VictorJuiz/thesis huggingface dataset:
Active mountain-building in Mongolia and Iran
Keywords: faulting
Earthquakes
tectonics

In this thesis I use a multi-disciplinary approach to investigate two areas of active mountain-building within the Alpine-Himalayan belt: the Altai range in western Mongolia, and the Zagros mountains in southern Iran. I begin by studying a clustered earthquake sequence that struck a previously unrecognised fault zone in the NW Altai mountains in 2003. By combining seismology and field observations with satellite radar interferometry (InSAR), I attempt to unravel the detailed history of faulting in time and space. Differences between body-wave and InSAR-based models prevent me from matching individual seismic events with individual fault segments, and I explore the cause of these discrepancies. In the following two chapters, I establish late Quaternary slip-rates on major right-lateral and thrust faults in the eastern part of the Altai. In particular, I explore the use of in situ-produced cosmogenic Be-10 and Optically Stimulated Luminescence (OSL) for dating offset alluvial fans and river terraces. My results suggest that faulting has migrated toward the eastern margin of the range from the high, interior Altai, presumably in response to stresses introduced by topography. In the final, main chapter, I investigate a link between buried reverse faulting and surface folding in the Zagros Simply Folded Belt. Using surface displacements measured with InSAR, I show that a major anticline on Qeshm Island was uplifted during an earthquake in 2005. However, the pattern of uplift is discordant with the growth of neighbouring folds, preventing us from establishing a simple connection between faulting and folding. All in all, my work demonstrates the importance of using several techniques in parallel when studying regions of active continental deformation.
On the significance of neutral spaces in adaptive evolution
Keywords: genotype-phenotype map
evolvability
evolutionary dynamics
mutational robustness

Evolutionary dynamics arise from the interplay of mutation and selection. Fundamentally, these two processes operate at different levels: Mutations modify genetic information (the genotype), which is passed from parent to offspring. Selection is triggered by variation in reproductive success, which depends on the physical properties (the phenotype) of an organism and its environment. Thus the genotype-phenotype map determines if and how mutations can lead to selection. The aim of this dissertation is to incorporate this map explicitly into a theoretical description of evolutionary dynamics. The first part of the analysis presented here is concerned with the static properties of simple models of these maps, which are studied using exhaustive enumeration. The two most important observations are phenotypic bias – some phenotypes are realized by many more genotypes than most other phenotypes – and the existence of neutral spaces – genotypes with the same phenotype can often be reached from each other by single mutational steps.
The remainder of the dissertation provides a theoretical description of evolutionary dynamics on and across neutral spaces. Two different mean-field approximations lead to simple analytic results for the first discovery of alternative phenotypes, highlighting the importance of phenotypic bias: Rare phenotypes are hard to find by evolutionary search. These results are used to discuss the relationship of robustness, the ability to withstand mutational change, and evolvability, the ability to create variation through mutation. Several types of fluctuations beyond the mean-field limit are studied, both theoretically and in simulations. The discrete structure of genotype spaces can lead to strong correlations in the spectra of phenotypes produced, increasing the probability that a particular phenotype is fixed in the population quickly after its discovery. Structural correlations between genotypes can increase the effect of phenotypic bias, while the qualitative features of the mean-field description remain valid. All these results highlight that neutral spaces impact evolutionary dynamics in many non-trivial ways, in particular by favouring phenotypes of high accessibly, but comparably low fitness over those phenotypes that are highly fit, but very hard to discover.
Investigation of the effects of IGF-1 receptor blockade on  chemoresistance of advanced melanoma
Keywords: alkylating agent
melanoma
IGF-1 receptor
chemotherapy
resistance

Advanced melanoma poses a major therapeutic challenge, and despite the development of recent promising therapeutic agents, resistance to treatment remains a problem. Until recently, despite low response rates, alkylating agents dacarbazine and temozolomide (TMZ) were the standard of care for the treatment of advanced melanoma. The cytotoxic effects of these agents relies upon the formation of alkylated base lesions such as O6-methylguanine (O6MeG), which is repaired by a protein implicated in TMZ resistance called O6-methylguanine-DNA methyltransferase (MGMT). Failure to resolve such alkylated bases results in DNA replication-associated double-strand breaks (DSBs). The type 1 insulin-like growth factor receptor (IGF-1R) mediates a number of characteristics common to cancers, including proliferation and survival, and evidence suggests it may also contribute to resistance to many anticancer agents. The aims of this study were to test whether melanoma cells could be sensitized to TMZ by small molecule IGF1R inhibitors, and to explore the mechanism of any chemosensitization. This study found an association between basal IGF1R phosphorylation and in vitro TMZ resistance in seven MGMT-proficient melanoma cell lines, suggesting that IGF1R activation may be linked with TMZ resistance. Furthermore, IGF1R inhibition caused dose-dependent sensitization of melanoma cells to TMZ, regardless of BRAF mutation status. This reduction in cell survival was not accompanied by an increase in apoptosis, but rather Chk2 activation and an accumulation of cells in the G2/M phase of the cell cycle, suggesting a possible effect of IGF1R inhibition on DNA repair. IGF1R depletion was found to increase MGMT protein levels and activity, but this effect was not seen in IGF1R inhibited cells. In addition, IGF1R inhibition was not epistatic with MGMT inhibition, and IGF1R inhibition reduced survival of TMZ treated MGMT-null cells. This suggested that TMZ sensitization by IGF1R inhibition was independent of MGMT. IGF1R inhibition did however cause an increase in the accumulation of TMZ-induced RPA foci, and delay in resolution of RAD51 foci. Together with the finding that IGF1R inhibition reduced survival in PARP inhibited melanoma cells, these results suggested that IGF1R inhibition influenced DSB repair by homologous recombination. Finally, the combination of IGF1R inhibition with TMZ was tested in a mouse model and was found to be tolerable. TMZ or IGF-1R inhibitor alone caused minor reduction in melanoma xenograft growth rates (rate reduction by 13% and 25% respectively), while combination treatment caused supra-additive growth delay (72%) that was significantly different from other treatment groups (p<0.05). The findings of this study suggest IGF1R inhibition as a possible option in overcoming alkylating drug resistance in melanoma.
The distribution and dispersion of herpetofauna in lowland farmland: with a focus on the common toad (Bufo bufo)
Keywords: habitat
Bufo bufo
agri-environment schemes
farmland
conservation

Concern over unexplained population declines in the common toad (Bufo bufo) has led to it being recognised as a priority species for conservation research. The general consensus among herpetologists is that the most important cause of the declines seen as part of a global amphibian extinction crisis is habitat loss and degradation.
The aim of thesis is to investigate the effect of habitat availability and quality on common toad populations in the United Kingdom, with a particular emphasis on the effect of land under agricultural use. I use occupancy modelling, resource selection function modelling and genetic techniques to determine the effects of both terrestrial and aquatic habitat on common toads. Based on my findings, I consider the impacts of habitat at local, landscape and national scales.
My research revealed the importance of pond density and presence of woodland in increasing relative probability of toad occurrence in the terrestrial habitat (Chapters 2 and 3) and the importance of water quality, woodland coverage and available terrestrial habitat coverage in determining common toad presence in ponds. The isolating effect of urban areas is demonstrated in Chapter 4 where Isolation By Barriers (IBB) explains genetic distance between common toad breeding populations better than Isolation By Distance (IBD). In Chapter 5 I again use the resource selection function for terrestrial habitat use developed in Chapter 3, to investigate the importance of terrestrial habitat availability in determining pond use by common toads at a national scale.
In my concluding chapter, I make recommendations for management and further research including consideration of potential interactions between the effect of habitat loss, fragmentation and degradation with other potential causes of common toad decline.
The within- and among-host evolution of chronically-infecting human RNA viruses
Keywords: within-host evolution
evolution
computational biology
phylogenetics
virology
molecular evolution

This thesis examines the evolutionary biology of the RNA viruses, a diverse group of pathogens that cause significant diseases. The focus of this work is the relationship between the processes driving the evolution of virus populations within individual hosts and at the epidemic level. First, Chapter One reviews the basic biology of RNA viruses, the current state of knowledge in relevant topics of evolutionary virology, and the principles that underlie the most commonly used methods in this thesis. In Chapter Two, I develop and test a novel framework to estimate the significance of phylogeny-trait association in viral phylogenies. The method incorporates phylogenetic uncertainty through the use of posterior sets of trees (PST) produced in Bayesian MCMC analyses. In Chapter Three, I conduct a comprehensive analysis of the substitution rate of hepatitis C virus (HCV) in within- and between-host data sets using a relaxed molecular clock. I find that within-host substitution rates are more rapid than previously appreciated, that heterotachy is rife in within-host data sets, and that selection is likely to be a primary driver. In Chapter Four I apply the techniques developed in Chapter Two to successfully detect compartmentalization between peripheral blood and cervical tissues in a large data set of human immunodeficiency virus (HIV) patients. I propose that compartmentalization in the cervix is maintained by selection. I extend the framework developed in Chapter Two in Chapter Five and explore the Type II error of the statistics used. In Chapter Six I review the findings of this thesis and conclude with a general discussion of the relationship between within- and among-host evolution in viruses, and some of the limitations of current techniques.
Political institutions, skill formation, and pension policy: the political-economic logic of China’s pension system
Keywords: varieties of capitalism
pension
skill formation
China
labour market
comparative political economy of the welfare state

A central theme in the comparative political economy of the welfare state is the complementaries between political institutions, social policy, and labour markets. Yet little has been written to uncover this political-economic nexus in China, the world’s second largest economy. This thesis partly addresses this gap by studying the country’s public pension arrangement, the most expensive component of the Chinese welfare state. It reveals the working of the political-economic nexus in contemporary China by showing how it leads to two puzzling characteristics of the Chinese pension system, namely the rapid expansion in the absence of electoral pressures and the persistent regional fragmentation despite an authoritarian central government. It argues that the decentralised authoritarianism, in which China’s authoritarian central state delegates to regional governments and motivates them to achieve its developmental goals, drives municipal authorities to compete with each other in generating economic growth. In the inter-municipal economic competition, local leaders adopt an expansionary yet localising pension policy. This facilitates the formation of specific industrial skills, which are productive for particular local industries, and the retention of skilled industrial workers. All of this is important to local economic development in a context of industrial upgrading and labour market tightening. It is argued this is the political-economic logic of China’s pension system.
The changing structure of occupations and wage inequality
Keywords: social class
wage inequality
occupations

This thesis investigates the co-evolution of the changing structure of occupations and the growth in wage inequality in Britain since the 1970s and the subsequent stabilisation during the 2000s. Occupations provide the single most important unit of analysis for economic inequality in stratification research, providing the basis for socioeconomic status, prestige scales, job desirability scores, and social class schemas. Although there was a ‘massive rise’ in wage inequality, relatively little is known about the relationship between the occupational structure and the growth in wage inequality. Since sociologists tend to place a lot of emphasis on the role of occupations in structuring economic inequalities, we might expect them to play a key role in accounting for trends in overall wage inequality. More recent strands of sociological theory, however, argue that the link between occupations and economic inequalities might have been weakening over time.
This thesis assesses these claims in relation to the over time trends in between- and within-occupation-inequality. It finds that the growth in overall wage inequality was largely due to growing inequality between occupations, not within them. The growth in between-occupation inequality was largely due to higher-paying occupations receiving the largest wage gains. Furthermore, and perhaps surprisingly, only a handful of occupations account for the majority of the rise in wage inequality, indicating caution should be exercised in generating accounts about the role for occupations in accounting for overall inequality. Along the way, this thesis attempts to address the extent to which the structuring of the growth in wage inequality by occupations was due to the changing composition of incumbents within occupations (namely the rise in educational attainment), in spite of data limitations. Finally, this thesis takes to task what the implications of the ‘massive rise’ in wage inequality implies for the broader categories sociologists use to capture economic inequalities based on aggregations of occupations.
The role of tracing in claiming 
Keywords: Equity
Debt
Value
Restitution
Property
Tracing

The central tenet of tracing theory is that in certain circumstances it is possible to show that one asset stands in the place of another, such that any claims in relation to the original asset can be transmitted to its substitute. Since at least 2001 academic and judicial orthodoxy has been that this is done by following the path of value from one asset to the other, and can be aided in more complex cases by the application of evidential rules or presumptions. These ideas are at the heart of existing accounts of proprietary claims against trustees who deal with trust assets without authority, and personal and proprietary claims against strangers to the trust. They are also at the heart of calls to 'unify' the rules of tracing at law and in equity, removing existing distinctions drawn between claimants who are owed fiduciary duties and those who are not.
In this thesis it is argued that there are no independent processes of following and identifying value, and that the language of 'tracing value' has lent the appearance of neutrality and conceptual unity to disparate heads of fiduciary and non-fiduciary liability. Most importantly, it has led to the assumption that in any case in which a claimant can demonstrate that a series of transactions links some right in the defendant’s hands with a right previously held by or for the claimant, the claimant can claim that right. In this thesis it is argued that far from creating an arbitrary practical obstacle for claimants seeking to trace and locate value, the fiduciary relationship is at the heart of the justification for any claim that exists to a new right in the hands of someone else.
The rise of the leisure painter: artistic creativity within the experience of ordinary life in postwar Britain, c. 1945-2000
Keywords: social democracy
art
affluence
british
history
market liberalism
modern
amateur

Since John Ruskin and William Morris's protestations against mass production in the nineteenth century, critics of mass consumption thought that it not only reduced the necessity, but also the desire, to make things for personal use and enjoyment. The history of leisure painting in art societies and adult education, and of the amateur artist’s consumption of art materials and self-help literature, shows that, on the contrary, affluence both inspired and facilitated a quest for self-actualisation amongst the rank and file. Creative activities such as drawing and painting served this quest at little financial cost to the individual. Following the Second World War, a significant increase in the take-up of leisure painting was encouraged by the state as part of the broader postwar settlement. The pursuit of personal wellbeing through creative activity was regarded as a public good, of benefit not only to individuals but also to the communities of which they were a part. In the last quarter of the twentieth century, state support for recreational pursuits such as leisure painting was pared back: in the shift from collectivist social democracy towards individualist market liberalism, personal enjoyment was recast as a private affair for which the consumer must pay. Painting continued to grow in popularity, supported by expanding consumer markets in self-help literature and affordable art materials. Yet while consumerism sustained the popularity of amateur art-making, the ways in which amateur artists participated in the arts changed. Personal creativity emerges here as an inherently social activity: the private experience of creativity is mediated and structured by society. Consumerism was not bad for personal creativity per se, but the replacement of a communitarian approach with a consumerist model restricted the breadth and reach of creative aspiration nurtured as part of the postwar settlement. By the end of the century, most amateurs were painting alone.
The role and regulation of Asterless in the centrosome cycle
Keywords: Centriole
centrosome
Drosophila

Centrosomes are the main microtubule organizing centres in animal cells and are formed by a pair of centrioles together with surrounding pericentriolar material (PCM). Cycling cells duplicate their centrosomes strictly once per cell cycle. This process is driven by the semi-conservative duplication of the centrioles that are found at the centrosome core. During the exit from mitosis the two centrioles within the single inherited centrosome separate, and upon the start of S-phase each of these inherited mother centrioles assembles an adjacent daughter at its side. This process results in two complete centrosomes that can form the poles of the mitotic spindle, and thus segregate evenly to the next cell generation.
The formation of a daughter centriole suppresses the initiation of new duplication events from the same templating mother centriole until this daughter separates - disengages - at the end of the cell cycle. This regulation - that acts to repress centriole amplification - is summarized in the 'licensing model of centriole duplication' (Tsou and Stearns, 2006). This model states that centriole disengagement provides the license for the re-duplication of mother centrioles. Importantly, experiments show that while abolishing centriole engagement is sufficient to allow mother centrioles to re-duplicate within the same cycle, it is insufficient to allow daughter centrioles the assembly of a granddaughter before they mature into mothers towards the end of their first cell cycle. The molecular nature of this daughter-to-mother transition remains mysterious.
In this thesis I show that in Drosophila embryos the essential centriole duplication protein Asl is not incorporated into daughter centrioles as they assemble during S-phase, but is only incorporated once mother and daughter separate at the end of mitosis. The initial incorporation of Asterless (Asl) is irreversible, and is dependent on centriolar DSas-4. Crucially, Asl incorporation is essential for daughter centrioles to mature into mothers that can support centriole duplication. I propose that Asl acts as a permanent primary license that allows new centrioles to duplicate for the first time. Once acquired, this primary license is not lost but rather further regulation is taken over by the reduplication licensing mechanism, disengagement. This work extends the previously proposed licensing model to also explain how new centrioles are licensed for their first duplication event.
Duties in the wake of atrocity: a normative analysis of post-atrocity peacebuilding
Keywords: jus post bellum
mass atrocities
just war theory; humanitarian intevention

Over the last two decades, the international community has taken on the task of rebuilding societies in the aftermath of mass-atrocities. Through a combination of trial and error and vigorous academic research, a relatively clear (and semi-malleable) blueprint of post-atrocity peacebuilding has developed. This includes setting up a temporary international transitional authority, establishing democracy, facilitating economic development, and holding war crime trials. Though there are volumes of studies which address the pragmatic strengths and weaknesses of these key elements of peacebuilding, to date political theorists have not critically analyzed the moral legitimacy of these policies. My thesis aims to fill this gap.
The overarching question of this thesis is this: What moral duties does the international community have to post-atrocity societies? To answer this question, I critically examine the normative issues involved in the four key aspects of peacebuilding (identified above). Using the framework of just war theory and a cosmopolitan theory of fundamental human rights, I argue that, in most post-atrocity cases, the international community has duties to remove atrocity-committing regimes from power, occupy the target-state and act as a transitional authority, help facilitate the creation of democracy and economic development, and hold war crimes trials. These duties, of course, are extremely complicated and limited and these qualifications are examined and developed throughout. Running through the construction of my theory of post-atrocity duties is a clear message: we – the international community – have obligations to the victims and survivors of atrocities. In other words, providing assistance in the wake of mass-atrocities is not a supererogatory act of charity, rather, it is a duty which we owe to the victims of these horrible crimes.