VictorJuiz/thesis huggingface dataset:
An investigation of the interaction of soil micro-organisms with special reference to the study of the bacterial population of plant root systems

Experiments and a critical review of the literature of the technique of soil microbiology have shown that the agar plate method for the estimation of soil microbes may lead to severe errors.
(1)The number of micro-organisms developing from a soil innoculum to colonies on agar media, and which are counted and used to estimate the soil population, do not always all develop. Of these organisms which can reproduce or grow on the medium provided, a proportion is not represented if the colonies are too crowded. The relationship between amount of soil innoculum and the number of colonies developing from it, is not then linear. When the development of some colonies is suppressed in this way, microbial populations estimated from the plate counts may be severely underestimated. The late developing colonies in particular are suppressed when the density of colonies on plates is high.
The suppression of the development of microbial types into colonies is differential, and so changes in the degree of crowding of colonies on agar plates may bring about changes in the proportional representation of specific groups of microbes. The proportional representation of actinomycetes for example, is depressed at high densities, and yellow chromogens may be depressed or proportionately increased in different populations. It is shown that both the quantitative and qualitative effects of plating density can be attributed to microbial interaction, and that these effects are very significant within the conventional range of plating densities 70-200 colonies per 9cm. diamter plate.
It is shown that there is a general relationship between the proportional representation of microbial types and the estimated total population of soils in the experimental results reported by a number of investigators. Many of the differences between rhizospheres and soil populations which have been claimed by investigators, and which show this relationship can be interpreted as plating density artifacts and it is pointed out that until many of the rhizosphere experiments which have been reported have been confirmed, making due allowance for or excluding the density effect, the results must be suspect.
Statistical methods have been used to show differential rhizosphere effects (in the presence of the density effect) between three fen plants growing in peat, and between banana varieties. There is a correlation between the rhizosphere flora of the banana varieties examined and resistance to Panama disease. Within the genetic pairs Congo - Gros Michel, and Silk Fig - Guindy, the susceptible variety supports a larger microflora on its roots than the resistant. The power of the varieties to support a varied microbial flora is correlated with the size of population supported on root systems in the field.
Antibacterial and antifungal substances were isolated from the rhizomes of a number of banana varieties, but no correlation with disease resistance could be found.
Novel aspects of the reactions of hydrogenases with small molecule inhibitors

Hydrogenases catalyse the reversible oxidation and production of H₂. They have been the subject of intense interest in recent years since these enzymes, or catalysts inspired by them, may greatly enhance our exploitation of H₂ as an energy carrier in a future ‘green’ H₂-based economy. However, a major challenge to the future use of these catalysts is their reactions with small molecule inhibitors, such as O₂ or CO.
This thesis presents studies using Protein Film Electrochemistry, in which an enzyme is adsorbed onto an electrode to give an electroactive film. Although most hydrogenases are inhibited or irreversibly damaged by even trace O₂, certain O₂-tolerant hydrogenases are unusual in that they are able to sustain H₂ oxidation activity in the presence of O₂. Results outlined in this thesis suggest that the O₂ tolerance of the membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha relies upon O₂ attack generating exclusively the ‘Ready’ inactive state (formed by complete, four-electron reduction of O₂), which subsequently reactivates both rapidly and at high potential. The results contributed to a new explanation for how hydrogenases in certain microbes survive O₂. Electrochemical studies performed on a variant enzyme suggest that a modified proximal FeS cluster plays a role in conferring this O₂ tolerance. Studies of an enzymatic H₂/O₂ fuel cell employing the O₂-tolerant [NiFe]-hydrogenase Hyd1 from Escherichia coli as the anodic catalyst highlight the subtle influence of the reactions of the hydrogenase with O₂ on the power characteristics of the fuel cell under various operating conditions.
This research also identifies straight-chain aldehydes as unprecedented inhibitors of H₂ production by the [FeFe]-hydrogenases. However, some of these results cannot currently be made freely available as they are to be published at a later date in academic journals.

Keywords: hydrogenase
electrochemistry
Advisor: Armstrong, F
Superstrings

Much of the low energy phenomenology which can be extracted from the field theory limit of the intrinsically ten dimensional E 8 ® E 8 heterotic superstring depends upon the topological and geometrical properties of the six dimensional compactified component of spacetime. After briefly reviewing the topological constraints on the latter manifold which ensure the survival of N=l four dimensional supersymmetry, we present and apply the mathematics necessary for the rigorous construction of vacuum solutions and the determination of the four dimensional massless field content.
Two phenomenologically attractive classes of solutions, with unbroken E8 ⨂ SU(5) and E8 ⨂ SO(10) gauge groups, arise if the vacuum configuration contains a Ricci flat Kahler manifold with SU(3) holonomy (Calabi-Yau manifold), which admits certain SU(5) or SU(4) vector bundles. Further reduction of the gauge group and emergence of naturally light weak Higgs doublets may also occur by flux breaking if the Calabi Yau manifold is multiply connected. We analyse the feasibility of such scenarios for Calabi Yau manifolds with any possible fundamental group. Phenomenological considerations place severe constraints on the dimensions and transformation properties of certain cohomology groups and thereby lead to a highly restricted class of acceptable models.
We then present the mathematical analysis of a three generation heterotic superstring inspired model, with E8 ⨂ E6 gauge symmetry. A detailed description of the manifold of compactification is given, along with a determination of its Hodge numbers and of the associated light supermultiplet structure. For a particular choice of vacuum moduli we derive this manifold's symmetry group, and determine its action on the massless fields in the theory. Preliminary investigation indicates that these transformation properties give rise to a remarkably realistic model.
In the second volume we derive cosmological constraints on a supersymmetric extension of the standard model in which weak gauge symmery breaking is triggered at the tree level by a Higgs singlet superfield. The fermionic component of this gauge singlet (the "nino") is shown to be the lightest supersymmetric particle with a relic abundance near the critical closure density for a surprisingly wide range of the unconstrained parameters.
The previously favoured photino dark matter scenario has been eliminated by the non observation of high energy solar neutrinos. After briefly reviewing this argument, we extend the analysis to eliminate Higgsino dark matter scenarios with and#60H1°and#62 ≠ and#60H2°and#62. We show that the nino produces an acceptably low level of solar neutrinos and that it may also account for the anomalously high level of cosmic ray antiproton flux.

Advisor: Ross, G
Binney, J
Automated quantitative software verification

Many software systems exhibit probabilistic behaviour, either added explicitly, to improve performance or to break symmetry, or implicitly, through interaction with unreliable networks or faulty hardware. When employed in safety-critical applications, it is important to rigorously analyse the behaviour of these systems. This can be done with a formal verification technique called model checking, which establishes properties of systems by algorithmically considering all execution scenarios. In the presence of probabilistic behaviour, we consider quantitative properties such as "the worst-case probability that the airbag fails to deploy within 10ms", instead of qualitative properties such as "the airbag eventually deploys". Although many model checking techniques exist to verify qualitative properties of software, quantitative model checking techniques typically focus on manually derived models of systems and cannot directly verify software.
In this thesis, we present two quantitative model checking techniques for probabilistic software. The first is a quantitative adaptation of a successful model checking technique called counter-example guided abstraction refinement which uses stochastic two-player games as abstractions of probabilistic software. We show how to achieve abstraction and refinement in a probabilistic setting and investigate theoretical extensions of stochastic two-player game abstractions. Our second technique instruments probabilistic software in such a way that existing, non-probabilistic software verification methods can be used to compute bounds on quantitative properties of the original, uninstrumented software.
Our techniques are the first to target real, compilable software in a probabilistic setting. We present an experimental evaluation of both approaches on a large range of case studies and evaluate several extensions and heuristics. We demonstrate that, with our methods, we can successfully compute quantitative properties of real network clients comprising approximately 1,000 lines of complex ANSI-C code — the verification of such software is far beyond the capabilities of existing quantitative model checking techniques.

Keywords: software verification
software
formal verification
formal methods
verification
quantitative
model checking
Advisor: Kwiatkowska, M
Dynamical System Decomposition and Analysis Using Convex Optimization

This thesis is concerned with investigating new methods for the analysis of large-scale dynamical systems using convex optimization. The proposed methodology is based on composite Lyapunov theory and is computationally implemented using polynomial programming techniques. The main result of this work is the development of a system decomposition framework that makes it possible to analyze systems that are of such a scale that traditional methods cannot cope with.
We begin by addressing the problem of model invalidation. A barrier certificate method for invalidating models in the presence of uncertain data is presented for both continuous and discrete time models. It is shown how a re-parameterization of the time dependent variables can improve the numerical conditioning of the underlying optimization problem.
The main contribution of this thesis is the development of an automated dynamical system decomposition framework that permits us to verify the stability of systems that typically have a state dimension large enough to render traditional computational methods intractable. The underlying idea is to decompose a system into a set of lower order subsystems connected in feedback in such a manner that composite methods for stability verification may be employed. What is unique about the algorithm presented is that it takes into account both dynamics and the topology of the interconnection graph.
In the first instance we illustrate the methodology with an ecological network and primal Internet congestion control scheme. The versatility of the decomposition framework is also highlighted when it is shown that when applied to a model of the EGF-MAPK signaling pathway it is capable of identifying biologically relevant subsystems in addition to stability verification.
Finally we introduce stability metrics for interconnected dynamical systems based on the theory of dissipativity. We conclude by outlining a clustering based decomposition algorithm that explicitly takes into account the input and output dynamics when determining the system decomposition.

Keywords: Dynamical systems
Convex optimization
Advisor: Papachristodoulou, A
Moral theological method in the theological ethics of Martin Luther and Arthur Rich, with particular reference to their economic ethics

This thesis seeks to expand the self-critical resources of contemporary theological economic ethics by bringing the method of a pre-modern theologian and social commentator, Martin Luther (1483-1546), into interaction with that of a modern contribution to social ethics, the Swiss theologian Arthur Rich (1910-92). This thesis is the first substantial treatment in English of Rich’s magnum opus, Wirtschaftsethik. The demonstration of the thesis is undertaken by a close engagement with a selected publication of Luther (his 1519/20 Großer Sermon von dem Wucher) and of Rich (his masterwork, Wirtschaftsethik, published in two volumes in 1984 and 1990 respectively). The thesis does not simply describe Luther’s and Rich’s economic ethics, but demonstrates the way in which they operate, that is, their method.
An introduction sets out the thesis, and defends its method. Chapter 1 introduces Luther’s sermon on usury, and situates it in its context. It then gives a commentary on Luther’s method, discussing its genre, the way in which Luther deploys Scripture and exploits doctrines with respect to ethics, and his concept of the twofold government of God. It analyses how Luther brings these theological motifs to bear on a particular economic question. Chapter 2 sketches Arthur Rich’s life and work, and presents Rich������s method as set out in Wirtschaftsethik. It discusses his understanding of ethics, his approach to Scripture, and his adoption of the thought of Max Weber and John Rawls. Chapter 3 brings our study of Luther to bear on Rich’s approach, noting strengths and weaknesses of Rich’s method. It questions some of Rich’s assumptions, and notes ways in which a more self-critical approach could have made his project more successful. A conclusion then summarises the argument, and makes tentative suggestions as to the wider applicability of the critical questions posed to Rich’s method by the analysis of Luther.

Keywords: christian ethics
ethics
economic ethics
Martin Luther
Arthur Rich
Advisor: Wannenwetsch, B
The economy and politics in Quebec, 1774-1791

If we accept that the British empire of the later eighteenth century was a mercantilist one, that there was in general a substantive connection between political and commercial matters, and that the ultimate authority in both spheres lay in the mother country, then it becomes clear that there are at least two major omissions in what has been written about Quebec during this period. The first is that, on the whole, there has been insufficient examination of the relationship between commerce and politics in Quebec's development; and as a corollary to this there has been a tendency towards a too Canada-centred examination of her history, which ignores or skims over events in London.
Among British historians the imperial standpoint has been most popular. Professor Harlow has looked at Canada's place in the empire along traditionally political, legal and constitutional lines, while Professor Graham has investigated her position within the imperial mercantile system. But there has been no attempt to relate in detail imperial political and economic ideas and events with the struggle for commercial and constitutional change in Quebec itself.
Canadian historians have, on the other hand, largely ignored Quebec's wider imperial setting and concentrated on local events, treating political, legal and constitutional developments in isolation from economic matters. Symptomatic of this is the way in which general histories, such as those of Professors Burt and Neatby, while recognising the role played by merchants in Quebec politics, have avoided a detailed examination of them, and have indeed reserved separate chapters for their treatment of trade and commerce. More recently though, Fernand Ouellet has gone some way towards filling this gap with his joint study in the economic and social history of Quebec, in which he combines imperial perspectives with the local affairs which form the main body of his book.
[Please see pdf. for full abstract.]
Design and synthesis of inositol phosphate-based probes

Inositol phosphates play a fundamental role in many intracellular processes. Of particular importance is the role of phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] in the protein kinase B (PKB/Akt) signalling pathway. PtdIns(3,4,5)P3 recruits PKB to the cell membrane through binding interactions with its pleckstrin homology (PH) domain. In several human cancers, this signalling pathway is upregulated, resulting in increased cell growth and proliferation. In order to investigate the therapeutic potential of the PtdIns(3,4,5)P3–PH domain binding interaction, it is necessary to develop inositol phosphate-based probes.
This DPhil dissertation highlights the synthesis of a number of derivatives of the PtdIns(3,4,5)P3 head group – inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P4]. These derivatives incorporated phosphate isosteres at both the 3- and 5-positions of Ins(1,3,4,5)P4, through the utilisation of novel protection and deprotection strategies. In addition, this dissertation highlights the efficient synthesis of the natural product inositol 1,3-bisphosphate [Ins(1,3)P2] and our work towards the synthesis of inositol pyrophosphate derivatives.

Keywords: Inositol
Inositol Pyrophosphate
Inositol Phosphate
Protein Kinase B
Organic Synthesis
Advisor: Conway, S
Familiar collaboration and women writers in eighteenth-century Britain: Elizabeth Griffith, Sarah Fielding and Susannah and Margaret Minifie

Between 1740 and 1770, a number of women writers choose to make explicit in their printed texts their collaboration with a ‘familiar’: a family member or close friend. In so doing, they strategically enact their personal relationships through the medium of print in order to claim for themselves a level of literary power and delineate the terms on which they entered the marketplace as authors. This thesis argues that familiar relations expressed along a horizontal axis – those of husband, wife, brother, sister and friend – offer a relatively flexible model of familiar relations in which women could acquire a level of agency in self-definition, supported by ideologies that valued women’s contribution to the polite sphere of sociable conversation. It demonstrates that Elizabeth Griffith, Sarah Fielding, Jane Collier, and Susannah and Margaret Minifie not only engage in collaborative literary production that is thoroughly inflected with the pressures of their historical context but that through familiar collaboration women writers display their professional authorial personae and generate social and literary criticism. Through close readings of carefully selected collaborative texts in the corpus of each writer, including the material history of the texts themselves, and the relationships expressed through those texts, this thesis highlights the complexity with which family relations interacted with print culture in the period. Far from using the familiar relation as a means of modestly retiring to the domestic sphere these women writers used their familiar relations as a basis from which to launch, describe and defend their authorial careers.

Keywords: sociability
criticism
collaboration
women
Advisor: Ballaster, R
Social networks, community-based development and empirical methodologies

This thesis consists of two parts: Part I (Chapters 2 and 3) critically assesses a set of methodological tools that are widely used in the literature and that are applied to the empirical analysis in Part II (Chapters 4 and 5).
Using a randomised experiment, the first chapter compares pen-and-paper interviewing (PAPI) with computer-assisted personal interviewing (CAPI). We observe a large error count in PAPI, which is likely to introduce sample bias. We examine the effect of PAPI consumption measurement error on poverty analysis and compare both applications in terms of interview length, costs and respondents’ perceptions.
Next, we formalise an unproven source of ordinary least squares estimation bias in standard linear-in-means peer effects models. Deriving a formula for the magnitude of the bias, we discuss its underlying parameters. We show when the bias is aggravated in models adding cluster fixed effects and how it affects inference and interpretation of estimation results. We reveal that two-stage least squares (2SLS) estimation strategies eliminate the bias and provide illustrative simulations. The results may explain some counter-intuitive findings in the social interaction literature.
We then use the linear-in-means model to estimate endogenous peer effects on the awareness of a community-based development programme of vulnerable groups in rural Tanzania. We denote the geographically nearest neighbours set as the relevant peer group in this context and employ a popular 2SLS estimation strategy on a unique spatial household dataset, collected using CAPI, to identify significant average and heterogeneous endogenous peer effects.
The final chapter investigates social network effects in decentralised food aid (free food and food for work) allocation processes in Ethiopia, in the aftermath of a serious drought. We find that food aid is responsive to need, as well as being targeted at households with less access to informal support. However, we also find strong correlations with political connections, especially in the immediate aftermath of the drought.

Keywords: Ethiopia
political connections
targeting effectiveness
PAPI
peer effects
local government
awareness
bias
Social networks
CAPI
data quality
exclusion bias
Tanzania
food aid
consumption measurement
community-based development
information spread
Advisor: Dercon, S