VictorJuiz/thesis huggingface dataset:
Expropriation, extraction, and evasion decisions in the design of taxation regimes for the natural resources industry

This dissertation provides three models pertaining expropriation and production decisions in the natural resources industries.
The first two chapters are intertwined: in these, the government relies on two tools to capture the rents from privately-owned Natural Resources Companies, a corporate income tax and the possibility of expropriating the assets. A real options model is used to assess the effect that progressiveness in taxation has on the political risk of a natural resources project.
In the first chapter, we discover that under certain conditions for the underlying commodity: –low prices or forward curves in backwardation– the introduction of an equivalent but more progressive tax regime decreases the political risk and the corresponding deadweight loss. However, when initial prices are too high or initial futures curves are in strong contango, the introduction of a progressive tax regime ends up significantly increasing the risks.
In the second chapter, producers are able to foresee the risks of expropriation and thus change their behaviour: the results are mixed. As in the previous case, with lower prices and less tendency to expropriate, the scheduling of production allows for gains in the value of the operation for the firms. More progressive tax regimes end up being detrimental to the government, which in some cases can even result in a non-stable equilibrium with the producers and governments trying to outguess each other and end up cycling both the production and the expropriation probability in order to maximise their respective expected value for the operations. This has a detrimental effect for all parties involved.
Finally, the third chapter introduces the possibility that a government levies royalties over sales. The development of home-based institutions is going to affect the amount of tax evasion that a government will face and thus determine the appropriate combination of taxes that it must choose. We find that when the host country's tax and technological capacity are too low, a state has no incentives to improve its institutions and becomes trapped in a low tax, low revenue situation: what we call a Royalty Trap. We end up by showing the evolution of tax capture in Chile during the 20th century to illustrate how these concepts might be applied.

Keywords: Taxation
Political risk
Royalties
Multiple real option
Real options
Expropriation risk
Income shifting
Non-renewable resources
Advisor: Venables, A
Modelling the pharmacokinetics and pharmacodynamics of macromolecules for the treatment of wet AMD

Wet age related macular degeneration (wet AMD) is a highly debilitating retinal disease, the third leading cause of blindness in the world and one the most expensive ocular conditions to care for. Wet AMD is characterised by the proliferation of neovasculature through the retinal posterior and theorised to be, at least in part, induced and driven by excess vascular endothelial growth factor (VEGF). Many current treatments for wet AMD utilise anti-VEGF macromolecules that bind to VEGF. The retina, however, remains a largely inaccessible, and delicate, anatomical region. Due to difficulties in collecting clinical and experimental data, mathematical modelling is playing an increasingly prominent role in understanding the distribution (Pharmacokinetics, PK) and drug-to-target interactions (Pharmacodynamics, PD) for treatments of wet AMD. This thesis will focus on ordinary/partial differential equation (ODE/PDE) models for the PK/PD of anti-VEGF therapeutics, administered via intravitreal (IVT) injection into the mammalian eye. We start in Chapter 2 with a 2-compartment PK/PD ODE model of drug-VEGF interactions in the eye, analysing a clinical dataset to estimate key binding parameters between VEGF and the typical anti-VEGF molecule, ranibizumab. In Chapter 3, we extend the PK ODE framework of the 2-compartment model to include a mechanistic description of the retina, to estimate retinal permeability to macromolecules used for treating wet AMD. In Chapter 4, using the retinal PK model, we reintroduce VEGF to predict concentrations of free VEGF in the retina post-IVT injection. Chapters 5 and 6 model a hypothetical class of anti-VEGF molecules designed to bind not only VEGF but also existing vitreal superstructures, analysing how dose and binding kinetics impact ocular retention. Alongside these models we present analogous PDE models, addressing whether the assumption that concentrations are homogeneous across anatomical regions, as implicit in ODE models, is appropriate for macromolecular PK/PD in the mammalian eye.

Keywords: mathematical modelling
wet amd
PK/PD
IVT injection
Advisor: Gaffney, E
Maini, P
Byrne, H
The synthesis and study of titanium amidinate complexes as olefin polymerisation catalysts

This Thesis is concerned with the synthesis of post-metallocene group 4 amidinate complexes as pre-catalysts for the polymerisation and oligomerisation of α-olefins. Activation of half-sandwich group 4 amidinate complexes with 1,3-conjugated dienes is also investigated and their underlying chemistry is explored.
Chapter 1 introduces homogeneous Ziegler-Natta catalysis, with a specific focus on group 4 compounds. A review of metallocene and post-metallocene complexes of group 4 will also be presented and their behaviour in olefin polymerisation will be discussed.
Chapter 2 describes the synthesis and characterisation of k1-amidinate supported titanium complexes. Base-free activation of the titanium cyclopentadienyl-amidinate dialkyl complexes will be investigated and the resulting cationic species will be further explored with commonly applied trapping agents. The synthesis and characterisation of new titanium cyclopentadienyl-amidinate diene complexes and their corresponding tri(pentafluorophenyl)borane-activated zwitterionic compounds will also be described and their performance in the co-polymerisation of ethylene and propylene will be discussed.
Chapter 3 explores the addition of 1,3-conjugated diene reagents to titanium cyclopentadienyl-amidinate and guanidinate alkyl cations. Mechanistic and computational studies of allyl and diene formation will also be described. The polymerisation capabilities of the newly formed complex will be discussed and compared to previously reported dialkyl complexes.
Chapter 4 describes the synthesis and characterisation of aminopyridinato titanium complexes and k1-k2-bis(amidinate) titanium complexes. The activation chemistry of the newly formed dialkyl complexes will be investigated. Furthermore, the synthesis of a new bis(aminopyridinato) titanium complex will also be discussed alongside their activity in EPM and EPDM polymerisation.
Chapter 5 describes the performance of the aminopyridinato titanium complexes (synthesised in Chapter 4) in EPDM polymerisation. The sensitivity of the aforementioned complexes towards hindered phenols will also be discussed and their behaviour in ethylene oligomerisation will be explored.
Chapter 6 presents full experimental procedures and characterising data for the new complexes reported in this Thesis.

Keywords: reactivity studies
postmetallocene catalysis
Advisor: Mountford, P
On collective behaviour of coupled micro/nano electromechanical sensors

With advances in nanotechnology, resonant sensors based on micro/nano electromechanical systems (M/NEMS) have been manufactured utilising a process similar to that of microelectronics. By providing a frequency shift proportional to the mass/stiffness change, these small resonators enable rapid detection of extremely minute changes in mass and force. For example, they can be used to trace the concentration of pathogens. M/NEMS resonators also demonstrate excellent compatibility with electronic circuits, hence offering multi-function and single-chip solutions for next-generation sensing applications. Resonators are coupled to provide extra degrees of freedom for multi-sensing, while reducing a majority of connections required. The collective behaviour of coupled systems gives rise to new sensing methods such as eigenvalue and eigenvector sensing, which exhibit enhanced sensitivity and linearity as opposed to the traditional frequency-shift approach.
However, the mechanisms of coupling have not yet been fully exploited. Coupled micro/nano systems are exposed to several challenges. First, process variability is known to degrade sensor performance. Moreover, the readout and signal processing issues in large arrays have not been addressed. Hence, actuating and testing coupled sensors are expensive and time-consuming. These hurdles can be circumvented using a novel inverse eigenvalue analysis (IEA) method proposed in this thesis, which is capable of characterising coupled systems based on inverse and forward analysis. The method extracts the system matrix, which carries deterministic information about process and sensitivity, by attaching a peripheral electrical resonator to the MEMS array, therefore providing the advantages of simplified actuation, accurate calibration and sensitivity trimming. To explore the ultimate limit of scaling, prototype sensors consisting of different numbers of coupled resonators have been designed, fabricated and tested for sensing. By investigating the unique behaviour of eigenvalues, various approaches have been proposed to enhance the accuracy of inverse eigenvalue sensing in large coupled systems.

Advisor: Choubey, B
Modulations in movement by animals

Movement is a fundamental aspect of life, which is intrinsically linked to almost every ecological and evolutionary process. Thus, a large fraction of an individual’s energy budget is invested in movement. Managing energy expenditure in relation to energy acquisition is critical for survival and is a primary focus for natural selection. Therefore, investigating how, when and why animals modulate their movement is crucial to understand behavioural ecology and, ultimately, the driving forces shaping evolution. The aim of my DPhil is to investigate how animals modulate their movement in response to their navigational capacity, the external presence of conspecifics and their internal reproductive state using two model species: the homing pigeon (Columba livia) and the African savannah elephant (Loxodonta africana). In Chapter 2, I report that homing pigeons modulate their wingbeat characteristics as a function of navigational knowledge, which suggests, for the first time, that navigation may have physical (biomechanical) manifestations. In Chapter 3, I show that pigeons increase their wingbeat frequency by c.18% when flying in pairs relative to flying solo. My results demonstrate that there is a substantial cost to flying together, and that the ultimate drivers of flocking, including predator protection and navigational knowledge, must outweigh these proximate costs. By contrast, in Chapter 4 I reveal that gestation, parturition and the presence of a neonatal calf has little impact on the movements of multiparous elephants, which could suggest that elephants’ unusually long gestation period evolved to facilitate an advanced stage of physical development. In my final data chapter, I show that reproductively active male elephants significantly increase their speed with age, suggesting that elephants increase energetic investments into reproduction as their probability of reproductive success increases. Overall, the results of my thesis provide key new insights into proximate and ultimate causes of movement and its modulation in animals.

Advisor: Vollrath, F
Biro, D
Portugal, S
Peptidoglycan recycling in the Gram-positive bacterium Staphylococcus aureus and its role in host-pathogen interaction

Bacteria are enclosed by a peptidoglycan sacculus, an exoskeleton-like polymer composed of glycan strands cross-linked by short peptides. The sacculus surrounds the cell in a closed bag-like structure and forms the main structural component of the bacterial cell wall. As bacteria grow and divide, cell wall remodelling by peptidoglycan hydrolases results in the release of peptidoglycan fragments from the sacculus. In Gram-negative bacteria, these fragments are efficiently trapped and recycled. Gram-positive bacteria however shed large quantities of peptidoglycan fragments into the environment. For nearly five decades, Gram-positive bacteria were thus assumed not to recycle peptidoglycan and this process has remained enigmatic until recently. In this thesis, the occurrence and physiological role of peptidoglycan recycling in the Gram-positive pathogen Staphylococcus aureus was investigated. S. aureus is an important pathogen, and is becoming increasingly resistant to many antibiotics. Through bioinformatic and experimental means it was determined that S. aureus may potentially recycle components of peptidoglycan and novel peptidoglycan recycling components were identified and characterised. Though disruption of putative peptidoglycan recycling in S. aureus appears not affect growth or gross morphology of this bacterium, potential roles for peptidoglycan recycling in cell wall homeostasis and in virulence were identified. This is to my knowledge the first demonstration of a potential role of peptidoglycan recycling in either of these aspects of bacterial physiology in any Gram-positive bacterium. This is an important step forward in understanding the basic biology of Gram-positive bacteria, and in understanding the mechanisms of virulence in S. aureus. Future study of this process in S. aureus and other Gram-positive bacteria promises to reveal yet further facets of this process and its functions, potentially leading to the identification of novel therapeutic approaches to combat infections.

Keywords: infection
staphyloccus aureus
aminosugar recycling
host-pathogen interaction
virulence
bacterial cell wall
peptidoglycan turnover
peptidoglycan hydrolase
peptidoglycan recycling
Advisor: Ligoxygakis, P
Secular assemblages: affect, Orientalism, and power in the French enlightenment

Taking Saba Mahmood’s question ‘Can secularism be other-wise?’ (2010) as the starting point for a critical-historical investigation of the ‘secular body’ (Asad 2003; Hirschkind 2011), my thesis develops in two stages. In the first, I argue that current works of secular theory—particularly A Secular Age (Taylor 2007)—tend to rely on an excessively rationalistic conception of Enlightenment thought for the construction of their central conceptual categories (e.g. the ‘immanent frame’, ‘buffered self’, or ‘modern exclusive humanism’), thus reinforcing a double-binary linking rationality to Euro-American secularity, and emotion to subaltern ‘religion’. Against Taylor and others, I emphasise the contradictory, ‘assembled’ nature of Enlightenment discourse, and point to alternative, more body-centred strands of thought in key figures of the seventeenth-eighteenth-century French Enlightenment, such as Descartes, Montesquieu, Voltaire, Diderot, Helvétius, and Holbach. Against common perceptions, and drawing on a range of philosophical works, institutional reports, and stage plays in French and in translation, I suggest these figures in some ways reinstated emotion and the body against the rationalistic tendencies of the past. Insofar as ‘the secular’ was shaped by the Enlightenment, it emerged out of a conscious project of nationalist cultivation, based fundamentally on manipulating the body and emotions.
In the second stage, I consider the way Orientalist representations of non-Western religions meshed with prevalent theories of political manipulation to generate an affective system of anti-Catholic propaganda geared towards the national good. Though existing critiques of Taylor tend to focus on the importance of religious (i.e. Christian) constructions of Oriental religions for the genealogy of secularity (e.g. Mahmood 2010), I suggest a distinctively secular form of Orientalism emerged in the eighteenth century, in which anti-religion, racism, and nationalism merged into a powerful weapon of republican discourse, congruent with ambient theories of emotion. The aesthetic manipulation of racist and Orientalist tropes in Montesquieu’s Lettres Persanes (1721) and Voltaire’s Le Fanatisme (1741), for example, can be read as a practical response to existing theory on the power of images to regulate people’s passions in the national interest.

Keywords: Descartes
Enlightenment
Holbach
Islam
The secular
Race
Montesquieu
Voltaire
Postsecularism
Charles Taylor
Secularism
Advisor: Schaefer, D
Hausner, S
The three-dimensional regulatory landscapes of the globin genes

One of the most important outstanding questions in biology involves the precise spatial and temporal regulation of gene activity, which enables different cell types to express the specific set of genes required for their function and is therefore a cornerstone for complex biological life. Cis-regulatory elements, such as gene promoters and enhancers, play a key role in controlling gene activity. These elements physically interact with the genes they regulate within structural chromatin domains. The organisation of chromosomes into these domains is critical for specific regulation of gene expression and disruption of these structures underlies common human disease. However, it is not understood how chromatin domains form, how interactions between the cis-regulatory elements contained within them are established, or how such interactions influence gene expression.
The major hurdles in addressing these questions are to determine chromatin structures with high resolution and sensitivity and to examine their dynamic nature within single cells. To overcome these, I have developed Tri-C, a new chromosome conformation capture assay that can analyse concurrent chromatin interactions at single alleles at high resolution. By combining Tri-C with conventional chromosome conformation capture techniques, I have analysed the three-dimensional regulatory landscapes of the well-characterised murine globin loci at unprecedented depth. Additionally, to examine the roles of cis-regulatory elements in establishing chromatin architecture, I have analysed how engineered deletions in enhancers and CTCF-binding elements in the murine alpha-globin locus disrupt its chromatin landscape.
These analyses reveal that the chromatin domains containing the globin genes represent compartmentalised structures, which are delimited by CTCF boundaries. The heterogeneity of interactions in these domains between individual cells is indicative for a dynamic process of loop extrusion underlying their formation. Within chromatin domains, preferential structures are formed in which multiple enhancers and promoters interact simultaneously. These complexes provide a structural basis for understanding how multiple cis-regulatory elements cooperate to establish robust regulation of gene expression. Importantly, these complex, tissue-specific structures, cannot be explained by loop extrusion alone and indicate other, independent mechanisms contributing to chromosome architecture, likely involving interactions mediated by multi-protein complexes. Together, these analyses show that the current view of genome organisation, in which chromosomes are organised by stable loops and domains that self-assemble into hierarchical structures, is not correct. Rather, chromatin architecture reflects a complex interplay between distinct molecular mechanisms contributing to the formation of regulatory landscapes that facilitate precise, robust control of gene expression.

Keywords: Chromosome structure and organisation
Globin
Gene regulation
Genetics
Advisor: Hughes, J
Higgs, D
Where are the digital natives? Identifying and mapping digital literacy skills of students and teachers in an international college

This research aimed to identify and map the digital literacy skills of students and teachers in an international college. Digital literacy is increasing in importance: effective digital literacy skills now determine the level of access to an individual’s economic future and full digital citizenship. Conversely, a lack of digital skills excludes individuals from digital life, including being able to contribute to the discourses that are shaping their future. In the college, the contact time for teaching basic digital literacy skills to students has been cut by 50%. In addition to this, the weekly hours for providing training and mentoring support for teachers to develop their digital literacy, through the Advanced Practitioner team, have been cut by 50%. Therefore there was a need to find out how the digital literacy skills of students and teachers are developing in this environment. This study firstly carried out an extensive review of the current empirical research in this field before proceeding with three action research cycles, which involved 69 research participants: 24 students and 45 teachers. The data collection methods included 5 online student learning journals, an online survey (skills audit) for teachers and feedback sheets gathered from a focus group of teachers. Collaboration with teachers to develop the action research cycles was a key feature of the study and Activity Theory was used as an additional analytical lens. The findings revealed that students have limited access to opportunities to develop their digital literacy in lessons. They are asking for help to develop their digital literacy skills and knowledge, whilst acknowledging that they have gaps in their knowledge. Furthermore, they want teachers to develop their digital expertise so that they can collaborate with them to help them navigate the digital world. The findings of the skills audit revealed that with a few exceptions, generally teachers in the college only feel confident in the basic use of learning technologies. The findings evidence that digital literacy is an important issue that has been overlooked in this setting, with ramifications for how the college and the wider organisation are perceived by potential students/future customers. The key recommendation is for a strategic approach to the issue of digital literacy to be adopted by the college/wider organisation, which must include: improving access to learning technologies for students by further embedding digital literacy across the curriculum; plus upskilling teachers by providing a comprehensive time-tabled programme of digital literacy training.

Keywords: MLT
MLT2015
Improving the educational outcomes for a 'looked after' child in Year 10: a case study

Michael is a looked-after child at the school where I am the Vice-Principal (Pastoral). He was placed in foster care at the age of 10 as a result of being emotionally abused by his biological mother. Michael presents with very challenging behaviour and was at risk of suspension and/or expulsion – outcomes which would only serve to further compound his difficulties and contribute to poor educational outcomes. As such, the basis of our intervention was to provide staff with training which would enable them to better understand how Michael’s insecure attachment and history of maltreatment contributes to the problem behaviour he exhibits. This piece of research suggests that when equipped with this understanding, teachers respond to Michael’s behavioural difficulties in a more empathetic and less punitive manner, helping to ensure his continued enrolment at the school. Other findings include: the valuable role that an educational psychologist played in delivering this school-based training; the intervention being strengthened by the role Michael played in its design; the need for greater collaboration between the school and Michael’s social worker; and concluded that although important, attachment theory should not be the sole framework used to help ameliorate the behaviour of looked-after children.

Keywords: MLT
MLT2015