VictorJuiz/thesis huggingface dataset:
Chromosomal variation of the common shrew Sorex araneus L. in Britain

Throughout the range of the common shrew (Sorex araneus Linnaeus 1767), repeated Robertsonian fusion mutations have led to a karyotypic polymorphism dividing the species into chromosome races. Studies of fertility were undertaken in the male, both of homozygotes and of heterozygotes forming meiotic multivalents of varying complexity.
Observations made at pachytene, diakinesis/metaphase I and metaphase II did not provide evidence for fertility impairment in homozygotes or simple heterozygotes. Males forming a chain of seven chromosomes during meiotic prophase I were produced through a program of captive breeding, and were brought to premature sexual maturity through photoperiod manipulation. In these more complex heterozygotes, incomplete pachytene pairing was frequently observed (68% of cells), germ cell death was found to be elevated (23%), and data from analysis of metaphase II spreads are indicative of an increase in nondisjunction above background of approximately 10%.
At the interface between two chromosome races, a complex of clines of chromosome frequency can be found. Field studies determined the routes and widths of four such clines (ko, 8.6km; kg, 28.4km; no, 37.1km; pr, 47.9km), and concluded that the courses taken are entirely consistent with maintenance through a mechanism of heterozygote disadvantage. Estimates of disadvantage made from cline width were in close agreement with those derived from the fertility studies.

Advisor: Searle, J
Engineered genetic sterility of pest insects

In the light of increasing pesticides resistance in agricultural pests and in insect vectors of human diseases, leading to the rise in occurrence of mosquito-borne diseases, new, efficient and environmentally friendly methods of pest control are needed.
Sterile Insect Technique (SIT), relying on mass releases of radiation sterilised males to reduce reproductive potential of target pest populations, although not new, offers an alternative to the use of pesticides and is an environmentally non-polluting method of insect control. Many insect species, however, are not very amenable to classical SIT, due to detrimental side-effects of radiation treatment.
We propose a new method, a genetically engineered modification of classical SIT, replacing radiation with genetically induced sterility. Based on conditional expression of male-germline targeted nucleases which introduce double strand breaks into the male germline DNA to render males sterile, this method emulates SIT mechanism, at the same time eliminating radiation and associated detrimental side-effects.
Different variants of such a system were investigated in this project, eventually leading to the creation of functional conditional male-sterility systems in two model organisms – the Yellow fever mosquito, Aedes aegypti and the Mediterranean fruit fly, Ceratitis capitata. Both systems utilise chimeric nuclease composed of protamine and FokI cleavage domain fusion. The sperm-specificity and the conditionality of the sterile phenotype have been achieved through the use of tetracycline repressible expression system driven by the β2-tubulin promoter in Ceratitis capitata and by the Topi promoter in Aedes aegypti.

Keywords: sterile male
RIDL
FokI nuclease
genetic pest control
sterile insect technique
transgenic insects
Advisor: Alphey, L
Shimeld, S
The non-sovereign self - Arendt, Butler and Cavell on the subject, community and otherness 

This thesis examines the idea of the non-sovereign self and the role it plays in the work of Hannah Arendt, Judith Butler, and Stanley Cavell. Based on their critiques of the subject a philosophical anthropology is forwarded that stresses that humans can only be understood in relation to their environment. This highlights the role of language, embodiment, and psychic attachment for the notion of the non-sovereign self and maintains that humans are finite and contingent beings. The finiteness of the self's knowledge of itself and others also implies that the self cannot give a cohesive narrative account of its emergence. Moreover, its relationship to the unknowable other is constitutive for the relational self. The notion of the other signifies not only the concrete other person, but also those other living beings and social structures on whom the self depends for its survival.
From this notion of non-sovereign, relational selfhood the thesis forwards an argument about the interrelation between ethical and political thought. Ethics is defined not in terms of the subject's accountability for its past actions, but by a primary responsibility for the other. By showing that ethical and political thought are closely intertwined, an understanding of political community is forwarded that highlights the role of responsibility towards those excluded from current forms of political representation. Turning to the role of affects for our understanding of political agency the role of cohesiveness, permeability and durability for political communities is interrogated. Stressing that the self remains a 'structure in formation' allows to account for the possibility of political agency which is not bound to a pre-established, shared social identity, but is motivated by one's ethical responsibility for others.

Keywords: otherness
community
subject
responsibility
political philosophy
Advisor: McNay, L
The Karaites, a religious and linguistic minority in Eastern Galicia (Ukraine) 1772-1945

The dissertation is dedicated to the history of the East European Karaite Jews (Karaites), a highly interesting ethno-religious Jewish group. It focuses on the Karaites of Galicia (Ukraine) from 1772 to 1945.
The first four chapters of the dissertation are devoted to the Austrian period in the history of the Galician Karaites (1772-1918). Chapter One demonstrates that the Karaites represent an unparalleled example of preferential treatment of a Jewish community by the Austrian administration. Chapter Two provides readers with an overview of the "internal" history of the Karaite communities of Halicz and Kukizow. Chapter Three outlines the religious and ethnographic customs and traditions of the Galician Karaites. Chapter Four focuses on relations between the Karaites and their ethnic neighbours - the Slavs and the Ashkenazic Jews. Chapter Five is dedicated to the history of the Karaites in Polish Galicia between the two world wars. It is in this period that the Karaites started to become more and more separated from the Ashkenazic Jews. Chapter Six reconstructs the process of dejudaization and Turkicization of the Karaite community, highlighting the role of Seraja Szapszal, the Karaite ideological leader. It ends with an analysis of the history of the community during the period of the Nazi occupation. Chapter Seven outlines the ultimate decline of the Galician community after the Second World War. It also describes the current state of the Galician Karaite community and its historical legacy. The conclusion provides some essential remarks regarding the position of the Karaite case within the wider framework of Jewish and European history.

Advisor: Evans, R
Identifying genetic determinants of impaired PfEMP1 export in Plasmodium falciparum-infected erythrocytes

The virulence of Plasmodium falciparum is largely attributed to the ability of asexual blood-stage parasites to cytoadhere to the microvascular endothelium of the human host. This pathogenic behavior is mediated by the primary parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1), an understanding of which is crucial to develop interventions to ameliorate the morbidity and mortality of P. falciparum malaria. The work presented in this thesis describes the application of a phenotype-to-genotype experimental approach to identify novel parasite proteins involved in the trafficking and display of PfEMP1. Guided by the overall hypothesis that the in vitro culture-adapted parasite line 3D7 harbors 1 or more genetic determinants of impaired PfEMP1 trafficking, surface PfEMP1 levels were first measured in 3D7, the presumably trafficking-competent parasite line HB3, and 16 unique progeny from an HB3 x 3D7 genetic cross (chapter 2). These phenotypes were then combined with genome-wide SNP data in QTL analysis to identify genetic polymorphisms potentially responsible for the impaired trafficking in 3D7 (chapter 3). A near-significant QTL containing a single protein-coding gene, the putative kinesin Pf3D7_1245600, was identified, characterized, and investigated in CRISPR-Cas9-driven allele-exchange parasite transfection experiments to establish a causal link between the gene and PfEMP1 trafficking (chapter 4). The parasite transfections were unsuccessful, but the potential role of Pf3D7_1245600 in PfEMP1 trafficking was indirectly assessed through the disruption of microtubules with colchicine (chapter 4), which significantly impacted the surface PfEMP1 levels of HB3 but not 3D7. The findings of this thesis suggest that kinesins and microtubules may play previously unconsidered roles in the regulation, production, or trafficking of PfEMP1.

Keywords: PfEMP1
Plasmodium falciparum
QTL Analysis
Kinesin
Virulence
Advisor: Newbold, C
Fairhurst, R
Elections, context, and institutions: the determinants of rent extraction in high-income democracies

Why is there significant variation in rent extraction amongst high-income democracies? A large number of political economy investigations into this research question have found that a long period of democratic rule and high per capita income are associated with less rent extraction amongst public policy-makers. However, attempts to explain the residual, yet significant, variation in rent extraction amongst countries that possess both these characteristics have been significantly more circumspect and disputed.
The thesis explores how the distribution of policy-making responsibilities between electorally accountable decision-makers (EDD) and their electorally unaccountable (NEDD) public policy-making counterparts, determines the optimal level of rents extracted in any given high-income democracy context. Specifically, the thesis formally models how: (1) variation in the EDD/NEDD ratio, by altering (2) voters’ evaluation of incumbent competency, changes (3) the incentives that policy-makers, wishing to remain in office, have to minimize their short term level of rent extraction in order to signal their competency and hopefully retain office. Given these ‘career concerns’ the theoretical model predicts that an increase or decrease in the EDD/NEDD ratio will be associated with more or less rent extraction.
This hypothesis is then tested empirically, primarily using an augmented version of Persson and Tabellini’s (2003) dataset. Specifically, the thesis tests whether (1) the EDD/NEDD ratio can predict variation in rent extraction only amongst high-income democracies; (2) whether voters, and not just elites, use the EDD/NEDD ratio to update their beliefs regarding the determinants of rent extraction; and (3) whether the EDD/NEDD ratio affects the level of rent extraction, once controlling for other institutional variables (Efficacy of Elections) also associated with variation in voter evaluation of incumbents’ competency.
Establishing that the EDD/NEDD ratio does robustly predict variation in rent extraction is a significant finding, as it can enable analysts to predict how changes in policy-making contexts may affect the incentive for good governance in this sub-set of countries. However, the results are (1) exploratory in nature, and also (2) contingent on other factors (regime type and institutional variation), meaning that while significant, they cannot be generalized to non-democratic contexts.

Keywords: rent-seeking
rent-extraction
corruption
public economics
political economy
Advisor: Duch, R
King, D
Bayesian methods for estimating human ancestry using whole genome SNP data

The past five years has seen the discovery of a wealth of genetics variants associated with an incredible range of diseases and traits that have been identified in genome- wide association studies (GWAS). These GWAS have typically been performed in in- dividuals of European descent, prompting a call for such studies to be conducted over a more diverse range of populations. These include groups such as African Ameri- cans and Latinos as they are recognised as bearing a disproportionately large burden of disease in the U.S. population.
The variation in ancestry among such groups must be correctly accounted for in association studies to avoid spurious hits arising due to differences in ancestry between cases and controls. Such ancestral variation is not all problematic as it may also be exploited to uncover loci associated with disease in an approach known as admixture mapping, or to estimate recombination rates in admixed individuals. Many models have been proposed to infer genetic ancestry and they differ in their accuracy, the type of data they employ, their computational efficiency, and whether or not they can handle multi-way admixture. Despite the number of existing models, there is an unfulfilled requirement for a model that performs well even when the ancestral populations are closely related, is extendible to multi-way admixture scenarios, and can handle whole- genome data while remaining computationally efficient.
In this thesis we present a novel method of ancestry estimation named MULTIMIX that satisfies these criteria. The underlying model we propose uses a multivariate nor- mal to approximate the distribution of a haplotype at a window of contiguous SNPs given the ancestral origin of that part of the genome. The observed allele types and the ancestry states that we aim to infer are incorporated in to a hidden Markov model to capture the correlations in ancestry that we expect to exist between neighbouring sites. We show via simulation studies that its performance on two-way and three-way admixture is competitive with state-of-the-art methods, and apply it to several real admixed samples of the International HapMap Project and the 1000 Genomes Project.

Keywords: Bayesian
genotype
MCMC
admixture
Advisor: Marchini, J
Ambiguous artefacts: towards a cognitive anthropology of art 

This thesis proposes elements for a cognitive anthropology of visual art. Most works of art are human-made objects that cannot be approached in purely functional terms, and as such they frustrate important cognitive expectations that people have about artefacts. For this reason, it is hypothesised that art triggers speculation about the artist’s intention, and that it is intuitively approached as a form of communication. By application of Bloom’s (1996) theory of artefact categorisation, and Sperber and Wilson’s (1986/1995) relevance theory of communication, a series of predictions are generated for art categorisation (or definition), art appreciation, and art cultural distribution. Two empirical studies involving more than 1,000 participants tested the most important of these predictions. In study 1, a relationship was found between how much a series of works of art were liked and how easy they were to understand. Study 2 comprised four experiments. In experiment 1, a series of hyperrealistic paintings were preferred when they were labelled as paintings than when they were labelled as photographs. In experiments 2a and 2b, a series of paintings were considered easier to understand and, under some conditions, were preferred, when they were accompanied by titles that made it easier to understand the artist’s intention. In experiment 3, a series of artefacts were more likely to be considered “art” when they were thought to have been created intentionally than when they were thought to have been created accidentally. The results of studies 1 and 2 confirmed the predictions tested, and are interpreted in the framework of relevance theory. The art experience involves speculation about the artist’s intention, and it is partly assessed as a form of communication that is constrained by relevance dynamics. Implications for anthropology of art, psychology of art, and the art world are discussed.

Keywords: intention
function
anthropology of art
affordances
Tate Gallery
aesthetics
hyperrealism
artefact
cognitive anthropology
culture and cognition
communication
title
art
relevance theory
Advisor: Barrett, J
Whitehouse, H
Discontinuity in conversation speech

The occurrence of discontinuity in conversational speech raises a variety of theoretical problems for the study of verbal communication. According to the dominant explanatory models of language, discontinuities in the form of pauses, self-corrections, repeats, false starts, and the like are errors'of language performance. Consequently, when, in - conversational speech, discontinuities do occur, it is natural that questions should arise regarding (a) why they occur and (b) given that they do occur, how speakers and hearers are able to deal with them. It is argued that no coherent answers may be offered to these questions under the prevalent conceptualization of discontinuity.
As a feature of verbal performance, discontinuity has been studied primarily by researchers from the related disciplines of psychology, sociology, ethnomethodology, and discourse analysis. Although the explanatory approaches differ greatly, there is an underlying presuppositional unity to them. Whether discontinuity is studied as an indication of the speaker's cognitive processing, as a feature of social differentiation, or as an essential aspect of the speaker and hearer's management of conversational interaction, it is always assumed that discontinuities occur as the result of speaker error. This assumption, in turn, is shown to be derived from an unrecognised written-language (or 'scriptist') bias in the study of verbal communication. This conceptual bias, it is argued, is a shared weakness in the otherwise differing theoretical approaches to the explanation of discontinuity in conversational speech.
The theoretical discussion of the thesis is supplemented by an appendix containing a selection of transcribed examples of discontinuities compiled with the aid of a computer concordance program. These examples are used as comparative evidence throughout the central chapters of the thesis.
Studies towards the total synthesis of manzamine A

This thesis describes studies towards the total synthesis of manzamine A (9), a marine alkaloid. Two routes are presented.
The first route applied a novel palladium-catalysed arylative allene spirocyclisation cascade to the synthesis of manzamine A (9). In the first generation, a short route was developed to access the tricyclic ACE core 263a in only nine steps. The second generation applied the palladium-catalysed cascade to a similar system which utilised non-terminal allene pro-nucleophile 450 in an attempt to access a homologated derivative of the ACE core.
The second route relied on a diastereoselective Michael addition between nitro-olefin 473 and 8,5-fused ring system 146 comprising rings C and E of manzamine A (9). Further elaboration of the Michael addition product enabled the synthesis of tetracyclic ABCE core precursor 464 to be carried out and preliminary investigations into ring B formation were investigated.

Keywords: MANZAMINE A
ORGANIC CHEMISTRY
TOTAL SYNTHESIS
Advisor: Dixon, D
Governing Montreal

In comparison with Toronto and Winnipeg, structural reform of metropolitan governmental institutions in Montreal has taken considerably longer and has been far less comprehensive. Why? The main objective of this thesis is to answer this question. The answer centres mainly on the existence of two major linguistic communities--a condition not present in the other two cities.
The thesis suggests that there have been three different varieties of motivational factors behind the metropolitan reform movement in Montreal: 1) the need to establish new metropolitan institutions to respond to particular crises resulting from the breakdown of local government services; 2) the desire to establish a set of metropolitan structures which meet the requirements of organizational rationality; and 3) the desire of Quebec nationalists to re-arrange local institutions in such a way as to eliminate any official recognition of the English-speaking minority.
The first variety of factors serves to explain the creation of the Montreal Urban Community in 1969. The second variety was behind the attempts in the early 1970s to restructure municipal boundaries, to integrate the various municipal police forces, and to re-organize the social service network. The third variety has been important primarily in relation to debates about the re-organization of Montreal's school boards. Judging from recent events, it is likely to become even more apparent in other fields in the near future.
Insofar as organizational rationality involves the simplification of governmental structures, the aims of many Quebec nationalists are likely to promote this type of reform rather than hinder it. However, in Montreal, unlike Toronto and Winnipeg, reforms justified solely on the basis of organizational rationality have either not been implemented at all or have been done so in a very slow or modified manner. This can be explained prinarily in terms of the impact of Montreal's linguistic cleavage.
Intra-gate fault diagnosis of CMOS integrated circuits

Knowing the root cause of why an Integrated Circuit (1C) device fails to function properly is the key to provide the corrective measures to increase the yield and shorten the time to market. In recent years, electrical fault diagnosis method has received growing attention due to the effective and indispensable guiding role it plays in modern fault localization practice when physical measures are more and more confined by the shrinking feature size and condensed internal structure.
While most of the fault diagnosis tools are based on gate level fault models, many faults are actually at the transistor level (the intra-gate fault). This thesis provides an innovative method to diagnose the intra-gate faults. It covers a wide range of different types of intra-gate faults. The method extends the capability of gate level fault diagnosis tools to the intra-gate domain by building connections with these intra-gate faults to particular types of gate level faults. Intra-gate faults are transformed to gate level representations so that they can be diagnosed directly by the widely available and well developed gate level diagnosis tools. Real diagnosis of intra-gate faults from wafer data and physical failure analysis photos are provided as solid proofs of the effectiveness of this method.

Advisor: Moore, W