VictorJuiz/thesis huggingface dataset:
Demographic consequences of a changing environment on a population of Trinidadian guppies (Poecilia Reticulata)

Ecologists are interested in the complex relationships between populations and their environment. Feedbacks from ecological interactions can change the biotic and abiotic landscape, impacting numerous aspects of a population. Selective pressures on phenotypic traits from processes such as predation and intraspecific competition can change the structure of populations. Structured models can be used to predict how individual level processes can determine population level responses and build an overall understanding of population dynamics. When these models are structured by fitness related phenotypic traits, they can simultaneously be used to provide insights into phenotypic change.
In this thesis, I explore ecological drivers of the population and body size dynamics of Trinidadian guppies (Poecilia reticulata) following a change in predation environment. I used individual based data to explore how the life history of individuals across size classes is determined by population density and size-dynamics in a varying environment. I (i) used a modelling approach to determine how much female body size, population density, and the interaction between body size and density explain the temporal variation in demographic rates of individuals (ii) parameterized and analysed a density-dependent Integral Projection Model to make predictions about population dynamics. This thesis contributes to our understanding of the factors that determine phenotypic trait dynamics and population demography in a seasonally fluctuating environment. Understanding how populations respond to environmental variation over the long term has important implications as anthropogenic forces rapidly disrupt seasonal dynamics, with serious consequences for populations.

Keywords: ecology
population dynamics
population demography
life history
guppies
Advisor: Coulson, T
Bassar, R
Particle interactions in a magnetophoretic system

The continuous flow separation of magnetic particles from a mixture of particles could improve the performance of magnetic bead based assays but the formation of agglomerates limit the separation efficiency. Bead agglomerates are formed as a result of magnetic binding forces while the hydrodynamic fluid environment strongly influences their movement. The ability to predict the interaction between nearby beads will help to determine a threshold separation distance which will be recommended for use when obtaining measurement within a magnetic bead assay for a specified time interval.
The introductory part of this thesis explored the development of a two dimensional numerical model in Matlab which predicts the trajectory pattern as well as magnetic induced velocities between a pair of super-paramagnetic beads suspended in water within a uniform field.
The movement of a bead pair interacting due to both magnetic and hydrodynamic forces within a magnetophoretic system was recorded using an optical system; the beads’ movements were compared with the simulated trajectories and gave a good agreement. The model was used to predict the shortest agglomeration time for a given separation distance which is of practical benefit to users of bead based assays.
The concluding part of this thesis expanded the simulation into a three dimensional model to predict the interactions among three super-paramagnetic beads within a magnetophoretic system. In order to determine the height of the magnetic beads, a Huygens-Fresnel model was implemented in Matlab which was compared with off-focused diffracted images of the beads viewed under an optical system. A good comparison was obtained by comparing the simulated three-dimensional trajectories with experimental data.

Keywords: Microfluidics
Super-paramagnetic Bead
Lab-on-a-chip
Magnetic Interaction
Magnetic Separation
Magnetophoretic
Magnetic Field
Magnetic Bead Agglomerate
Bio-sensor
Immunoassay
Hydrodynamic Interaction
Advisor: Sheard, S
Mechanisms of Non-Progressing Paediatric HIV-1 Infection

HIV-infected children progress more rapidly to AIDS than adults and, in sub-Saharan Africa, without antiretroviral therapy (ART), more than 50% will die before their second birthday. However, a minority of perinatally infected children will become paediatric non-progressors (PNP). The reasons for this rapid disease progression and the immunological correlates of protection against rapid progression are incompletely understood. This thesis focuses principally on paediatric HIV infection, and addresses the immunological and viral influences on disease progression.
This work shows that Human Leukocyte Antigen (HLA) class I variation does not significantly influence progression rates in paediatric HIV infection, in stark contrast to adult HIV infection where HLA class I allele variation substantially impacts disease progression. This study describes potent broadly neutralizing antibody responses along with strong virus-specific T-cell activity in HIV-infected children. These virus-specific immune responses, however, do not protect against progression. The primary driver of non-progression in HIV infected children is low levels of T cell immune activation despite persistently high viraemia. This suggests close similarities with mechanisms evolved over thousands of years of non-pathogenic SIV infection in non-human primates.
Further evaluation of the mechanisms underlying paediatric non-progression is relevant both to reaching a better understanding of HIV pathogenesis and to underpin future HIV cure strategies.

Advisor: Goulder, P
International criminal justice and the global south: extraversion and state agency

Why do states of the Global South initiate international criminal justice processes for domestic atrocity crimes? The phenomenon of Southern agency regarding international criminal justice presents an empirical and theoretical puzzle given the Southern states' defence of Westphalian sovereignty, or the juridical equality of states and domestic non-intervention. International criminal justice challenges this notion of sovereignty by directly prosecuting individuals under international law through international courts. This thesis rejects this theoretical notion that international criminal justice curbs sovereignty, and argues that the initiative for international criminal justice processes is a type of short-term political strategy adopted by Southern state actors to strengthen specific aspects of their statehood. In doing so, the thesis challenges the dominant theoretical explanations of Southern state preference that relies on their relative weakness and the power of external factors, such as Great Power interests or transnational activist networks, and reclaims the possibility of agency for Southern state actors. The argument is derived from a theory developed in this thesis, referred to as judicial extraversion, or a counter-structural theory of strategic action that links the politics of statehood in the Global South and the political opportunities inherent in the nature of international criminal justice, namely, the individualisation of responsibility, criminalisation of specific forms of violence, and the privileged status of the state in the international criminal justice system. It develops this theory through the qualitative case studies of Uganda’s self-referral to the International Criminal Court (ICC), Cambodia’s request for an international criminal tribunal to the UN, and the counterexample of Colombia’s special domestic criminal justice process for paramilitary demobilisation. The thesis finds that relative weakness of Southern states is insufficient to explain engagement with international criminal justice, and highlights the possibility of paradoxical agency. Finally, the findings suggest that, under particular circumstances, international criminal justice can be used to entrench the authority of weaker states in the international system.

Advisor: Welsh, J
Hurrell, A
18F-labelling of new chemotypes for drug discovery

In this thesis, the 18F-labelling of new "chemotypes" will be described with the aim of application in pharmaceutically interesting targets. In Chapter 1, a general introduction to the effect of fluorine substituents on molecular properties and reactivity is provided. This includes the application of organofluorine in both medicinal chemistry and positron emission tomography. Chapter 2 describes a novel silver-mediated 18F-labelling of Ar-SCF3, Ar OCF3 and Ar-OCF2H, including [18F]Riluzole, the 18F labelled version of a drug for treatment of amyotrophic lateral sclerosis (ALS). This work demonstrates that AgOTf can induce halogen exchange nucleophilic 18F-fluorination under mild reaction conditions with a wide range of substrates. In addition, the 18F-labelled Ar-SCF3 substrate is further transformed into the [18F]Umemoto reagent in a single step.
The Umemoto reagent has been extensively used for electrophilic trifluoromethylation of various functional groups. Therefore the labelling of this reagent could potentially expand the radiochemical space available for PET applications. To augment the utility of this reagent, we developed a late-stage stereoselective trifluoromethylation-thiocyclisation of alkenes using electrophilic trifluoromethylating reagents such as Umemoto reagent or Togni reagent, which will be discussed in Chapter 3. In this process, thiourea acts as both S-nucleophile and CF3 radical initiator; therefore no metal or photoredox catalyst is required. The reaction affords novel trifluoromethylated 2-amino-thiazolines and 2-amino-thiazines, important scaffolds in the development of aspartate beta-secretase enzyme (BACE–1) inhibitors, a therapeutic target for Alzheimer's disease.
Chapter 4 investigates the 18F-labelling of α,α-difluoro-α-aryloxyacetic acid, a class of substrate that can serve as a versatile intermediate which can undergo various decarboxylative functionalisation reactions to afford a wide range of novel 18F labelled α fluorinated aryl ethers. Finally, Chapter 5 gives full experimental procedures and characterisation data for all compounds.

Advisor: Gouverneur, V
The struggle that has no name: race, space and policing in post-Duggan Britain

State violence, and policing in particular, continue to shape the black British experience, racialising geographical areas associated with African and African-Caribbean communities. The history of black struggles in the UK has often centred on spaces of racial violence and resistance to it. But black-led social movements of previous decades have, for the most part, seen a decline in both political mobilisations, and the militant anti-racist slogans and discourses that accompanied them. Neoliberalism, through securitisation, resource reallocation, privatisation of space and the de-racialising of language, has made radical black activism an increasingly difficult endeavour. But this does not mean that black struggle against policing has disappeared. What it does mean, however, is that there have been significant changes in how anti-racist activism against policing is articulated and carried out. Three high-profile black deaths at the hands of police in 2011 led to widespread protest and civil unrest. These movements of resistance were strengthened when the Black Lives Matter movement in the United States mobilised hundreds of young people in solidarity actions in England. In this thesis, I argue that, over time, racist metonyms used to describe places racialised as black (Handsworth, Brixton etc.) and people racialised as black (Stephen Lawrence, Mark Duggan etc.), have led to the rise of metonymic anti-racism. While metonymic anti-racism was used alongside more overt anti-racist language in the period between the 1950s and early 1990s, I argue that such overt anti-racist language is becoming rarer in the post-2011 period, particularly in radical black grassroots organisations that address policing. Intersecting with metonymic anti-racism are gender dynamics brought to the surface by female-led campaigns against police violence, and forms of resistance which target spaces of post-industrial consumer capitalism. Understanding how police racism, and resistance to it, are being reconceptualised through language, and reconfigured through different forms of activism, provides a fresh understanding of grassroots black struggle in Britain.

Keywords: resistance
polcing
racism
britain
Advisor: Daley, P
Networks for school support and improvement: a mixed methods study

From 2010 to 2016, public schools in New York City were required to affiliate with one of approximately 60 Children First Networks (CFN). These networks were designed to provide a broad range of support for instruction, leadership, curriculum, and operations in schools, as well as facilitating collaboration between schools, with the ultimate goal of raising student achievement. Using mixed methods, the research presented in this thesis investigates relationships between these networks and student achievement, and explores processes and interactions relevant to collaboration and school improvement within and between schools and their affiliated networks.
The overall explanatory sequential mixed methods design began with a quantitative phase, in which secondary data were analyzed using multilevel modeling to determine whether there was an overall effect of networks on student achievement on state assessments in literacy and mathematics. Contextualised value added (CVA) school effects were also investigated at this stage, and the results were used to inform the sampling of schools for the qualitative strand of the project. Qualitative inquiry used a case study approach, with the "case" defined as the network structure as a whole, and embedded cases consisting of 10 schools in several different networks. Interviews were conducted with various stakeholders (principals, teachers, and network staff) to access multiple perspectives and experiences of network roles, participation and collaboration in networks, and how these relate to school improvement.
Main findings from the quantitative analysis demonstrate little evidence of an overall effect of networks on student achievement, but show significant variation between schools’ CVA effects. Qualitative findings offer insight relevant to these results, as accounts of participants at different levels of the network structure vary regarding the nature, extent and impact of schools’ involvement with networks.
Focusing on an under-researched network structure and applying rigorous methods from educational effectiveness research within a mixed methods design to study networking and collaboration in education, this study makes an original and substantive contribution to both of these fields. Findings have the potential to inform relevant policy in New York City, and though results from this context must be generalized cautiously, this research may provide useful considerations for policymakers in other settings by adding to the broader evidence base on the effects of school networks and the processes and interactions within them.

Keywords: multilevel modeling
mixed methods
educational effectiveness
networks and collaboration
school improvement
Advisor: Sammons, P
The prehistory of material signification: tracing the nature and emergence of early body ornamentation through a pragmatic and enactive theory of cognitive semiotics

This thesis explores the nature and emergence of early body ornamentation, which has long been at the forefront of the debate on modern human origins. According to most prehistorians, ornamental shell beads are unequivocal proxies for behavioural and cognitive "modernity", for they are considered the arbitrary products of symbolically-capable brains. In my dissertation, I argue against the "symbolic" dictum of reducing material signification to linguistic terms, and attributing its creation to a representational mechanism. For one, the significative meaning of material culture is not entirely arbitrary, because concepts can be founded on physical properties and affordances. Moreover, material signification is not the epiphenomenal product of innate cognitive modules, for the mind is not a computational device that processes internal representations before externalising them through behaviour.
I thus suggest that these theoretical fallacies about the nature and emergence of material signification can be overcome by combining a pragmatic semiotic approach with an enactive theory of cognition. Briefly put, a pragmatic semiotic theory describes the nature of material signification by recognising that significative concepts can be founded on physical qualities and relations, whereas an enactive theory of cognition accounts for the emergence of material signification by explaining how significative concepts are brought forth via the constitutive entwinement of mind and matter. Through the synergistic fusion of these theoretical tenets, the origins of early body ornamentation can be examined from a developmental perspective that treats the generation of significative meaning as the emergent product of material engagement. In its light, the preoccupation of most evolutionary archaeologists with the notion of "modernity" appears to be inherently problematic. It is therefore ultimately proposed that the dominant symbolic interpretation of material signification need be replaced with a pragmatic and enactive theory of cognitive semiotics that is suitably geared to trace the evolution of prehistoric material signs.

Keywords: Symbolism
Early body ornaments
Material Signification
Advisor: Malafouris, L
Public accountability and the case of the NHS foundation trust policy:  An exploration of the views and experiences of policy makers, regulators, directors and governors

Scholars have suggested that reforms associated with a shift from government to governance have fundamentally altered the accountability landscapes of modern welfare states. The promotion of policies in favour of organisational autonomy, coupled with the rise of New Public Management Practices (NPM), have been correlated with the proliferation of innovative, and increasingly hybrid accountability arrangements, which have supplanted, or at the very least, supplemented traditional vertical forms of political accountability. In some contexts, the policies have promoted the role of organisational mechanisms that encourage the public to be involved and to hold their public services to account. While some scholars have emphasised the possibilities, as well as the limitations, associated with the new forms of public accountability, further research is required to critically explore the realities of the processes and the outcomes of such mechanisms.
The contribution of this thesis is intended to provide insights into the themes, key issues and tensions which relate to the functioning of direct forms of public accountability in practice. Through drawing on the in-depth case of the NHS Foundation Trust policy, that was passed into law in 2003, and which introduced an innovative direct form of public accountability, this study examines the perspectives and experiences of the directors, the governors, the policy makers and the regulators concerning the implementation of this new mechanism, in one NHS Foundation Trust, in order to analyse the factors which shape the practices of public accountability. The analysis also considers the identified outcomes of the mechanism and it addresses the implications for the conceptualised possibilities and limitations of public accountability.
While the approach adopted is, in part, exploratory, the analysis is guided by close reference to current theoretical understandings, drawn from accountability theory, new institutional theory, and organisational and management studies. Through an in-depth analysis the NHS Foundation Trust policy reform, this thesis is intended to make an important contribution to the central debates and to the existing body of knowledge that is defined as accountability scholarship.

Advisor: Bennett, F
A theological defence of Burkean conservatism and a critique of contractarian liberalism

In this thesis I have provided a critique of the stream of contractarian liberalism which finds its source in the work of John Locke, tracing its influence through the French Revolution and into our own era in the work of the contemporary liberal theorist John Rawls. I have drawn particular attention to the substantive and methodological assumptions which unify these three instantiations of the contractarian tradition. I have challenged this stream of liberalism by offering an exposition of the thought of Edmund Burke. During the course of the thesis I have looked at the central themes which characterised Burke's thought, drawing particular attention to Burke's understanding of the British constitution, common law and his regard for the institutional church. Secondly, I have analysed the theological content of Burke's political thought, demonstrating that Burke's political thought emerged from his Christian faith and his concomitant belief in the natural law. I have argued that, as a result, there is a profound consonance between the central principles of the Christian faith and the conservative tradition which followed Burke. In the course of this argument I have defended the natural law school of Burkean scholarship and presented a clear link between Burke and the thought of Thomas Aquinas. Thirdly, I have unearthed some of the theological convictions which were historically resident in the British legal tradition that informed Burke's thought and I have shown how these assumptions run counter to the central ideas of the contractarian tradition. I have concluded by arguing that there are specifiable aspects of contractarian liberalism which should be treated with suspicion by Christians.

Keywords: common law
Contractarian Liberalism
Philosophes
Edmund Burke
John Fortescue
natural law
Burkean
Edward Coke
Political Theology
John Locke
Burkean conservatism
John Rawls
John Selden
Conservatism
Christianity
Advisor: Biggar, N
Electronic and optoelectronic devices using chemical vapour deposited 2D materials

Two dimensional (2D) materials bear a lot of expectations on playing important role in next generation electronics and optoelectronics. Driven by the thrust of this, this project studies the electronic and optoelectronic properties of 2D materials through device fabrication with 2D materials. Graphene and WS2 are the representative 2D materials studied in this thesis.
In the study of graphene, a simple method to grow uniform continuous layer of graphene via chemical vapour deposition (CVD) is developed. Factors cause micro-defects like cracks and holes in the graphene sheet are revealed. Our study helps to develop the growth and transfer method of producing chip-sized continuous single layer graphene. This growth and transfer method is currently used as the routine for high quality graphene production in our lab.
The study on graphene device fabrication soon extends to device fabrication with other 2D materials like WS2. WS2 photo conductor is fabricated with the CVD WS2. Large gain factor up to several hundred is achieved in WS2 photo conductor. A close link between the large gain and trapped states between WS2 and metal contact is revealed. A photo induced Schottky barrier lowering is measured in this study.
Subsequent studies aim to deepen the understanding on the relation between WS2 microstructure and its electronic properties results the fabrication of in-situ electronic devices. A novel in-situ electronic measurement TEM chip is designed and fabricated. Our measurement reveals the detailed atomic structure of WS2 after electronic break-down. Furthermore we developed a one-step method to synthesis WS2 nanoparticles decorated graphene film by electric shock. Our in-situ electronic measurement concludes with a discovery of negative electronic responsivity in the conductance of suspended WS2 single crystal domain. This result cast light on the fabrication of novel 2D direct electron detector.

Advisor: Warner, J
Briggs, A