VictorJuiz/thesis huggingface dataset:
Lanthanide architectures, rotaxanes and responsive d-f assemblies

This work describes the use of copper catalysed "Click" chemistry in the synthesis of lanthanide containing compounds and outlines the application of the products in modulation of luminescence, anion sensing, bioconjugation and multiemissive probes.
Chapter one discusses the fundamental properties of lanthanides with a focus on luminescence and magnetism. A brief literature review on the use of emissive lanthanide probes for sensing application is given. The chapter concludes with an overview on "click" chemistry and its use in the design of lanthanide containing architectures.
A redox switchable luminescent lanthanide complex using a ferrocene group as antenna is described in chapter 2. Insights into the mechanism of modulation of the luminescence signal are given. Other complexes containing redox active aryl chromophores were prepared and their luminescence properties elucidated.
In chapter three, a lanthanide complex is coupled with a rotaxane by Cu(I) "click" reaction. A detailed study of the anion sensing ability of this supramolecular structure follows.
Chapter 4 describes the synthesis of orthogonally functionalised synthons containing azide and alkyne groups that are amenable to form macrocyclic structures upon Cu(I) "click" reaction.
Chapter 5 describes the preparation and study of a novel class of lanthanide complexes containing an appended azide group, and their luminescence properties are studied. The chapter continues with the description of heterobimetallic f-f’ complexes prepared using Cu(I) "click" chemistry.
Chapter six describes the synthesis of lanthanide bioconjugates able to target the dopamine transporter (DAT) protein.
Chapter seven delineates the overarching conclusions from the thesis and possible future work in the field, while chapter eight provides experimental procedures.

Keywords: supramolecular chemistry
click-chemistry
lanthanides
luminescence
Advisor: Faulkner, S
Beer, P
Ecology and sustainability of the marine ornamental trade in Puerto Rico

The marine ornamental fishery (MOF), in which fish and invertebrates are harvested for the live aquarium trade, has been growing in the last years. It is a worldwide market where species are mainly harvested directly from coral reefs in tropical countries. In the island of Puerto Rico, in the US Caribbean, resource managers have little information about the impact of this harvest on the stock populations of the species in the trade. Due to concern about the potential for over-exploitation of the fishery, a regulation was passed in 2004 limiting the permitted species to be harvested and exported. This action caused significant conflict with ornamental fishers and exporters. In order to better manage the resource, more precise ecological and market information was needed, as well as a regulation that more accurately reflected the status of the resource. This study analyzed the marine ornamental trade in Puerto Rico, in order to provide baseline information and public policy recommendations. It evaluated management needs, enforcement, fishers' perspectives and practices, market forces, ecological assessment of the species, as well as explored a management tool for the commercial (edible species) fishery involving the ornamental trade.
The findings of the study are split into two broad topics, a) socio-economics and b) ecology. a) The number of dedicated ornamental fishers on the island is quite small, possibly allowing for the trade to become a seasonal alternative to commercial fishers during closed seasons for edible species. Certifications that promote correct harvesting and handling of the species were found to be of interest to fishermen and managers. b) Reef surveys of fish and invertebrates around Puerto Rico found associations of fish species with habitat characteristics including depth and rugosity. Fish and invertebrate richness and abundance did not vary markedly between different sites and regions around the island, and no evidence could be detected of ornamental fishing impacts. It is suggested that more species of fish could be added to the permitted species list, without damaging their population densities. From both ecological and market perspectives, MOF in Puerto Rico is a viable and sustainable small industry that could be expanded to benefit local people and international traders alike.

Keywords: socio-economics
coral reef
Puerto Rico
aquarium trade
tropical fish
Advisor: Speight, M
Liquid crystals and novel gain materials for thin-film photonic devices

This thesis describes work to create a variety of thin-film photonic devices based upon liquid crystalline materials. Firstly, a variety of liquid crystal phases are polymer- templated by combining a liquid crystalline material with photo-polymerisable reactive mesogens. Upon photo-curing, a polymer scaffold, which is a template of the original phase, is formed with liquid crystal molecules in interstitial sites. This liquid crystal is removed to yield a polymer scaffold which can be used to template the original phase. Here, polymer-templating is used to template the smectic A liquid crystal alignment onto nematic liquid crystals for the first time; this results in materials with improved contrast ratios and faster response times than conventional nematic devices. Next, a study is performed to compare the electro-optic properties of polymer-templated and polymer-stabilised chiral nematic liquid crystals. The enhanced tuning range of polymer-templated liquid crystals is applied to create a polymer-templated liquid crystal laser and to electrically tune its emission wavelength. Subsequently, thin-film elastomeric liquid crystal lasers are created. The lasing wavelength of these films can be reversibly and selectively tuned without hysteresis by subjecting them to a mechanical stress. Finally, work is performed to study the potential of inorganic materials for use in liquid crystal lasers. Transition metal clustomesogens (liquid crystalline materials that contain highly emissive molybdenum clusters) and inorganic-organic perovskites are considered here. The dispersal and emissive properties of clustomesogens in liquid crystals are studied, and they are used to create circularly polarised light sources with a polarisation that can be controlled using electric fields. Layered structures of inorganic- organic perovskite and liquid crystal are created; these exhibit enhanced amplified spontaneous emission. Then, perovskites are used as the gain materials in distributed feedback lasers for the first time. These lasers may be wavelength-tuned by varying the grating spacing of the structure.

Advisor: Morris, S
Investigating the psychological factors associated with obesity

Obesity is one of the most serious public health challenges of the 21st century, associated with a range of adverse physical, psychological, social and economic consequences. The aetiology of obesity is complex; however, the psychological factors associated with overweight and obesity remain poorly understood.
The first paper critically appraises evidence for three of the most developed psychological theories of obesity. Based on these findings, literature from the fields of emotion regulation and attachment are reviewed, and a novel developmental theory of obesity based on an integration of these theoretical constructs is proposed. Recommendations for future research based on a theoretical framework of emotion regulation are made, and implications for clinical practice including a focus on enhancing caregiver sensitivity are highlighted.
The second paper explores the applicability of an established cognitive model of Bulimia Nervosa (BN) and binge eating to an overweight and obese sample. Findings support the relevance of cognitive aspects of the model in an overweight and obese sample, and highlight the potential role of early attachment relationships in the formation of cognitions that make an individual vulnerable to overweight and obesity in later life. Theoretical and clinical implications based on the established cognitive model are considered. Limitations include reliance on self-report and the correlational nature of analyses used. Recommendations for future research with larger, more representative samples to address these limitations are made.
Overall, this dissertation makes a unique contribution to the psychological understanding of overweight and obesity, which has the potential to enhance treatment outcomes and suggests useful avenues for further research.

Keywords: attachment
cognition
psychology
BMI
emotion regulation
A compact borehole, thermal-infrared radiometer and infrared reflectometer for the characterization of subsurface habitability and presence of water ice on Mars

One of the most important steps in the search for life on Mars is to determine if a specific sub-surface location it is "habitable", or that it provides the conditions and requirements to support life as we know it. In this thesis, I present a miniature, thermal-IR radiometer and reflectometer designed to determine temperature, the presence of water ice, and the discrimination of minerals, all necessary for a habitable environment.
A dual use detector was selected for the thermal and five reflectance channels. The IR source is provided by five LEDs. These components were embedded in a thermally controlled aluminium block. Integrated electronics provided signal amplification and demodulation. This device will be suitable for drilling applications with less than 25 mm diameter boreholes and with limited available power (&LT;5watts).
Thermal testing was within a simulated borehole mounted in a thermal vacuum chamber. The results were compared to a theoretical model of the expected temperature. The maximum temperature error between predicted and measured was 0.21 K (&Tilde;0.08%). The total RMS error of all sources were calculated to be &LT;3%.
Reflectance testing in all five channels included a variety of minerals and a two point calibration method. The results were compared to the predicted reflectance values for the samples. The results of the reflectance channel testing demonstrated that the measured values matched the predicted values with a 2.5% measured error. The total RMS error was 6.1%.
Detection and discrimination of water ice and hydrated minerals included a non-linear mixing model and/or testing. The model predicted that water ice mixed in a pyroxene mineral matrix can be detected and discriminated from 5% to 60% concentration by weight. Testing with a hydrated mineral mixed within a non-hydrated mineral matrix demonstrated that the measured result matched the predicted result from 5-45% concentration by weight.

Keywords: NIR reflectometer
Mars Technologies
Thermal IR Radiometer
Advisor: Bowles, N
Beyond removal: Indians, states, and sovereignties in the American South, 1812-1860

In 1830, the US Congress passed the Indian Removal Act; within a decade, 65,000 of the South's original inhabitants had left the region. Two centuries later, historians still see removal as a pivot that transformed indigenous South into Cotton Kingdom. This dissertation tells a different story. Contrary to officials’ hopes, thousands of indigenous Southerners remained. This dissertation provides the first account of non-removal as a massive cross-regional phenomenon which affected not only indigenous Southerners, but also American officials, local residents, and continental dynamics of sovereignty, state development, and empire.
Historians have tended to see an inescapable choice between assimilation and removal. This dissertation demonstrates that thousands of indigenous Southerners successfully carved out a third option, creating their own alternate routes to remain. By fleeing into impenetrable terrain or passing as white, many people avoided agents’ attempts to see and control them. Others cooperated with American officials, subverting state policies to remain hidden in plain sight.
Because they sought to evade officials, many of these people simply do not appear in traditional archives, especially federal documents. This dissertation reinterprets these silences, reading them not as moments where nothing happened, but where indigenous Southerners took actions which statesmen could not see. In doing so, it reveals the world as officials saw it, but also the many blind spots that also marred their vision. This optic cautions against over-easy interpretations of the reach of the early nineteenth-century American state, demonstrating both its enormous capacities and its glaring weaknesses.
Ultimately, this dissertation challenges understandings of removal a transition to American control over the South, and demonstrates that the line between nineteenth-century American expansion and sovereignty was not always an automatic one. Behind slaveholders' illusion of a binary racial universe lay an enduring indigenous world, often illegible to outsiders.

Advisor: Hamalainen, P
Growth laws in morphoelasticity

Many living biological tissues are known to grow in response to their mechanical environment, such as changes in the surrounding pressure. This growth response can be seen, for instance, in the adaptation of heart chamber size and arterial wall thickness to changes in blood pressure. Moreover, many living elastic tissues actively maintain a preferred level of mechanical internal (residual) stress, called the mechanical homeostasis. The tissue-level feedback mechanism by which changes of the local mechanical stresses affect growth is called a growth law within the theory of morphoelasticity, a theory for understanding the coupling between mechanics and geometry in growing and evolving biological material. The goal of this thesis is to develop mathematical techniques to analyse growth laws that are biologically plausible, and to explore issues of heterogeneity and growth stability.
Firstly, we review attempts based on the Second Law of Thermodynamics (Coleman-Noll procedure) concluding that they cannot universally restrict the mathematical form of growth laws. In light of these results we focus on the phenomenological concept of homeostasis. We hypothesize that growth laws are functions of homeostatic stress (homeostasis-driven growth).
Secondly, we demonstrate that for a static residually stressed network made of elastic bars connected in series and parallel, the network response has the same functional form as the response of individual bars (similarly to electrical circuits). For a dynamically evolving network, on the other hand, the macroscopic network response is a nonlinear function of microscopic homeostasis-driven growth laws with no electrical counterpart. We characterise the macroscopic growth dynamics as non-monotonic and non-oscillatory.
Thirdly, we discuss the growth dynamics of tubular structures, which are very common in biology (e.g. arteries, plant stems, airways). We model the homeostasis-driven growth dynamics of tubes which produces spatially inhomogeneous residual stress. We show that the stability of the homeostatic state nontrivially depends on the anisotropy of the growth response. The key role of anisotropy may provide a foundation for experimental testing of homeostasis-driven growth laws.
Fourthly, we apply our theoretical framework to the growth of Ammonites' seashells. We demonstrate how homeostasis-driven growth produces seashell morphology that is consistent with observation and that cannot readily be captured with previous models.

Advisor: Goriely, A
Moulton, D
Effects of an experimentally evolved defensive microbe on its host-microbiome system

Defensive microbes readily influence hosts and their microbiome. And, since hosts and their microbiome are not disparate but comprise an integrated hostmicrobiome system, it follows that defensive microbes should alter the system as a whole. Nonetheless, direct evidence on how defensive microbes influence hostmicrobiome systems is lacking. Using C. elegans and their natural microbiome as a model host-microbiome system and an experimentally evolved defensive E. faecalis strain, I integrated host RNA sequencing, microbiome 16S rRNA sequencing, and phenotypic assays to show effects of a defensive microbe on its host-microbiome system. My results indicate that a defensive microbe can substantially alter its host transcriptome while influencing little change on its host’s microbiome. Additionally, that a defensive microbe can colonize better than its non-defensive counterparts and maintain protective effects even amongst a natural microbiome. This thesis reveals some outcomes and utility of defensive microbes that can be translated to both natural and applied contexts. Additionally, this thesis promotes experimental evolution as a key tool in investigating evolutionary and ecological outcomes of symbiosis.

Advisor: King, K
Frustration and disorder: classical spin liquids and Floquet-Anderson insulators

In this thesis, the physics of two systems is investigated, both of which support unconventional phases of matter. We investigate a frustrated system which has a classical spin liquid regime in the paramagnetic phase. We also consider a periodically-driven, disordered system and explore nonequilibrium regimes. Both systems exhibit macroscopic behaviour which differs strongly from the behaviour in standard scenarios.
First, the properties of frustrated magnets and related systems are discussed. We introduce three-dimensional generalisations of a well-studied two-dimensional frustrated system. These generalisations consist of coupled layers of two-dimensional triangular lattice Ising antiferromagnets. We study three stackings that have nearest-neighbour interactions: two frustrated stackings (abc and abab) and the unfrustrated stacking (aaa). We use a combination of methods, including numerics and analytics, to show that these generalisations exhibit a strongly correlated, highly fluctuating regime known as a classical spin liquid. We show this by investigating the structure factor and correlations directly and by describing a mapping to a continuum field theory that gives further clarity about the classical spin liquid regime using a renormalisation group analysis and consideration of low-lying excitations in these systems.
Second, we study the response of a disordered system to a time-periodic driving potential. We start in the context of Mott's work on a.c. conductivity in Anderson insulators and move beyond this to study the Floquet (long-time) regimes beyond linear response. Using Landau-Zener physics, we construct a description of the various regimes which are possible. We also present the results of thorough numerical studies of these systems.

Advisor: Chalker, J
Information, self-management and common sense: an ethnography of NHS mental healthcare as an accountable bureaucracy

This thesis presents mental healthcare as an 'accountable bureaucracy.' I find a resemblance between clinical expertise and the ethos of the office. Accountable clinicians must produce documentation of disinterested, standardised, justifiable decisions. What staff members consider to be good clinical practice emerges as being good, accountable bureaucratic practice.
My fieldwork investigates an attempt to promote patient 'empowerment.' I use the term empowerment to refer to a set of interlocking clinical goals that pertain to increased patient input to decision-making, more equal clinical relationships, and a wider reconfiguring of services. Patient empowerment is thought of as correcting inappropriate and outdated paternalism in healthcare, leading to better quality care, improved outcomes and reduced costs.
I argue that patient empowerment and accountability are contradictory, in such a way that thin conceptions of empowerment may be compatible with accountability, but thicker conceptions are not. Contradictions between empowerment and accountability exist at the level of basic concepts, clinical style, documentary practices, and clinical relationships. In typical care, accountability is primary, and much of what clinicians consider to be empowering is ignored or excluded. To deliver routinized care, clinicians simplify, and think in terms of reified mental disorders. As they require standardised knowledge about patients, clinicians become adept at 'routinized intimacy.' Attempts to promote empowerment face serious obstacles. Thinner conceptions of empowerment are bureaucratically less problematic, but unsatisfying to many clinicians. Thicker versions of empowerment make care harder to document, control, justify and standardise, and risk escalates.
My findings shed light on an under-acknowledged but important contradiction. I contribute to anthropological literature on accountability, ignorance and uncertainty, professional knowledge and ethics, responsibility and patient self-care, and mental healthcare as a source of disempowerment.

Advisor: Hsu, E
The rule of strangers: empire, Islam, and the invention of "politics" in Egypt, 1867–1914

At the centre of the thesis is puzzle of why Egypt appears to have contributed little to the global corpus of political thought. Although the country witnessed two major revolutions in 1882 and 1919, there are virtually no histories of the ideas they generated or the thought that fuelled them. Colonial observers frequently suggested that Egyptians were 'political ciphers'. They pointed to the absence of abstract political theory in the post-Classical Islamicate world as evidence for that assertion. By extension, contemporary historians have accepted those claims uncritically. They have often held that Muslim clerics, jurists and intellectuals, though long engaged in brokering power, have had little interest in theorising its workings.
Against those claims, the thesis asserts that this apparent deficit of ideas was rather the product of foundational assumptions on the part of intellectual historians. These include a dependence on a Eurocentric concept of 'politics', which emerged in the 19th century and eclipsed older modes of thinking about sovereignty, and a reliance on colonial distinctions between 'religion' and 'politics'. Further, the dichotomy between political 'thought' and 'action' (and the presumption that the former precedes the latter) upon which intellectual history of the Middle East has relied not only oversimplified a complex reality, but justified imperial domination then, and now obscures the intellectual contributions of anticolonial activists.
Drawing on overlooked and fragmentary sources, I provide a history of political ideas for a place that, it is said, failed to produce any. I reconstruct the sophisticated political theology behind the precolonial system of rule that would be dismissed as 'Oriental despotism'. I then examine how British imperial perceptions of despotism and the Egyptian subject on which it was predicated determined their programme of reform as well as generated theory for an academic 'Science of Politics' in Britain. I end by charting responses to those reforms by political activists, who would evince with remarkable clarity insights—generated through struggle rather than armchair speculation—that would decades later be described as postcolonial theory.

Advisor: Rogan, E