VictorJuiz/thesis huggingface dataset:
The demand for money, asset substitution and the inflation tax in a liberalizing economy

This thesis develops empirical econometric models of the private sector aggregate demand for real and financial assets in Kenya over the period 1973 to 1990. Single-equation error-correction models of the demand for money are estimated using systems cointegration methods developed by Johansen (1988). The models are found to be statistically stable functions throughout the period, and are capable of encompassing existing studies. Across a range of monetary aggregates, including a Divisia index aggregate for broad money, the models describe demand for money functions in which inflation and illegal foreign currency substitution are significant determinants of money holdings, and where the private sector adjusts rapidly to deviations from its stable longrun equilibrium real money demand.
The demand for money is then integrated within a neo-classical model of asset demands, which examines the behaviour of the aggregate private sector asset portfolio in response to changes in relative prices between assets and to external shocks to the economy, principally the 1976-77 coffee boom. A variant of the Almost Ideal Demand System model developed by Deaton and Muellbauer (1980) is estimated for a class of six assets: base money, banking system deposits, government securities, tradable capital, nontradable capital and inventories. The asset substitution model, which also takes an errorcorrection form, and which allows for credit rationing, generates results which are consistent with the earlier demand for money models, where private agents are also denied access to foreign-denominated assets. Using this model, the maintenance of policies of financial repression are shown to cause the private sector to offset inflationary shocks through the accumulation of real assets, principally in the form of non-tradable capital in the construction and property sectors.
The evidence from the two models is used to analyze the fiscal effects of the inflation tax and financial repression measures. Policies of financial liberalization are shown to reduce the revenue maximizing rate of inflation (estimated to be 14% per annum) and the implicit tax on domestic holders of government liabilities. This dampens asset substitution in response to inflationary shocks and offsets the adverse effects of "construction-boom" investment on non-tradable capital prices.
Nitric oxide: a chemical effector of pathogenesis in magnaporthe oryzae

Research detailed in this thesis investigated the generation of Nitric Oxide (NO) and its role in the pathogenesis of the rice blast fungus Magnaporthe oryzae. Two putative nitric oxide synthase genes and single copy nitrate and nitrite reductase genes were cloned as potential sources of NO in M. oryzae. Single and double gene disrupted mutants were generated and their phenotypes assessed.
Detection of NO is problematic. Herein, a fluorescent plate reader assay was developed, exploiting the NO sensitive dye DAR-4M AM and the NO scavenger PTIO, to compare wildtype NO generation with the mutant strains. All strains were assessed for infection-related development on an artificial surface inductive to appressorium formation and maturation in the wildtype strain. Appressorium formation in the presence of PTIO and the NO donor DETANONOate was recorded for all strains on this surface. The pathogenicity of the wildtype and mutant strains were assessed, in terms of their ability to infect rice and barley plants. Finally, the capacity of each strain to metabolise nitrogen was evaluated to confirm the disruption of the nitrate and nitrite reductase genes.
Collectively, the data demonstrate that the plate reader assay provides robust evidence for the generation of NO in M. oryzae. However, none of the various mutant strains showed a reduction in NO emission during germling morphogenesis. However, they exhibited significantly different infection-related development on an inductive artificial surface as compared with the wildtype strain. Moreover, exogenous application of PTIO to the wildtype strain provided evidence for NO and its involvement in germination and appressorium development. No significant differences in the infection of rice and barley leaves were observed between the wildtype and mutant strains, indicating their disrupted genes are dispensable for pathogenesis. The nitrate and nitrite reductase genes were found to be essential for nitrate assimilation.
In summary, this work provides the most robust evidence for the generation of NO in fungi to-date, but the molecular mechanism underpinning the generation of NO in M. oryzae remains elusive.

Keywords: Nitric Oxide
Magnaporthe oryzae
Advisor: Gurr, S
Fricker, M
Modelling optimal strategies for novel genetics-based pest management

Genetic transformation techniques for pest insects have enabled the development of novel methods to mitigate the enormous harm done by insects to human health (through transmission of diseases) and to agriculture (through damage to crops or livestock). I use mathematical modelling to analyse strategies using autocidal genetic constructs (dominant lethal genes that are repressible during mass-rearing); in parallel several research groups are developing the strains and the laboratory and field experimental work. Engineered insects would be released in large numbers and compete for mates, and their progeny would inherit one copy of a dominant lethal gene and die. The lethal mechanism can be made stage- or sex-specific. The aim is to reduce the number of pest insects in a population, suppressing numbers to a less harmful level or local elimination. I examine the evolutionary, ecological, and economic cost and benefit aspects of these novel interventions. I consider application of this genetic technology against agricultural pest insects, combined with genetically modified crop plants engineered to produce insecticidal toxins, to which field-evolved resistance is emerging. Using a theoretical framework, I analyse the gene frequency evolution of resistant alleles and show that strategies using genetic constructs that are selectively lethal only to females could help to manage both pests and resistance. I investigate potential resistance to the lethal mechanism of the genetic construct itself. I use population genetics and population dynamics models to explore the impact of heritable biochemically-based resistance on the effectiveness of genetic strategies for reducing populations of important pests in agriculture or public health. Released insects are homozygous for susceptibility to the lethal construct; this has an inherent element of resistance dilution. Finally, I analyse genetic vector control methods to reduce the transmission of human disease. I combine vector population dynamics and epidemiological models with techniques for assessing cost-effectiveness of a genetic strategy for controlling a vector mosquito, and show that disease elimination is feasible on a practical timescale and economically beneficial.

Keywords: mathematical modelling
Advisor: Bonsall, M
Alphey, L
Transient free radicals studied by laser magnetic resonance spectroscopy

A liquid nitrogen cooled, carbon monoxide laser magnetic resonance spectrometer was used to study mid-infrared vibration-rotation transitions in the gaseous free radical NCO, in its ̅X2Π state, at very high resolution. The use of an intracavity absorption cell made possible the observation of some transitions with sub-Doppler resolution. Developments to the spectrometer extended the range of operation of the CO laser. Most importantly, a CO laser operating on overtone transitions, Δν = 2, was operated in Oxford. The Δν = 2 CO laser operates over the range 2450-3800cm-1 (4.08-2.63 μm), and the Δν = 1 CO laser over the range 1200-2100 cm-1 (8.33-4.76 μm).
NCO exhibits a Renner-Teller effect in its ground electronic state, an interaction between the motion of the electrons and the bending motion of the nuclei. Vibration-rotation transitions were observed in a sequence of bands involving the excitation of the out-of-phase stretching vibration, in the region of 1900cm-1. Some of the bands involved the excited bending vibration. The Zeeman effect behaviour of the molecular energy levels, particularly in the 2Σ vibronic states, clearly showed the manifestation of the Renner-Teller effect. The Zeeman effect in the 2Σ vibronic states was considered in detail. Many of the 2Σ LMR spectra were recorded at sub-Doppler resolution. NCO is complicated to model, and unassigned LMR spectra remain.
A harmonic Renner-Teller model was developed for the analysis. It was implemented by constructing an explicit matrix representation of the single electronic state N2 effective Hamiltonian, which was diagonalised exactly. A new term in this Hamiltonian, describing centrifugal distortion corrections to the Renner-Teller coupling term, was developed for the 2Σ vibronic states in order to account for anharmonic vibronic interactions.
Substrate recognition by the proteasome 

The ubiquitin proteasome system targets proteins to the proteasome where they are degraded. Substrate recognition and processing prior to degradation take place at the 19S regulatory particle of the proteasome. A polyubiquitin chain, linked through isopeptide bonds formed between the C-terminal G76 and K48, is the signal responsible for delivery to the proteasome. Because chains linked via any of the seven lysine residues of ubiquitin exist in vivo and encode signals unrelated to protein degradation it is crucial for cells to avoid crosstalk between these different pathways. Several ubiquitin receptors related to proteasomal degradation have been identified but the selectivity between the different ubiquitin chains has not been assessed quantitatively while avoiding artefacts attributed to GST-dimerisation. By employing isothermal titration calorimetry, analytical ultracentrifugation and nuclear magnetic resonance, discrimination between K48- and K63-linked diubiquitin was established for the S. pombe proteasomal receptor Rpn10 and the shuttle protein Rhp23. The same methods allowed us to propose a discriminatory model for Rpn10. The crystal structures of the 19S regulatory particle subunits Rpn101-193 and Rpn121-224 have been determined and possible protein-protein interaction sites were identified by surface conservation and electrostatics analysis. Rpn12 surface residues were identified that had a negative effect on Rpn10-binding. This interaction was studied by surface plasmon resonance, fluorescence anisotropy and nuclear magnetic resonance. These experiments revealed a binding site on Rpn10 that is exclusively occupied by either ubiquitin or Rpn12 and for the first time demonstrated the interaction of a ubiquitin interacting motif with a protein other than ubiquitin.

Keywords: SPR
ITC
fluorescence anisotropy
proteasome
NMR
x-ray crystallography
ubiquitin
Advisor: Endicott, J
Campbell, I
Structure–function studies of the oxidoreductase bilirubin oxidase from Myrothecium verrucaria using an electrochemical quartz crystal microbalance with dissipation

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces.
Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis.
The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.

Keywords: adsorption
voltammetry
reduction
laccase
Electrochemical quartz-crystal microbalance
QCM
enzyme catalysis
surface chemistry
fuel cell
bilirubin oxidase
E-QCM
redox enzyme
oxygen reduction
gold electrodes
Quartz-crystal microbalance
electrochemistry
Advisor: Blanford, C
Wong, L
Characterisation of engineered nanoparticles and their interaction with natural biological and non-biological material

Form, mobility, toxicity and the eventual fate of engineered nanomaterials in environmental ecosystems are currently not well defined and are needed to improve risk assessment and legislation. The present study subjected uncoated zinc oxide (ZnO) nanoparticles (30nm and 200nm) and coated silver (Ag) nanoparticles (Paraffin: 3-8nm and citrate/PVP: 50nm) to different ionic strength media and different types of algal/bacterial extracellular-polymeric species (EPS) at long (6 months) and short (2 weeks) timescales. Changes in particle size distribution and stability were examined using a multi-method approach. Sample concentration and sample polydispersity are important factors when selecting techniques. Uncoated ZnO nanoparticles aggregated heavily in water at high concentrations (1000mg/L). However silver nanoparticles (1-10mg/L) remained stable at all ionic strengths and EPS in this study due to the steric component of their coatings. Nano-toxicological experiments involving cyanobacteria S.leopoliensis and green algae C.reinhardtii showed size-dependent toxicity from coated nanosilver particles. Smaller nanoparticles (3-8nm) showed greater dissolution over 72h and greater toxicity to both species than 50nm particles indicating silver ions are an important toxicity mechanism. Nanoparticle coatings were likely important in controlling dissolution levels. Cell viability and production of reactive oxygen species (ROS) were shown to be important mechanisms of toxicity to phycological species. Species specific effects were noted for both silver nanoparticles. EPS from S.leopoliensis were noted to remove ionic silver from suspension and different types of C.reinhardtii EPS were produced when particles underwent different levels of toxic stress indicating that EPS could both affect particle toxicity and be affected by it. This work has demonstrated that coated nanoparticles could remain stable under various ionic strengths and with exposure to algal organic matter for timescales up to 6 months. This could result in adverse effects to aquatic organisms were they to reach environmental systems and is of concern to nanomaterial risk assessors.

Keywords: Zinc Oxide
ROS
Reactive Oxygen Species
EPS
Suspension
Extra-cellular Polymeric Species
Silver
Algae
Ecotoxicology Nanoparticle Characterisation Nanoparticle Fate Nanoparticle Toxicity Algae and Cyanobacteria
Fate
Cell Viability
Ecotoxicology
Cyanobacteria
Stability
Toxicity
Coatings
Materials
Advisor: Crossley, A
Grovenor, C
Robust pricing and hedging beyond one marginal

The robust pricing and hedging approach in Mathematical Finance, pioneered by Hobson (1998), makes statements about non-traded derivative contracts by imposing very little assumptions about the underlying financial model but directly using information contained in traded options, typically call or put option prices. These prices are informative about marginal distributions of the asset. Mathematically, the theory of Skorokhod embeddings provides one possibility to approach robust problems.
In this thesis we consider mostly robust pricing and hedging problems of Lookback options (options written on the terminal maximum of an asset) and Convex Vanilla Options (options written on the terminal value of an asset) and extend the analysis which is predominately found in the literature on robust problems by two features: Firstly, options with multiple maturities are available for trading (mathematically this corresponds to multiple marginal constraints) and secondly, restrictions on the total realized variance of asset trajectories are imposed. Probabilistically, in both cases, we develop new optimal solutions to the Skorokhod embedding problem.
More precisely, in Part I we start by constructing an iterated Azema-Yor type embedding (a solution to the n-marginal Skorokhod embedding problem, see Chapter 2. Subsequently, its implications are presented in Chapter 3. From a Mathematical Finance perspective we obtain explicitly the optimal superhedging strategy for Barrier/Lookback options. From a probability theory perspective, we find the maximum maximum of a martingale which is constrained by finitely many intermediate marginal laws. Further, as a by-product, we discover a new class of martingale inequalities for the terminal maximum of a cadlag submartingale, see Chapter 4. These inequalities enable us to re-derive the sharp versions of Doob's inequalities. In Chapter 5 a different problem is solved. Motivated by the fact that in some markets both Vanilla and Barrier options with multiple maturities are traded, we characterize the set of market models in this case.
In Part II we incorporate the restriction that the total realized variance of every asset trajectory is bounded by a constant. This has been previously suggested by Mykland (2000). We further assume that finitely many put options with one fixed maturity are traded. After introducing the general framework in Chapter 6, we analyse the associated robust pricing and hedging problem for convex Vanilla and Lookback options in Chapters 7 and 8. Robust pricing is achieved through construction of appropriate Root solutions to the Skorokhod embedding problem. Robust hedging and pathwise duality are obtained by a careful development of dynamic pathwise superhedging strategies. Further, we characterize existence of market models with a suitable notion of arbitrage.

Keywords: semi-static superhedging
robust pricing and hedging
Skorokhod embedding problem
model uncertainty
Advisor: Obloj, J
Monitoring cell and tissue damage during ablation by high-intensity focussed ultrasound

High Intensity Focussed Ultrasound (HIFU) ablation is a promising technology for the non-invasive, targeted treatment of certain types of cancer. The technique functions by subjecting tumours to a cytotoxic level of intense, localised heating, while leaving the surrounding tissue unharmed. However, a number of limitations in the available HIFU treatment monitoring methods are currently hampering the effectiveness and clinical adoption of the therapy.
This work aims to develop improved metrics of HIFU-induced biological damage that are specifically suited to monitoring and controlling HIFU ablation. Firstly, an optical method that enables straightforward quantification of thermal damage in protein-embedding hydrogels is developed. Secondly, hydrogels embedded with different cell lines are used to assess the performance of common temperature-based metrics of cell death across a range of HIFU-relevant conditions. Finally, a novel, passive acoustic detector designed for the real-time monitoring of HIFU-induced tissue damage is proposed. The detector is shown to predict lesioning with over 80% accuracy in regimes that are very likely to create lesions (60 J of acoustic energy or more), with an error rate of less than 6% for exposures that are too short to cause lesioning (up to 1 s long). The proposed detector could therefore provide a low-cost means of effectively monitoring clinical HIFU treatments passively and in real time.

Keywords: ablation
cancer therapy
ultrasound
biomedical engineering
HIFU
Advisor: Coussios, C
Computing with functions in two dimensions

New numerical methods are proposed for computing with smooth scalar and vector valued functions of two variables defined on rectangular domains. Functions are approximated to essentially machine precision by an iterative variant of Gaussian elimination that constructs near-optimal low rank approximations. Operations such as integration, differentiation, and function evaluation are particularly efficient. Explicit convergence rates are shown for the singular values of differentiable and separately analytic functions, and examples are given to demonstrate some paradoxical features of low rank approximation theory.
Analogues of QR, LU, and Cholesky factorizations are introduced for matrices that are continuous in one or both directions, deriving a continuous linear algebra. New notions of triangular structures are proposed and the convergence of the infinite series associated with these factorizations is proved under certain smoothness assumptions.
A robust numerical bivariate rootfinder is developed for computing the common zeros of two smooth functions via a resultant method. Using several specialized techniques the algorithm can accurately find the simple common zeros of two functions with polynomial approximants of high degree (&geq; 1,000).
Lastly, low rank ideas are extended to linear partial differential equations (PDEs) with variable coefficients defined on rectangles. When these ideas are used in conjunction with a new one-dimensional spectral method the resulting solver is spectrally accurate and efficient, requiring O(n2) operations for rank 1
partial differential operators, O(n3) for rank 2, and O(n4) for rank &geq;,3 to compute an n x n matrix of bivariate Chebyshev expansion coefficients for the PDE solution.
The algorithms in this thesis are realized in a software package called Chebfun2, which is an integrated two-dimensional component of Chebfun.

Keywords: low rank
Chebfun
Chebyshev
Advisor: Trefethen, L