VictorJuiz/thesis huggingface dataset:
Privacy: a political approach
Keywords: privacy
privacy policy
privacy and democracy
history of privacy
concept of privacy

This thesis is concerned with two central questions on the subject of privacy: (1) how should we conceptualize privacy? And (2), on what basis can laws and regulations to protect privacy be justified? The goal of this thesis is to provide an account of privacy that is both more persuasive than existing accounts and more capable of meeting the challenges to privacy in the modern day.
The first part of the thesis advances the argument that privacy is a normatively dependent concept. A normatively dependent concept is defined as a concept that relies on outside normative frameworks for its meaning or value. This thesis argues that privacy has this quality because it exists in a relationship of opposition to “the public” and thus lacks any essential characteristic other than being not-public, not-visible, or not in the common view. An examination of four historic reformulations of what it means to be private, spanning two thousand years of western history, confirms that privacy has shifted considerably over time and that attempts to essentialize it are misplaced. In addition, the modern disarray of the privacy debate—characterized by deep disagreement over both the definition and the purpose of privacy—reflects privacy’s normative dependence and in particular reveals our over-reliance on liberal-individualist conceptions of privacy that wrongly prioritize consent and control.
The second part of this thesis argues for adopting a wholly new approach to understanding privacy: the political approach. More specifically, this thesis argues for abandoning traditional liberal frameworks in favor of demonstrating how privacy supports central features of modern democracies, such as the ability to form a distinct political identity, the right to free expression, and the right of free assembly. Furthermore, this thesis argues that democracy even presupposes an “epistemic veil” of privacy around citizens, which motivates the practices of deliberation and voting. It can thus be shown that a commitment to democracy entails a commitment to certain privacy rights—a finding that circumvents the difficulty in establishing a common basis for privacy protections by appealing to all citizens who live under democratic regimes. In abandoning familiar understandings of privacy, the political approach to privacy does away with the problematic emphasis on consent, adapts privacy to an ever-changing surveillance environment, addresses prominent critiques of privacy rights, and provides a common basis of justification for future privacy legislation.
Protein folding investigated by NMR spectroscopy
Keywords: small heat-shock proteins
NMR spectroscopy
protein folding
molecular chaperones

Proteins are biological molecules that perform diverse cellular roles, including metabolizing energy sources to regulating the acidity of blood. The collective actions of proteins and their interactions with nucleic acids at the molecular level enable life at the macroscopic level. If protein folding is delayed or has faltered, unwanted associations between exposed hydrophobic amino acids can lead to cytotoxic protein aggregation, which is implicated in diseases such as Parkinson’s, Alzheimer’s, and type II diabetes. However, cells have armed themselves with an evolutionarily conserved defense mechanism to combat protein misfolding: a class of proteins known as molecular chaperones that can recognize misfolded, aggregation-prone proteins and either correctly refold them or target them for degradation and recycling.
The focus of this thesis is to understand aspects of protein folding and the activity of molecular chaperones at the atomic level. Nuclear magnetic resonance (NMR) spectroscopy methods have been applied to characterize the molecular chaperone HSP27. My results reveal that HSP27 locally unfolds upon monomerization and becomes highly active. Further, I characterize a single amino acid variant of HSP27 implicated in the onset of Charcot-Marie-Tooth disease, a commonly inherited motor neuropathy, and find to be devoid of chaperone activity, while also forming oligomers that are significantly larger than the wild-type protein.
Rapid pressure-jump NMR experiments are developed and deployed to monitor protein folding with millisecond resolution via the protection from solvent exchange. These data provide insight into the folding mechanism of a pressure-sensitized variant of ubiquitin. The extent of cis-proline formation is characterized in unfolded proteins with NMR, and the degree of polypeptide collapse in low denaturant conditions is probed by translational diffusion. Finally, the accuracy and precision of Carr-Purcell-Meiboom-Gill relaxation dispersion, a powerful NMR method to investigate transiently populated folding intermediates, is analyzed in the presence of limited input data.
Applications of single-cell Raman microspectroscopy in bacteria metabolism and physiology
Keywords: Raman spectroscopy
Single cell
Bacteria metabolism

Bacteria play important roles in almost all ecosystems, including the natural environment and the human body, and they are extremely abundant and versatile. New generations of sequencing technologies can provide phylogenetic diversity and metagenomic profiling of microbial communities, but metabolic functions of individual microbes and their molecular mechanisms are often elusive, owing to the limited culturability and the complexity of microbial communities.
Single-cell Raman microspectroscopy (SCRM) is label-free vibrational spectroscopy that measures a collection of molecular vibrations coming from all biomolecules in a single bacterial cell. This thesis emphasises the capabilities of SCRM in a wide spectrum of applications for investigating bacterial metabolism and physiology. SCRM is applied to study bacterial phenotypes in a symbiotic setting with a plant host. SCRM is combined with deuterium-isotope-probing (DIP) and applied to study carbon metabolism in pure cultures, as well as in vivo metabolic adaptations by human-invasive pathogens. Especially, the power of single-cell analysis in studies of heterogeneous bacterial populations is explored and highlighted.
This thesis also outlines an analytical pipeline to standardise and automate the process of spectral analysis in SCRM studies, from data tidying and data preprocessing to a variety of analytical approaches for either exploratory or diagnostic purposes. By following the established pipeline and executing the developed programming script, single-cell Raman analysis can be performed in a simple and rapid manner.
To conclude, by applying SCRM to provide intrinsic biochemical fingerprints of individual bacterial cells and connecting SCRM with the power of computational analysis, this thesis provides the possibility of probing bacterial metabolism and physiological states in ever-changing and multifaceted ecological settings.
Understanding the effects of a large development sector on the labour market of a small low-income country: Evidence from Sierra Leone
Keywords: Foreign aid
Labour markets
Sierra Leone
Development sector

This thesis examines the effects of a large and ever-present development sector on the labour market of aid-dependent low-income countries, using Sierra Leone as a case study. The thread that connects the substantive chapters of this thesis is the positioning of the development sector as a third sector in the labour market. Alongside the public and private sectors, the development sector is also an employer and skills developer in host-countries. Embedding the development sector as a sector in itself, makes apparent a channel of aid transmission in the domestic economy, via the labour market - a channel that is often overlooked in both academic and policy discourses. This in turn brings to the debate the short-term and the long-term effects on the labour market of host-countries. The thesis is novel as it applies analytical methods that are primarily used in the economics discipline, to the types of questions which sit within critical development studies.
The main findings are that the presence of a large development sector affects occupational choice of graduates and the skills available in the labour market. These effects interplay with: (i) cognitive ability of graduates – higher ability graduates are more likely to choose employment with a donor organisation, non-governmental organisation or international non-governmental organisation; (ii) patronage in the labour market – in low trust environments where patronage exist in the labour market the development sector emerges as a more transparent recruiter and thus attracts talent; and (iii) skills training programmes at vocational and university levels have been directly affected by donor policies and actions. This process of change in the labour market and skills composition is important in itself; but there are also potential implications for sustainable home-grown growth and continued aid dependence.
Business power in the making of social policies: the case of old-age pensions in Chile, 1973-2017
Keywords: economic elite
business
Latin America
social policies
power

The 1980-1981 reform to the pension system in Chile represents the most notable case of pension privatisation as it pioneered private-oriented pension reforms worldwide. After almost four decades since its inception, the main pillars of this old-age pension system remain largely intact in spite of significant insufficiencies such as low effective coverage and low benefits. Hence, this dissertation aims to explain, in the first place, why and how pension privatisation took off during the authoritarian regime (1973- 1990). Secondly, it seeks to address the question of why the scheme has proved so resilient during thirty years of democracy dominated mostly by centre-left administrations, growing public opposition and increasing electoral competition. In so doing, this work combines a long-term historical approach (stretching back to the early 1960s) with an in-depth analysis of five pension policymaking processes developed during the 1973-2017 period. The research is based on extensive archival research and more than ninety interviews with key informants. In this context, I argue that in order to have a more accurate picture of the system’s inception in 1981 and the subsequent lack of paradigmatic changes in democracy, we need to pay more attention to the role played by the economic elite as a whole and by its different segments. Among other findings, this thesis shows the significance of including in the analysis ideational elements of power, which have been overlooked so far in the literature on business politics. Specifically, I show the significant influence of long-term, strategic investments carried out by the economic elite in order to avoid the overt exercising of power -which usually entails high costs and risks- through the dissemination of dominant ideological frameworks. At a more empirical level, this research shows the extraordinary adaptive capacity of the Chilean economic elite throughout the period under analysis. Through a vast repertoire of sources of power, this group has been able to overcome different challenges from below and safeguard their minority interests.
Investigating the effects of autophagic perturbations on mitochondrial function in Parkinson’s Disease
Keywords: mt-mKeima
Autophagy
Mitophagy
Mitotimer
Parkinson's Disease
Alpha synuclein

Parkinson’s disease is among the fastest growing neurodegenerative disease, projected to impact over 12 million individuals worldwide by 2040. Though extensive research has identified that alpha-synuclein, a canonical Parkinson’s disease gene, impacts proper autophagy and mitophagy, its exact role in the pathogenesis of the disease remains contested. This thesis aims to develop an assay for measuring rates of mitophagy in vivo and to use that assay to understand how alpha-synuclein impacts rates of mitophagy.
The fluorescent protein MitoTimer is trafficked to mitochondria where it displays a time-dependent fluorescent profile. Though this temporal profile was robust, a single pulse of expression did not recapitulate prior reports of sensitivity to oxidative stress; rather, observed changes correlated more strongly with cell death. An alternative double-pulse protocol did not detect any changes in mitochondria following FCCP treatment. Together, these data suggest that MitoTimer is not ideal for measuring rates of mitophagy.
mt-mKeima revealed accumulation of acidic puncta over time, indicating active basal mitophagy. This basal mitophagy was inhibited by autophagic inhibitors (wortmannin, VPS34IN1) and increased by autophagic activators (rapamycin, torin). Overexpression of alpha-synuclein appeared to decrease rates of mitophagy, though the effect did not reach statistical significance. Assays in patient-derived, iPSC dopaminergic neurons carrying a triplication in alpha-synuclein revealed decreased levels of MFN2, indicative of increased rates of mitophagy. Furthermore, treatments with MLi2, a LRRK2 inhibitor, appeared to recover this phenotype. Overall, these data indicate that alpha-synuclein impacts strongly on rates of mitophagy, though the effect varies by model, and that LRRK2 inhibition may have therapeutic potential for Parkinson’s disease.
Would-be great powers, status, and stigma: the case of Brazil, 1970-1979
Keywords: Great Powers
Status
Brazil

This thesis critically engages the dominant theoretical account of would-be great power status-seeking behaviour in International Relations (IR), namely Larson and Shevchenko’s social identity theory (SIT) framework. This critical engagement involves bringing the SIT framework into dialogue with a literature that it has hitherto neglected: the emerging scholarship on stigma in IR. Through this dialogical synthesis, I make two theoretical arguments. First, I argue that the SIT account of would-be great power status-seeking has theoretically overemphasised the extent to which these states strive for ‘positive distinctiveness’ because of their ‘need for distinctive identities’ in their quest for higher status. This overemphasis has overshadowed another crucial drive animating these states’ attempts to move up the international pecking order. I contend that this has led to neglect of the other principal motive, which I draw from the literature on stigma, relating to desires by these actors to be seen and accepted as ‘normal’. Thus, in contrast to the one-dimensional account offered by the dominant SIT framework, I suggest that would-be great power status-seeking is Janus-faced, animated both by a desire to be positively distinct and by attempts to be seen and accepted as ‘normal’. I develop a new conceptual framework to account for this dualistic conception of status. Second, I attempt to theorise the effects that being stigmatised as ‘underdeveloped’ has on would-be great powers’ quest for higher status. I suggest that being stigmatised as such makes these states extremely wary, bordering on paranoid, of any sort of relationship of political and economic dependence, and that this mindset powerfully shapes their quest for higher standing in world politics. I substantiate these claims using original archival research based on Brazil’s near-brush with great power status in the 1970s in the face of underdevelopment.
The genomics of diversification in South Pacific Silvereyes (Zosterops lateralis)
Keywords: Silvereye
Divergence
Genomics
Natural selection
Diversification
Bird
Genetic drift
Speciation
Adaptation
Genomic landscape

Speciation is a dynamic process, shaped by interactions among different evolutionary mechanisms including natural selection, genetic drift, gene flow, and mutation. Over 150 years since the publication of ‘On the Origin of Species’ a major challenge in evolutionary biology is to determine the relative importance of these different mechanisms in the speciation process. In the era of genomics, a step towards addressing this challenge is to study the progression of speciation at the level of the genome. Using island colonisations by the silvereye (Zosterops lateralis), in this thesis I investigate the roles of gene flow, selection and drift in shaping patterns of divergence at both the genomic and phenotypic level. In Chapter 2, using populations where divergence timeframes and gene flow histories are known a priori, I documented how genomic patterns accumulate as populations progress along the speciation continuum. This chapter challenges the ubiquity of existing verbal models that explain the accumulation of genomic differences via the growth of genomic islands and instead supports the idea that divergence both within and outside of genomic islands is important during the speciation process. In Chapter 3, using the recent sequential colonization of south Pacific islands by the Tasmanian silvereye subspecies I provide the first assessment of how patterns of genomic divergence are shaped by the stochastic effects of drift following population founding. By tracking divergence across the genome, I demonstrate that population founding has an idiosyncratic effect on the buildup of divergence. In Chapter 4, using the human- mediated introduction of the silvereye to French Polynesia, I assess the role of drift and selection in driving rapid morphological change following the establishment of new populations. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, but the magnitude of these changes are not large enough, considering effective population sizes, to require directional natural selection to explain them; instead drift alone is a sufficient explanation at the phenotypic level. However, identification of outlier loci at genes previously identified as candidates for bill size and body shape, also suggests selective processes are operating within this population. As a whole, this body of work furthers understanding of how different evolutionary mechanisms shape patterns of divergence at the level of the genome and how divergence unfolds following the establishment of new populations.
Route boundary inference with vision and LiDAR
Keywords: curb detection and inference
scene understanding
lateral localisation
deep learning
road segmentation
road boundary detection

The purpose of roads is to carry vehicles. Human drivers can easily distinguish roads and their components (e.g., surfaces, boundaries) using direct and indirect (contextual) clues as they are designed with driving in mind. The colour of road tarmacs, shape of road turns, smoothness of road surfaces, traffic signs, road boundaries, buildings, or even other vehicles provide clues about roads. For autonomous vehicles to safely navigate to a desired location in complex driving scenarios they are required to perceive their surrounding environment even in the presence of occlusions. This requires the use of contextual information in a similar fashion to human perception.
In this thesis, we focus primarily on road boundary detection and present a deep learning based approach to capture contextual information for dealing with occlusions. Many scenes present large-scale occlusion by other road users, preventing direct approaches from fully detecting road boundaries. Conventional neural network architectures fail to infer the exact location of an occluded, narrow, continuous curve running through the image. We tackle this problem with a coupled approach that generates multi-scale parameterised outputs in a discrete-continuous form. We combine the power of deep learning with the data obtained from our novel annotation framework to detect and infer road boundaries irrespective of whether or not the boundaries are visible by taking inspiration from human perception, which uses contextual information to perceive beyond the visible spectrum. Our semi-supervised data annotation framework leverages visual localisation and facilitates the use of deep networks by providing an efficient way to generate thousands of training samples. We present two road boundary detection approaches, camera-based and LiDAR-based, that capture scene context and achieve accurate results. We also demonstrate that the presented approaches have utility in scene understanding and localisation.
Between integrals and optima: new methods for scalable machine learning
Keywords: First-Order Optimization
Approximate Bayesian Inference
Gradient Estimation

The success of machine learning is due in part to the effectiveness of scalable computational methods, like stochastic gradient descent or Monte Carlo methods, that undergird learning algorithms. This thesis contributes four new scalable methods for distinct problems that arise in machine learning. It introduces a new method for gradient estimation in discrete variable models, a new objective for maximum likelihood learning in the presence of latent variables, and two new gradient-based differentiable optimization methods. Although quite different, these contributions address distinct, critical parts of a typical machine learning workflow. Furthermore, each contribution is inspired by an interplay between the numerical problems of optimization and integration, an interplay that forms the central theme of this thesis.
Abolishing franking credit refunds: evidence from an event study
Keywords: Dividend taxation
Franking credits
Company tax
Corporation tax
Dividend imputation
Event study

Competing asset pricing models offer different predictions on whether dividend taxes affect share prices. This thesis conducts an event study of the announcement of a reform to Australia’s dividend imputation system. The reform would have abolished refunds to taxpayers with excess franking credits, which would have had the effect of raising taxes on dividends paid to domestic shareholders. The results provide no evidence that the announcement reduced share prices.
TEX264 in DNA replication and genome stability
Keywords: DNA repair
DNA replication
DNA-protein crosslinks

DNA damage drives numerous human pathologies, including cancer and ageing. However, it can also be exploited in cancer therapy, where most chemotherapeutics exert their effects by inducing DNA damage. A common type of DNA lesion induced by chemotherapeutics is DNA-protein crosslinks (DPC). DPCs are also very common endogenous DNA lesions which impede DNA replication, transcription, and mitosis. However, very little is known about the mechanisms by which they are repaired.
Our laboratory recently characterised a genetic syndrome, known as Ruijs-Aalfs syndrome (RJALS), characterised by premature ageing and early onset hepatocellular carcinoma, caused by mutations in the SPRTN gene. This thesis contributes to the characterisation of SPRTN as an essential DPC repair protease that promotes DNA replication progression.
We identify topoisomerase 1 cleavage complexes (TOP1cc) as SPRTN substrates. TOP1ccs are composed of the enzyme, TOP1, covalently bound to DNA. TOP1ccs are highly cytotoxic endogenous lesions which can also be induced by the frontline class of anti-cancer drugs known as camptothecins. In addition, we identify the previously uncharacterised protein, testes expressed 264 (TEX264), as being critical for TOP1cc repair. TEX264 recognises unmodified and SUMO1-modified TOP1 and promotes TOP1cc repair by recruiting p97 and SPRTN. Thus, TEX264 promotes DNA replication fork progression and preserves genome stability. Furthermore, this study identifies SPRTN as a biomarker of clinical resistance to the camptothecin derivative, irinotecan, in patients with metastatic colorectal cancer.