VictorJuiz/thesis huggingface dataset:
Private investment and public policy in Egypt, 1960-1986

The determinants of private investment and the role of government policy in Egypt are analyzed with a focus on the debate over "crowding out" versus "crowding in," the implications of administered interest rates, and the consequences of uncertainty. A theoretical model of investment is developed that integrates the microfoundations of firm decision making with the determinants of investment at the macroeconomic level. The model, which draws on case studies of fifty private firms in Egypt, is characterized by oligopolistic markets, putty-clay technology, credit rationing, and rigidities in the supply of capital goods. Econometric testing of the model uses the recent literature on cointegration and error correction to address the problem of spurious correlations while retaining long run information about the equilibrium relationship between aggregate investment and its determinants.
The empirical evidence shows that the investment decision depends on expected profits which are a function of demand, costs and mark ups. The impact of government policy on private capital formation operates through these determinants, such as the positive effects of protection or restrictive licensing on private sector mark ups. Using the model to analyze the oil boom of the 1970s, it is possible to explain the sectoral distribution of private investment, which diverged from the predictions of conventional Dutch disease theory about the consequences of a trade shock.
The findings indicate that the sharp rise in the private investment ratio during the 1970s in Egypt stemmed more from the consequences of the foreign exchange windfall on demand, costs, and mark ups than from the effect of fiscal incentives introduced by the state. However, government policy was crucial in determining the structure of incentives in the economy which favoured capital intensive, heavily indebted, import substituting investments in protected sectors. The private sector responded to this incentive structure by concentrating on those activities where economic rents were highest.
Binary hypotheses for bipolar mass loss in transients

We investigate binary hypotheses for the formation of bipolar nebulae using the smoothed particle hydrodynamics code Gadget-2. In the general case, we present a parameter study of mass loss from very simple common envelope models, which seems to show a strongly bipolar trend for sufficiently oblate envelopes and low enough spiral-in injection energy. The density profiles of the envelopes produce differing structure within the ejecta.
We also investigate 3 specific bipolar mass loss events. In the case of the outer nebula of SN 1987A, we study the effects of fast polar jets interacting with a pre- existing progenitor wind and find that these are consistent with the observed light echoes from the nebula, in particular for the feature known as ’Napoleon’s Hat’. In the case of Cas A, we briefly study the effects of close binarity on supernova ejecta and suggest the influence of a close, compact companion may lead to at least one jet-like disturbance that may be observable in a supernova remnant. Finally, we study whether a fast bipolar wind, similar to that of Eta Car’s present wind, may inflate ejecta similar to that produced in the common envelope models to a shape consistent with that of Eta Car’s Homunculus Nebula.

Keywords: Stellar
87A
Planetary Nebula
Common Envelope
Stellar Merger
Planetary Nebulae
SPH
Cassiopeia A
Bipolar
Napoleon's Hat
SN 1987A
Eta Carinae
Advisor: Podsiadlowski, P
Theoretical advances in the modelling and interrogation of biochemical reaction systems: alternative formulations of the chemical Langevin equation and optimal experiment design for model discrimination

This thesis is concerned with methodologies for the accurate quantitative modelling of molecular biological systems. The first part is devoted to the chemical Langevin equation (CLE), a stochastic differential equation driven by a multidimensional Wiener process. The CLE is an approximation to the standard discrete Markov jump process model of chemical reaction kinetics. It is valid in the regime where molecular populations are abundant enough to assume their concentrations change continuously, but stochastic fluctuations still play a major role. We observe that the CLE is not a single equation, but a family of equations with shared finite-dimensional distributions. On the theoretical side, we prove that as many Wiener processes are sufficient to formulate the CLE as there are independent variables in the equation, which is just the rank of the stoichiometric matrix. On the practical side, we show that in the case where there are m_1 pairs of reversible reactions and m_2 irreversible reactions, there is another, simple formulation of the CLE with only m_1+m_2 Wiener processes, whereas the standard approach uses 2m_1+m_2. Considerable computational savings are achieved with this latter formulation. A flaw of the CLE model is identified: trajectories may leave the nonnegative orthant with positive probability.
The second part addresses the challenge when alternative, structurally different ordinary differential equation models of similar complexity fit the available experimental data equally well. We review optimal experiment design methods for choosing the initial state and structural changes on the biological system to maximally discriminate between the outputs of rival models in terms of L_2-distance. We determine the optimal stimulus (input) profile for externally excitable systems. The numerical implementation relies on sum of squares decompositions and is demonstrated on two rival models of signal processing in starving Dictyostelium amoebae. Such experiments accelerate the perfection of our understanding of biochemical mechanisms.

Keywords: diffusion processes
control theory
systems biology
chemical reaction kinetics
experiment design
chemical Langevin equation
model discrimination
Advisor: Etheridge, A
Papachristodoulou, A
Investigation of Escherichia coli Tat (twin arginine translocase) transport in vitro

The Twin arginine translocase (Tat) system catalyzes movement of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plant chloroplasts. This transport process requires energy in the form of the transmembrane proton motive force (PMF). The Tat system can be studied in vitro using inner membrane vesicles (IMVs) from E. coli overproducing the Tat components, TatA, TatB and TatC. However, the transport efficiencies of current in vitro Tat transport assays are low.
In this work, current in vitro Tat transport assays were compared and parameters that affect transport efficiencies were identified. Mild French press treatment of IMVs resulted in larger IMVs with higher transport efficiencies. Chloride ions were shown to inhibit Tat transport in vitro. Generation of a PMF by the activity of ATP synthase gave higher transport efficiencies than generating a PMF by NADH respiration. This understanding was applied to develop an optimized in vitro Tat transport assay that showed a higher transport efficiency than currently published methods. Fluorescently labelled Tat substrates were developed to allow quantitative analysis of Tat transport.
The transport of the purified native Tat substrate, CueO into IMVs was characterized using the optimized in vitro Tat transport assay. It was shown that the proton concentration (ΔpH) component of the PMF was sufficient to support Tat transport in vitro. It was observed that transport of CueO ceased in a time-dependent manner in the in vitro Tat transport assays. This loss of transport efficiency could be due, at least in part, to the presence of a PMF since transport efficiency was reduced when IMVs were pre-energized.
Substrates for future in vitro single molecule fluorescence microscopy studies of the Tat transport were developed in this work. One of the substrates is fluorescently labelled CueO. The second substrate is the native Tat substrate alkaline phosphatase PhoX from Vibrio fischeri which was able to cleave the fluorogenic compound AttoPhos® and can thus be used as an enzymatic reporter of Tat transport.
The structure of a native Tat substrate from Pseudomonas fluorescens, PhoX, was solved by X-ray crystallography at a resolution of 1.4Å. PhoX is a monomeric six blade β propeller with two α-helical bundle subdomains. PhoX was shown to have optimum activity at pH8.0. PhoX has a novel catalytic site which requires two Fe3+ (including a Cys-coordinated Fe3+) and three Ca2+ as cofactors. Mutagenesis studies showed that all the metal ions are required for the integrity of the active site. Co-crystallization of PhoX with vanadate, an inhibitor of PhoX which mimics the transition state, showed that hydrolysis of phosphomonoesters does not involve formation of a covalent phosphoenzyme intermediate. Instead, dephosphorylation of substrates is proposed to occur via a SN2 reaction with OH- as the attacking nucleophile.

Keywords: twin arginine translocase system
PhoX
alkaline phosphatase
Advisor: Berks, B
Empirical Modelling and Model Selection for Forecasting Inflation in a Non-stationary World.

Selection and forecasting are integral to econometric modelling and this thesis addresses both issues, with an application to UK inflation. Two automatic model selection algorithms, PcGets and RETINA, are evaluated on time-series and cross-section data. PcGets aims to select an undominated, congruent model of the phenomena of interest, whereas RETINA selects a parsimonious set of regressors that have predictive ability. Monte Carlo simulation results assess the null and non-null rejection frequencies of the algorithms in the presence of nonlinear functions. Both algorithms have the same properties as those for linear models under orthogonality, but collinearity increases null rejection frequencies and reduces non-null rejection frequencies. Simple operational rules that ‘double de-mean’ all functions are proposed to mitigate that problem. A nonlinear model selection strategy is proposed, that commences with a new test for nonlinearity, specifies the general model using polynomial functions as approximations, and undertakes a general-to-specific reduction using a multi-stage procedure. Nonlinearity poses a number of problems, including collinearity generated by nonlinear transformations, extreme observations leading to non-normal (fat-tailed) distributions, and often more variables than observations from general expansions approximating the nonlinearity, yet one must avoid excess retention of irrelevant variables. Solutions to all of these problems are proposed. A successful algorithm requires the synthesis of all of these developments to be implemented, as exclusion of one component of the algorithm can lead to severely erroneous conclusions. A model of inflation is built in which many determinants of inflation play a role in its explanation. The single cause explanation of inflation is refuted, along with a generic business cycle explanation. As forecast failure is prevalent, with naive devices often outperforming econometric models, a forecast competition is undertaken for UK annual and quarterly inflation, in which equilibrium correction models are compared to various forecasting rules. Robust forecasting devices prove useful in forecasting macroeconomic time-series, and they often outperform econometric models, both when there are structural breaks in the data and when the underlying process appears to be stable but with breaks in the explanatory variables. Increasing the information set does lead to improvements in forecasting performance suggesting that disaggregation can yield benefits. It is observed that much of the forecast error in the structural models is driven by the deterministic terms. Breaks in the mean of the cointegrating vector or the growth rate of the system will cause forecast ‘failure’, and results show how sensitive forecasts are to errors in these terms.
Numerical solutions to a class of stochastic partial differential equations arising in finance

We propose two alternative approaches to evaluate numerically credit basket derivatives in a N-name structural model where the number of entities, N, is large, and where the names are independent and identically distributed random variables conditional on common random factors.
In the ﬁrst framework, we treat a N-name model as a set of N Bernoulli random variables indicating a default or a survival. We show that certain expected functionals of the proportion LN of variables in a given state converge at rate 1/N as N [right arrow - infinity]. Based on these results, we propose a multi-level simulation algorithm using a family of sequences with increasing length, to obtain estimators for these expected functionals with a mean-square error of epsilon 2 and computational complexity of order epsilon−2, independent of N. In particular, this optimal complexity order also holds for the inﬁnite-dimensional limit. Numerical examples are presented for tranche spreads of basket credit derivatives.
In the second framework, we extend the approximation of Bush et al. [13] to a structural jump-diﬀusion model with discretely monitored defaults. Under this approach, a N-name model is represented as a system of particles with an absorbing boundary that is active in a discrete time set, and the loss of a portfolio is given as the function of empirical measure of the system. We show that, for the inﬁnite system, the empirical measure has a density with respect to the Lebesgue measure that satisﬁes a stochastic partial differential equation. Then, we develop an algorithm to efficiently estimate CDO index and tranche spreads consistent with underlying credit default swaps, using a ﬁnite diﬀerence simulation for the resulting SPDE. We verify the validity of this approximation numerically by comparison with results obtained by direct Monte Carlo simulation of the basket constituents.
A calibration exercise assesses the ﬂexibility of the model and its extensions to match CDO spreads from precrisis and crisis periods.

Keywords: Monte Carlo simulations
Stochastic PDEs
Credit basket derivatives
Advisor: Reisinger, C
Publishing sub-Saharan Africa in Paris 1945 - 67

This thesis is an investigation of literary institutions and print culture in France during the two decades following the Second World War. It demonstrates how the changing metropolitan literary marketplace, driven by new methods of book production and bookselling; the rise of internationalism and tiers-mondisme; and a nascent notion of francophonie, accommodated writing of and on sub-Saharan Africa. The first half of the thesis focuses on three institutions of particular significance: the publishing houses of Le Seuil and Présence Africaine, and the Association nationale des écrivains de la mer et de l’outre-mer, known for the literary prizes it administered. Diverse strategies for evaluating representations of sub-Saharan Africa are explored through new research in the archives of these institutions. The tensions between specialist and more commercially orientated publishing, between anti-colonial and exotic representations of sub-Saharan Africa do not map cleanly onto separate institutional contexts in this period. These tensions are underpinned by shared political and aesthetic debates, technological resources, and social contexts. The second half of the thesis analyses in greater detail the publishing process of selection, production and distribution in seven individual case-studies of novels by Christine Garnier, Abdoulaye Sadji, Cheikh Hamidou Kane, Malick Fall, Amos Tutuola, Chinua Achebe and Peter Abrahams. Aspects considered include: readers’ reports and editorial revision; the use of pseudonyms; the development of named collections; the role of literary translators. My methodological approach works with, and at times against, a Bourdieusian framework, to describe the literary field in this period. More specifically, Pascale Casanova’s depiction of Paris as capital of the “World Republic of Letters” is tested and nuanced through the historical focus on the period 1945 – 67. Rather than a passive annexation to the colonial centre, African literary production is shown to be intrinsic to and constitutive of the restless political and aesthetic landscape of post-war reconstruction and decolonisation in the French-speaking world.

Advisor: Boehmer, E
Garfitt, J
Biological studies of distraction osteogenesis

The development of limb lengthening techniques has made possible the treatment of many congenital and acquired disorders of the adult and developing skeleton by generating new bone tissue at appropriate sites. The studies described in this thesis have attempted to elucidate some of the biological aspects of this process which is called distraction osteogenesis.
A rabbit model of distraction osteogenesis has been used in the present study. Lengthening at four different distraction rates (0.3, 0.7, 1.3 and 2.7 mm/day) has been investigated radiographically and histologically. The most satisfactory histology and radiology results were observed in the group distracted at a rate of 0.7 mm/day. The present study indicated that the proliferation of osteoprogenitor cells during distraction osteogenesis was affected by the rate of distraction. The rate of cell proliferation in the regenerating tissues was found to increase as the rate of lengthening increased from 0.3 to 0.7 mm/day. However, a further increase of cell proliferation did not occur at higher distraction rates.
In-situ hybridization techniques using non-radioactive labelling probes and imrnunohistochemistry using specific collagen antibodies have been used in the study. The localization of the mRNAs and proteins for types I and II collagen in the distraction regenerates indicates that bone is formed mainly in an intramembranous manner during distraction osteogenesis. However, higher rates of distraction resulted in increased chondrogenesis in the regenerating tissues. The osteoblasts and chondrocytes within the regenerate originate from the same pool of progenitor cells and their differentiation appeared to be altered by the rate of distraction.
In addition, the present study has characterized the localization of BMP-4 mRNA expression in the regenerating tissues produced by distraction osteogenesis. The BMP-4 gene was expressed mainly by less differentiated osteoprogenitor cells in the regenerating tissue, indicating that BMP-4 may play an important role in controlling the early differentiation and proliferation of osteoprogenitor cells during distraction osteogenesis.
The demonstration of a mixture of proliferative and apoptotic cells in the regenerating tissues, suggested that apoptosis and cell proliferation may be regulated closely during the rapid cell or tissue turnover seen in distraction osteogenesis. The changes of cells undergoing apoptosis and proliferation in the different regions of the distraction regenerate, suggested that apoptosis is an important mechanism controlling cell or tissue turnover and bone remodelling during distraction osteogenesis.
The neovascularization process is affected by the rate of distraction during distraction osteogenesis. A slow rate of distraction (0.3 mm/day) did not maximally stimulate angiogenesis, while the highest rate (2.7 mm/day) of distraction inhibited angiogenesis. The angiogenic response was the best at distraction rates of 0.7 and 1.3 mm/day. The clinical relevance of the present findings has been discussed and future work are suggested.
Interspecific competition between Blue and Great tits

Great tits (Aves: Passeriformes; Parus major) and blue tits (Parus caeruleus) nested in boxes in Wytham Woods near Oxford. The breeding densities of both species were limited by the availability of nest sites. The larger great tits were dominant in obtaining nest boxes. This was most important where breeding sites were scarce. The two species did not maintain interspecific territories or interfere with interspecific nest site spacing beyond the immediate vicinity of the nest. Blue and great tit numbers fluctuated in parallel where nest sites were not limiting resources. Annual changes in breeding numbers of great tits were negatively related to blue tit breeding density but great tit density did not seem to affect changes in the blue tit population.
Overlap in the feeding sites of blue and great tits was greatest during the summer and interference competition was lowest at this time. The nestling diets of the two species were very similar. Despite an apparent abundance of food for nestlings, adults were pressed to feed large broods. Food for nestlings was probably a limiting and depletable resource.
The date of clutch initiation of great tits, but not blue tits, was retarded at high densities of blue or great tits. The clutch sizes of both species were probably negatively affected by high breeding densities of congeners but the results were not clear cut.
Heavy great tit fledglings are most likely to survive to breed. Great tit fledglings were heavier at low densities of blue tits. An experiment in which blue tit young were removed from a section of the Woods, showed that great tit nestlings were heavier and developed faster, and that female condition was better, than in a control section or section where blue tit broods were supplemented.
In terms of resource competition, blue tits were the better scramble competitors and great tits the better interference competitors.

Advisor: Perrins, C