VictorJuiz/thesis huggingface dataset:
Measuring antineutrino oscillations with the MINOS experiment

MINOS is a long baseline neutrino oscillation experiment. A manmade beam of predominantly muon neutrinos is detected both 1 km and 735 km from the production point by two functionally identical detectors. A comparison of the energy spectra measured by the two detectors shows the energy-dependent disappearance of muon neutrinos characteristic of oscillations and allows a measurement of the parameters governing the oscillations. This thesis presents work leading to measurements of disappearance in the 6% v̅μ background in that beam.
A calibration is developed to correct for time-dependent changes in the responses of both detectors, reducing the corresponding uncertainty on hadronic energy measurements from 1.8% to 0.4% in the near detector and from 0.8% to 0.4% in the far detector. A method of selecting charged current v̅μ events is developed, with purities (efficiencies) of 96.5% (74.4%) at the near detector, and 98.8% (70.9%) at the far detector in the region below 10~GeV reconstructed neutrino energy. A method of using the measured near detector neutrino energy spectrum to predict that expected at the far detector is discussed, and developed for use in the v̅μ analysis. Sources of systematic uncertainty contributing to the oscillation measurements are discussed.
In the far detector, 32 v̅μ events are observed below a reconstructed energy of 30 GeV, compared to an expectation of 47.8 for Δm̅2atm = Δm2atm, sin2(2̅θ23) = sin2(2θ23). This deficit, in such a low statistics sample, makes the result difficult to interpret in the context of an oscillation parameter measurement. Possible sources for the discrepancy are discussed, concluding that considerably more data are required for a definitive solution. Running MINOS with a dedicated v̅μ beam would be the ideal continuation of this work.

Keywords: MINOS
oscillation
neutrino
antineutrino
NuMI
Advisor: Barr, G
The formation and development of Latin medical vocabulary

This is a study of the substantival medical terminology of Aulus Cornelius Celsus (early 1st c.) and Cassius Felix (mid 5th c.), in the fields of Anatomy and Physiology; Pathology; and Therapeutics. Two broad questions are considered: (1) What were the possible and the preferred means of extending the Latin vocabulary in these technical areas in the first and the fifth century A.D.? (2) May any linguistic features be identified as proper or peculiar to Latin medical - or, more generally, technical - terminology?
Chapter 1 presents a general characterisation, based on examples of medical language, of modern technical terminology. Certain features of the structure and composition of the modern terminology are observed also in our Latin authors, especially in Cassius Felix.
Chapters 2-5 focus each on one linguistic means of term-formation in Celsus and Cassius Felix. These are (Ch.2:) the use of Greek medical terms within the Latin terminology; (Ch.3:) the use of semantic extension, that is the deployment of established Latin words with new, medical reference (sutura 'stitching' → 'cranial suture'); (Ch.4:) the minimal use of compounding (dentifricium 'tooth-rub'), and the use as single terminological units of lexicalised Noun Phrases, Noun + Adjective (ignis sacer a type of skin-disease) or Noun + Genitive (difficultas urinae 'dysury'), here called "Phrasal Terms"; (Ch.5:) the favouring of certain suffixes in deriving Nouns (and some Adjectives) and the striking correlation between suffix and the lexical-semantic field of the derivative (-or and clinical signs and symptoms: dolor, rubor).
Chapter 6 presents comparative figures for the two authors and a general working hypothesis that emerges: namely that divergences between Cassius Felix and Celsus may be interpreted as symptoms of the development of a Latin technical medical terminology (notably the integration of Greek and Latin terminology; reduction in the use of non-metaphorical polysemy; increased use of Phrasal Terms in fixed word order; extended use of suffixation to signal the semantic organisation of the terminology and, additionally, to form nominalisations as part of the development of a heavily-nominal style). A programme is adumbrated for testing this hypothesis.
Volume II contains brief historical introductions to Celsus and Cassius Felix, the authors and their works; a Glossary of their medical terminology in three parts (ANATOMY and PHYSIOLOGY; PATHOLOGY; THERAPEUTICS); and full word indexes to both authors listed on microfiche.
Identification and characterisation of homologous recombination genes in Schizosaccharomyces pombe

DNA double-strand breaks (DSBs) are highly genotoxic lesions, which can promote chromosomal rearrangements and tumorigenesis through oncogene activation or loss of heterozygosity (LOH) at tumour suppressor loci. To identify new genes involved in DSB repair and genome stability, an S. pombe deletion library was screened for mutants which exhibited sensitivity to the DNA damaging agents bleomycin and/or MMS. 192 mutants were isolated which exhibited increased sensitivity to one or both of these agents. These mutants were further analysed in a sectoring assay and mutants sought which exhibited elevated levels of break-induced loss and rearrangement of a non-essential minichromosome. Using this approach 57 genes were identified, including all known homologous recombination (HR) and DNA damage checkpoint genes present in the library. Further, quantitative analysis of DSB repair indicated that 25 of these genes functioned to promote efficient HR repair, thus representing a comprehensive HR gene set in fission yeast. Included in this gene set are 10 genes not previously implicated in HR repair; nse5⁺, nse6⁺, ddb1⁺, cdt2⁺, alm1⁺, snz1⁺, kin1⁺, pal1⁺, SPAC31G5.18c⁺ and SPCC613.03⁺. Detailed characterisation of ddb1Δ and cdt2Δ established a role for the Ddb1-Cul4Cdt2 ubiquitin ligase complex in HR. The findings presented here support a model in which break-induced Rad3 and Ddb1-Cul4Cdt2 ubiquitin ligase-dependent Spd1 degradation promotes ribonucleotide reductase activation and nucleotide biosynthesis, which is required for post-synaptic ssDNA gap filling during HR repair.
Lastly, the role of HR genes in suppressing chromosome loss and rearrangements was examined. A striking inverse correlation between levels of gene conversion and levels of both chromosome loss and LOH was observed across the HR gene deletion set. These findings support a common and likely evolutionarily conserved role for HR genes in suppressing both chromosome loss and break-induced chromosomal rearrangements resulting from extensive end processing associated with failed HR repair.

Keywords: DNA double-strand break
Schizosaccharomyces pombe
DNA repair
genome instability
Advisor: Humphrey, T
Investigating the function of Drosophila MAPs Msd1 and dTD-60 in mitotic spindle assembly

Mitosis is the process by which new cells are formed. Following accurate duplication of chromosomes, a cell must segregate its chromosomes into separate daughter cells with great accuracy. Failure to do so can result in genomic instability. Thus, entry into mitosis is tightly regulated via complex protein interactions. Microtubules (MTs) are versatile Tubulin polymers that constitute a considerable portion of the cytoskeleton, and it is the dramatic rearrangement of MTs upon mitotic entry that is required to build the mitotic spindle – the structure responsible for segregating the duplicated sister chromatids. MTs are modulated by MT-Associated Proteins (MAPs) that enact major MT rearrangements during mitosis. Identifying and understanding the role of MAPs is essential to the study of MT behaviour during mitosis.
Recently, an RNAi screen for Drosophila MAPs identified two proteins that are the subject of this thesis; Msd1 and dTD-60. This thesis demonstrates that Msd1 is a novel MAP that is a component of the recently identified Augmin complex – the action of which is to generate a novel and redundant population of MTs within the mitotic spindle from existing MTs. Experiments described below demonstrate that Msd1 is required for Augmin-directed MT generation, and further investigate the role of this novel population of MTs within the developing fruit fly. Furthermore, a role for Msd1 in central spindle formation during anaphase in Drosophila is identified.
dTD-60, the Drosophila homologue of human TD-60 (hTD-60), is the subject of another study described in this thesis. While hTD-60 has a role in metaphase progression through interaction with the Chromosomal Passenger Complex, a contrasting role for dTD-60 is investigated here. This thesis describes both a divergent localisation and phenotype of dTD-60, and further investigates the role of dTD-60 and its interactors in mitotic spindle formation.

Keywords: Augmin
Drosophila
Msd1
Microtubule
Advisor: James, W
Human obesity and Arctic adaptation: epidemiological patterns, metabolic effects and evolutionary implications

The objective of this dissertation is to investigate the occurrence, determinants and consequences of obesity among the Inuit people in the central Canadian Arctic, based on the Keewatin Health Assessment Study (KHAS), conducted during 1990/91 in 8 Inuit communities in the Northwest Territories (n=434 adults aged 18yr+). Data from three other surveys are included for comparison: (1) the 1190 Manitoba Heart Health Survey among 2200 predominantly Caucasian residents of the province of Manitoba; (2) the 1986-87 Northern Indian Chronic Disease Study among 704 Cree-Ojibwa Indians from Northern Ontario and Manitoba; and (3) the 1990-91 Chukotka Chronic Disease Survey among 362 Chuckchi and Inuit in coastal Chukotka in the Russian Far North.
Judged by both body mass index and two skinfold thicknesses, obesity among the Inuit in the Keewatin region is as prevalent as it is in the general North American population. This is a new development over the past two or three decades, the result of rapidly changing physical activity, diet and other lifestyles. Obesity is more prevalent among women, among whom there is also a higher prevalence of central fat patterning.
Age, education and non-smoking status (females only) are consistently identified as independent predictors of various obesity indices on multivariate analysis. While better educated men are more likely to be obese, the relationship is reversed in women, possibly due to the different sex roles and their associated stress levels in a rapidly acculturating and modernizing society.
When different categories of obesity indices are compared, there is a consistent pattern of an increasing trend in blood pressure and one or more of the lipids but no significant change in glucose or insulin level. This observation distinguishes the Inuit and Chukchi from Caucasians and Amerindians. Even where a relationship exists, as with triglycerides and HDL-cholesterol, the magnitude of response is also lower among the Inuit.
The differential effect of obesity on glucose, blood pressure and lipids in Inuit compared to non-Inuit suggests a type of selective insulin resistance, the underlying mechanism of obesity and several chronic diseases. The Inuit metabolism reflects their almost exclusive diet of fat and proteins. Apart from its public health importance, the study of Inuit obesity can shed some light into issues related to the peopling of the Americas: are the Inuit "exempt" from the "New World syndrome", and can the "thrifty genotype" explain the differential occurrence of diabetes among Arctic and Subarctic hunter-gatherers? It provides an opportunity to elucidate fundamental questions relating to the interaction of genetic and environmental factors in disease causation and distribution.

Keywords: Inuit
Arctic
Canada
Advisor: Harrison, G
A measurement of the W boson charge asymmetry with the ATLAS detector

Uncertainties on the parton distribution functions (PDFs), in particular those of the valence quarks, can be constrained at LHC energies using the charge asymmetry in the production of W± bosons.
This thesis presents a measurement of the electron channel, lepton charge asymmetry using 497 pb-1 of data recorded with the ATLAS detector in 2011. The measurement is included in PDF fits using the machinery of HERAPDF and is found to have some constraining power beyond that of existing W charge asymmetry measurements.

Keywords: Parton Distribution Function
W boson
ATLAS
LHC
charge asymmetry
PDF fit
Advisor: Weidberg, A
The effects of contact patterns and genetic specificity on host and parasite evolution

Many bacteria, viruses and other parasites cause severe morbidity or mortality in their host populations, creating strong selection for physiological or behavioural mechanisms to avoid disease. Likewise, changes in host susceptibility and contact patterns can dramatically influence the spread of infectious diseases, and hence selection for traits such as virulence and infectivity range in parasites. Understanding how ecological and evolutionary changes in one population affect selection in another represents a key challenge for theoreticians and empiricists alike, and is essential for gaining further insights into host-parasite relationships.
This thesis contains theoretical models that explore how genetic and environmental factors shape the evolutionary and coevolutionary dynamics of hosts and parasites. In particular, the roles of genetic specificity (i.e. genotype-by-genotype interactions) and population mixing patterns are investigated, using both mathematical models and computer simulations. A broad range of scenarios are covered, including the coevolution of broad resistance and infectivity ranges (generalism), the persistence of coevolutionary cycling and the maintenance of sex, the effects of mating behaviour on disease prevalence and evolution, and the evolution of sexual and social behaviour. The models presented herein develop our understanding of host-parasite relationships and highlight the importance of genetic interactions and ecological feedbacks.

Keywords: generalism
Red Queen
Host-parasite
resistance
infectious disease
virulence
infectivity
sociality
castration
coevolution
Advisor: Gupta, S
Buckling, A
The relationship between Russia and Ukraine, Belarus and Kazakhstan from 2000-10: A post-Imperial perspective

This study aims to account for the high degree of influence and intensity displayed in bi-lateral relations between Russia and the other post-Soviet states – specifically Belarus, Ukraine and Kazakhstan (BUK.) It seeks to do so by employing an analytical framework based around the concept of ‘post-Imperialism,’ arguing that persistent legacies of the imperial past have both ensured a high degree of intensity in bilateral relationships as well as providing pathways of influence over certain policy areas – primarily for Russia, but in some instances for BUK as well. It also seeks to examine imperial legacy issues as distinct ‘types’ – from physical economic and military infrastructure, to cross-border constellations of elite personnel to the normative and cognitive inheritances of imperialism amongst both the elite and the population at large. It concludes that Russia has been able to mobilise and employ power resources not available to alternative actors in order to ‘punch above its weight’ when competing with other powers for influence in the post-Soviet space, and preserve certain Soviet era patterns of relations. It is not the focus of this study, but it is to be hoped that the framework will prove useful for researchers in other former imperial polities in future.

Keywords: Russia
soft power
constructivism
Belarus
Imperialism
Kazakhstan
Post-imperialism
Advisor: Pravda, A
The cerebral connexions of the visual system

In the mammalian visual system the experimental investigation of the effect of sensory experience on the postnatal brain was facilitated by the detailed information that was already available on the structure and function of the normal adult and the relative ease with which the animal's visual environment could be modified by eyelid suture. When performed in young kittens this procedure produced a cellular atrophy in the lateral geniculate nucleus which resembled histologically the transneuronal degeneration studied in the same site after eye enucleation (Wiesel & Hubel 1963a). The physiological studies (Hubel & Wiesel 1965) pointed out the role of a process of competition between deprived and non-deprived visual inputs in the postnatal development of the visual pathways. This idea of competition was applied as a mechanism to explain the cellular atrophy in the lateral geniculate nucleus following lid suture in kittens after the observation that the degeneration was confined to the binocular segments of the geniculate (Guillery & Stelzner, 1970). It was postulated that cells in the binocular portion of the visual cortex may be regarded as receiving axons from 2 adjacent geniculate laminae and there may be a competition for synaptic space on the cortical cell with the neurons from the non-deprived laminae of the lateral geniculate nucleus forming greater axonal arborisations at the expense of those from the deprived laminae. This abnormally restricted cortical arborisation of the deprived geniculo-cortical cells could be reflected in a retrograde fashion in a smaller perikaryal size of the deprived cells than the non-deprived cells with a rich arborisation. Secondly the monocular segment of retina-geniculate-cortex pathway could be a site in which competition was not occurring so that the lack of degeneration here was a reflection of the absence of competition.
[Please see thesis for full abstract.]
The impact of socioeconomic position of severe maternal morbidity outcomes amongst women in the UK and Australia

Aims: The aims of this thesis are to investigate the risk of severe maternal morbidity amongst women from different socioeconomic groups in the UK, explore why these differences exist and compare these findings to the setting in Australia.
Methods: Three separate analyses were conducted. The first used UK Obstetric Surveillance System (UKOSS) data to assess the incidence and independent odds of severe maternal morbidity by socioeconomic group in the UK. The second analysis used quantitative and qualitative data from the 2010 UK National Maternity Survey (NMS) to explore the possible reasons for the difference in odds of morbidity between socioeconomic groups in the UK. The third analysis used data from the Victorian Perinatal Data Collection (VPDC) unit in Australia to assess the incidence and odds of severe maternal morbidity by socioeconomic group in Victoria.
Results: The UKOSS analysis showed that compared with women from the highest socioeconomic group, women in the lowest ‘unemployed’ group had 1.22 (95%CI: 0.92 – 1.61) times greater odds associated with severe maternal morbidity. The NMS analysis demonstrated that independent of ethnicity, age and parity, women from the lowest socioeconomic quintile were 60% less likely to have had any antenatal care (aOR 0.40; 95%CI 0.18 – 0.87), 40% less likely to have been seen by a health professional prior to 12 weeks gestation (aOR 0.62; 95%CI 0.45 – 0.85) and 45% less likely to have had a postnatal check with their doctor (aOR 0.55; 95%CI 0.42 – 0.70) compared to women from the highest quintile. The Victorian analysis showed that women from the lowest socioeconomic group were 21% (aOR 1.21; 95%CI 1.00 – 1.47) more likely and that Aboriginal and Torres Strait Islander women were twice (aOR 2.02; 95%CI 1.32 – 3.09) as likely to experience severe morbidity.
Discussion: The results suggest that women from the lowest socioeconomic group in the UK and in Victoria have increased odds of severe maternal morbidity. Further research is needed into why these differences exist and efforts must be made to ensure that these women are appropriately prioritised in the future planning of maternity services provision in the UK and Australia.

Keywords: socioeconomic
morbidity
maternal
disadvantage
Advisor: Knight, M
Kurinczuk, J
Semi-robust static Hedging of Barrier Options

We explore how to put the theory on static hedges of barrier options into use. We discuss a polynomial expansion of the exact static hedge in a stationary diffusion model provided by [9] and we develop an explicit expression of an asymptotic static hedge, which is constructed to perform well for short maturities. We derive a semi-robust static hedge in a sense, that it is model independent and depends upon one's beliefs about the future values of implied volatility only.
The industrial organization of input markets

This thesis consists of three closely connected pieces of work and an enhanced version of my M.Phil. thesis. The first three substantive chapters analyse vertical contracting in input markets under the exercise of differential buyer power. Chapters 2 and 3 consider the case of a supplier selling its output via a supermarket that offers captive demand (due to customers who anyway make a trip for their weekly shopping), which its rival, a local store is not able to offer. It is shown that the supermarket can negotiate an input price lower than the local store's only if its advantage translates into sufficient bargaining strength in setting contracts. The existence of a waterbed effect, the implications of a partially covered market, a nonlinear pricing structure and welfare implications of a ban in discrimination are also explored. Chapter 4 modifies the standard model where size determines buyer power to show that if quantities need to be decided in advance, an increase in a retailer's size is always welfare improving. For the presence of waterbed effects, we propose a novel insight that runs across different classes of models: following a discount to one retailer, the supplier faces two competing incentives - it wants to extract profits from the rival retailer but it also wants to transfer sales towards it. The waterbed effect is shown to be present only if the discount to the retailer is small, so incentives for profit extraction outweigh those for transferring business.
Finally chapter 5 studies a firm's strategic incentive to outsource when its product displays network effects. It shows that a firm would choose to increase its observable marginal cost to make its competitor less aggressive and thereby increase its own probability of winning competition for the market. This is robust to small levels of uncertainty.

Keywords: waterbed effect
buyer power
price discrimination
Advisor: Thanassoulis, J