VictorJuiz/thesis huggingface dataset:
Designing boron nitride nanotubes and their macroscopic assemblies via sacrificial templating
Keywords: BNNTs
atmospheric pressure CVD
buckypapers
nanotube assemblies
CNTs
carbon nanotubes
nanotube synthesis
boron nitride nanotubes
heteronanotubes
ammonia borane
boric acid
sacrificial templating

Hexagonal boron nitride nanotubes (BNNTs) have properties advantageous for the development of next generation materials and advanced composites that exhibit improved mechanical strength, high temperature resistance and thermal conductivity.
The future exploitation of BNNTs depends on the development of economically accessible and safe production methods. These should also present a scope for BNNT structural tunability, and output a high purity of BNNTs versus other possible hexagonal boron nitride (h-BN) structures. In this thesis, a novel synthesis technique is validated that is primarily motivated by a demand to address these issues.
Here, atmospheric pressure chemical vapour deposition (APCVD) is employed in conjunction with a safe and easy-to-handle compound, ammonia borane (H3N−BH3),to deposit h-BN coaxially onto the surface of multi-wall carbon nanotubes (MWCNTs). Subsequently, thermal oxidation is demonstrated to remove/sacrifice the MWCNTs, thereby leaving BNNTs as shells that exhibit diameter dependence on their MWCNT templates. By this method, BNNTs with walls 2-3 nm thick are synthesised, and nanotube outer diameters 16±2 nm and 40±16 nm are obtained using separate grades of MWCNT templates. The achieved BNNT diameter control exemplifies the versatility of MWCNT as a template material, which is justified by its structural compatibility to BNNTs, commercial scale availability and established morphological diversity. It is also argued here that use of H3N−BH3 precursor favours the van der Waals isolation of the deposited h-BN from the MWCNT template, which is advantageous for the h-BN purity of the BNNT shell.
The work presented here also establishes that the proposed APCVD and sacrificial templating method, when implemented in combination with vacuum filtration, is a novel and adaptable means of fabricating macroscopic assemblies of BNNTs. This is achieved at the cm-scale for BNNTs randomly entangled within a low density, self-supporting and sheet-like architecture with thicknesses <100µm. Furthermore, platelet crystals discovered on the surface of these BNNT assemblies, revealed to be boric acid, provide evidence in support of a new theory on the oxidation behaviour and moisture sensitivity of BNNTs.
Throughout this work, newly synthesised nanomaterials (non-assembled and assembled) are characterised by multiple techniques including electron microscopy, spectroscopy and thermogravimetry, in order to determine their qualities such as dimensionality, crystallinity, chemical composition and thermal stability.
The repair mechanisms of DNA damage induced by G-quadruplexes stabilisation in BRCA1/2-deficient cells
Keywords: small molecules
BRCA1/2
pyridostatin
G4s
DNA damage
olaparib
NHEJ
HR
DSBs
DNA-PKcs inhibitors
PARP inhibitors
G-quadruplexes

Mutations in the breast cancer type 1 or 2 susceptibility protein (BRCA1 or BRCA2 respectively) predispose to the onset of breast and ovarian cancer. Indeed, cells lacking homologous recombination (HR) rely mainly on error-prone mechanisms to repair DNA double-strand breaks (DSBs) and have an inherently increased sensitivity to replication stress. These defects can be exploited therapeutically with chemicals such as poly [ADP-ribose] polymerase (PARP) inhibitors. Among this family of inhibitors, olaparib has been approved by the Food and Drug Administration (FDA) in January 2018 as a maintenance treatment for breast cancer patients with BRCA defects. However, tumours ultimately develop resistance to olaparib treatment, stressing the need to develop new pproaches to target resistant tumours. G-quadruplexes (G4s) are thermodynamically stable secondary DNA structures resulting from the folding of guanine-rich DNA sequences. During replication, unresolved G4s due to small molecules stabilisation,can induce fork stalling, ultimately leading to DSBs formation. Among these small molecules, pyridostatin (PDS) has been shown to effectively stabilise G4 structures. In BRCA-deficient cells HR is impaired, thus PDS leads to DSBs accumulation and genomic instability. Surprisingly, we observed that DSBs induced by PDS could be repaired in BRCA2-deficient cells. We identified classical non-homologous end joining (cNHEJ) as a repair mechanism for PDS-induced DNA damage in our cell models including those with HR-deficient background using two chemical inhibitors of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a protein ensuring effective cNHEJ functions. Indeed, we described that PDS and DNA-PKcs inhibitors have a synergistic effect in BRCA-deficient cells. Furthermore, we showed that PDS-induced lesions seem retained longer in BRCA-deficient cells that have acquired resistance to PARP inhibitors via the loss of the p53 binding protein 1 (53BP1). Whether this is due to the roles of 53BP1 in regulating cNHEJ activity or end resection remains to be elucidated. In summary, our results provide new insights into G4 ligands-induced DNA damage and their repair in HR-defective models. This knowledge could be further exploited towards a new therapeutic approach to treat mutated BRCA carriers with breast cancer that have developed PARP inhibitors resistance.
The roles of BRCA2 in chromosome integrity
Keywords: BRCA2
cancer biology
DNA damage

High frequency of fork stalling and fork degradation are associated with DNA damage accumulation and represent key replication pathologies in cells lacking BRCA2. As a consequence, these cells enter mitosis with under-replicated DNA, which leads to interlinks between sister chromatids in anaphase. Failure to resolve these interlinks causes chromosome mis-segregation, aneuploidy and micronuclei. Here we show that BRCA2 loss leads to micronuclei formation, which triggers an innate immune response signalling via activation of the cGAS- STING pathway. However, cleavage of these interlinks by the MUS81 endonuclease activates mitotic DNA synthesis (MiDAS), thereby completing genome replication and ensuring correct chromosome segregation. Which genomic loci require BRCA2 for their replication and therefore become unstable upon BRCA2 inactivation remains unknown. Here we label mitotic nascent DNA and perform EdU-seq to monitor at high-resolution sites where MiDAS occurs in absence of BRCA2. Our findings reveal that loss of BRCA2 triggers MiDAS at 150 genomic loci, which map within regions replicating in early S phase and are therefore distinct from aphidicolin-induced common fragile sites. Our results suggest that BRCA2 inactivation causes replication failure at early-replicating genomic regions, a subset of which completes replication during mitosis.
My neighbour the Animalien: constructing Japanese national cultural identity from invasive alien animal species discourse in the 21st century
Keywords: banal nationalism
invasive alien species
Japan
TV
identity construction

In this study, I analyse the verbal and visual language used in Japanese mass media materials (newspaper pieces and a TV variety show) and state pamphlets to understand why the invasive alien animal as an Other persists despite decades of residency from a cultural angle, rather than ecological. As an example of banal nationalism, I examine this discourse for the languages in which 21st century national identity is expressed and constructed in terms of identity coordinates in space-time. With humans using these ‘animaliens’ as ‘space transformers’ and ‘time telescopes’ for self-reflection in their encounters, I find that invasive alien animals are also opportunistically used as props for teaching national cultural symbol literacy and the languages to express membership to the national culture. These languages are folklore, nostalgia and self-responsibility. Folkloric language turns individual self-exploratory fantasy spaces into nationalised exploratory fantasies. Nostalgia and self-responsibility languages build relationships with past and future-communities that serve the present. The alien animals’ Othering persists because it is useful to the majority. This approach to animaliens fills a literature gap where the human cultural coexistence with these animals has been largely ignored in favour of conservation biology.
Incorporation of biological factors in radiation therapy treatment planning
Keywords: feasibility seeking
double strand breaks
particle therapy
inverse problem
dose volume constraints
radiobiology
radiotherapy
proton therapy

Radiation therapy plays a crucial role in the treatment of cancer. Major developments in the field, including 3D tomographic imaging, intensity modulation and novel particle modalities, have all contributed to iterative improvements in precise dose delivery. These advances have enabled highly conformal tumouricidal dose deposition with improved healthy tissue sparing. Proton therapy, in particular, has become an increasingly adopted modality due to its favourable depth-dose profile, allowing for much of the dose to be localised within the target region, with virtually no dose leakage to tissues beyond the target. However, physical dose does not tell the full story; radiobiological mechanisms and their intermodality differences must be well-understood, as these explain the processes by which the energy deposited in cells leads to cell death and, ultimately, to clinical outcomes.
Densely ionising particle tracks offer an enhanced cell killing efficiency over x-rays, which may be quantified through the relative biological effectiveness (RBE). The RBE is a multiplicative factor converting the proton dose to an x-ray dose equivalent that yields the same biological endpoint. In standard clinical practice a constant RBE of 1.1 is used, assuming protons are 10% more effective than x-rays for the same dose, though recently there has been an increased focus on more sophisticated, variable RBE models. Many decades of clinical experience with x-rays enables RBE-weighted proton dose planning under a familiar framework. The dose is shaped according to both absolute and volume-based tolerance doses. Although, in many modern treatment planning systems, dose-volume constraints (DVCs) are approximated as their exact formulation poses a non-convex optimisation problem.
This thesis proposes novel methods and recommendations for the inclusion of radiobiological factors in treatment planning through (1) a variable but pragmatic RBE model based on DNA double strand break induction, and (2) a flexible, projection-based inverse planning algorithm, suited to non-convex settings, that comprehensively addresses dose-volume effects through the exact modeling of DVCs. This author hypothesises that inclusion of these strategies will enable confident and effective treatment planning not only in terms of physical dose deposition but, crucially, in biological effect.
Concert governance: how informal intergovernmental organizations orchestrate global governance

Keywords: G7
IIGO
rising powers
global public goods
international institutions
G20
money laundering
transgovernmentalism
concert diplomacy
orchestration
technology
financial regulation
global governance

Concert governance is a defining feature of contemporary international organization: just as the Concert of Europe shaped 19th century international politics, informal intergovernmental organizations (IIGOs) like the G7 and G20 steer 21st century governance of global issues ranging from financial stability to technology regulation. States use IIGOs to govern indirectly by leveraging their collective power and influence to orchestrate other international institutions. Even though the field explores why states choose informal intergovernmentalism, how IIGOs orchestrate global governance has not yet received systematic attention.
In this thesis, I study IIGO orchestration through a series of interrelated research articles. I first identify the international origins of IIGO orchestration, highlighting the increased international issue complexity and state actor heterogeneity as key factors. I then examine the governance logic of IIGO orchestration, which walks a fine line between exerting control over the multilateral system and undermining the competence of the universal organizations that form its bedrock. I establish theoretically that IIGOs can manage this balance through strategic regime design and show empirically that the G7 and G20 embed universal organizations in differentiated regime complexes to govern cross-border regulatory challenges. Finally, I analyze the organizational foundations of IIGO orchestration, which raise questions about the limits of informality for supporting the expansive state interactions that accompany the orchestration of global governance. I theorize IIGOs’ functional scope and illustrate how the G20 adapted organizationally as it graduated from a crisis management vehicle to a global steering body.
By expanding the frontier of scholarly knowledge on IIGOs, the thesis also contributes more broadly to the study of indirect governance, regime complexity, and international institutions. While IIGO orchestration is consolidating as a pillar of global governance, this thesis provides a reference for academics and policymakers looking to study and shape multilateral responses to critical and emerging global issues.
The predictive view of Bayesian inference
Keywords: Bayesian nonparametrics
Bayesian bootstrap
marginal likelihood
predictive inference

This thesis considers the direct connection between the prediction of future observations and Bayesian inference. Using prediction as a guide, we generalize the Bayesian framework and introduce new methodologies for parameter inference and model selection which improve scalability and performance under model misspecification.
We begin with an introduction in Chapter 1 on methodologies for generalizing Bayesian inference, including the Bayesian bootstrap and general Bayesian updating. A summary of the current role of prediction in Bayesian inference is then provided.
In Chapter 2, we present a novel perspective on Bayesian inference which points to missing observations as the source of statistical uncertainty. We formally connect the Bayesian posterior on the parameter with the joint predictive distribution on the unobserved remainder of the population. Using this connection, we introduce the martingale posterior, which generalizes the Bayesian posterior. The martingale posterior only requires the elicitation of a predictive model, thus removing the need for the likelihood and prior. We discuss notions of predictive coherence and further introduce new nonparametric predictive models based on a bivariate copula update.
In Chapter 3, we investigate the computational benefits of Bayesian nonparametric learning using the Dirichlet process. This is closely related to the Bayesian bootstrap and is a special case of the martingale posterior. We find that the method is robust to model misspecification and is highly scalable due to its parallelizable nature. We further demonstrate that the posterior bootstrap, which approximately samples from the nonparametric posterior, is particularly proficient at targeting multimodal posteriors.
In Chapter 4, we introduce a notion of coherent model scoring under general Bayesian updating. We then explore the formal connection between the Bayesian marginal likelihood and cross-validation, and introduce a cumulative cross-validation score which alleviates some of the deficiencies of the marginal likelihood.
We provide a summary and discussion of future work in Chapter 5.
Learner strategies when listening to teacher talk in EMI settings
Keywords: L2 listening strategies
listening strategies
listening abilities
learner strategies
self-regulation
EMI

As English Medium Instruction (EMI) is becoming widespread in both secondary and higher educational settings, listening to the teacher speaking in English becomes an everyday task for many students who are taught mainstream curriculum subjects in their second language (L2). The strategies students use during such a listening task are of importance for teaching practitioners aiming to enhance learners’ comprehension of academic content in English. This mixed-methods study looks at L2 strategies used by EMI upper-secondary students (N = 20) of B2-C2 Common European Framework of Reference (CEFR) proficiency levels when listening to teacher talk. It explores which strategies learners use when they begin EMI, whether their strategies differ according to listening abilities, and whether strategies develop or change over a six-month period of EMI exposure. The data have been collected from a questionnaire, a lesson observation, and follow-up interviews at two time points. The findings show a wide variety of strategies and two most common strategy combinations deployed by the participants. No statistically significant correlation between strategy use and listening abilities has been found; however, differences in approaches to note-taking and summarisation/appropriation between participants with lower and higher listening abilities have been detected. Some development in strategy use over time has been recorded. The implications for teaching strategies are discussed.
(Not)withstanding minority rights: re-thinking Canada's notwithstanding clause
Keywords: notwithstanding clause
the override
Canadian Charter of Rights and Freedoms
Section 33
minority rights

On October 22, 2018, Ontario Premier Doug Ford announced that he would be using the Canadian Charter of Rights and Freedoms notwithstanding clause to override an Ontario Superior Court decision which held that his government’s municipal election legislation was unconstitutional. Ford went so far as to say that he ‘won’t be shy’ about using the clause in the future. Several months later, Quebec Premier Francois Legault used the notwithstanding clause in legislation to ban the wearing of religious symbols in public service roles. The recent actions of both Ford and Legault reignited the debate over the notwithstanding clause, upon which current scholarship is dominated by discussions of balance of power between the legislative and judicial branches. In this paper, I argue that the current scholarship that focuses primarily on the relationship between the courts and legislatures, overlooks the threat the notwithstanding clause poses to constitutional minority rights protections. Ford’s threat and Legault’s use of the notwithstanding clause reveal the ways in which minority rights are uniquely vulnerable to the current Canadian constitutional structure and must be further examined.
The impact of genetic drift on the distribution and uses of linkage disequilibrium
Keywords: statistics
genetics

With the advent of Genome Wide Association Studies (GWAS), researchers have gained unprecedented access to data in order to examine associations between variants and complex traits and diseases. To analyze these studies, researchers have typically utilized measurements of Linkage Disequilibrium (LD) from the GWAS population or from a reference population which may be genetically drifted relative to the GWAS. However, these measurements are only point estimates and thus, do not capture the stochastic nature of forces such as recombination and genetic drift. Moreover, point estimates from reference populations do not take into consideration errors and inconsistencies in the ancestral composition between the reference and GWAS population. Therefore, in this thesis, we instead model LD as a distribution and demonstrate the extent to which statistical genetic applications can be improved in terms of their robustness and calibration by modelling uncertainty in LD.
First, we characterise the distribution of LD and demonstrate that genetic drift between populations can result in a high degree of variation of the measurements of LD. Additionally, we demonstrate that this variation leads to variation downstream within the accuracy of statistical genetic applications including summary statistic imputation and fine-mapping.
Secondly, to generate LD measurements in a genetically drifted population, we use a reference population and weight the individual reference haplotypes. We demonstrate how repeatedly sampling these weights provides a process to obtain the distribution of LD in the drifted population and how the weights can be updated in a marginal fashion.
Thirdly, using GWAS summary statistics and a reference population, we derive a Maximum Likelihood Estimate (MLE) which infers both the level of noise in the GWAS population as well as the drift between the GWAS and the reference population.
Lastly, we show that by repeatedly updating the weights on our reference haplotypes while incorporating GWAS summary statistic data leads to a method to infer the in-sample distributions of LD from a GWAS. The benefits of our approach over using LD obtained from a reference population is illustrated in the context of fine-mapping admixed populations.
We end by discussing more sophisticated methods for generating our weighted reference haplotypes, the ability to leverage distributions of LD in statistical genetic applications and the effective and efficient data sharing of LD distributions.
Intentional community: a qualitative analysis of social organization in a mixed-income neighborhood
Keywords: social capital
mixed-income
housing

Mixed-income housing policy initiatives in the United States have attempted to reduce the social disorganization associated with concentrated urban poverty. Using a Portland, Oregon HOPE VI project as a single case study site, this thesis examined how residents’ socio-economic status, correlated closely with tenure, informed neighborhood choice, social networks, social exchange and informal social control. The latter three concepts underpin collective efficacy for children, which provided the theoretical framework for this thesis. Research methods relied on 42 in- depth interviews with parents and adolescents from rented and owned homes, 10 in-depth interviews with Housing Authority of Portland staff members and neighborhood observation over a span of four months. The study revealed differences between lower-income renters’ and higher-income owners’ framing of neighborhood choice; these frames informed subsequent approaches to social ties, social exchange, and informal social control in the neighborhood.
Parents’ social networks typically did not span across tenures but adolescents’ networks were more flexible; families’ varied use of Portland’s school choice program influenced the nature of these ties and other elements of social organization in the neighborhood. Institutional resources, in the form of staff employed in youth services and community building efforts, were particularly important to social capital activation among renter families. Finally, governance forums and public spaces informed territoriality in the neighborhood and the related perception of boundaries between rented and owned households. The theoretical implications of this research relate to the utility of mixed-income housing policy as a tool for poverty reduction, as well as how social dynamics are informed by socio-economic status and delineated by physical space.