VictorJuiz/thesis huggingface dataset:
Historical reconstruction of Sennacherib's campaign against Judah and Jerusalem in 701 B.C.

This thesis has attempted a reconstruction of Sennacherib’s campaign against Judah in 701. The purpose of this resconstruction has not been to reach a definitive picture of the events of 701 but rather to come to the best possible hypothesis based upon a wide study of the relevant texts.
The best historical hypothesis concerning what happened in 701 must attempt to give equal weight to each piece of evidence in each relevant area, whether literary or archaeological. My justification for returning to this much-discussed area therefore is that previous scholarship has failed to meet this criterion for giving the best historical hypothesis. Over the course of my investigation I examined the relevant Assyrian inscriptions, not merely those relating to the third campaign, and the purported instances of biblical evidence, as well as engaging with archaeological and literary considerations. I showed that the most important theories offered up to this point each contradict or contend with an important piece of contrary evidence. Then, I suggested a view of my own which is, as far as possible, commensurate with all the evidence available.

Keywords: history
King of Assyria
campaigns
Sennacherib
Advisor: Day, J
A novel role for Atmin as a transcription factor controlling ciliogenesis

Cilia are cellular organelles involved in processing components of the hedgehog (hh) signalling pathway and determining left-right (L-R) axis formation in the embryo. An embryonic lethal mouse mutant, called gasping 6 (gpg6), was identified that demonstrated morphological and molecular defects associated with L-R development and hh signalling. gpg6 mutant embryos also demonstrate abnormally short cilia, which was hypothesised to be the primary morphological defect in gpg6 mutants.
The underlying genetic lesion in gpg6 is a mutation in the DNA repair gene Atmin. The base pair change results in an amino acid substitution in a critical residue in the third zinc finger of Atmin. The consequence of this change is the failure to activate transcriptional targets of Atmin. This raised the possibility that previously unidentified Atmin target genes are important for ciliogenesis. Consistent with this hypothesis, Dynein light chain-LC8 (Dynll1) is downregulated in gpg6 mutants. LC8 (a homolog of mouse Dynll1) is required, in the single cell eukaryotic organism Chlamydomonas, for retrograde intraflagellar transport (IFT), a process crucial for ciliogenesis.
These data led to the following hypothesis: Atmin activates expression of Dynll1, which functions in retrograde IFT to enable normal ciliogenesis. Knockdown of Atmin in a ciliated kidney cell line resulted in abnormally short cilia. Thus, Atmin functions in ciliogenesis. Investigation of gpg6 has therefore identified a novel role for Atmin in ciliogenesis and has added to the growing knowledge of genes that control cilia formation and embryonic development.

Keywords: mouse mutagenesis
Atmin
cilia
embryonic development
Advisor: Norris, D
Nixon, Kissinger and the Shah: US-Iran relations and the Cold War, 1969-1976

This thesis examines the nature and dynamics of U.S.-Iran relations during the Cold War under the leadership of U.S. President Richard Nixon, his adviser Henry Kissinger, and Shah Mohammad Reza Pahlavi of Iran. This revisionist account critically examines the popular view of Mohammad Reza Shah as a mere instrument of American strategies of containment during the Cold War. Relying on recently declassified American documents, British government papers, and the diaries, memoirs and oral histories of Iranian actors, this thesis restores agency to the shah as an autonomous Cold War actor and suggests that Iran evolved from a client to a partner of the United States under the Nixon Doctrine. This partnership was forged during Nixon’s first term in office between 1969 and 1972, as the United States embraced a policy of Iranian primacy in the Persian Gulf region. Thanks to a long-standing friendship with the president, the shah was able to exercise extraordinary influence in the Nixon White House. This partnership reached its peak during Nixon’s second term as the United States supported Iran’s regional primacy against the challenge from Iraq. The shah drew Nixon and Kissinger into Iran’s secret war against Iraq in Kurdistan in 1972, by portraying Iran’s long-standing regional conflict with Iraq as a Cold War confrontation with the Soviet-backed Ba’th regime in Baghdad. When the shah unilaterally decided to abandon the Kurds in a deal with Iraq’s Saddam Hussein in 1975, Kissinger had little choice but to acquiesce, despite the personal embarrassment and domestic recriminations that followed. The U.S.-Iran partnership declined following Watergate and Nixon’s resignation in 1974. In spite of the best efforts of the shah and Kissinger, between 1974 and 1976 the United States and Iran were unable to reach an agreement on U.S. nuclear exports to Iran. President Gerald Ford tried to impose a discriminatory nuclear agreement on Iran that was rejected by the shah because it violated Iran’s national sovereignty. Under Ford, the United States reverted to treating Iran as a client rather a partner of the United States.

Keywords: Richard Nixon
Mohammad Reza Pahlavi
Iran
Henry Kissinger
United States
Cold War
Advisor: Fawcett, L
Harpsichord and lute music in seventeenth-century France

The view that the lute exercised an important influence on the formation of French harpsichord style in the seventeenth century is a commonplace of musicology which has not until now been thoroughly investigated. This thesis is an attempt to determine the nature of that influence taking into account as much of the available relevant material as possible. The first chapter outlines the status and function of stringed keyboard instruments, particularly in the late sixteenth and early seventeenth centuries, using a wide variety of non-musical sources whether literary, archival, or documentary. It also charts the relative standing of the two instruments and the interrelationship of their repertoires as viewed by contemporaries throughout the seventeenth century. The second chapter provides a survey of the evolution of French lute style based on a detailed study of most of the French lute sources from the period cl600-cl670 and including the more important sources from cl670-cl700. The third chapter presents detailed comparisons of individual works existing in versions for both lute and keyboard. These are based on numerous parallel transcriptions presented in the second volume. The material for this section is provided by a concordance file for virtually all French seventeenth-century lute sources designed to be usable in conjunction with Gustafson's keyboard catalogue. The final chapter is an attempt to define the degree of affinity existing between particular features of the central harpsichord style and that of the lute on the basis of principles established in the previous discussions. This thesis contains the first detailed discussion of the works of the principal seventeenth-century French lutenists in the context of a survey of the general development of the lute style. Numerous illustrative examples of hitherto unpublished lute music are included in the second volume. The final chapter also discusses some new sources of French harpsichord music dating from the late sixteenth and early seventeenth centuries, with transcriptions. Also discussed for the first time is the Premier Livre (1687) of Elizabeth Jacquet de la Guerre, and a transcription of a suite supposedly written in imitation of the lute is given. A comprehensive concordance of pieces existing in versions for both lute and harpsichord is given in Volume II.
Chemical and dynamical evolution of early-type galaxies

In this work I have examined the spatially resolved properties of the local early-type galaxy population. Using Hubble Space Telescope and ground based photometry I constructed Jeans Anisotropic Multi Gaussian Expansion models of the SAURON sample of early-type galaxies, from which I determined the depth of the local gravitational potential well, quantified by the local escape velocity, Vesc. I found that Vesc correlated tightly with the three Lick indices: Mgb, Fe5015 and Hβ. The Mgb-Vesc relation within individual galaxies is identical to that between different galaxies; the relation is both local and global. The Mgb-Vesc relation is: log Mgb = (0.35 ± 0.01) log Vesc − (0.41 ± 0.03). While the metallicity, [Z/H] is correlated with Vesc it does not show the same local and global behaviour. Age (t) and alpha enhancement ([α/Fe]) are only weakly correlated with Vesc. A combination of [Z/H] and t is tightly correlated with Vesc, with scatter comparable to the Mgb-Vesc relation, and does show the local and global behaviour. This combination is given by: log Vesc = 0.85[Z/H] + 0.43 log t.
Using the volume limited ATLAS3D sample of 260 local ETGs I examined in detail the behaviour of the Mgb-Vesc relation and its dependence on other galaxy properties. I found that systematic deviations from the relation correlate with the local environmental density and molecular gas mass of a galaxy, and with the local [α/Fe] measurement. I found that there is a population of galaxies that do not follow the relation, found only at Vesc < 400 kms−1 . These galaxies have negative gradients, high central Hβ indices and young (t < 3 Gyrs) ages. Using stellar population models I demonstrated that these negative gradient galaxies are perturbed from the relation by recent star formation and will return to the relation as they age.
I also describe the observation, reduction and analysis of a new sample of ETGs in the core of the Coma cluster, the highest density environment in the local Universe, observed with the SWIFT Integral Field Spectrograph. I determined the fraction of slow rotators in the sample, comparing it to results from the ATLAS3D survey, and found an enhanced slow rotator fraction in the Coma cluster. I also determined the Fundamental Plane of Coma early-type galaxies, given by: log Re = (1.20 ± 0.22) log σe − (0.79 ± 0.09) log〈Ie〉.

Keywords: Early-type galaxies
Galaxy Evolution
Advisor: Davies, R
Cappellari, M
A Calpain-like multigene family in trypanosoma brucei

Trypanosomatid parasites are unicellular eukaryotes characterised by the presence of a subpellicular array of microtubules, a single flagellum, and a kinetoplast (containing the condensed mitochondrial DNA). The majority of trypanosomatid species undergo complex life-cycles, alternating between a mammalian host and an insect vector. Progression through this life-cycle requires the differentiation of trypanosomatids into distinct, niche adapted developmental forms. Differentiation into each life-cycle stage involves important biochemical and morphological changes, including the remodelling of the subpellicular cytoskeleton that defines cell shape. In higher eukaryotes, proteins from the calpain superfamily are involved in developmentally- and environmentally-regulated remodelling of the cytoskeleton and the dynamic organisation of signal transduction cascades. Interestingly, trypanosomatids contain unusually large families of calpain-related proteins, but there is little knowledge about the functional roles of these molecules during the life-cycle of trypanosomatid parasites.
In this thesis, I present the results of the bioinformatic analysis of calpain-like proteins in three trypanosomatid parasites, Trypanosoma brucei, Leishmania major and Leishmania infantum. From this analysis, I selected several calpain-related proteins tor RNAi functional analysis, on the bases of their domain composition and conservation across different species. The detailed analysis of the resulting RNAi phenotypes revealed the essential function of some calpain-like proteins for the correct morphogenesis of specific developmental forms of T. brucei, shedding some light on the mechanisms that regulate this parasite differentiation and cytoskeletal remodelling, and providing new putative therapeutic targets for African sleeping sickness.

Keywords: Molecular and Cellular Parasitology
Advisor: Gull, K
Ginger, M
The 'full liberty of public writers': special treatment of journalism in English law

This thesis investigates whether institutional journalism should receive special treatment at the hands of the law. Special treatment encompasses the affording of benefits to and the imposition of liabilities on journalistic institutions and the individuals who work for them. The arguments against special treatment are pragmatic and theoretical: pragmatic arguments emphasise, inter alia, the difficulty of providing a definition of journalism, and theoretical arguments emphasise the difficulty in explaining why special treatment can be coherent. The former can be addressed by describing how special treatment is already afforded to institutional journalism, both liabilities and benefits, to individuals and institutions, and showing that some of the problems foreseen by the pragmatic arguments have not proved as difficult as they appear. The arguments that special treatment is incoherent can be addressed by arguing that the credibility and assessability of institutional journalism still provide a prima facie rationale for special treatment irrespective of the rise of public speech on the Internet, when combined with the integral nature of journalism to democracy. Two basic arguments are advanced why this is so. The first, the free speech values argument, is a consequentialist account that holds that special treatment is appropriate when (or because) institutional journalism contributes to free speech values. It is attractive, but presents difficulties, both when considered in the abstract and when applied to the free speech value of democracy. The second, a rights-based argument, based on the notion that freedoms of speech and of the Press are distinguishable, can be based on either on Dworkin’s theory of rights as trumps or Raz’s theory of rights as interests. Raz’s account is preferable, as it complements the free speech values thesis in explaining the coherence of special treatment.

Keywords: press regulation.
journalism
media regulation
Leveson Inquiry
media diversity
privacy
contemporary theories of human rights
media plurality
information law
confidence
Press freedom in English law
defamation
contempt of court
journalists' rights
source protection (Norwich Pharmacal orders)
Media freedom in English law
Advisor: Young, A
The interaction between cognitive and linguistic categorisation in early word learning

This thesis investigates the strategies infants use to generalise labels to different objects in the early stages of lexical development. It aims to directly test the assumption that a taxonomic bias exists which guides infants to extend words to categories of objects instead of individual instances of them, against the hypothesis that infants discover the extension of words through exposure to multiple naming instances of different objects.Experiments One and Two attempted to teach two object-label pairings to infants at the end of their first year of life, and test generalisation of those labels to new objects from the same adult linguistic categories. This aim failed because infants showed evidence for prior knowledge of the words. Experiments Three and Four employed a more infant-controlled procedure using a habituation task during training; in the former a single exemplar from each adult category was used, whereas in the latter multiple exemplars from each category were used. In both Experiments evidence for word learning was provided at test, but infants failed to generalise the labels to other objects. Experiment Five used a training phase identical to Experiment Four but tested infants for perceptual categorisation in the absence of any labels. Some infants showed evidence for their ability to create such categories on the basis of the training set, suggesting that the inability to generalise in Experiments Three and Four was not due to a perceptual limitation. These findings suggest that infants at the end of their first year do not seem to be guided by any linguistic biases in their generalisation of labels. This thesis concludes that 10-month-old infants seem to have more advanced linguistic abilities than has previously been thought and constraint-like behaviour in later stages of lexical development might be a result of experience instead of a qualitative shift in cognitive processes.

Keywords: word learning
categorisation
lexical categorisation
Advisor: Plunkett, K
The role of the WspR responce regulator in the adaptive evolution of experimental populations of Pseudomonas Fluorescens SBW25

The role of ecological opportunity in adaptive radiation has been demonstrated by the diversification of the bacterium Pseudomonas fluorescens SBW25 in a spatially structured microcosm. This provides an ideal system for studying the genetics of adaptation and asking questions about the genes that matter in evolution. Previous studies have identified the genes that are necessary for the evolved, biofilm-forming, niche-specialist genotype, the wrinkly spreader (WS). These genes are organised in two operons: the wss operon that encodes the genes for cellulose biosynthesis, and the wsp operon that encodes a chemosensory pathway. The terminal gene in the wsp operon, wspR, encodes a novel response regulator thought to regulate the activity of the wss operon. This gene forms the basis of this study, which assesses the role of regulatory genes in adaptive evolution. The structure-function relationship of WspR is established through the phenotypic analysis of overexpressed wspR random point mutants. On this basis a model of WspR activity is proposed which is tested by molecular genetic analysis. The role of phosphorylation is demonstrated by site-directed mutagenesis, and domain liberation is used to study the interaction of WspR with the other components of the signalling pathway. As the overexpression of certain wspR mutant alleles mimics the evolutionary transition from ancestor to niche-specialist, the fitness effects of such overexpression are measured. It is found that some, but not all, wspR alleles do indeed cause adaptation. It is also found that a phenotypically-plastic genotype, with enhanced fitness, can be created by artificial manipulation, but does not occur naturally; this demonstrates the existence of a constraint on evolution. Sequence analysis of independently-isolated WS genotypes shows no evidence of wspR sequence variation, despite its capacity to enhance fitness. A further proteomic and phenotypic characterisation shows variation between ancestral and WS genotypes, and also between different WS genotypes. This demonstrates that there are different mutational routes to the same adaptation.

Advisor: Rainey, P
Functional genomics of variation in response to infection: insights into severe sepsis and common variable immune deficiency disorders

Functional genomics uses high throughput genome-wide technologies to investigate the functional consequences of genetic variants on gene expression and protein products. In the context of disease, using integrative functional genomic approaches to understand the genetic variation which underlies disease susceptibility and aetiology may contribute to better diagnosis, treatment and prevention. This thesis investigated genetic determinants of variation in response to infection by applying a functional genomics approach to investigate three clinical cohorts: patients with severe sepsis, an influenza challenge study and patients with common variable immune deficiency disorders.
The transcriptomic response to severe sepsis is reported here for the largest known adult severe sepsis community acquired pneumonia cohort. Two clusters within the cohort, based on gene expression signatures, which have different survival rates and identify individuals with distinct immune responses to sepsis, highlight the value of functional genomics for identifying heterogeneity within patient cohorts. This was further complemented by the resolution of gene expression signatures in healthy individuals following influenza challenge which identified individuals with moderate to severe disease. Shared gene expression signatures between the cohorts highlighted components of the immune response to viral infection important across multiple clinical settings and may assist with the identification of viral infections in the sepsis patients. Gene expression was mapped as a quantitative trait (eQTL). Comparison to data sets for healthy individuals and from innate immune stimulated cells identified regulatory variants specific to the context of sepsis.
Whole genome sequencing for a cohort of patients with common variable immune deficiency disorders was performed. This identified novel variants and pathways which may play a role in the underlying immunopathogenesis of disease. Integration with RNA-seq for a small number of patients allowed prioritisation of non-coding variants based on evidence of altered gene expression. Comparison to the sepsis cohort analysis identified key immune related genes involved in rare and common responses to bacterial infection.
This thesis has demonstrated the value of integrating multiple functional genomic techniques to further our understanding of the mechanisms underlying variation in the response to infection.

Keywords: Functional genomics
immunology
Advisor: Knight, J
The social expectations of Anglican clergy in England and Australia, 1850-1910

In the early nineteenth century, the ideal type of Anglican parish clergyman was a member of a gentlemanly profession. Although he had few formal duties, he exercised a benevolent influence in a small, deferential community. His liberal education, independent income and ample leisure enabled him to pursue scholarly hobbies. In every English village, he was a light of civilization. The parson was spiritual half-brother of the squire, and the Church as a whole was closely identified with the landed classes in the social rank, governing role (the magistracy) and political sympathies of the parochial clergy.
Urbanisation was the main force that largely destroyed the authenticity of this ideal. As society became horizontally divided, the power of locality dwindled. The Church's opponents - sceptics, Dissenters and organised labour - gained confidence. Rival authorities (to the pulpit) overwhelmingly established themselves in popular favour - especially the mass circulating press. The franchise was extended to the working classes, or at least to the aristocracy of labour with whom the Church of England had rarely felt easy. Finally, two of the props of the old ideal were knocked away - the prosperity of the agricultural sector, and the acceptance of the clergyman's calling as a learned profession.
In Australia, there were similar problems for the Anglican minister, although most were in a more intense form. A lack of endowment, the prevailing democratic and anti-clerical sentiment in much of the political debate, and the high degree of geographical and social mobility characteristic of much of the colonial population, made the problems of the Church and of her parochial ministers appear overwhelming. The result was the development of a form of careerism in the clerical order that seemed to some censorious contemporaries to have been not merely improper but quite destructive of the ideal of the parish priest, an ideal which was still upheld despite its manifest inappropriateness.