VictorJuiz/thesis huggingface dataset:
Accelerator mass spectrometry for radiocarbon dating

Accelerator mass spectrometry (AMS) has been used routinely for radiocarbon measurements for several years. During this period it has become evident neither the accuracy nor the range of the technique were as great as had originally been hoped. This thesis describes both theoretical work to understand the reasons for this and practical solutions to overcome some of the problems.
The production and transport of the ions used in the measurements are found to be the most crucial stages in the process. The theories behind ion production by sputtering are discussed and applied to the specific case of carbon sputtered by caesium. Experimental evidence is also examined in relation to the theories. The phenomena of space charge and lens aberrations are discussed along with the interaction between ion beams and gas molecules in the vacuum. Computer programs for calculating phase space transformations are then described; these are designed to help investigations of the effects of space charge and aberrations on AMS measurements. Calculations using these programs are discussed in relation both to measured ion beam profiles in phase space and to the current dependent transmission of ions through the Oxford radiocarbon accelerator. Improvements have been made to this accelerator and these are discussed in the context of the calculations.
There are many reasons for wishing to produce C- ions directly from carbon dioxide. The most suitable type of source for achieving this is the Middleton High Intensity Sputter Source. Experiments to evaluate the performance of such a source are described and detailed design criteria established.
An ion source designed and built specifically for radiocarbon measurements using carbon dioxide is described. Experiments to evaluate its performance and investigate the underlying physical processes are discussed. The source is found to have a high efficiency enabling small samples (<100 μg of carbon) to be measured. The cross contamination is measured to be low (<0.1%) and the background currents are small; the implications of these results are discussed.

Advisor: Hedges, R
Specification, implementation and verification of refactorings

Refactoring is the process of reorganising or restructuring code by means of behaviour-preserving program transformations, themselves called refactorings. Most modern development environments come with built-in support for refactoring in the form of automated refactorings that the user can perform at the push of a button. Implementing refactorings is notoriously complex, however, and even state-of-the-art implementations have very low standards of correctness and can introduce subtle changes of behaviour into refactored programs. In this thesis, we develop concepts and techniques that make it possible to give concise, modular specifications of refactorings. These specifications are precise enough to cover all details of the object language, and thus give rise to full featured, high-quality refactoring implementations. Their modularity, on the other hand, makes them amenable to formal proof, and hence opens the door to the rigorous verification of refactorings. We discuss a disciplined approach to maintaining name bindings and avoiding name capture by treating the binding from a name to the declaration it refers to as a dependency that the refactoring has to preserve. This approach readily generalises to other types of dependencies for capturing control flow, data flow and synchronisation behaviour. To implement complex refactorings, it is often helpful for the refactoring to internally work on a richer language with language extensions that make the transformation easier to express. We show how this allows the decomposition of refactorings into small microrefactorings that can be specified, implemented and verified in isolation. We evaluate our approach by giving specifications and implementations of many commonly used refactorings that are concise, yet match the implementations in the popular Java development environment Eclipse in terms of features, and outperform them in terms of correctness. We give detailed informal correctness proofs for some of our specifications, which are greatly aided by their modular structure. Finally, we discuss a rigorous formalisation of the central name binding framework used by most of our specifications in the theorem prover Coq, and show how its correctness can be established mechanically.

Keywords: verification of refactorings
attribute grammars
name analysis
language extensions
refactoring
Advisor: de Moor, O
On portfolio optimisation under drawdown and floor type constraints

This work is devoted to portfolio optimisation problem arising in the context of constrained optimisation. Despite the classical convex constraints imposed on proportion of wealth invested in the stock this work deals with the pathwise constraints. The drawdown constraint requires an investor's wealth process to dominate a given function of its up-to-date maximum. Typically, fund managers are required to post information about their maximum portfolio drawdowns as a part of the risk management procedure. One of the results of this work connects the drawdown constrained and the unconstrained asymptotic portfolio optimisation problems in an explicit manner. The main tools for achieving the connection are Azema-Yor processes which by their nature satisfy the drawdown condition.
The other result deals with the constraint given as a floor process which the wealth process is required to dominate. The motivation arises from the financial market where the class of products serve as a protection from a downfall, e.g. out of the money put options. The main result provides the wealth process which dominates any fraction of a given floor and preserves the optimality.
In the second part of this work we consider a problem of a lifetime utility of consumption maximisation subject to a drawdown constraint. One contribution to the existing literature consists of extending the results to incorporate a general drawdown constraint for a case of a zero interest rate market. The second result provides the first heuristic results for a problem in a presence of interest rates which differs qualitatively from a zero interest rate case. Also the last chapter concludes with the conjecture for the general case of the problem.

Keywords: portfolio optimisation
drawdown constraint
Azema-Yor processess
Advisor: Obloj, J
Upregulation of early inflammation to enhance fracture repair

Fractures of bone are very common, affecting 2% of the population per annum. Whilst the majority heal uneventfully, 10-15% exhibit delayed or non-union. These complications tend to occur in patients who have sustained high-energy open fractures, which are limb-threatening injuries, or low-energy osteoporotic fractures, which are associated with high morbidity and mortality rates. Enhancement or acceleration of fracture repair would confer significant benefit to these patients as well as reduce the public health burden.
Inflammation represents the earliest response following trauma and initiates a cascade of downstream events crucial for wound healing. However, the mechanism by which this occurs remains poorly defined. A detailed understanding of how these upstream events initiate fracture healing is a necessary step in the development of therapeutics to enhance this process. Our group previously reported that addition of low dose recombinant human TNF (rhTNF) at the fracture site accelerated fracture repair in a murine tibial fracture model. Here I show that local rhTNF treatment is only effective when administered within 24 hours of injury, when neutrophils represent the major inflammatory cell infiltrate. Endogenous TNF was expressed at the fracture site initially by neutrophils and after 3 days by monocytes/macrophages. Systemic administration of anti-TNF resulted in impaired fracture healing. The addition of rhTNF to the fracture environment in an air pouch model enhanced neutrophil recruitment, and promoted the recruitment of monocytes through CCL2 production. Conversely, inhibition of either neutrophils or the chemokine receptor CCR2 resulted in significantly impaired fracture healing. Fragility fractures represent a major unmet medical need and they are associated with permanent disability and premature death. Using a murine model of fragility fractures, rhTNF treatment improved fracture healing during the early phase of repair. Translated clinically, accelerated healing would permit earlier load bearing and reduce the morbidity and mortality associated with delayed patient mobilisation.

Keywords: healing
fracture
inflammation
innate immunity
Advisor: Nanchahal, J
Horwood, N
Mahoney, D
The novice mathematician’s encounter with mathematical abstraction: tensions in concept-image construction and formalisation

Mathematics is defined as an abstract way of thinking. Abstraction ranks among the least accessible mental activities. In an educational context the encounter with mathematical abstraction is the crucial step of the transition from informal school mathematics to the formalism of university mathematics. This transition is characterised by cognitive tensions. This study aimed at the identification and exploration of the tensions in the novice mathematician's encounter with mathematical abstraction. For this purpose twenty first-year mathematics undergraduates were observed in their weekly tutorials in four Oxford Colleges during Michaelmas and Hilary Term of Year 1. Tutorials were tape-recorded and fieldnotes kept during observation. The students were also interviewed at the end of each term of observation. The recordings of the observed tutorials and the interviews were transcribed and submitted to an analytical process of filtering out episodes that illuminate the novices' cognition. An analytical framework consisting of cognitive and sociocultural theories on learning was applied on sets of episodes within the mathematical areas of Foundational Analysis, Calculus, Linear Algebra and Group Theory. This topical analysis was followed by a cross-topical synthesis of themes that were found to characterise the novices' cognition. The novices' encounter with mathematical abstraction was described as a personal meaning-construction process and as an enculturation process: the new culture is Advanced Mathematics introduced by an expert, the tutor. The novices' interaction with the new concept definitions was obstructed by their unstable previous knowledge. Concept image construction was described as a construction of meaningful metaphors and an exploration of the 'raison-d'-être' of the new concepts and the new reasoning and was characterised by the tension between the Informal/Intuitive/Verbal and the Formal/Abstract/Symbolic — which was discussed in terms of semantics and reasoning. The novices were in difficulty with the mechanics of formal mathematical reasoning as well as with applying these mechanics in a contextualised manner. This decontextualised behaviour was linked to the fragility of their knowledge with regard to the nature of rigour in formal mathematics.

Keywords: university
education
formalism
abstraction
mathematics
Advisor: Jaworski, B
Measurement of particulate emissions from gasoline direct injection engines

Gasoline Direct Injection (GDI) engines have been considered to be the key enabler for reducing the CO2 emission from gasoline-powered vehicles. Compared to Port Fuel Injection (PFI) engines, GDI engines realize a higher compression ratio, a lower intake temperature and the absence of throttling which will deliver higher volumetric efficiency and lower fuel consumption. However, due to the reduced time for fuel atomization and the possibility of fuel impingement, GDI engines will inherently generate more Particulate Matter (PM) emissions than PFI engines. Previous research demonstrated that GDI engines typically emit one order of magnitude more PM than PFIs. Therefore, the number-based measurement of PM emissions from GDI engines is essential, for engine researchers and manufacturers to meet the number-based PM regulations in the near future.
This thesis undertakes to investigate: a) the effects of the after-treatment (Three-Way Catalyst) and various engine operational parameters, such as injection and ignition timing, injection strategy and valve timing on the PM emissions; b) the characteristics of GDI PM emissions using a range of gasoline/ethanol blends; c) The compositional information for GDI-generated PM emissions, i.e. the PM mass fractions in different volatility ranges. The first objective was achieved by using a Cambustion Ltd Differential Mobility Spectrometer 500 (DMS500) to simultaneously derive the PM size-resolved number concentrations and mass concentrations in the range of 5-1000 nm. The second objective was addressed by using the DMS500 together with other instruments such as a Photron high-speed camera, a Cambustion Ltd fast Flame Ionization Detector (FID). The third objective was realized by using Thermo-Gravimetric Analysis (TGA). These experiments are amongst the first of their kind and may well provide vehicle manufacturers and the fuel industry with useful data for PM control and abatement.
Data acquisition (DAQ) systems for two test engines, namely, a V8 GDI engine and a single-cylinder optical access engine, have been developed in LabVIEW to facilitate recording various experimental data at different sampling rates (1Hz to 300 kHz). The DAQ system in the single-cylinder engine is also capable for communicating with the engine controlling system to enable automatic data logging. A controlled automatic dilution system has been developed for taking filter samples in a way that is consistent with emissions legislation.

Keywords: DISI
GDI
DMS500
PM
Advisor: Stone, R
Mass transfer analysis of transdermal drug delivery using microneedles

Microneedle is a promising technique for delivering high molecular weight drugs across skin. The microneedles can offer a number of benefits over other drug delivery methods. For example, the drugs only diffuse over a short distance before reaching the blood circulation which enhances the absorption of drugs by the tissue. However, the drug transport behaviour in skin is affected by a complex interplay of many parameters (e.g., microneedle geometries, permeability across skin, etc).
In this thesis, many aspects of the microneedle field were examined. A mathematical model for drug transport from microneedle systems into skin was developed. Issues such as microneedle penetration, surface area of the microneedle arrays, etc. were investigated. This work helped us to focus into optimizing the design of microneedles by developing an in-house algorithm to enhance the performance of transdermal drug delivery using microneedles. Following the development of this algorithm, the influence of skin thickness with its classification (i.e., age group, race, etc.) on drug permeability across skin was studied. Attention was then given to determine the effective permeability (Peff) and the effective skin thickness (Heff) for various solid microneedle models. The outcome of this research allowed us to study the influence of microneedle dimensions on the drug concentration in blood (Cb). Furthermore, the 'pattern' (shape) of the microneedles array (i.e., square or rectangular) and the 'distribution' (arrangement) of the microneedles inside an array (i.e., triangular or diamond) were investigated to identify the optimum microneedle models. Finally, the effect of skin metabolism on both the patch (without microneedles) and the microneedle arrays on drug intake were examined.

Keywords: mass transfer
pharmacokinetic
modelling
microneedles
drug delivery
Advisor: Das, D
Cui, Z
Peace as societal transformation: intergenerational power-struggles and the role of youth in post-conflict Sierra Leone

Intergenerational solidarity and reciprocity are fundamental building blocks of any society. At the same time, socio-generational groups constantly struggle for influence and authority. In Sub-Saharan Africa, disproportionately male, gerontocratic and patrimonial systems governing economic, social and political life lend a special explosiveness to the social cleavage of generation. This dissertation draws on the concept of the generational contract to explore whether Sierra Leone’s decade-long civil war (1991-2001) – labelled a ‘revolt of youth’ – catalysed changes in the power-asymmetries between age groups. Based on fieldwork conducted between 2007 and 2010, I argue that youth in post-war Sierra Leone question fundamental norms of intergenerational relations and challenge local governance structures demanding changes to the generational contract. Amidst a strong continuity of gerontocratic dominance and counter-strategies from elders, youth draw on organisational forms and a local rights discourse to create spaces for contestation and negotiation. These openings hold potential for long-term rearrangements of societal relations in the medium to long-term future.

Keywords: social inequality
human rights
integration
intergenerational relationships
children and youth
social cleavages
social status
Africa
Rights (development)
social mobility
governance in Africa
conflict
history of Africa
local government
Advisor: de Oliveira, R
Quantitative analysis of core-shell nanoparticle catalysts by scanning transmission electron microscopy

This thesis concerns the application of aberration corrected scanning transmission electron microscopy (STEM) to the quantitative analysis of industrial Pd-Pt core-shell catalyst nanoparticles. High angle annular dark field imaging (HAADF), an incoherent imaging mode, is used to determine particle size distribution and particle morphology of various particle designs with differing amounts of Pt coverage. The limitations to imaging, discrete tomography and spectral analysis imposed by the sample’s sensitivity to the beam are also explored.
Since scattered intensity in HAADF is strongly dependent on both thickness and composition, determining the three dimensional structure of a particle and its bimetallic composition in each atomic column requires further analysis. A quantitative method was developed to interpret single images, obtained from commercially available microscopes, by analysis of the cross sections of HAADF scattering from individual atomic columns. This technique uses thorough detector calibrations and full dynamical simulations in order to allow comparison between experimentally measured cross section to simulated ones and is shown to be robust to many experimental parameters. Potential difficulties in its applications are discussed. The cross section approach is tested on model materials before applying it to the identification of column compositions of core-shell nanoparticles.
Energy dispersive X-ray analysis is then used to provide compositional sensitivity. The potential sources of error are discussed and steps towards optimisation of experimental parameters presented. Finally, a combination of HAADF cross section analysis and EDX spectrum imaging is used to investigate the core-shell nanoparticles and the results are correlated to findings regarding structure and catalyst activity from other techniques.
The results show that analysis by cross section combined with EDX spectrum mapping shows great promise in elucidating the atom-by-atom composition of individual columns in a core-shell nanoparticle. However, there is a clear need for further investigation to solve the thickness / composition dualism.

Keywords: energy dispersive X-ray analysis
high resolution
atomic resolution
high angle annular dark field
electron microscopy
catalyst
nanoparticles
specimen damage
Advisor: Nellist, P
Lozano-Perez, S
Ozkaya, D
Structural studies on DNP binding antibodies

This thesis is concerned with structural aspects of the recognition and effector functions of antibody molecules. The recognition process is investigated in the dinitrophenyl (DNP) binding mouse IgA produced by the myeloma MOPC 315. The studies on effector functions utilize a DNP binding mouse hybridoma IgG2a to examine the role of N-glycosylation in IgG.
The combining site of protein 315. The involvement of tyrosyl residues in the combining site of protein 315 was examined by preparing specifically nitrated NO2-Tyr-33H and NO2-Tyr-34L derivatives of the Fv fragment of this protein. The ionizations of tnese derivatives were studied in the presence and absence of various DNP-ligands. Perturbations to the nitrotyrosine ionizations were found to be caused by the side chains of certain of these ligands, allowing an indication of the distance of these tyrosines from the bound hapten. On examination of the compatibility of these data with the model of the combining site of protein 315 proposed by Dower et al
. (1977) (Biochem. J. 165, 207-225) it was found that while the location of Tyr-33H is consistent with this model, the position of Tyr-34L is not. A remodelled combining site using the modified ring-current treatment of Perkins and Dwek (1980) (Biochemistry 19, 245-258) is presented. This allows a better rationalization of the nitration data and of previous experimental observations on protein 315.
The role of the conserved C 2 domain oligosaccharide of IgG. This was examined by a functional comparison of native IgG with an aglycosylated IgG preparation. Aglycosylation was acheived by cell culture of the hybridoma cells in the presence of the glycosylation inhibitor tunicamycin. The conditions for preparation and purification of this aglycosyl IgG are described. Aglycosylated IgG is found to be correctly assembled as an H2L2 unit. It retains the antigen binding and Staphylococcal protein A binding abilities of the native glycosylated molecule. Using an assay system designed specifically to overcome certain problems in comparing Clq binding to different preparations of IgG it was found that the aglycosylated preparation showed only slightly reduced affinity for Clq. In addition the aglycosylated IgG is able to activate bound Cl. The above results are consistent with the structure of the Fc region being only minimally altered in the absence of oligosaccharide. The structural integrity of the aglycosylated molecule may be compromised however, as its ability to bind to monocyte Fc receptor is significantly reduced. In addition the aglycosylated molecule becomes much more susceptible to proteolytic digestion. A computational model-building analysis of the quaternary structure of Fc allows an explanation of at least some of the effects of aglycosylation in terms of reduced conformational stability of the CH2 domains.

Advisor: Dwek, R