VictorJuiz/thesis huggingface dataset:
Derivative-free algorithms for nonlinear optimisation problems
Keywords: derivative-free optimization
nonconvex optimization
trust region methods

Minimising a nonlinear function is a ubiquitous problem in applications, and standard algorithms need accurate evaluations of the function and its derivatives. However, if the function is black-box, expensive to evaluate, or noisy, it may be impractical or even impossible to obtain accurate derivatives, and we require derivative-free optimisation (DFO). Model-based DFO methods perform well in practice, taking many features from derivative-based methods, but can have lower performance for noisy problems and a high linear algebra cost. In this thesis, we aim to improve the flexibility, robustness and scalability of state-of-the-art methods for model-based DFO by designing, analysing, implementing and comprehensively testing three new algorithms for nonlinear optimisation, with a special focus on nonlinear least-squares problems (such as parameter fitting).
The first, DFO-LS, is designed for nonlinear least-squares problems, and is simpler than existing methods, constructing linear residual models with a flexible approach. DFO-LS can benefit from a reduced initialisation cost, and has improved scalability and runtime over existing methods without a performance penalty. DFO-LS also has features for noisy problems, including a novel multiple restarts mechanism, which are low cost in evaluations and linear algebra, giving DFO-LS better performance compared to existing techniques for handling noise.
We then introduce Py-BOBYQA, an extension of BOBYQA (Powell, 2009) with a similar multiple restarts mechanism to DFO-LS, amongst other new enhancements. It matches or outperforms BOBYQA and other state-of-the-art solvers on both smooth and noisy problems. We also propose a simple extension of Py-BOBYQA that may enable it to escape local minima and progress towards the global optima.
Lastly, we introduce, for large-scale nonlinear least-squares problems, DFBGN, the first model-based DFO method to optimise in low-dimensional subspaces at each iteration. DFBGN has lower linear algebra costs, improved runtime, and hence improved performance on large-scale problems than DFO-LS, as it can perform many more iterations within a reasonable runtime limit. It can also make progress under very small evaluation budgets, with a low runtime cost.
Computational mechanisms of moral inference
Keywords: moral character
person perception
Bayesian inference
computational psychiatry
impression formation

Accurately inferring the moral character of others is crucial for avoiding social threats. Putatively “bad” agents command more attention and are identified more quickly and accurately than benign or friendly agents. Such vigilance is adaptive but can also be costly in environments where people sometimes make mistakes, because incorrectly attributing bad character to good people damages existing relationships and discourages forming new ones. Evolutionary models demonstrate that responding to wrongdoers with probabilistic forgiveness can facilitate the evolution of cooperation, but the cognitive mechanisms that enable the implementation of forgiving strategies are unknown. In this dissertation, I explore these mechanisms using novel methods derived from computational science, social cognition, and behavioral economics. Part I of the dissertation demonstrates that moral inference is described by an asymmetric Bayesian updating mechanism, where beliefs about the morality of bad agents are more uncertain (and therefore more amenable to updating) than beliefs about the morality of good agents. The model and data reveal a cognitive mechanism that rapidly discounts prior expectations to permit flexible updating of beliefs about potentially threatening others, a mechanism that could facilitate forgiveness when initial bad impressions turn out to be inaccurate. Part II of the dissertation considers the consequences that ensue when these mechanisms break down. Disruptions in learning and decision-making lie at the heart of many populations characterized by maladaptive social functioning. Consequently, I examine moral inference in two populations associated with interpersonal disturbances: individuals exposed to community violence and patients with Borderline Personality Disorder. The data reveal novel cognitive processes that may explain the emergence of maladaptive behavior related to chronic exposure to violence and Borderline Personality Disorder. Collectively, the results in this dissertation provide insights into the computational mechanisms of moral inference and their role in adaptive and maladaptive social functioning.
The political economy of free zones in the GCC
Keywords: Commercialized rents
Duqm
Trade
Dubai
Neom
Investment
Jebel Ali
economic cities
Special Economic Zones

Free zones (FZs) in Gulf Cooperation Council (GCC) countries displayed substantial variation in the timing, scale, and scope of development between 1985 and 2017. This dissertation argues that the utilization of FZs as political instruments – both domestically and internationally – is critical for understanding FZ development outcomes in the region. The work tests this hypothesis using a comparative analysis of FZ development cases structured along three analytical dimensions: hydrocarbon dynamics, elite relationships, and global competition. Field visits to 44 of the 51 FZs observed in the work, 77 interviews with government and business officials associated with FZ development, and an extensive collection of primary source materials provide the data for this study.
As the first political economy analysis of the GCC’s FZ system, this research employs a qualified version of rentier state theory (RST) and a new conceptual categorization of rents associated with FZs – described in this work as commercialized rents. The concept builds upon existing scholarly applications of RST in the GCC by revealing previously unexplored rentier structures and the embeddedness of local and international elites in non-hydrocarbon development processes. Other aspects of FZ development trajectories, however, qualify RST’s ability to comprehensively account for economic development initiatives in the region.
The subsequent findings reveal that both resource-scarce and resource-abundant territories across the region employed FZs to generate rents, encourage rent-seeking behavior, and accomplish other political objectives. The specific trajectories of FZ development depended upon domestic, regional, and international factors, which could constrain or encourage FZ proliferation as well as shape FZ policies in a given territory. The work provides an academic foundation for future studies on FZs in the GCC and a broader methodological framework for researchers seeking to unpack the political economy of FZs in other countries and regions.
In-vacuum roll-to-roll patterning for functional devices
Keywords: printing
flexible electronics
organic electronics
flexography
metallization

This thesis investigates the viability and compatibility of an industrially-mature metal thin film patterning process, that uses flexography printing in vacuum environments, for application to functional organic devices.
The integral thermal mechanism of this process, called selective metallization, is modelled, showing its compatibility with functional organics (process temperature <60°C, Al sheet resistance <1.59Ω◻-1}). The first example of sub-10μm lateral patterning, using this technique, is presented. These results demonstrate that, for this process, the flexography ink transfer defines the pattern quality.
The pattern quality of the printed metal is optimised, using custom-built in-vacuum flexography equipment. The pattern quality metrics, quantified using specially developed image analysis code, vary parabolically with printing pressure and diminish with increased printing speeds. A hierarchical phenomenological model of ink transfer is developed, which fits the data well. Optimal printing parameters reduce line edge peak-to-peak roughness to <1/2 nominal pattern gap, enough to remove electrical defects.
These optimised printed patterns are used as electrical contacts for organic thin film transistors (OTFTs), as a proof of concept. Device characterisation shows a change in transistor performance, compared to batch-processed Au contacts, resulting from a charge carrier injection layer, MoOx(x<3), which is necessary for band matching of the organic semiconductor with the high work function Al. Overall, the changes with MoOx thickness and configuration demonstrate selective metallization is compatible with OTFTs, with a contact resistivity of 1Ωcm-2.
To conclude, exploratory results, of selective metallization applied to organic light emitting diodes, and in-vacuum printing of an organic dielectric material, demonstrate the potential wide applicability of in-vacuum flexography.
Norm contestation in international politics
Keywords: international security
norms
international law
United States - foreign relations
norm contestation

First generation norm scholars treat the meaning of a norm as if it was clear-cut and static in order to show the influence of international law on state behavior. Second generation norm scholars acknowledge that legal ambiguities and tensions give rise to debates. However, they tend to end rather than begin with the finding that norm contestation is a common occurrence in international affairs. This project begins with norm contestation as a problematic to understand norm development in international relations.
This study develops a theoretical framework on processes and possible outcomes of norm contestation that can guide empirical research. States can agree or disagree on both the norm frame (justification) and/or claim (action) when applying international law. Thus, norm contestation can have four different outcomes: norm clarification (frame and claim agreement), norm recognition (frame agreement/claim disagreement), norm neglect (frame disagreement/claim agreement) and norm impasse (frame and claim disagreement). These alternate endings have different effects on the clarity and strength of the contested norms, as well as on subsequent debate over them.
This “alternate endings” typology structures an empirical analysis using contentanalysis and elite interviews to compare the duration and effect of contestation over security norms. I further show that the malleability of norms does not make them epiphenomenal to power. States pay attention to the legal justifications they provide for their actions, so that norms both structure debates, and are constructed by them.
States act strategically when interpreting norms, but social dynamics intervene in the process, and influence the outcome: the kind of legal framing and legitimation strategy that a state or a third party to which norm interpretation was delegated to engages in matters. Next to this justificatory discourse, the reactions of in- and out-group members to norm interpretations decide over their sustainability.
Time-efficient methods for non-invasive brain blood flow imaging using arterial spin labelling MRI
Keywords: pulse sequence development
PCASL
arterial spin labelling
magnetic resonance imaging
arterial spin labeling
angiography
time-encoded
perfusion imaging

Accurate knowledge of brain tissue perfusion and clear visualisation of cerebral arteries are of great interest for the diagnosis and research of a range of diseases and conditions such as stroke, dementia, Moyamoya, and cancer, as well as in drug development. 15O-H20 PET imaging is considered the gold standard for measuring cerebral blood flow (CBF), while contrast-enhanced x-ray digital subtraction angiography is the gold standard for visualising cerebral arteries. However, both methods use ionising radiation and injectable contrast agents so carry some risks to the patient and are not appropriate for longitudinal monitoring or research.
There is growing interest in arterial spin labelling (ASL) magnetic resonance imaging (MRI), which uses magnetically labelled blood as an endogenous and freely diffusible tracer and can be flexibly used to visualise the arterial tree as well as to measure CBF. However, ASL is an intrinsically low SNR technique, requiring signal averaging and long scan times.
The main aim of this thesis is to improve the time-efficiency of ASL MRI perfusion and angiographic scans, increasing the accuracy and SNR of CBF measurements and vessel depiction in clinically relevant scan times.
First, a statistical framework was developed and validated for optimising multi- delay ASL perfusion protocol timings to improve the accuracy of CBF and arterial transit time measurements. This flexible framework can be targeted to improve the accuracy of specific parameters and provides a more informed method for designing ASL protocols.
Next, this framework was used to optimise and objectively compare a range of existing pseudo-continuous ASL (PCASL) perfusion protocol designs, including time- encoded preparations, from the literature and to explore novel protocol designs. These comparisons allowed the advantages and disadvantages of each approach to be explored, and recommendations about the best ASL experimental designs to be made.
Finally, the benefits of time-encoded PCASL preparations for ASL angiography were investigated. Angiography visualises the pass-through of labelled blood, in contrast to perfusion imaging which relies on the accumulation of labelled blood in tissue, and so the short label durations used in time-encoded PCASL have a greatly reduced impact on the magnitude of the ASL signal. A variable flip-angle approach was also used to remove signal discontinuities and demonstrate a significant SNR improvement over conventional PCASL angiography.
The cellular response to atherogenic lipid
Keywords: vascular smooth muscle
endothelial
atherosclerosis
chromatin
epigenetics
inflammation
histone modifications
monocytes

Atherosclerotic vascular disease is the leading cause of disease worldwide. It is an inflammatory condition affecting the arterial wall, and lesions are composed of vascular and immune cells. The purpose of this study is to understand how oxidised low density lipoprotein, a key risk factor for the development of atherosclerosis, affects immune and vascular cells involved in formation of the atherosclerotic lesion. Recent insights into the pathogenesis of atherosclerosis have highlighted changes in expression and activity of gene regulatory proteins (transcription factors) and epigenetic modifications, such as alterations in chromatin accessibility and histone marks, as important mechanisms of atherogenesis. To understand how these changes come about in atherosclerosis, genome-wide approaches have been used to investigate changes in gene expression, chromatin accessibility, and histone marks following exposure of primary human aortic endothelial cells, aortic vascular smooth muscle cells, CD4+ lymphocytes and CD14+ monocytes to oxidised low density lipoprotein.
Interactions of trypanosomatid Herpetomonas muscarum with dipteran Drosophila melanogaster
Keywords: Leishmaniasis
Insect
Drosophila
Herpetomonas
Leishmania
Parasite
Trypanosomatid

Trypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). With resistance to both vector-targeted pesticides and trypanocidal drugs being reported, there is a need for novel transmission blocking strategies to be developed. Studies using the blood-feeding vectors themselves are not broadly accessible, as such, new model systems are being developed to unpick insect-trypanosmatids interactions. In this thesis the interactions between model dipteran Drosophila melanogaster and its own natural trypanosomatid Herpetomonas muscarum are investigated from the perspective of the parasite. This work describes the sequencing and annotation of the H. muscarum genome, which was shown to be highly syntenic to disease-causing trypanosomatids, especially with those of the Leishmania genus. Infections of D. melanogaster were shown to be confined to adults, where H. muscarum persisted in the crop and midgut of the flies for 3-4 days. RNA-sequencing analysis of infected flies showed that rapid, large-scale transcriptomic changes, associated with autophagy, nutrient acquisition and cell surface remodelling, are triggered in H. muscarum after ingestion by the fly. Much of the transcriptomic changes observed reflect what is known for disease-causing trypanosomatids. As such, several of the identified surface proteins are of interest as putative transmission blocking targets. Further characterisation of these genes will be greatly aided by genetic manipulation methods developed for H. muscarum as part of this work. This thesis has described multiple, evolutionarily conserved, trypanosomatid responses to ingestion by dipterans by using a Drosophila-Herpetomonas model. Future studies of these conserved responses will inform development of novel, broad-spectrum transmission blocking strategies.
Quantum Steenrod squares, related operations, and their properties
Keywords: Gromov-Witten theory
Floer theory
Steenrod squares

In this thesis, we generalise the Steenrod square on the cohomology of a topological space to a quantum Steenrod square on the quantum cohomology of a symplectic manifold. We prove quantum versions of the Cartan and Adem relations, and use the former to calculate the quantum Steenrod square for CPn, as well as more generally giving the means to compute the operation for all monotone toric varieties. We calculate the quantum Steenrod squares for two examples of blowups along a subvariety, in which a quantum correction of the Steenrod square on the blowup is determined by the classical Steenrod square on the subvariety. We then relate the quantum Steenrod square to Seidel's equivariant pair-of-pants product for open convex weakly monotone symplectic manifolds, using an equivariant version of the PSS isomorphism. We proceed similarly for Z/2-equivariant symplectic cohomology, using an equivariant version of the c*-map. We prove a symplectic Cartan relation, pointing out the difficulties in stating it. We will give some chain level calculations of the equivariant pair-of-pants product for T*Sn. We calculate the quantum Steenrod square for the negative line bundles O(-1) → CPm, and use this to calculate the equivariant pair-of-pants square by extending previous results due to Ritter. We finish with a brief sketch of further ideas, involving a Z/2-equivariant version of the Chas-Sullivan product and the Viterbo isomorphism.
Diffusion MRI in premanifest Huntington's disease and early Parkinson's disease: tensor and tractography analyses
Keywords: Parkinson's disease
subthalamic nucleus
neuroimaging
diffusion tensor MRI
Huntington's disease
magnetic resonance imaging
basal ganglia
globus pallidus
brain imaging

Huntington’s and Parkinson’s disease are neurodegenerative movement disorders that both affect the basal ganglia, a system of interconnected deep cerebral nuclei that receive converging input from various cortical areas through white matter tracts. Here we have used diffusion MRI to investigate changes in the tissue microstructure of the basal ganglia, as well as the white matter in presymptomatic/early Huntington’s and early Parkinson’s disease. In the presymptomatic Huntington’s disease group longitudinal sensitivity of diffusion MRI across presymptomatic stages was investigated. We also have investigated the connectivity of the basal ganglia with the cortex, and derived connectivity-based parcellations of the gobus pallidus, and subthalamic nucleus, two important hubs of the basal ganglia system, into motor, limbic, and associative territories.
In presymptomatic Huntington’s disease distinct longitudinal changes in the microstructure of the posterior part of the basal ganglia and the splenium of the corpus callosum, as revealed by diffusion tensor metrics, were detectable at different presymptomatic stages. Both patients with Huntington’s and Parkinson’s disease showed micro-structural alterations in the internal segment of the globus pallidus,and the posterior limb of the internal capsule, two important neuroanatomical structures of the basal ganglia system. Huntington's disease patients also showed marked decreases in their structural connectivity in the motor basal ganglia pathway, and the cortico-subthalamic hyperdirect pathway. The volumes of connectivity-based territories of the globus pallidus, pars interna, and subthalamic nucleus undergo disease-specific alterations that capture opposing effects in Huntington’s vs. Parkinson’s disease. Connectivity-based territories undergo disease-related changes in their coordinates that might be of clinical importance. Neuroimaging outcomes were found to be correlated with clinical questionnaire data.
Successful breastfeeding? Investigating mothers' experiences of infant feeding policies in the United Kingdom
Keywords: Ethnography
Breastfeeding
Motherhood
Public Health Policy
Public Health
Biopolitics
Infant Feeding

This research investigates how women in the UK experience and navigate infant feeding policies which frame specific infant feeding practices as ‘optimal’ for maternal health and infant health and development. At the centre of the research are policies focussed on practices of exclusive breastfeeding for six months followed by the introduction of complementary foods alongside continued breastfeeding. Execution of these practices is termed ‘successful breastfeeding’ in health education. The thesis examines these policies as a contemporary example of biopolitical governance, aiming to advance understanding of how the attempted regulation of health behaviours such as infant feeding plays out in the daily lives of its subjects. This provides insights into the divergence between policy and practice as well as the potentially adverse effects of infant feeding policy. Ethnographic research was conducted in a community network of breastfeeding support services in Oxford, UK, over a period of twelve months, foregrounding the lived reality of mothers as the subjects of infant feeding governance. The findings indicate that mothers are held responsible for achieving successful breastfeeding according to ‘optimal’ practices, with limited acknowledgement in policy of the multiple factors – both within and beyond a mother’s control – that might prevent them from achieving this standard. Conflicts were identified in what constitutes ‘optimal’ infant feeding, and in how breastfeeding ‘success’ is and can be achieved. Mothers navigate these divergent and often conflicting ontologies of success through pragmatic strategies that enable them to negotiate the discrepant demands of early motherhood. These findings contribute to research that highlights the complexities involved in infant feeding decisions and practices, as well as to research that calls for a more ‘mother-centred’ approach to the promotion of breastfeeding.