis investigates whether bodily cues for race, gender and age (and the sense of similarity and difference that they convey), play a role in the non-verbal mundane interaction that takes place in city busses. The assumption that mundane non-verbal interaction in a time- and space-constrained setting such as a city bus could be influenced by obvious phenotypical similarities and differences between the bodies­ of the people that engage in this interaction, is also hereby explored.

    The empirical material utilized in this thesis has been generated through a carefully designed study of city bus riding that relies on participant observation (over a period of 10 months), and is based on the operationalization of an array of parameters to study non-verbal interaction in a theoretically-informed and systematic manner. The analyses performed allowed for the methodical study of what time, space and phenotypical variations mean to the non-verbal mundane interaction that takes place in city busses (a total 200 hours of observations were recorded in systematized field notes resulting in 136 interaction moments, which were coded along 307 parameters using ATLAS.ti).

    The results suggest that while previous research on urban bus riding alludes to three dimensions of social interaction that are worthy of our attention – time, space, and (travelling) bodies – there is also a fourth dimension that scholars of social interaction (both verbal and non-verbal) ought to take into account (i.e. codes for interaction). The results indicate also that it is through the systematic attention to interaction moments (by acknowledging their dimensions, by taking into account features of gestures, and through detailed comparisons with other interaction moments) that we can achieve a deeper and detailed understanding of mundane non-verbal interaction in everyday life. Thus, by exposing new aspects of social interaction that future research can explore, as well as offering an array of new angles that it ought to consider (such as different aspects of intensity of involvement and types of territorial orientation to name but a few), this thesis expands the micro-sociological imagination of what mundane non-verbal interaction entails.

    This thesis proposes that there is nothing inconsequential or fleeting about mundane non-verbal interaction in everyday life. This thesis shows namely that in the mundane non-verbal interaction that takes place in the public spaces that are city busses, the socially coded bodies of the riders, and therefore also the phenotypical similarities and differences between them, may be a part of the interaction space created and reshaped in each interaction moment. Thus, not only is mundane non-verbal interaction full of events, rhythms, and nuances in intensity, this interaction seems also to be heavily mediated by the phenotypical cues that are imprinted in our bodies, which is why labeling this interaction ‘mundane’ is deceiving.

  • Genome evolution of a bee-associated bacterium

    Author: Andrea García-Montaner
    Publication date: 2020-09-02 15:00

    The use of large-scale comparative genomics allows us to explore the genetic diversity and mechanisms of evolution of related organisms. This thesis has focused on the application of such approaches to study Lactobacillus kunkeei, a bacterial inhabitant of the honeybee gut.

    We produced 102 novel complete genomes from L. kunkeei, which were used in four large comparative studies. In the first study, 41 bacterial strains were isolated from the crop of honeybees whose populations were geographically isolated. Their genome sequences revealed differences in gene contents, including the mobilome, which were mostly phylogroup-specific. However, differences in strain diversity and co-occurrence between both locations were observed. In the second study, we obtained 61 bacterial isolates from neighboring hives at different timepoints during the summer. We observed that strain diversity seemed hive-specific and relatively constant in time. Surprisingly, the observed mobilome also showed hive specificity and was maintained through the summer.

    The novel genome data were combined with previously published genomes, allowing us to perform deep comparative analyses on the evolution of the species using a total of 126 genomes. We determined that, despite the large number of sequenced genomes, L. kunkeei has an open pangenome. Besides, we evaluated the effects of recombination on the species core genome, and concluded that it mainly evolves through mutation events.

    In the last study we described the mechanisms of evolution of a cluster of 5 giant genes (about 90 kb long in total) that are unique to L. kunkeei and the closest sister species. Their patterns of evolution do not reflect those of the species core genome. We concluded that they originated by duplication events, and have diverged by accumulation of both mutations and recombination events. We predicted a potential interaction between the proteins encoded by two of them, and we hypothesized a role in host-specific interaction for another protein.

    In conclusion, these studies have provided novel and cohesive knowledge on the composition and dynamics of different populations of L. kunkeei, and may have contributed to better understand its ecological niche.

  • Modelling and Simulation of Electro-catalysts for Green Energy : From Solvated Complexes to Solid-Liquid Interfaces

    Author: Jose Luis Lima de Jesus Silva
    Publication date: 2020-08-31 15:03

    In this thesis, I have worked with solid-liquid interfaces, adsorbed molecules on the surface, and solvated complexes using Density Functional Theory (DFT) calculations to find possible signatures that could help design suitable energy materials. More specifically, I have explored hybrid electrocatalysts for hydrogen evolution reaction (HER), XPS fingerprints of gas-phase melamine (monomer, dimer, trimer, and hexagonal packed arrangement), hexagonally packed melamine adsorbed on the Au(111) surface, and high-valence Ruthenium complexes along a reaction pathway in aqueous solution through a joint theory-experiment approach. First, I have explored single layer and hybrid-type systems as micro-reactors (current collector/catalysts) for HER with site-dependent calculations of the hydrogen binding free energy ΔGH to estimate the HER activity, electronic structure, and Schottky Barrier Height (SBH) to measure the resis-tance for charge injection across the interface. Furthermore, we have predicted a new hybrid electrocatalyst Td-WTe2/2H-MoS2 employing DFT-based trends. Additionally, we have built carbon-based hybrid systems from a bilayer of g-C3N4 coupled with Td-WTe2, 2H-MoS2, and Graphene, and used an implicit solvation model to obtain more realistic signatures. The results show that g-C3N4/Td-WTe2 has filled states in the Fermi level, which is a good indication of higher charge mobility. The SBH was evaluated with both GGA and HSE06, and Td-WTe2/g-C3N4 has shown lower resistance for charge injection across the interface. Further, the induced dipole (driving force for electron injection) increases under higher hydrogen coverages, enhanc-ing the catalytic activity. Finally, our results indicate that Td-WTe2/g-C3N4 could be classified as an efficient electrocatalyst for HER. In the last two papers, we have estimated XPS finger-prints of molecular and solid-state systems by calculating the core-level binding energy shifts using the Janak-Slater transition state approximation. Also, we have developed a new methodology by combing DFT calculations with Monte Carlo Simulations using explicit solvation to resolve the XPS and understand the chemical shifts of the [RuII -OH2]2+ species, as well as of multiple PCET oxidation states. This work also shows that the chemical shift of [RuIV =O]2+ is affected by the polarization of the explicit solvation model, and that we could only capture the experimental trend by using the complete first solvation shell and an XPS averaged spectra over a certain amount of snapshots from the Monte Carlo simulation. To the end, we also show that the nearest-neighbor potential contributions to the Ru 3d binding energies arising from atoms around the metallic center explain the higher 3d-state shifts of the oxo complex.

  • Human demographic history : Insights on the human past based on genomes from Southern through Central Africa

    Author: Gwenna Breton
    Publication date: 2020-08-28 10:18

    Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming.

    I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution.

    I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records.

    In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.

  • Negotiating who the ’Other’ is : Care providers talk about caring for dying patients with migrant backgrounds

    Author: Pernilla Ågård
    Publication date: 2020-08-28 09:01

    Most research at the intersection of ethno-cultural minority patients and end-of-life care has been preoccupied with two types of problems: the underrepresentation of patients with an ethno-cultural minority background in end-of-life care and the challenges that these patients are believed to pose to the deliverance of high-quality and user-friendly care. When scholars have focused on these issues, they have tended to assume that it is ethno-cultural diversity as such that poses these problems. Taking a different stance, this study stresses the importance of designing research in a way that does not assume at the outset that the difficulties depicted in the literature are caused by patients’ ethno-cultural diversity. Drawing upon the social constructionist tradition, this study examines care providers’ understandings of caring for patients with ethno-cultural minority backgrounds, and how they negotiate their understandings in talk. As such, this study differs from previous studies that have focused on professional care providers’ experiences of patients categorized as ethno-cultural minorities, in order to explore what precedes these experiences (i.e. their understandings of ethno-cultural diversity, and the expectations they themselves bring to the table when caring for these patients).

    Based on an analysis of focus groups interviews with end-of-life care professionals (n=60) in Sweden – a context where people with migrant backgrounds are often assumed to have an ethno-cultural minority background – this study aims to explore professional characterizations of patients with migrant backgrounds.

    Through its focus on talk – and the way in which understandings are negotiated when the professionals talk with one another about what ethno-cultural diversity means, and what caring for patients with migrant backgrounds is like – this study contributes to research about the implications of ethno-cultural diversity in end-of-life care. Thus, by shedding light on the argumentative side of meaning-making this study’s findings suggest that understandings play a greater role in how ethno-cultural diversity is addressed in end-of-life care. In particular, this study shows that the process through which understandings are negotiated plays a vital part in determining which understandings become legitimate descriptions of these patients, their families and interactions with them. The study highlights that the providers seemed to take for granted that patients categorized as ethno-cultural minorities, their families and the interactions they have with them differ from what they  consider to be  ‘normal’, i.e. patients categorized as Swedes, their families and the interactions with them. Therefore, this study concludes that the understandings brought to fore are underpinned by the notion of ‘Otherness’, and the assumption that ethno-cultural diversity poses challenges to the deliverance of high-quality and user-friendly end-of-life care even if one’s experience of providing care to patients with migrant backgrounds is limited and/or suggests otherwise.

  • Iron, Manganese and Iridium Complexes From Models of RNR and Catalase to Water Oxidation

    Author: Michele Bedin
    Publication date: 2020-08-27 15:06

    The focus of this thesis has been synthesise and study metal complexes that mimic the structure and function of the active site in two particular metalloenzymes, ribonucleotide reductase (RNR) and manganese catalase (MnCAT). These two metalloenzymes both have two transition metals ions in the cofactor: two manganese ions in MnCAT and either two iron, iron-manganese or two manganese ions in RNR.

    Three different ligands were synthetized to make model complexes for these cofactors. The first ligand, BPMP, can bind two metal ions and provides two symmetric pockets with two pyridine groups and one amine each, plus a phenolate group that can bridge the two metals. The second ligand DPCPMP had one carboxylate group instead of a pyridine group in one pocket, creating an asymmetric ligand, and the third ligand BPCPMP, had two carboxylate groups, one in each pocket. From the first and the second ligands it was possible to obtain six complexes: low-valent homometallic Mn/Mn and Fe/Fe complexes and a heterometallic complex for each ligand. For the third ligand, only the Fe/Fe complex was synthetized.

    All seven complexes were characterized by a number of spectroscopic methods. The presence of carboxylate groups in the ligand shifted the redox potential for the metal complexes towards more negative values, particularly in the case of the homometallic Fe/Fe complexes. Surprisingly, for the asymmetric ligand the placement of the metal ions in the two pockets was not dictated by the asymmetry. Additionally, the relative stability of the homometallic complexes versus the heterometallic complexes and the possibility to transform a homometallic complex into a heterometallic complex were investigated. By titrating one metal into a solution containing the other homometallic dimer it was possible to observe that Fe2+ added to a solution of a Mn/Mn complex led to the replacement of one Mn ion in the complex with a Fe ion.

    The manganese complex of DPCPMP was investigated as a functional model for MnCAT, catalysing the disproportionation of H2O2 to oxygen and water. In the presence of H2O2 this complex also forms a high-valent species with a di-µ-oxo bridge similar to the MnCAT and RNR.

    Finally, the methodology used for the study of these complexes was also applied to a set of Ir complexes that act as water oxidation catalysts, and we could show that the presence of a pendant group stabilizes the metal at higher oxidation states leading to higher activity for the catalyst.