Coming dissertations at Uppsala university
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Garnishing the smorgasbord of pharmacometric methods
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-518178
The smorgasbord of methods that we use within the field of pharmacometrics has developed steadily over several decades and is now a well-laid-out buffet. This thesis adds some garnish to the table in the form of small improvements to the handling of certain problems.
The first problem tackled by the thesis was the challenge of saddle points and local non-identifiability when estimating pharmacometric model parameters. Substituting the common method of randomly perturbing the initial parameter estimates with one saddle-reset step enhances the accuracy of maximum likelihood estimates by overcoming saddle points parameter values, a common issue in nonlinear mixed-effects models. This algorithm, as implemented in the NONMEM software, was applied to various identifiable and nonidentifiable pharmacometric models, showing improved performance over traditional methods.
Part of the thesis was dedicated to the development of a paediatric pharmacokinetic model for ethionamide, a drug used in treating multidrug-resistant tuberculosis. The resulting model was then used to simulate drug exposure under different dosing regimens, a new dosing regimen for children was proposed. The developed model, and therefore the proposed paediatric dosing regimen, considers factors like maturation of pharmacokinetic pathways and, administration by nasogastric tube, and concurrent rifampicin treatment. The regimen, with some modifications, was adopted in the 2022 update to the World Health Organization operational handbook on tuberculosis.
Finally, the thesis explored novel model-integrated evidence (MIE) approaches for bioequivalence (BE) determination. Such methods could offer more robust alternatives to standard BE approached using non-compartmental analysis (NCA). Model-based methods have been shown to be advantageous in sparse data situations, such as is found in studies of ophthalmic formulations, but have suffered from inflated type I error rates. MIE BE approaches using a single model or using model averaging were presented and shown to control type I error at the nominal level while demonstrating increased power in bioequivalence determination.
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Conservation genomics in inbred Scandinavian wolves using bioinformatic methods
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-517653
With the recent and unprecedented progress in retrieving DNA sequence information from a large number of individuals of any species, conservation genetic research has entered a new phase. Specifically, it has become possible to study how genomes of endangered species respond to reductions in population size. Using genomic and bioinformatic approaches, in this thesis I investigate the contemporary Scandinavian wolf population founded 40 years ago by only three individuals, after the original population had been extirpated some decades earlier. The origin of the founders has been the subject of controversy, so I aimed to trace their origin using first male-specific Y chromosome sequences, and then whole-genome sequence data. I compared Scandinavian wolves to wolves from the nearby Finnish-Russian population as well as to publicly available wolf and dog samples from around the northern hemisphere, and found that the Scandinavian founders shared Y-haplotypes only with Finnish wolves. Consistent with this observation, when assessing population structure on the genomic scale, founders clustered with Finnish and Russian wolves, and an admixture analysis showed no other ancestries, nor traces of introgression from dogs.
Small populations tend to have less genetic variation than larger populations, which might reduce their adaptive potential and increase the risk for extinction. A common measure used to investigate the genetic health of small populations is the genetic load, which is the fitness reduction of individuals due to accumulation of deleterious variants. I assessed the genetic load in Scandinavian wolves, divided into the components masked load (comprised of deleterious mutations in heterozygous state) and realized load (comprised of deleterious mutations in homozygous state), using both putatively deleterious single nucleotides and structural variants. I found that the realized load increased with every generation of inbreeding but was alleviated after genetic rescue events when new immigrants entered the population. Finally, I searched for the genetic basis of cryptorchidism, a testis condition that results in lowered fertility and is thought to be related to inbreeding depression. The trait is likely highly polygenic and the fact that only one significant association (to a region on the X chromosome) was found can be explained by that the number of available samples was very low, as is inevitable for small populations.
In conclusion, this thesis explores the origin and the genetic health status of a small and recently founded natural population, and gives insights into how patterns of genetic load are affected by inbreeding and genetic rescue.
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Daily Experiences and Perceived Quality of Care for Patients with Liver Cirrhosis
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-517092
Aim and methods: This thesis aimed to study patients’ experiences with illness in their day-to-day lives and their perceived quality of care before and after implementing a 24-month adjunctive registered nurse-based outpatient intervention in liver cirrhosis. Qualitative data was used to explore patient perspectives on day-to-day life and healthcare experiences related to liver cirrhosis. The patient-perceived quality of care following the adjunctive registered nurse-based outpatient care was studied in a pragmatic, randomised controlled multicentre study, preceded by a study protocol.
Results: Liver cirrhosis led to physical symptoms sometimes appearing rapidly. Fatigue, fear and social stigma affected daily life, resulting in cancelled activities and creating an unpredictable daily life situation. Patients with liver cirrhosis lacked adequate support to learn about the disease and manage it. They sought a trustworthy relationship with healthcare providers. When this was lacking, they felt neglected. After 12 months, the adjunctive registered nurse-based outpatient care revealed an improvement in patient-perceived quality of care. Enhancements were observed in 7 out of 22 questionnaire items regarding: patient participation, access to outpatient care, and feeling understood. However, these improvements were not sustained after 24 months.
Conclusions: Fluctuating liver cirrhosis symptoms and constant worry significantly impact patients’ daily lives. Patients expressed a wish to be more involved in their healthcare and support in understanding and managing their illness. Structured registered nurse-based outpatient care for liver cirrhosis could complement physician-based care to meet patient desires for a more person-centred approach, continuity and care coordination.