VictorJuiz/thesis huggingface dataset:
The moral self, moral knowledge and God

The principal aim of this work is to ascertain a clear understanding of Clarke's moral theory, one which has suffered from neglect and misunderstanding. The assumption that his 'rational intuitionism' is given little if any epistemological grounding, is shown to be erroneous. This is done by drawing on his extensive work in the Letter to Dodwell and its Defenses. The secondary aim of this thesis is to show the relevance of Clarke's work to contemporary discussions in philosophy of mind, moral theory, and moral theology.
The thesis has four parts. In Part I, the works of Clarke, relevant to his moral theory, are introduced. His influence in the eighteenth century is brought out, both in Britain and on the Continent. As regards his influence in moral theory, he is the likely goad that moved Hume to formulate 'Hume's Law,' that ought cannot be derived from is.
Part II is an analysis of Clarke's philosophical work on the nature of the 'rational and moral agent.' His views are ascertained, clarified, and presented as the epistemological foundation of his moral theory. One conclusion that follows from this material is that the influential work of Clarke is sharply at odds with the 'historiographic orthodoxy' that views British thought about the problem of knowledge to be progressive refinements of Locke's anti-innatism. The Defences are directed to Anthony Collins, a deist and late disciple of Locke.
There are also three major historical corrections that follow from the study of Clarke's work on the nature of mind. Two ideas that are usually attributed to Joseph Butler are actually Clarke's conceptions, e.g. the distinction between 'the strict' and 'the abstract'(or 'loose') concepts of personal identity, and the notion that memory does not constitute personal identity but rather presupposes and entails it. One other idea, usually attributed to Thomas Reid, is more properly credited to Clarke, namely, the theory of agent-causation. All three of these concepts are extremely important in contemporary philosophy of mind and theory of action. They constitute the epistemological ground of Clarke's moral theory.
In Part III the moral epistemology uncovered in Part II is linked with Clarke's more well known views found in the Discourse. His usually nebulous concept of 'fitness' is assessed and defended against the major criticisms of Hume (in Treatise 3.1.1) and Hutcheson. His often degraded analogy between morals and mathematics is defended, and his views are distinguished from those of Thomas Burnet, another anti- Lockean writer.
In Part IV, the moral theory proposed by Clarke argues for an employment of reason and revelation. It comes under sharp and extensive criticism from the deist Matthew Tindal. His criticisms, however, employ an either/or fallacy that is wholly inadequate as a refutation of Clarke's moral theology.
A comparison of key ideas in the moral theologies (metaphysics) of Leibniz and Clarke is made, and the principle of imitation of the holiness of God is found to be the coherent and full expression of Clarke's moral theology.
The use of, and controversy surrounding, the term atman in the Indian Buddhist tathagatagarbha literature.

The tathāgatagarbha doctrine of Mahāyāna Buddhism affirms the existence of some permanent, significant content of sentient beings that is of the same character as a Buddha. While this alone was an important innovation within Buddhist thought, some of its authors ventured further to deem this significant content an ātman: a ‘self’, in apparent contradiction to the central Buddhist teaching of the absence of self (anātman) in the constitution of all beings.
The aims of this thesis are two. Firstly, to examine usage of the term ātman in the Indian tathāgatagarbha sources which develop use of this expression. This entails a close reading of relevant sources (primarily Mahāyāna sūtra literature), and attention to how this term is used in the context of each. These sources present different perspectives on the tathāgatagarbha and its designation as a self; this study aims to examine significant differences between, and similarities across, these texts and their respective doctrines.
The second aim is to attempt an account of why authors of these texts ventured to designate the tathāgatagarbha with the term ātman, especially when some of our sources suggest that this innovation received some opposition, while others deem it in requirement of strong qualification, or to be simply inappropriate. It is not my objective to account for whether or not the tathāgatagarbha is or is not implicitly what we may deem ‘a self’ on the terms of Buddhist tradition; rather, I am concerned with the manner in which this expression itself was adopted, and – in light of clear difficulties raises by it – what may have motivated those authors responsible.
I argue not only that we can trace the development of this designation across the tathāgatagarbha literature, but also that those authors responsible for its earliest usage adopted an attitude towards non-Buddhist discourses on the self that requires special attention. This, I believe, had its roots in an account of the Buddha and his influence that advances our understanding of one tradition of Mahāyāna Buddhology, and its ambition to affirm its superiority over other Indian religious traditions.

Keywords: Sanskrit
tathagatagarbha
Buddhism
Mahayana
atman
tirthika.
sutra
Advisor: Zacchetti, S
Roesler, U
Free-will, responsibility and punishment

One of the purposes of this thesis is to try to examine the concepts of mental sickness and responsibility (and some other related concepts) and see whether or not they can be defended against some of the criticisms that have been made against them. It has, for instance, been argued that the concept mental sickness is culture relative in a bad sense. If this criticism is valid, then we cannot be justified in saying that mental sickness has impaired a person's responsibility.
Another criticism that has been made is that arguments that use mental sickness to explain and excuse criminal behaviour are circular.
Most of the criticisms that I have discussed are intended to be general, i.e. they are criticisms of the concept of mental disorder im general, not just of a particular kind of mental disorder. Thus though Lady Wootton says that arguments that try to explain the psychopath's anti-social behaviour are circular, she thinks (at least in her more radical moments) that the circular process prevails in other mental disorders as well (e.g. with mental defectives. See Social Science and Social Pathology, page 256 ff.).
Similarly, the argument that different standards of mental defect prevail in different cultures, and that therefore there is something wrong with the concept of mental defect, is intended to be (at least in her more radical moments) a general one, i.e. it is intended to apply, mutatis mutandis against other kinds of mental disorders also.
[Please see pdf. for full abstract.]
Generation of chimeric P-glycoprotein for functional and structural investigations

A major challenge in cancer treatment is acquired or intrinsic multidrug resistance (MDR) to chemotherapeutics. A notorious mediator of MDR is P-glycoprotein (P-gp, ABCB1), product of the human MDR1 gene, which actively effluxes cytotoxic drugs from cancer cells, resulting in sub-therapeutic intracellular concentrations. Understanding how P-gp interacts with drugs has been severely limited by the lack of high-resolution structures of P-gp. Although numerous efforts to obtain an X-ray crystal structure of P-gp have been attempted, human P-gp has never been crystallized. However, mouse P-gp (87% homologous to human P-gp) has been crystallized, and several structures of mouse P-gp have been recently reported. Despite a high degree of homology, it is currently unknown why mouse P-gp can be crystallized while human P-gp cannot. The studies presented in this thesis describe the creation of novel chimeras of mouse and human P-gp as an approach to investigate whether specific protein domains are responsible for differences in the ability to form crystals between mouse and human P-gp. A range of chimeras, created by protein domain swapping, were expressed in mammalian cells and all were found to retain MDR transport function demonstrating that P-gp can tolerate major structural changes. High-level expression of all chimeras was achieved by baculovirus-mediated heterologous protein expression. Chimeric proteins were purified by a multi-step process including immobilized metal affinity chromatography and size exclusion chromatography. Crystallization screening obtained protein crystals for two of the chimeras, indicating the approach adopted is a successful strategy, and an advance along the path towards a high-resolution structure of human P-gp.

Keywords: chimera
multidrug resistance
P-glycoprotein
Advisor: Gill, D
Complicity in international law

This thesis is concerned with the ways in which international law regulates state and individual complicity. Complicity is a derivative form of responsibility that links an accomplice to wrongdoing by a principal actor. Whenever complicity is prohibited, certain questions arise about the scope and structure of the complicity rule. To answer these questions, this thesis proposes an analytical framework in which complicity rules may be assessed, and defends a normative claim as to their optimal structure. This framework and normative claim anchor the thesis’ analysis of complicity in international law. The thesis shows that international criminal law regulates individual complicity in a comprehensive way, using the doctrines of instigation and aiding and abetting to inculpate complicit participants in international crimes. These doctrines are marked by the breadth of the complicit conduct prohibited, a standard of knowledge in the fault required of the accomplice, and an underused nexus requirement between the accomplice’s acts and the principal’s wrong. In contrast, international law’s regulation of state complicity was historically marked by an absence of complicity rules. In respect of state complicity in the wrongdoing of another state, international law now imposes both specific and general complicity obligations, the latter prohibiting states from aiding or assisting another state in the commission of any internationally wrongful act. In respect of the ways that states participate in harms caused by non-state actors, the traditional normative structure of international law, which imposed obligations only on states, foreclosed the possibility of regulating the state’s participation as a form of complicity. As that traditional normative structure has evolved, so the possibility of holding states responsible for complicity in the wrongdoing of non-state actors has emerged. More and more, both the wrongs that international actors commit, and the wrongs they help or encourage others to commit, matter.

Keywords: participation
international criminal law
state responsibility
aiding and abetting
complicity
Advisor: Akande, D
'Things that matter': missionaries, government, and patients in the shaping of Uganda's leprosy settlements, 1927-1951

This thesis examines the role of missionaries, the colonial government, and leprosy patients in the formation of leprosy settlements in Uganda, from the first inception of the settlements in 1927, until 1951 when the nature of leprosy control in Uganda changed, with the government appointment of a Protectorate leprologist and the creation of more treatment centres. It focuses on four leprosy settlements opened between 1930 and 1934 by the Anglican Church Missionary Society (CMS) and the British and Irish Catholic Franciscan Missionary Sisters for Africa (FMSA) and Mill Hill Mission (MHM).
Firstly, this thesis explores the ways in which the differing goals, ideologies, and resources of the Protestant CMS and the Catholic FMSA and MHM shaped the formation of and social environment within leprosy settlements in a highly Christianised and denominationally divided Uganda. Secondly, it examines the relationship between the CMS and Franciscan leprosy missions and the government, exploring the cooperation and conflict that their spiritual and medical priorities had upon the social lives of patients within Uganda’s leprosy settlements. Thirdly, this thesis assesses the extent to which missionaries consciously endeavoured to engineer a social environment for leprosy patients within settlements that conformed to their ideal of Christianised, modern African communities, as well the roles that healthy and leprous Ugandans chose to play in response to these attempts at social engineering. Missionaries and Ugandan leprosy patients had different priorities, but far from being passive receptacles of the ‘civilising’ mission, most leprosy patients were active agents in pursuing their own medical, social, and economic priorities through life in the settlements.

Keywords: Leprosy
Uganda
Missionaries
Advisor: Mahone, S
The early socio-demographic impact of the HIV-1 epidemic in rural Zimbabwe

Theoretical work indicates that HIV-1 epidemics in sub-Saharan Africa will cause major demographic changes. The current study assesses the extent to which these changes can already be seen in two rural areas of Manicaland, Zimbabwe and investigates the determinants of the epidemic and its demographic impact. The study utilizes demographic survey methods and qualitative sociological techniques. Data analysis is conducted using statistical packages and is guided by insights generated from mathematical models of the epidemiology and demographic impact of HIV-1 infections.
HIV-1 prevalence is high in both areas. Among women, HIV-1 infection is associated with age and marital status. Indirect evidence indicates that religion, education, migration and socio-economic characteristics of husband may also be important determinants. Each of these factors influences the pattern of sexual behaviour. Rates of sexual partner change are heterogeneous for women but appear more homogeneous for men. Mixing patterns are disassortative: men form partnerships with women with high and low rates of partner change.
Mortality has undergone a recent upturn, almost certainly associated with HIV-1 infections. Adults aged 20-45 years and men, in particular, are most affected at this (early) stage of the epidemic. Religion is an important local determinant of demographic patterns, whose influence on mortality appears to be changing vua its effect on sexual behaviour and the spread of HIV-1. Orphanhood has increased, but, as yet, there is little change in population structure. Fertility has declined since the late 1970s. It is too early in the AIDS epidemic to see an impact of HIV-1 at the population level. However, some signs of behaviour changes which affect the proximate determinants of fertility were detected. These changes may accelerate the decline in birth rates, especially at younger ages.
New demographic projections for Zimbabwe are developed, based on observed trends in HIV- 1 infection and fertility, and underlying behaviour patterns. These indicate substantial further increases in mortality, particularly among women and young children, greatly reduced population growth, relative shortages of young children and older adults, and further increases in orphanhood. Families and communities will require support in facing this slowly unfolding disaster.

Advisor: Anderson, R
Aspects of Yang-Mills theory in twistor space

This thesis carries out a detailed investigation of the action for pure Yang-Mills theory which L. Mason formulated in twistor space. The rich structure of twistor space results in greater gauge freedom compared to the theory in ordinary space-time. One particular gauge choice, the CSW gauge, allows simplifications to be made at both the classical and quantum level. The equations of motion have an interesting form in the CSW gauge, which suggests a possible solution procedure. This is explored in three special cases. Explicit solutions are found in each case and connections with earlier work are examined. The equations are then reformulated in Minkowski space, in order to deal with an initial-value, rather than boundary-value, problem. An interesting form of the Yang-Mills equation is obtained, for which we propose an iteration procedure. The quantum theory is also simplified by adopting the CSW gauge. The Feynman rules are derived and are shown to reproduce the MHV diagram formalism straightforwardly, once LSZ reduction is taken into account. The three-point amplitude missing in the MHV formalism can be recovered in our theory. Finally, relations to Mansfield’s canonical transformation approach are elucidated.

Keywords: scattering
Yang-Mills
twistors
Advisor: Candelas, P
Covenant and reformed identity in England 1525-1555

This study examines Reformed identity as an aspect of religious identity formation during the early Reformation period. It contributes towards an understanding of the character of the English Reformation by examining the reception of Swiss theology. The research is principally focussed upon the theological concept of covenant which blossomed in a distinctively bilateral and conditional form in early Reformation Switzerland. Patterns of thought discerned in English theology are related to this Swiss pattern, thereby assisting the process of identifying individual reformers according to continental models and elucidating an important theological development of the period. The concept of covenant had implications for contemporary discourses regarding the doctrines of justification and sanctification. It also made an impact upon sacramental theology in the way that sacraments were viewed as covenant signs. Despite the essential uniformity of the Swiss Reformed concept of covenant, three distinct emphases arose in Swiss Reformed sacramental theology with regard to the efficacy of the sacraments as means of grace. Having identified cases of English reception of the Swiss concept of covenant, their specific influences are determined using patterns of sacramental theology.
Chapter one considers the problems involved in discerning different forms of religious identity in this period. Evidence for Reformed identity in England from the 1520s to the 1550s is surveyed from various different angles. The transmission of Swiss ideas through the Low Countries is considered, and alternative explanations for the failure of English Lutheranism are evaluated, particularly Lollardy and humanism. Chapter two demonstrates the essential consistency of the concepts of covenant espoused by leading Swiss reformers. Chapter three examines the concepts of covenant of four English reformers. Chapter four highlights different patterns in Swiss sacramental theology, and chapter five analyses English cases in light of those Swiss models.

Keywords: covenant theology
soteriology
sacraments
Reformation
Advisor: Brigden, S
Methuen, C
Real recurrence sets

Classical theorems such as the Poincaré recurrence theorem, the van der Corput theorem about equidistribution of sequences or the F. and M. Riesz theorem about measures on the torus show properties of the set ℕ. However, In particular the Poincaré recurrence easily allows to extend the recurrence result to sets such as mℕ for any m ∈ ℕ.
This motivates the notion of recurrence sets, i.e. sets Ɗ ⊆ ℕ (or Ɗ ⊆ ℤ) which are "strong" enough to force certain recurrence properties, and a thorough study of these sets and their relations with each other has been undertaken since the late 1970s.
This thesis deals with real recurrence sets Ɗ ⊆ ℝ. Our first result shows that integer properties and most associated implications can be transferred to the real setting and allow a similar treatment.
For a set Ɗ⊆ ℤ, the integer and real recurrence property coincide for many properties. This gives non-trivial recurrence examples from the integer theory, but also yields some counterexamples showing that some recurrence properties are distinct.
Using continuity and appropriate product systems, we show that we can reduce recurrence sets such as Poincaré or operator recurrence sets, in particular, every such recurrence set has a countable subset ~D⊆   ∪|n|>N([sn-ε,sn+ε] ∩ Ɗ) for arbitrary small ε > 0 and arbitrarily large N ∈ ℕ having the same recurrence property.
We finally indicate how to further extend this topic by discussing topological dynamical systems, a quantitative analysis of recurrence sets and the use of locally compact abelian groups instead of ℤ and ℝ.

Keywords: Recurrence
Advisor: Batty, C
Cytoplasmic polyadenylation in S. pombe

Cid1 is a cytoplasmic member of a novel class of regulatory poly(A) polymerases discovered recently in yeast, worms and vertebrates. Previous genetic studies in the fission yeast, Schizosaccharomyces pombe, suggested a role for Cid1 in the checkpoint response to replication stress, but it was not known how a poly(A) polymerase might contribute to this response. Further investigations into the mode of action of Cid1 were therefore undertaken in this study. Cid1 is likely to target specific RNAs for polyadenylation; potential RNA substrates were identified using the complementary methods of microarray hybridisation and whole proteome analysis using two-dimensional liquid chromatography. These experiments revealed that Cid1 does not affect RNAs during normal, unperturbed growth but instead alters the expression of specific subsets of genes during replication stress. Many RNAs affected by Cid1 in these circumstances were cell-cycle dependent and telomeric transcripts, including those encoding histones and a novel RecQ helicase, Rqh2. As Cid1 lacks an RNA recognition motif, it is unlikely to bind selectively to RNA targets on its own. Cid1-interacting proteins were identified using yeast two-hybrid and tandem affinity purification methods. From these studies, novel members of a Cid1 complex have been discovered including: a previously uncharacterised metallo-beta-lactamase, RNA-binding proteins, ribosomal proteins and a telomere-binding protein. Together, these approaches are leading to a model for the role of cytoplasmic polyadenylation by Cid1 in checkpoint control.

Advisor: Norbury, C
Matching with mismatches and assorted applications

This thesis consists of three parts, each of independent interest, yet tied together by the problem of matching with mismatches. In the first chapter, we present a motivated exposition of a new randomized algorithm for indexed matching with mismatches which, for constant error (substitution) rates, locates a substring of length m within a string of length n faster than existing algorithms by a factor of O(m/ log(n)).
The second chapter turns from this theoretical problem to an entirely practical concern: delta compression of executable code. In contrast to earlier work which has either generated very large deltas when applied to executable code, or has generated small deltas by utilizing platform and processor-specific knowledge, we present a naïve approach — that is, one which does not rely upon any external knowledge — which nevertheless constructs deltas of size comparable to those produced by a platformspecific approach. In the course of this construction, we utilize the result from the first chapter, although it is of primary utility only when producing deltas between very similar executables.
The third chapter lies between the horn and ivory gates, being both highly interesting from a theoretical viewpoint and of great practical value. Using the algorithm for matching with mismatches from the first chapter, combined with error correcting codes, we give a practical algorithm for “universal” delta compression (often called “feedback-free file synchronization”) which can operate in the presence of multiple indels and a large number of substitutions.

Keywords: data compression
statistical matching
Advisor: McColl, W
Brent, R