VictorJuiz/thesis huggingface dataset:
Colloidal rods in confinement

We study colloidal rods in conﬁnement and under ﬂow on the single particle level using optical microscopy and laser scanning confocal microscopy. First, we investigate liquid crystals in conﬁnement. A mathematical method for calculating distortion energies is developed and illustrated by applying it to both artiﬁcial data and experimental results. Next, we study an isotropic phase in strong conﬁnement, and observe a capillary nematisation transition. This is the ﬁrst observation of capillary nematisation in a colloidal liquid crystal. The results are compared to the Zwanzig model and a DFT model for semi-ﬂexible rods, and we ﬁnd good agreement with both. The DFT model, in which rod orientations are unrestricted and rod flexibility is taken into account, was found to have a better quantitative agreement with the experiments. In the second half of this thesis, we study single colloidal rods ﬂowing in a plane Poiseuille ﬂow. For the most simple case of non-magnetic Brownian rods in water, we observe aperiodic kayaking and xy-tumbling behaviour. The results are compared to Jeﬀery theory for non-Brownian rods in a simple shear ﬂow and to multi-particle collision dynamics simulations. The experimental results were found to undergo the same type of behaviour as predicted by Jeﬀery’s theory, but without periodicity, and particles were seen to switch from one type of behaviour to another. We ﬁnd qualitative agreement between the experiment and simulations, which indicates that the presence of Brownian motion can explain the diﬀerences between theory and experiment. Following on, we investigate further deviations from Jeﬀery theory by studying the eﬀect of an external magnetic ﬁeld and of a non-Newtonian ﬂuid on the orientational behaviour of rods. We ﬁnd that a magnetic ﬁeld shows somewhat similar behaviour as the kayaking and tumbling found in the non-magnetic system, but suppressed towards a plane perpendicular to the magnetic ﬁeld. Rods ﬂowing through a non-Newtonian ﬂuid are found to be aligned in the direction of ﬂow, and do not undergo any tumbling behaviour. The absence of tumbling can be explained by the depletion interaction between rods and the wall. It is unclear why the preferred orientation for rods is along the direction of ﬂow.

Advisor: Aarts, D
Yeomans, J
Dimensions of allusion synthesis affecting craft in the works of Huw Belling and in 20th and 21st century composition

This examination of my own works (presented largely in chronological order) and of related music by others, broadly concerns itself with appropriation and allusion on the part of twentieth and twenty-first century composers. It considers how the deliberate synthesis of existing works affects the responding composers' own output. To this end, whether surveying my own music or others', I do so within a four-pronged framework:
1. The philosophical premise and aesthetic of pieces which somehow appropriate existing composition (as claimed overtly by the composer, or inferred from available research).
2. The compositional procedure and techniques employed in the process of composing works which allude to or synthesise other pieces.
3. The product resulting from the interaction of the above two factors (naturally the latter is more concrete).
4. Critics' and scholars’ responses: the basic phenomenology of the allusive element, synthesis, or stylistic appropriation, and the ethical problems surrounding any appropriation.
My analyses address one or more of these connected points. They raise a number of significant questions. Is synthesis and re-composition (the latter taken to be more specifically referential) affective or effective? That is to say, is it aesthetically prescriptive? Can composers manage to quarantine 'Les objets trouvés' from their individual practice? Of interest are composers with individual credibility as innovators, whose craft is its own defence against criticism on dogmatic grounds. I consider what is to be gained, in terms of technique, and in terms of developing an aesthetic, from the process of specifically engaging with other pieces, and explore the effects of differing methods of synthesis as compared across compositional practices.

Keywords: Allusion
Composition
Advisor: Saxton, R
Multi-modal people detection from aerial video

There has been great interest in the use of small robotic helicopter vehicles over the last few years. Although there are regulatory issues involved in flying these that are still to be solved, they have the potential to provide a practical mobile aerial platform for a small fraction of the cost of a conventional manned helicopter. One potential class of applications for these is in searching for people, and this thesis explores a new generation of cameras which are suitable for this purpose.
We propose HeatTrack, a novel algorithm to detect and track people in aerial imagery taken from a combined infrared/visible camera rig. A Local Binary Patterns (LBP) detector finds silhouettes in the infrared image which are used guide the search in the visible light image, and a Kalman filter combines information from both modalities in order to track a person more accurately than if only a single modality were available. We introduce a method for matching the thermal signature of a person to their corresponding patch in the visible modality, and show that this is more accurate than traditional homography-based matching. Furthermore, we propose a method for cancelling out camera motion which allows us to estimate a velocity for the person, and this helps in determining the location of a person in subsequent frames.
HeatTrack demonstrates several advantages over tracking in the visible domain only, particularly in cases where the person shows up clearly in infrared. By narrowing down the search to the warmer parts of a scene, the detection of a person is faster than if the whole image were searched. The use of two imaging modalities instead of one makes the system more robust to occlusion; this, in combination with estimation of the velocity of a person, enables tracking even when information is lacking in either modality. To the best of our knowledge, this is the first published algorithm for tracking people in aerial imagery using a combined infrared/visible camera setup.

Advisor: Cameron, S
Why comply? The politics of the international refugee regime in non-party Southeast Asian states

A majority of Southeast Asian states are not party to the international refugee regime, and thus have not formally consented to be bound by its normative obligations. This thesis examines changes in State refugee policies absent formal commitments to the regime, using process tracing and archival evidence in four case studies (Malaysia, Thailand, Indonesia and the Philippines) to inductively explain shifts in each states’ compliance. It employs rationalist and constructivist lenses, contributing to the literature on compliance absent formalised international legal commitments, and that on forced migration.

Keywords: Philippines
Thailand
refugee convention
compliance
Malaysia
Indonesia
Advisor: Keene, E
Linking ageing and arthritis: The role of the longevityrelated SIRT1 molecule in age-related cartilage degeneration and osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis worldwide and is characterised by the progressive degradation of articular cartilage. Ageing is the primary risk factor associated with OA. However, the roles of ageing-related mechanisms in cartilage homeostasis are poorly understood. The class three histone deacetylase, Silent mating type information regulation 2 homolog (SIRT1) has been extensively shown to regulate lifespan in lower organisms and signalling pathways linked to mammalian ageing. My thesis explores the role of Sirtuin 1 in cartilage homeostasis and OA.
I used in vitro experiments with chondrocyte cell lines, human clinical samples, novel genetically modified cartilage specific and whole body SIRT1 deficient mice alongside molecular biological tools to investigate my research questions.
Human OA cartilage showed decreased SIRT1 compared to healthy cartilage. Mice with cartilage-specific SIRT1 deletion showed greater cartilage degradation during ageing and in an experimental OA model. In vitro and in vivo studies showed SIRT1 to directly regulate autophagy in chondrocytes. More importantly, the activation of autophagy using spermidine protected against experimental OA in wild-type mice but not in cartilage-specific SIRT1 deficient mice. In addition, my data revealed whole body SIRT1 deficient mice had increased early joint inflammation in repose to injury but displayed less cartilage loss over time in an experimental OA model.
Together I have shown that SIRT1 declines with age and contributes to OA due to dysregulated autophagy. However, chronic low grade inflammation caused by SIRT1 loss was protective. My data suggest these pathways can be targeted to treat OA.

Keywords: SIRT1
Osteoarthritis
Inflammation
Autophagy
Ageing Biology
Experimental therapeutic
Advisor: Edwards, J
Vincent, T
Mechanisms underlying navigational leadership hierarchies: studies with avian and fish models

For animals moving together in groups, navigating collectively requires group members to reach consensus decisions about, among other things, the direction in which to travel. This thesis focuses on how consensus collective decisions are made when certain individuals have a disproportionate influence on the group’s movement decisions. The specific focus is on hierarchical decision-making during collective movement, whereby an individual's position in the hierarchy corresponds to its relative contribution to the directional decision-making process. I used two model species, homing pigeons (Columba livia) and the Characin fish (Astyanax mexicanus) to explore the mechanisms and consequences of leadership hierarchies, using a combination of GPS tracking and high-resolution video recording. Across several experiments, the following key results emerged:
Previous navigational experience contributes to structuring navigational leadership hierarchies in homing pigeons, but only at the most influential positions. Birds with local experience occupy the top hierarchical positions significantly more often than inexperienced birds. This suggests there is an advantage to individuals in having an experienced leader when homing as a group.
When leader birds hold highly inaccurate information, leadership hierarchies are spontaneously rearranged causing the original leaders to lose influence over flocks. This demonstrates the importance flexibility in decision-making structures, which may thus prevent the propagation of navigational errors – detrimental to all individuals within the flock – through the hierarchy.
Homing pigeon navigational leadership hierarchies can be stable over long periods of time, but only in flocks with high levels of inter-individual variation in age and experience. Flocks homogeneous in age and experience showed no hierarchy stability. This highlights the importance of flock composition in determining the stability of navigational leadership hierarchies, which potentially impacts on the advantages of these decision-making structures.
Three-dimensional data are not a necessary requirement for identifying leadership hierarchies in animals that move and interact in three dimensions. A two-dimensional directional correlation delay model was able to correctly identify leader-follower interactions in three-dimensional shoals of Astyanax mexicanus.
Overall, this thesis has shed light on the mechanisms of consensus decision-making, involving hierarchies of influence, during group movement. Through this knowledge we can further our understanding of the adaptive significance of collective behaviour.

Advisor: de Perera, T
Biro, D
The role of dendritic cells in determining the breadth and epitope specificity of the initial CD8+ T cell response during acute HIV-1 infection

During acute HIV-1 infection (AHI), CD8+ T cell responses are initially induced to only 1-3 viral epitopes in many patients, and Nef-derived epitopes are very commonly targeted. The earliest CD8+ T cell responses decrease in magnitude as viraemia begins to decline, and are followed by delayed expansion of subsequent waves of responses of broader epitope-specificity. In this thesis, the hypotheses that prevalent presentation of Nef-derived epitopes by dendritic cells (DCs) favours priming of Nef-biased CD8+ T cell responses in AHI, and that impairments in DC function after the first responses are primed delay expansion of responses of additional specificities, were explored. Mechanisms of impairment of DC function in AHI were not definitely identified, although preexposure of monocyte-derived DCs to IFN&alpa;, which is rapidly induced during AHI, was shown to reduce TLR3-induced co-stimulatory molecule expression and affect the quality of the CD8+ T cell response primed in vitro. Using mass spectrometry-based immunopeptidomics, novel HLA class Irestricted HIV-1 epitopes presented by HIV-1-infected CD4+ T cells were characterised, including epitopes derived from the 5' "untranslated" region of the HIV-1 genome. High ratios of Nef/Gag protein were found associated with extracellular vesicles (EVs) in the plasma of HIV-1+ patients during early, chronic and treated infection. Rather than CD4+ T cells, HIV-1-infected macrophages were identified as a potential source of these Nef-containing EVs. Utilising an in vitro DC crosspresentation assay incorporating immunopeptidomics, cross-presented epitopes were found to derive preferentially from proteins that were more abundant or membrane-associated. Multiple crosspresented HIV-1 (mainly Gag-, Pol- and Env-derived) epitopes were identified, but HIV-1-infected CD4+ T cells were not found to be a source of Nef for cross-presentation. Collectively, these results extend understanding of how DCs control CD8+ T cell immunodominance and expansion during AHI, and could potentially be exploited in future development of novel prophylactic and therapeutic strategies against HIV-1.

Advisor: Borrow, P
Kessler, B
The sustainable use of species-rich grasslands for forage and biogas production

The rapid loss of species-rich grasslands in the UK may have profound environmental and socio-economic ramifications. Although they were once the foundation of livestock production systems, the agricultural use of these landscapes has rapidly declined since the ‘Green Revolution’ of the 1950s due to increased economic incentives to replace species-rich grasslands with agriculturally improved leys and arable fields. In this thesis, I examined the agricultural value of species-rich grasslands in lowland England and the potential ecological impact of losing these landscapes. My research had four main objectives: (1) to determine whether the nutritional composition of forage from species-rich grasslands was comparable to commercial livestock feeds, (2) to assess the bioenergy output of biomass from species-rich grasslands compared to current bioenergy feedstocks, (3) to determine the effect of land use change and agricultural intensification on microbial diversity, and (4) to determine whether grassland biodiversity was stable or changed (temporally and spatially) over time. I show that the forage quality of species-rich grasslands is comparable to that of forage from improved leys and contains extra nutrients (minerals and phytochemicals) which contribute to livestock health. I demonstrate that biomass from species-rich grasslands can compete with other bioenergy crops, especially Miscanthus (the primary bioenergy feedstock in the region) and that species richness and species composition contributes strongly to the biogas yield of grasslands. Through soil metagenomic analysis I found that while bacterial diversity does not decline with agricultural intensification, fungal diversity decreases and plant, human and livestock microbial pathogens shown to be pathogenic in other ecosystems dramatically increase on agriculturally improved fields compared to species-rich grasslands. Finally, by combining palaeoecological and modern vegetation data I demonstrate that grassland biodiversity was temporally and spatially linked to long-term human management and would revert to oscillating between open grassland and woodland if this management ceases. Grassland biodiversity is thus a finite natural resource with a strong economic and environmental value that can contribute to the development of more sustainable agricultural and bioenergy production systems in the UK.

Advisor: Turnbull, L
Charles, M
Technology and employment: tasks, capabilities, and tastes

This thesis explores the consequences of 'increasingly capable machines' on earnings and employment. A new literature, the task-based approach, has been developed for this purpose. And this literature presents an optimistic account of the prospects for labour in the 21st century. The central claim in this literature is that "people tend to overstate the extent of machine substitution for labour and ignore the complementarities".
This thesis challenges this optimism. I argue that such optimism is based on two assumptions, neither of which is justified. The first is that the supply-side analysis in this literature is based on outdated reasoning about how these machines operate. The result is that the models arbitrarily constrain what machines are capable of doing. The second is that the demand-side analysis in this literature is either altogether missing, or is carried out in a way that is constrained by the arbitrary supply-side assumption.
In this thesis I build a new range of task-based models that are based on more justifiable assumptions. The first set of models show that updated reasoning about how machines operate leads to a pessimistic account of the prospects for labour. The second set of models show that the demand-side has an important role in either strengthening, or weakening, this pessimism that is reached when the supply-side is looked at in isolation. This analysis leads to the identification of an important new 'race' in the labour market.

Keywords: automation
technological Unemployment
computerisation
technology
future of Work
economics
Advisor: Vines, D
Genetic risk and resilience for Alzheimer’s disease: The effect of the three APOE alleles on brain function across life

The human apolipoprotein E (APOE) gene has three alleles (ε2, ε3 and ε4). Relative to the most common ε3 allele, ε4 is associated with a higher risk of developing sporadic late-onset Alzheimer’s disease (AD) whereas ε2 is believed to confer a protection to AD. Because of ε4's close association with cognitive decline, the majority of APOE-research has focused on this allele, with ε2 receiving little attention. This DPhil thesis used advanced multi-modal magnetic resonance imaging techniques in cognitively healthy young (20-40 years), middle-age (35-55 years) and older (60-85 years) adults to fulfil two objectives: (1) to present the first detailed examination of the effects of ε2 on brain structure and function across life, and (2) to study the early-life effects of APOE on cerebrovascular and neurochemical health, both of which are characteristically impaired in AD but have not been investigated in relation to APOE. We found that while APOE did not exert strong effects on brain structure or neurochemistry across the lifespan, there were significant allele-specific changes in brain function and vascular health. APOE’s effects on functional connectivity of the posterior cingulate cortex varied with age (connectivity in young adults: ε4 &GT; (ε2 and ε3); older adults: (ε2 and ε3) &GT; ε4). APOE ε2 carriers displayed an upward and ε4 carriers a declining trend in functional connectivity from young to older ages, with the middle-age range serving as a crossing point for the two opposing trajectories. Notably, similar increases in brain activity were observed within the hippocampus during a memory-encoding task in young ε4 carriers relative to non-carriers, suggesting a link between ε4 and early-life functional hyperactivity. We also found that young ε4 carriers had the worst and ε2 carriers the most robust measures of cerebrovascular reactivity (measured as the compensatory blood flow to the brain in response to breathing carbon dioxide, i.e. CO2-CVR). Early-life changes in cerebrovascular function may explain why ε4 carriers are more vulnerable to amyloid deposition and by contrast, why ε2 carriers remain relatively protected from AD-related neuropathology. Evidence suggests that impairments in CO2-CVR can be pharmacologically restored, making this measure a particularly useful preclinical marker of AD risk. Overall, this thesis provides valuable insights into the effects of APOE in the brain, and lends support to our growing understanding of AD as a vascular disorder.

Keywords: MRI
Ageing
APOE gene
Advisor: Mackay, C
Filippini, N
The cosmology and astrophysics of axion-like particles

In this thesis I study astrophysical and cosmological effects of axion-like particles (ALPs). ALPs are pseudo-scalar particles, which are generally very weakly-interacting, with a coupling 𝑎/M E · B to electromagnetism. They are predicted by many theories which extend the standard model (SM) of particle physics, most notably string theory. String theory compactifications also predict many scalar fields called moduli which describe the size and shape of the extra, compact dimensions.
In string theory models generically the moduli fields are responsible for reheating the universe after inflation. Being gravitationally-coupled, they will also decay to any other particles or sectors of the theory, including any light ALPs, of which there are usually many. The ALPs produced by moduli decay will contribute to dark radiation, additional relativistic energy density. The amount of dark radiation is tightly constrained by observations, this bounds the branching fraction of moduli decays into ALPs, which constrains the string theory model itself. I calculate the amount of dark radiation produced in a model with one light modulus, solely responsible for reheating, called the Large Volume Scenario. I study a minimal version of this model with one ALP and a visible sector comprised of the minimal supersymmetric SM. The dominant visible sector decay mode is to two Higgses, I include radiative corrections to this decay and find that ALP dark radiation is over-produced in this minimal version of the model, effectively ruling it out.
The production of ALPs from moduli decay at reheating seems to be a generic feature of string theory models. These ALPs would exist today as a homogeneous cosmic ALP background (CAB). The coupling of ALPs to electromagnetism allows ALPs to convert to photons and vice versa in a magnetic field, leading to potential observable astrophysical signals of this CAB. Observations have shown an excess in soft X-ray emission from many galaxy clusters. I use detailed simulations of galaxy cluster magnetic fields to show that a CAB can explain these observations by conversion of ALPs into X-ray photons. I simulate ALP–photon conversion in four galaxy clusters and compare to soft X-ray observations. I show the excesses (or lack thereof) can be fit consistently across the clusters for a CAB with ALP–photon inverse coupling of M = 6 − 12 × 1012 GeV, if the CAB spectrum has energy &Tilde; 200 eV.
I also study the possibility of using galaxy clusters to search for and constrain the ALP coupling to photons using cluster X-ray emission. Conversion of X-ray photons into ALPs will cause spectral distortions to the thermal X-ray spectrum emitted by galaxy clusters. I show that the non-observation of these distortions is able to produce the strongest constraints to date on the ALP–photon inverse coupling, M &gsim; 7 × 1011 GeV.

Advisor: Conlon, J