Background: Coronary heart disease (CHD) is one of the leading causes of death worldwide, and global mortality rates are expected to continue to rise over the coming decades. In Pakistan in particular, chronic diseases are responsible for 50% of the total disease burden. Circulating lipids are strongly and linearly associated with risk of CHD; however, despite considerable efforts to demonstrate causality, available evidence is conflicting and insufficient. Study of the underlying metabolic pathways implicated in the association between lipids and CHD would help to disentangle and elucidate these complex relationships. Objectives: The primary objectives of this dissertation were to (1) identify the genetic determinants of lipid metabolites and (2) advance understanding of the effect of perturbations in lipid metabolite levels on CHD and its risk factors. Methods: Direct infusion high-resolution mass spectrometry was performed on 5662 participants from the Pakistan Risk of Myocardial Infarction Study to obtain signals for 444 known lipid metabolites. Correlations and associations of the lipids with smoking, physical activity, circulating biomarkers, and other CHD risk factors were assessed. Genome-wide analyses were conducted to analyse the association of each lipid with over 6.7 million imputed single nucleotide polymorphisms. Functional annotation and Gaussian Graphical Modelling were used to link the variants associated with each lipid to the most likely mediating gene, discern the underlying metabolic pathways, and provide a visual representation of the genetic determinants of human metabolism. Mendelian randomisation was also implemented to examine the causal effect of lipids on risk of CHD. Results: The lipids were highly correlated with each other and with levels of major circulating lipids, and they exhibited significant associations with several CHD risk factors. There were 254 lipids that had significant associations with one or more genetic variants and 355 associations between lipids and variants, with a total of 89 sentinel variants from 23 independent loci. The analyses described in this dissertation resulted in the discovery of four novel loci, identified novel relationships between genetic variants and lipids, and revealed new biological insights into lipid metabolism. Conclusion: Analyses of lipid metabolites in large epidemiological studies can contribute to enhanced understanding of mechanisms for CHD development and identification of novel causal pathways and new therapeutic targets.

<p>Complex traits are influenced by genetic and environmental factors and their interactions. Most common human disorders such as cardiovascular, metabolic, autoimmune, and neurological diseases are complex. Understanding their genetic architecture and etiology is an important step to prevent, diagnose and treat these conditions. Genome Wide Association Studies (GWAS) have emerged as a powerful and widely used tool that can be used to explore and identify the genetic variants associated with complex traits. In this dissertation, we present some of the downstream applications of GWAS studies to analyze and understand the genetic risk and etiology of complex traits and provide important insights into the genetic architecture and background of several complex phenotypes. First, we examined whether prevalence of complex disorders around the world correlates to Polygenic Risk Scores (PRS). To do so, we determined the average PRS of 14 such complex disorders across 24 world populations using results of GWAS studies. We found variation in risk across populations and significant correlation was obtained between average disease risk and prevalence for seven of the studied disorders. Further exploring the power of PRS- based calculations, we performed a PRS - based phenome wide association study (PheWAS) for Tourette Syndrome (TS) and identified 57 phenotypic outcomes significantly associated with TS PRS. The strongest associations were found between TS PRS and mental health factors. Cross- disorder comparisons of phenotypic associations with genetic risk for other childhood-onset disorders (e.g.: attention deficit hyperactivity disorder [ADHD], autism spectrum disorder [ASD], and obsessive-compulsive disorder [OCD]) indicated an overlap in associations between TS and these disorders. Furthermore, we performed a sex specific PheWAS that highlighted differences in associations of complex disorders with TS PRS in males and females. Finally, we used large- scale GWAS results to identify causal associations between different biological markers (proteins, metabolites, and microbes) and subcortical brain structure volumes using Mendelian Randomization (MR) analysis. We identified eleven proteins and six metabolites to be significantly associated with subcortical brain volume structures. Enrichment analysis indicated that the associated proteins were enriched for proteolytic functions and regulation of apoptotic pathways. Overall, our work demonstrates the power of GWAS studies to help disentangle the genetic basis of complex diseases and also provides important insights into the etiology of the studied complex traits. </p>

The rapid growth of centralised social media platforms such as Twitter and Facebook has raised concerns about privacy and the concentration of power held by the companies behind these services. In response, decentralised social media platforms have emerged as alternatives, forming federations of various instances without a single owner. However, these decentralised platforms have faced challenges with centralisation, as users tend to gather on larger instances. This paper examines Mastodon, one of the most popular decentralised platforms, to explore whether its onboarding flow and website design can be modified to encourage less centralisation. The study maps Mastodon's onboarding flow and identifies potential modifications to mitigate centralisation. Additionally, a new design for the official website is proposed. User tests involving five participants were conducted to evaluate the effectiveness of these changes. The results indicate that modifying the design can influence users to choose smaller servers. One effective modification is randomising the order in which servers are presented, eliminating the advantage of larger servers. Another proposed change is to improve user awareness about how feeds and interactions on Mastodon spans servers, enabling users to interact beyond their own server and removing a motivation for choosing a larger one. But the impact of this information on user behaviour remains inconclusive in the user tests. Overall, this research suggests that through design modifications, Mastodon can encourage users to select smaller servers and foster a more decentralised social media environment. / Den snabba tillväxten av centraliserade sociala medieplattformar som Twitter och Facebook har väckt oro över personlig integritet och koncentrationen av makt hos företagen bakom dessa tjänster. Som svar har decentraliserade sociala medieplattformar dykt upp, där plattformen består av en federation av olika instanser utan en enda ägare. Dessa decentraliserade plattformar har dock stött på utmaningar med centralisering eftersom användare tenderar att samlas på större instanser. Den här rapporten undersöker Mastodon, en av de mest populära decentraliserade plattformarna, för att undersöka om dess onboardingflöde och designen av deras webbplats kan modifieras för att uppmuntra mindre centralisering. Studien kartlägger Mastodons nuvarande onboardingflöde och identifierar potentiella ändringar som kan mildra centraliseringen. Dessutom föreslås en ny design för den officiella webbplatsen. Användartester med fem deltagare genomfördes för att utvärdera effektiviteten av dessa förändringar. Resultaten indikerar att den modifierade designen kan påverka användare och få dem att välja mindre servrar. En effektiv förändring är att randomisera ordningen i vilken servrar presenteras, vilket eliminerar fördelen större servrar har i hur synliga de är. En annan föreslagen förändring är att förbättra användarnas medvetenhet om att flöden och interaktioner på Mastodon sträcker sig över servrar, vilket gör det möjligt för användare att interagera utanför sin egen server och tar bort ett av motiven användare har för att välja en större server. Vilken effekt det här har på användarnas beteende när det gäller deras val av server var dock oklart i användartesterna som utfördes. Sammantaget tyder denna undersökning på att Mastodon genom designändringar potentiellt kan uppmuntra användare att välja mindre servrar och främja en mer decentraliserad miljö för sociala media.

Die vorliegende Dissertation besteht aus zwei Teilen, deren gemeinsames Thema in der Frage besteht, wie mächtig Zufall als Berechnungsressource ist. Im ersten Teil beschäftigen wir uns mit zufälligen Strukturen, die -- mit hoher Wahrscheinlichkeit -- Eigenschaften haben können, die von Computeralgorithmen genutzt werden können. In zwei konkreten Fällen geben wir bis dahin unbekannte deterministische Konstruktionen solcher Strukturen: Wir derandomisieren eine randomisierte Reduktion von Alekhnovich und Razborov, indem wir bestimmte unbalancierte bipartite Expandergraphen konstruieren, und wir geben eine Reduktion von einem Problem über bipartite Graphen auf das Problem, den minmax-Wert in Dreipersonenspielen zu berechnen. Im zweiten Teil untersuchen wir die Ausdrucksstärke verschiedener Logiken, wenn sie durch zufällige Relationssymbole angereichert werden. Unser Ziel ist es, Techniken aus der deskriptiven Komplexitätstheorie für die Untersuchung randomisierter Komplexitätsklassen nutzbar zu machen, und tatsächlich können wir zeigen, dass unsere randomisierten Logiken randomisierte Komlexitätsklassen einfangen, die in der Komplexitätstheorie untersucht werden. Unter Benutzung starker Ergebnisse über die Logik erster Stufe und die Berechnungsstärke von Schaltkreisen beschränkter Tiefe geben wir sowohl positive als auch negative Derandomisierungsergebnisse für unsere Logiken. Auf der negativen Seite zeigen wir, dass randomisierte erststufige Logik gegenüber normaler erststufiger Logik an Ausdrucksstärke gewinnt, sogar auf Strukturen mit einer eingebauten Additionsrelation. Außerdem ist sie nicht auf geordneten Strukturen in monadischer zweitstufiger Logik enthalten, und auch nicht in infinitärer Zähllogik auf beliebigen Strukturen. Auf der positiven Seite zeigen wir, dass randomisierte erststufige Logik auf Strukturen mit einem unären Vokabular derandomisiert werden kann und auf additiven Strukturen in monadischer Logik zweiter Stufe enthalten ist. / This thesis is comprised of two main parts whose common theme is the question of how powerful randomness as a computational resource is. In the first part we deal with random structures which possess -- with high probability -- properties than can be exploited by computer algorithms. We then give two new deterministic constructions for such structures: We derandomise a randomised reduction due to Alekhnovich and Razborov by constructing certain unbalanced bipartite expander graphs, and we give a reduction from a problem concerning bipartite graphs to the problem of computing the minmax-value in three-player games. In the second part we study the expressive power of various logics when they are enriched by random relation symbols. Our goal is to bridge techniques from descriptive complexity with the study of randomised complexity classes, and indeed we show that our randomised logics do capture complexity classes under study in complexity theory. Using strong results on the expressive power of first-order logic and the computational power of bounded-depth circuits, we give both positive and negative derandomisation results for our logics. On the negative side, we show that randomised first-order logic gains expressive power over standard first-order logic even on structures with a built-in addition relation. Furthermore, it is not contained in monadic second-order logic on ordered structures, nor in infinitary counting logic on arbitrary structures. On the positive side, we show that randomised first-order logic can be derandomised on structures with a unary vocabulary and is contained in monadic second-order logic on additive structures.

Human ageing is accompanied by characteristic metabolic and endocrine changes, including altered hormone profiles, insulin resistance and deterioration of skeletal muscle. Obesity and diabetes may themselves drive an accelerated ageing phenotype. Untangling the causal web between ageing, obesity and diabetes is a priority in order to understand their aetiology and improve prevention and management. The role of biological ageing in determining the risk of obesity and associated conditions has often been examined using mean leukocyte telomere length (LTL), a marker of replicative fatigue and senescence. However, considering phenotypes which represent different domains of biological and functional ageing as exposures for obesity and related traits could allow the elucidation of new understudied phenotypes relevant to cardio-metabolic risk in the wider population. This PhD considers the causal role of (1) hand grip strength (HGS), a marker of overall strength and physical functioning, and (2) resting energy expenditure, an indicator of overall energy metabolism and the major component of daily energy expenditure, in cardio-metabolic risk. I also characterise a new and readily-quantifiable marker of age-related genomic instability, mosaic loss of the Y chromosome (mLOY). Observational evidence implicates each of these phenotypes in cardio-metabolic conditions and intermediate phenotypes. However, it is not possible to infer causality from these observational associations due to confounding and reverse-causality. Mendelian randomisation offers a solution to these limitations and can allow the causal nature of these relationships to be investigated. Using population-based data including UK Biobank, this thesis presents the first large-scale genetic discovery effort for each trait and provides new biological insight into their shared and separate aetiology. I used identified variants to investigate the bidirectional causal associations of each trait with cardio-metabolic outcomes, intermediate phenotypes and other related traits such as frailty and mortality. In total I identified 16 loci for hand grip strength, 19 for mLOY, and one signal for REE. I have shown that HGS is likely to be causally linked to fracture risk, and I have identified the important shared genetic architecture between mLOY, glycaemic traits and cancer. I have also demonstrated that at least one known genetic variant contributing to obesity risk acts partially via reduced REE. Overall the findings of my PhD contribute to our wider understanding of the aetiological role of ageing processes in metabolic dysfunction, and have implications for both basic science and translational applications.

This research is important because it has identified a gap in the existing knowledge base. A term is therefore coined to label a computer-based test mode effect, the so-called Item Randomisation Effect, discussed in detail in this thesis. Item Randomisation Effect is a test mode effect occurring in computer-based testing contexts, especially noticeable in test-takers that may be susceptible to test anxiety. The practise of randomising multiple choice items in computer-based test venues is commonplace, mainly as a deterrent for cheating. Previous research attempted to determine the degree of equivalence across testing modalities of any test. The need was to ensure test-takers in paper-based tests would not have an advantage/disadvantage over test-takers given the same test in a computer-based mode. Such studies have a nomothetic perspective. This research contrasts with those earlier studies in that it has an ideographic perspective because it is concerned with the performance of individuals taking any test in the computer-based modality. This subtle difference in perspective may account for the apparent gap in the existing educational research literature. Evidence of Item Randomisation Effect was found in this study but further research into this test mode effect is necessary. / Dissertation (MEd (Computer-Integrated Education))--University of Pretoria, 2008. / Curriculum Studies / unrestricted

Introduction and background Recruitment to cancer clinical trials needs to be improved, as does patient understanding about clinical trials, to enable patients to make an informed choice about whether or not to take part. The main reason that clinically eligible patients do not take part in clinical trials is because they refuse; poor understanding of the research has been associated with patient refusal. Audiovisual patient information (AVPI) has been shown to improve knowledge/understanding in various areas of practice but there is limited information about its effect in the cancer clinical trial setting, particularly in relation to recruitment rates. Understanding the research is necessary for informed consent, and it was hypothesised that if patient understanding about clinical trials was increased with AVPI, then this could result in a reduction in the number of patients refusing clinical trials, and therefore provide an ethical approach to improving recruitment. This study aimed to test the impact of an audiovisual patient information intervention on recruitment to randomised cancer clinical trials (refusal rates), patient understanding of the information given, and levels of anxiety. Reasons for patients’ decisions about trial participation were also assessed. Method An AVPI intervention was developed that aimed to address the common misconceptions associated with randomisation and clinical equipoise, as well as improve patient understanding generally of randomised cancer trials, and of other core clinical trial informational requirements, such as voluntariness. Patients were randomised to receive either AVPI in addition to the standard trial-specific written information, or the written information alone. A new questionnaire was developed to assess patient understanding (also referred to as knowledge) in the randomised trial setting and, following testing with patients and research nurses, this was shown to be reliable and valid. Patients completed self-report questionnaires to assess their understanding (new knowledge questionnaire) and anxiety (Spielberger State-Trait Anxiety Inventory), at baseline and after they had made their decision about clinical trial entry, when their perceptions of the intervention, as well as factors contributing to their decision were also determined (this tool incorporated Jenkins and Fallowfield’s (2005) questionnaire which assessed reasons for accepting and declining randomised cancer trials). Results A total of 173 patients with breast cancer (65%), colorectal cancer (32%) and lung cancer (3%) were entered into the main study. The median age was 60 (range 37-92 years). There was no difference in clinical trial recruitment rates between the two groups: 72.1% in the AVPI group and 75.9% in the standard information group. The estimated odds ratio for refusal (intervention/no intervention) was 1.19 (95% ci 0.55-2.58, p=0.661). Knowledge scores increased more in the intervention group compared to the standard group (U= 2029, p=0.0072). The change in anxiety score between the arms was also statistically significant (p=0.011) with anxiety improving in the intervention arm more than in the no-intervention arm. The estimated difference in the median anxiety change score between the groups is –4.6 (95% ci –7.0 to –2.0). Clinical trial entry was not influenced by tumour type, stage of cancer, age, educational qualifications or previous research experience, however, there was a modest association with deprivation status (p=0.046) where more affluent patients were the least likely to consent to a trial. Educational qualifications and stage of cancer were independently associated with knowledge: patients who were better educated had higher levels of knowledge about randomised trials, and patients who had limited stage of cancer had higher baseline knowledge than patients with advanced cancer. Acceptability of the intervention was high with 93% of those who watched it finding it useful, and 42% stating that it made them want to take part in the clinical trial. Personal benefit and altruism were key motivating factors for clinical trial participation, with reasons for refusal being less clear. Discussion and conclusions Although the potential for AVPI to increase clinical trial recruitment rates was highlighted in the literature, in this study, AVPI was not shown to have any effect on refusal rates to randomised cancer trials. However, by improving patient understanding prior to decision making, AVPI was shown to be a useful addition to the consent process for randomised cancer trials. AVPI addresses the fundamental ethical challenges of informed consent by improving patient understanding, and supports the ethical framework integral to Faden and Beauchamp’s (1986) theory of informed consent. The new knowledge questionnaire was shown to be a sensitive and effective instrument for measuring understanding of randomised clinical trials in the cancer setting, although it would benefit from further testing. The AVPI appears to reduce anxiety at the decision making time point and has been shown to be an acceptable medium for patients. This study confirms existing findings from studies assessing factors affecting decision making, with personal benefit and altruism being key motivating factors, and reasons for refusal being less clear. The need for further qualitative work in this area is highlighted to gain a deeper understanding of what is important to patients, in terms of why they refuse clinical trial participation. Implications for practice and further research Several implications for practice have been identified, including using AVPI as part of the standard information package for patients considering randomised cancer trials, and focussing on patient and staff education in this area. The knowledge questionnaire could be introduced to routine practice as a tool to determine patient understanding prior to decision making, allowing clinicians the opportunity to correct any misconceptions prior to consent. Further research focussing on AVPI specific to individual trials would be helpful, to determine if a more customised approach would be of benefit in terms of clinical trial recruitment. The importance of studying other aspects of the consent process such as the interaction between the clinician and the patient, in addition to more detailed exploration of the factors affecting patients’ decisions were highlighted.

La variabilité de la réponse aux médicaments entre les individus est en grande partie attribuable aux différences génétiques causées par des mutations génétiques. Ces mutations ont émergé au cours de l'évolution humaine et peuvent être neutres, bénéfiques ou délétères en termes de survie ou de succès reproductif. Bien que de nombreuses études identifient des variants génétiques associés à des phénotypes, comme la réponse aux médicaments, peu d'attention est accordée à l'origine de ces mutations ou à leur présence au sein des populations. La médecine évolutive entre alors en jeu en étudiant les origines évolutives des mutations associées à des phénotypes. Ce domaine se situe à l'intersection de la médecine et de la biologie évolutive, et il cherche à comprendre comment le corps humain est devenu ce qu'il est aujourd'hui. Cette thèse se concentrera sur l'évolution des gènes impliqués dans la réponse aux médicaments. La première partie de cette thèse se penchera sur la relation entre les gènes ADCY9 et CETP, qui sont liés à la réponse au médicament dalcetrapib visant à réduire les événements cardiovasculaires en ciblant la protéine CETP. Une mutation dans le gène ADCY9 a été précédemment identifiée comme modulant la réponse à ce médicament. Nous avons identifié plusieurs pressions de sélection dans le gène ADCY9, mais nous avons concentré nos analyses sur son interaction épistasique, c'est-à-dire non linéaire, co-évolutive avec le gène CETP. Des effets de cette interaction sur plusieurs phénotypes ont été observés, et des mécanismes potentiels sous-tendant cette pression co-évolutive et son association avec le médicament ont été identifiés. La deuxième partie de cette thèse sera la suite d'un projet portant sur l'étude des pressions de sélection sur la superfamille des cytochromes P450. Les gènes de cette superfamille sont généralement impliqués dans la détoxification de l'organisme, y compris par la métabolisation d'environ 75% des médicaments couramment prescrits. Des analyses préliminaires ont révélé des enrichissements de pression de sélection dans deux sous-familles, à savoir les CYP3A et les CYP4F. Des phénotypes potentiellement sous pressions de sélection ont été identifiés dans la sous-famille des CYP3A au sein de la population africaine. En conclusion, l'intégration de la génétique des populations avec la transcriptomique et les études d'association phénotypiques enrichit notre compréhension des liens entre les pharmacogènes au sein de diverses populations. Cette approche représente un pas de plus vers l'amélioration de la médecine de précision. / Variability in drug response between individuals is largely due to genetic differences caused by genetic mutations. These mutations have emerged in the course of human evolution and can be neutral, beneficial or deleterious in terms of survival or reproductive success. Although many studies identify genetic variants associated with phenotypes such as drug response, little attention is paid to the origin of these mutations or their presence in the population. This is where evolutionary medicine comes in, studying the evolutionary origins of mutations associated with phenotypes. This field lies at the intersection of medicine and evolutionary biology, and seeks to understand how the human body became what it is today. This thesis will focus on the evolution of genes involved in drug response. The first part of this thesis will look at the relationship between the genes ADCY9 and CETP, linked to the response to the drug dalcetrapib aimed at reducing cardiovascular events by targeting the CETP protein. A mutation in the ADCY9 gene has been previously identified as modulating the response to this drug. We identified several selection pressures in the ADCY9 gene, but focused our analyses on the co-evolutionary epistatic interactions, meaning non-linear. Effects of this interaction on several phenotypes were observed, and potential mechanisms underlying this co-evolutionary pressure and its association with the drug were identified. The second part of this thesis will follow on from a project investigating selection pressures on the cytochrome P450 superfamily. Genes in this superfamily are generally involved in the detoxification of the body, including the metabolization of around 75% of commonly prescribed drugs. Preliminary analyses have revealed selective pressure enrichments in two subfamilies, CYP3A and CYP4F. Potential phenotypes under selective pressure were identified in the CYP3A subfamily in the African population. In conclusion, the integration of population genetics with transcriptomics and phenotypic association studies enhances our understanding of the connections among pharmacogenes across diverse populations. This approach signifies another stride towards advancing precision medicine.

I performed two randomised controlled trials (RCTs) to determine the best treatments for enteric fever in Kathmandu, Nepal, an area with a high proportion of nalidixic acid resistant S. Typhi and S. Paratyphi A isolates. I recruited 844 patients with suspected enteric fever to compare chloramphenicol versus gatifloxacin. 352 patients were culture confirmed. 14/175 patients treated with chloramphenicol and 12/177 patients treated with gatifloxacin experienced treatment failure (HR=0.86 (95% CI 0.40 to 1.86), p=0.70). The median times to fever clearance were 3.95 and 3.90 days, respectively (HR=1.06 [CI 0.86 to 1.32], p=0.59). The second RCT compared ofloxacin versus gatifloxacin and recruited 627 patients. Of the 170 patients infected with nalidixic acid resistant strains, the number of patients with treatment failure was 6/83 in the ofloxacin group and 5/87 in the gatifloxacin group (Hazard Ratio, HR=0.81, 95% CI 0.25 to 2.65; p=0.73); the median times to fever clearance were 4.7 and 3.3 days respectively (HR=1.59 [CI 1.16 to 2.18], p=0.004). I compared conventional blood culture against an electricity free culture approach. 66 of 304 patients with suspected enteric fever were positive for S. Typhi or S. Paratyphi A, 55 (85%) isolates were identified by the conventional blood culture and 60 (92%) isolates were identified by the experimental method. The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% and 96.0%, respectively. This electricity free blood culture system may have utility in resource-limited settings or potentially in disaster relief and refugee camps. I performed a literature review of RCTs of enteric fever which showed that trial design varied greatly. I was interested in the perspective of patients and what they regarded as cure. 1,481 patients were interviewed at the start of treatment, 860 (58%) reported that the resolution of fever would mean cure to them. At the completion of treatment, 877/1,448 (60.6%) reported that they felt cured when fever was completely gone. We suggest that fever clearance time is the best surrogate for clinical cure in patients with enteric fever and should be used as the primary outcome in future RCTs for the treatment of enteric fever.

No description available.