VictorJuiz/thesis huggingface dataset:
The role of homeobox gene NKX3.1 in prostate cancer
Keywords: cancer stem cells
NKX3.1
prostate cancer

NKX3.1, a prostate specific homeobox gene is a known marker of prostate epithelium during embryogenesis and is also expressed subsequently through different stages of prostate differentiation. However, all studies on NKX3.1 are focused on its regulation by androgen receptor (AR). The aim of this project is to establish the role of NKX3.1 in differentiation in prostate cancer, independent of AR regulation. In this thesis, I characterize the cell lines in terms of their differentiation capabilities in 3D, expression levels of NKX3.1 and the mismatch repair status. The genes potentially involved in differentiation and regulators of NKX3.1 are also identified using microarray data of the cell lines (Chapter 3). Although NKX3.1 plays a key role in prostate development no studies have been conducted on the effect of NKX3.1 expression on differentiation capabilities of prostate cell lines. In Chapter 4, this was investigated by siRNA mediated knockdown of NKX3.1 in 22Rv1 cell line and overexpression of NKX3.1 in PC3 (designated PC3-Nkx3.1) and PNT1a cells followed by growth in 3D. These functional studies show that the expression of NKX3.1 is vital for lumen formation in 3D, which is used as a measure of differentiation. The microarray data and overexpression of NKX3.1 studies suggest that this gene may also be involved in inhibiting epithelial to mesenchymal transition (EMT). Homeobox B13 (HOXB13) was identified as one of the downstream targets of NKX3.1. NKX3.1 and HOXB13 expression levels are positively correlated not only in the panel of prostate cell lines but also in the NKX3.1 overexpression and knockdown studies (Chapter 5). The results of the work presented in this thesis demonstrate that there is a striking parallel between the function of NKX3.1 in prostate and Caudal-type homeobox 1 (CDX1) in the colon and rectum. In conclusion, NKX3.1 plays a key role as a tumour suppressor in prostate cancer by controlling differentiation of prostate cancer cells.
The processing, microstructure and creep properties of Pb-free solders for harsh environments
Keywords: harsh environments
Pb-free solders
microstructure
creep

The constitutive mechanical behaviour with a focus on creep of Sn-Pb and various Sn-Ag-Cu based Pb-free solders in the 25-150°C temperature range has been studied using nanoindentation and various new meso-scale tests. All alloys have been studied as bulk wave soldering bars, as-received solder balls and solder joints. Ball Grid Array (BGA) solder joints in a typical electronic configuration were manufactured in-house using both Cu and Pd-Ag metallizations. Microstructural characterisation of all configurations used various types of optical and electron microscopy and showed that the solder pad metallization type played a major role in intermetallic compound (IMC) formation. There were comparatively fine and coarse-grained microstructures in both as-received solder balls and BGA solder joints depending on ball diameter. Nanoindentation creep measurements in the stress range 20-500MPa showed that grain boundary sliding occurred together with dislocation glide and dislocation climb in the low temperature (25-50°C) and high temperature (100-150°C) regimes respectively. Smaller grain sizes (<20µm) encouraged grain boundary sliding that enhanced creep.
New elevated temperature mechanical tests were developed using the nanoindentation platform to enable testing of entire solder joints in shear and compression, with stresses in the 1E-2 - 3MPa range, more relevant to in-service conditions than those in nanoindentation. Meso-scale spherical indentation creep behaviour in compression on as-reflowed solder balls showed good agreement with that obtained by conventional nanoindentation. However, when BGAs were tested in shear, the solder microstructure had relatively little influence on the creep response, which was significantly less creep resistant than individual phases in the ball obtained by nanoindentation or the ball itself obtained by meso-scale spherical indentation. In shear, the creep conformed to diffusion controlled behaviour and interfacial microstructure was suggested to now control creep response, with the microstructure of the majority of the solder joint playing only a minor role.
Unpacking faculty development in Japan: an ethnography of faculty development practitioners 
Keywords: Japan
ethnography
academic development
higher education
faculty development

This thesis provides an ethnographic account of the lived experiences of faculty development practitioners in Japan. Through participatory observation and ethnographic interviews, it seeks to understand the following research question:
“How do faculty development practitioners make sense of the concept of faculty development as a professional identity and a lived experience in Japan?”
The Ministry of Education, Culture, Sports, Science and Technology, MEXT, introduced and recommended institutional ‘fakaruthī diberoppumento (faculty development)’ or ‘FD’ in 1999 and later mandated it in 2008. As a result, universities created the role and position of FD practitioner. Those FD practitioners have been involved in crafting a genre of faculty development that reconcile policy requirements, university’s requirements, and their personal understanding. This leads to a daily struggle between acting as FD practitioner according to external requirements and sustaining or constructing one’s own professional identity and values especially as an academic. By incorporating notions of ‘identity’ and ‘community’, I describe practitioners’ constant negotiation of their position between an academic and a FD practitioner.
I have three arguments. First, the title of ‘FD tantōsha’ that is most commonly used in Japan creates a semantic space for negotiations to take place between different types of identities, both practiced and/or idealized. ‘Tantōsha’ literally means the person in charge and it is relatively 7 neutral label to describe the position. Second, alphabetically written ‘FD’ prevents the evolution of the concept. The term ‘FD’ is just a symbolic noun therefore it allows various interpretations but it does not allow evolution of the concept like in the USA and the UK. As an English term, ‘faculty development’ means ‘to develop’ ‘faculty’. As the focus of faculty development shifted, the term also changed, leading to terms such as ‘educational development’. Third, the temporariness of the position prevents practitioners to engage with the community for faculty development practitioners in Japan and in other countries. Therefore interpretation of the concept of faculty development, creation of the common language and knowledge base as a field, and construction of professional identity have yet to be observed.
Accessing complex genomic variation in Plasmodium falciparum natural infections
Keywords: genomics
malaria
computational biology
drug resistance
bioinformatics

Genetic polymorphism in Plasmodium falciparum is a considerable obstacle to malaria intervention. Parasites have repeatedly evolved to overcome every front-line antimalarial deployed throughout history, and artemisinin resistant populations are expanding in Southeast Asia. Promising vaccine candidates routinely fail when challenged by the genetic diversity of natural parasite populations, and a recent trial using a blood-stage antigen showed immunity was allele specific. Modern sequencing technologies have revolutionized our understanding of parasite genomics and population genetics by providing access to single nucleotide variation, but characterizing more complex polymorphism remains a key challenge. Solving this problem is important because the selective pressures from drugs and host immunity often create complex polymorphism in the most clinically relevant genes that is missed using standard genotyping methods. In three sections, this thesis is a narrative about 1) encountering complex variation, 2) overcoming it with novel tools, and then 3) innovatively applying those tools to old and new questions. I first show examples of complex variation in a vaccine candidate (EBA-175) and a drug resistance gene (pfcrt) while reporting SNP based analyses of Kenyan and Tanzanian field isolates. While introducing this complex variation I also describe biological insights discovered in these populations. In Kenya I show evidence that chloroquine resistance selects for parasites that are primaquine sensitive, use a GWAS approach to discover new drug resistance loci, and catalogue variation in known resistance genes. In Tanzania I describe the population structure and allele frequencies of parasites from two geographic regions. In the second section of the thesis I develop methods for accessing complex variation and demonstrate their utility by producing de novo assemblies of eba-175, pfcrt, ama1, and msp3.4 from thousands of sequenced samples. Finally, in the third section I apply these tools in depth to eba-175. I comprehensively characterize the SNP and structural variation in eba-175 using an alignment of 1419 de novo assemblies. I use this resource to illustrate the profiles of positive selection across the gene, and corroborate these signals of balancing selection by showing the geographic distribution of the F/C indels and a lesser known 6bp indel positioned between the DBL domains. I then use the alignments to design Sequenom genotyping assays that facilitate a genome wide association study, testing for human associations with the eba-175 indels in the infecting parasite. I close by reporting a potential association on human chromosome 14 with the 6bp indel in eba-175.
Implied constitutional principles
Keywords: Ronald Dworkin
constitutional interpretation
living tree
implied bill of rights
rule of recognition
HLA Hart
judicial independence
parliamentary sovereignty
unwritten constitution
rule of law

This thesis challenges some of the current limits to the grounds for judicial review of legislation accepted by most Canadian jurists. More specifically, it makes a common law-based argument in favour of the priority over legislation of principles which are implied from the Imperial Constitution Acts 1867-1982 and which originally derive from the English constitution – namely implied constitutional principles. The argument faces two main interrelated legal objections: Parliamentary sovereignty and the Framers’ intentions. The first objection is rebutted by arguing that Parliamentary sovereignty possesses an ability to change in a way that can incorporate substantive legal limitations. The most prevalent common law-based theories of change to Parliamentary sovereignty suggest that the courts can authoritatively determine if implied constitutional principles can check legislation. The second objection is rebutted by reference to the notion of progressive interpretation as conceived under Hartian and Dworkinian theories of law and adjudication. Under these theories, progressive interpretation is an aspect of the courts’ best overall interpretation of the constitution, which includes implied constitutional principles. Such progressive interpretation can result in these principles constraining legislative authority.
Justification of the progressive interpretation of implied constitutional principles can be based on the rule of law from which derive a number of these principles. One plausible conception of the Canadian rule of law is that it rejects the view that implied constitutional principles can prevail when in conflict with legislation. However, the better conception is that, as an attempt to adapt implied constitutional principles to relevant changes in society and to protect their underlying values, the judiciary should interpret these principles as capable of checking legislation to the extent that they form part of the core content of the rule of law. Such a conception and an operation of implied constitutional principles can properly be explained by Hartian or Dworkinian common law-based progressive interpretation of these principles and by their relationship with legislative authority.
Breast cancer radiotherapy and heart disease
Keywords: breast cancer
cardiac toxicity
radiotherapy
radiation-induced heart disease

Introduction: Some past breast cancer radiotherapy regimens led to an increased risk of death from heart disease. Although heart dose from breast cancer radiotherapy has generally reduced over the past few decades, there may still be some cardiac risk. Estimation of future risk for women irradiated today requires both measurement of their cardiac dose and dose-response relationships, which depend on cardiac dosimetry of past regimens, in conjunction with long-term follow-up data. Methods: Virtual simulation and computed tomography 3-dimensional treatment planning on a representative patient were used to estimate mean heart and coronary artery doses for women irradiated since 1950 in 71 randomised trials in the Early Breast Cancer Trialists’ Collaborative Group (EBCTCG) overview. Patient-to-patient variability in cardiac dose was assessed. Heart and coronary artery doses were also calculated for breast cancer radiotherapy regimens used since the 1950s in Sweden. Cardiac doses from contemporary (year 2006) radiotherapy were assessed for 55 patients who received tangential breast cancer irradiation at a large UK radiotherapy centre. The maximum heart distance (i.e. the maximum distance between the anterior cardiac contour and the posterior tangential field edges) was measured for the left-sided patients, and its value as a predictor of cardiac doses assessed. Results: Mean heart dose for women irradiated in the EBCTCG trials varied from <1 to 18 Gray, and mean coronary artery dose from <1 to 57 Gray. Patient-to-patient variability was moderate. Mean heart dose for women irradiated in Sweden since the 1950s varied from <1 to 24 Gray, and mean coronary artery dose from <1 to 46 Gray. Heart dose from tangential irradiation has reduced over the past four decades. However, mean heart dose for left-sided patients irradiated in 2006 was 2 Gray and around half of them still received >20 Gray to parts of the heart and left anterior descending coronary artery. For these patients, maximum heart distance was a reliable predictor of cardiac doses. For the other patients, mean heart dose varied little and was usually less than 2 Gray. Conclusions: Cardiac doses from breast cancer radiotherapy can be estimated reliably and are now available for use in deriving dose-response relationships in the EBCTCG data and in a Scandinavian case-control study. Cardiac dose has reduced over the past four decades. Therefore the cardiac risk is also likely to have reduced. Nevertheless, for some patients, parts of the heart still receive >20 Gray in the year 2006.
Representing modular tensor categories: a computer algebra system for topological quantum computing
Keywords: quantum computing
physics
topological quantum computing
anyons
category theory
mathematics
computer science
modular tensor categories
2-Categories

Topological quantum computation (TQC) is a new fault-tolerant approach to quantum information, where computations are carried out by braiding particles called anyons. Anyons are quasiparticles that exist in 2 + 1 dimensions and are neither bosons or fermions. Modular tensor categories capture the structure of anyon systems and thus serve as models for topological quantum computation. However, program of using category theory to find higher-level structures and protocols has yet to be applied to TQC due to the difficulty of working with modular tensor categories. This difficulty could be greatly mitigated by the development of a computer algebra system to represent such categories. Thus, a computer algebra system for representing modular tensor categories within the symmetric monoidal 2-category 2Vect was developed.
A general representation for 2Vect is described. This involves extending basic linear algebra operations to handle matrices of zero-dimension and 2-matrices (matrices of matrices). Then, representations for the 0-cells, 1-cells, and 2-cells of 2Vect are found. Due to the chosen representation, various structural isomorphisms are required to ensure equations expected of 1-categories hold in the 2-categories setting. These structural isomorphisms are explicitly constructed.
In order to identify special categories, such as modular tensor categories, a diagrammatic language of monoidal categories is extended for 2-categories. This language is used to construct the axioms for these special categories within 2Vect. Finally, a way of implementing these axioms within 2Vect in the computer algebra system is described. This system will now be used for the investigation of higher-level structures within modular tensor categories to better understand the structure of topological quantum computing.
New mathematical models for splash dynamics
Keywords: matched asymptotics
splash jets
Fluid dynamics
impact theory

In this thesis, we derive, extend and generalise various aspects of impact theory and splash dynamics. Our methods throughout will involve isolating small parameters in our models, which we can utilise using the language of matched asymptotics.
In Chapter 1 we briefly motivate the field of impact theory and outline the structure of the thesis. In Chapter 2, we give a detailed review of classical small-deadrise water entry, Wagner theory, in both two and three dimensions, highlighting the key results that we will use in our extensions of the theory. We study oblique water entry in Chapter 3, in which we use a novel transformation to relate an oblique impact with its normal-impact counterpart. This allows us to derive a wide range of solutions to both two- and three-dimensional oblique impacts, as well as discuss the limitations and breakdown of Wagner theory. We return to vertical water-entry in Chapter 4, but introduce the air layer trapped between the impacting body and the liquid it is entering. We extend the classical theory to include this air layer and in the limit in which the density ratio between the air and liquid is sufficiently small, we derive the first-order correction to the Wagner solution due to the presence of the surrounding air. The model is presented in both two dimensions and axisymmetric geometries. In Chapter 5 we move away from Wagner theory and systematically derive a series of splash jet models in order to find possible mechanisms for phenomena seen in droplet impact and droplet spreading experiments. Our canonical model is a thin jet of liquid shot over a substrate with a thin air layer trapped between the jet and the substrate. We consider a variety of parameter regimes and investigate the stability of the jet in each regime. We then use this model as part of a growing-jet problem, in which we attempt to include effects due to the jet tip. In the final chapter we summarise the main results of the thesis and outline directions for future work.
Bismuth oxybromide-based photocatalysts for solar energy utilisation and environmental remediation
Keywords: environmental remediation
surface engineering
photocatalysis
semiconductor

This thesis reports the investigation of Bismuth oxybromide (BiOBr) semiconductor material as an efficient photocatalyst for the sunlight harvesting as well as environmental cleanup. I have utilised different synthetic methodologies to obtain BiOBr and its derivatives, such as co-precipitation, ultrasonification, and photo-deposition; and have studied their structural and optical properties by X-ray diffraction and surface analysis techniques. I report the synthesis and characterisation of two new p-n heterojunction systems, AgBr-BiOBr and BiOBr-ZnFe2O4, and have performed initial studies on photocatalytic reaction and their catalytic decomposition mechanisms. I have also reported the surface modification method including the deposition of noble metal on BiOBr to investigate the role played by the noble metal and the interactions between semiconductor and metal using various characterisation measurements. Furthermore, a continuous series of BiOBr-BiOI solid solutions were synthesised, characterised and the photocatalytic degradation was performed on the as-obtained semiconductors, to study the band structure properties of the solid solutions.
The construction of nationalist politics : the MHP, 1965-1980.
Keywords: Student Activism
Middle East
Religion
Nationalism
Turkey

This thesis presents an analysis of the political discourse and strategies of the MHP (Milliyetçi Hareket Partisi-Nationalist Movement Party) between 1965 and 1980. It particularly focuses on the role of young militants in the development of the nationalist movement in Turkey during this period. The 1960s and 1970s in Turkey saw military coups, street clashes, violence perpetrated by university students, and the rapid proliferation of civil organizations. Yet this turbulent period in modern Turkish history has received no systematic historical investigation. The MHP was one of the principal actors of this period. The study argues that the change in the profile of the CKMP-MHP leadership and the recruitment of young nationalist students, who became increasingly involved in physical confrontations with the socialists, had multiple effects on nationalist discourse and strategies. Retired soldiers involved in the 27 May 1960 military coup sought to develop a nationalist party based on secular-Kemalist principles, but those people who held conservative views of nationalism started to join the CKMP-MHP. The anti-Republican discourse of this current of thought involved the re-appropriation of Ottoman history and culture and certain religious themes into nationalist discourse. This ideological orientation appealed to most of young nationalists organized around the ülkü ocakları. However, the thesis demonstrates that there were various channels of ideological indoctrination in the nationalist movement, a diversity of positions that sometimes stirred conflicts among the nationalists themselves. The question of political strategy involved paradoxical aspects as well. Young nationalists were willing to take on the mission of becoming the future elites of the country yet were simultaneously involved in violent confrontations with socialists. Most of the party leadership, on the other hand, was preoccupied with parliamentarian goals and the long-term administrative success of nationalist activists in the state apparatus. The thesis shows that viewing the party activities and paramilitary operations in the same framework gave rise to serious tensions within the nationalist movement. The findings of this study also shed light on the institutional and ideological evolution of the nationalist movement after 1980.
Palladium-catalysed heterocycle synthesis 
Keywords: catalysis
heterocycles
palladium

Chapter 1 is a literature review of selected palladium-catalysed aryl C-N and C-S bond forming reactions. The application of these reactions to the synthesis of heterocycles is also discussed.
Chapter 2 highlights the importance of the benzimidazole motif and gives a brief discussion of the existing routes to this scaffold. The utility of N-(o-halophenyl)imidoyl chlorides and imidates as precursors to heterocycles is demonstrated in a palladium-catalysed reaction with N-nucleophiles to afford benzimidazole products.
Chapter 3 provides a brief introduction to the synthesis of benzothiazoles and describes efforts towards the use of our established substrates for the preparation of these heterocycles. This is achieved via reaction of N-(o-chlorophenyl)imidoyl chlorides with a sulfur nucleophile in a metal-free process.
Chapter 4 is a literature review of palladium-catalysed carbonylation chemistry with specific focus on aminocarbonylation and thiocarbonylation reactions of aryl halides. Heterocycle syntheses which employ such carbonylative methods are also discussed.
Chapter 5 describes existing protocols for the synthesis of quinazolinones. A novel palladium-catalysed synthesis of these heterocycles from the reaction of our imidate substrates with an amine and carbon monoxide is described. This further demonstrates their utility as general heterocycle precursors