VictorJuiz/thesis huggingface dataset:
The at-sea behaviour of the Manx shearwater
Keywords: animal behaviour
biologging
seabird
foraging

Seabirds are vulnerable to a wide range of impacts at sea and function as important indicators of ocean health. A detailed understanding of their movements and distributions at sea, as well as the types of behaviour in which they engage and the extent to which those activities make them vulnerable to different impacts is critical in effective conservation planning. But their elusive lifestyles and mobility have hampered studies of their at-sea behaviour. Using miniature data loggers deployed on Manx shearwaters Puffinus puffinus this thesis explores the movements, distribution and behaviour of a small-medium pelagic, procellariiform seabird during foraging trips at sea.
Foraging distributions were most variable during the pre-laying period when females departed the colony to build their egg. Females foraged close to the colony when local resources were adequate, but more typically foraged in distant shelf edge waters. Males returned frequently to the colony during this period and typically foraged close by, but also in shelf edge waters when local resources were poor.
During incubation and chick-rearing the foraging movements of birds tracked from up to four colonies showed considerable inter-annual variability, but were largely constrained to the Irish and Celtic Seas and the inshore waters of west Scotland. Birds from each of the colonies foraged in waters local to their own colony, but also in more distant locations, including the productive Western Irish Sea and Western Irish Sea Front where birds from multiple colonies co-foraged, presumably at high densities.
At-sea behaviour was organized into three principal activities representing: (1) sustained direct flight, (2) sitting on the sea surface, and (3) foraging, comprising tortuous flight interspersed with periods of immersion and diving in pursuit of prey. Foraging was highly constrained to daylight hours during which birds engaged in bouts of diving separated by periods of flight or rest on the surface. Most dives were up to 6 m deep, lasting up to 13 s, but some much deeper dives (maximum 55.5 m) were also made.
During chick-rearing the use of short and long duration trips may allow parents to control provisioning effort and their own body condition. However, reducing parents’ requirement to provision their chick (by supplemental chick feeding) did not appear to alter the at-sea movements and behaviour of parents, suggesting that at-sea behaviour probably is controlled more by foraging conditions and prey distributions than by the nutritional demands of the chick.
Imidazolium- and triazolium-based interlocked structures for anion recognition and sensing
Keywords: sensing
molecular recognition
template synthesis
supramolecular
anions
rotaxane

This thesis describes the synthesis and investigation of novel anion templated interlocked structures which incorporate the positively charged imidazolium and triazolium binding motifs for applications in anion recognition and sensing.
Chapter One introduces the fields of anion supramolecular chemistry and mechanically interlocked structures, focusing on topics of particular relevance to this thesis, including anion recognition, anion sensing and the templated synthesis of interlocked architectures.
Chapter Two details the incorporation of the imidazolium motif into the axle components of anion templated rotaxane hosts to achieve selective anion recognition by virtue of their interlocked binding cavities. The effects of exploiting imidazolium motifs with contrasting hydrogen bond donor arrangements and reducing the macrocycle size on the anion recognition properties of such systems were investigated using 1H NMR spectroscopy.
Chapter Three reports the work undertaken to utilise fluorescent reporter groups as stoppers in the synthesis of anion sensing rotaxanes. Imidazolium- and triazolium based systems containing either luminescent ruthenium(II) bipyridyl complexes or the organic fluorophore anthracene were prepared and their anion sensing behaviours explored using fluorescence spectroscopy. Synthetic efforts to construct suitable photo-active rotaxanes are detailed.
Chapter Four describes investigations of the novel naphthalimide triazolium motif both for use in interlocked molecular motion systems, and for fluorescence sensing applications. The preparation of a naphthalimide triazolium rotaxane, capable of selective, anion-induced, uni-directional shuttling which was investigated extensively using 1H NMR spectroscopy and optically signalled by perturbations in the UV/Vis spectrum, is detailed. Preliminary research studies into the potential to exploit this motif for surface based fluorescence sensing devices are also included.
Chapter Five presents research into the utilisation of acyclic receptors displaying considerable binding induced conformational changes for fluorescence anion sensing. The recognition properties of a series of imidazolium-based receptors were studied, whilst the ability of a pyrene appended analogue to signal anion complexation via changes in excimer emission is reported. The control of interpenetrated assembly formation using anion-induced conformational changes within the threading component of a pseudorotaxane is also discussed.
Chapter Six provides the experimental procedures and characterisation details for the compounds synthesised in this thesis.
Chapter Seven is a summary of conclusions from Chapters Two, Three, Four and Five.
Supplementary information relating to titration protocols, crystallographic data and surface studies is provided in the Appendices.
Investigation of the bend transition in Pi-cell devices
Keywords: Pi-cell
anchoring breaking
order reconstruction
bend transition speed

The Pi-cell is known to have the fastest response time amongst commercialised nematic LCD applications due to the bend configuration. The Bend configuration can be obtained when a high voltage is applied to a Pi-cell initially treated to have a splay configuration, but transition is complex because the splay and the bend states are topologically not identical. Although two possible mechanisms (anchoring breaking and order reconstruction) can explain the bend transition, it is still difficult to be certain of the mechanism in some cases. In this thesis, therefore, the bend transition mechanism in the Pi-cell is investigated.
Whichever mechanism is present, the bend transition speed is expected to increase when a high voltage is applied to the cell. However, in some cases, the application of a higher voltage reduces the bend transition speed. These phenomena are discussed based on various experimental results, and the reasons are also discussed. Four different regimes are suggested depending on the bend transition speed change. From these results, it is possible to understand the best way to obtain the bend state quickly in a TFT-LCD in the Pi-cell mode.
During the experiments, unexpected light leakage was observed in the extinction position. It was proved that the light leakage came from the residual twist angle caused by the manufacturing process. In addition, two new methods were suggested for measuring the residual twist angle from the light leakage. One of the methods, the analytic method, was extended to the TN-cell.
Allowing for the residual twist angle in the Pi-cell, the reason for lower CR compared to other LCD modes is discussed, and methods are suggested in this thesis to improve the CR of Pi-cell devices.
Genetics of chronic otitis media: a mouse to man approach
Keywords: mouse
otitis media
hypoxia
genetics
Down syndrome

Chronic otitis media (OM) is an archetypal complex disease, which is particularly prevalent in childhood. Epidemiological data suggest high heritability for disease susceptibility, but previous genetic association studies have had methodological flaws, and none have specifically focused on chronic OM phenotypes.
Mouse models represent one way to ascertain candidate loci for human association testing. A number of mouse models of middle ear inflammation have been reported, but many susceptibility loci remain undiscovered. I demonstrate that oto-endoscopy is a robust and scalable phenotyping platform for OM in the mouse, and discuss its value in new model discovery.
Chronic OM is also a feature of trisomy HSA21 (Down Syndrome). Through an interrogation of the mouse library of segmental trisomy models of Down Syndrome, I identify a critical trisomic region for chronic otitis media. This region may underlie OM susceptibility in Down Syndrome, but could also contribute to disease susceptibility in non-syndromic disease.
Mouse models can also be used to interrogate disease mechanisms. Our previous work has shown that the chronically inflamed middle ear is hypoxic, and that hypoxia signalling is a potential therapeutic target. Exploiting the Junbo mouse model, I demonstrate that surgical ventilation of the Junbo ear improves inflammation, and that this is associated with loss of hypoxia signalling. I present preliminary results from transcript analyses of human middle ear effusions showing marked upregulation of hypoxia signalling.
A systematic review of existing mouse models suggests that the loci FBXO11, EVI1, SMAD2, and TGIF1 are good candidates genes for human association testing. I detail recruitment and collection of DNA from families in the UK where a child is undergoing grommet insertion. Association testing using a variant of the transmission disequilibrium test shows susceptibility associated with polymorphisms at FBXO11, and possibly also SMAD2 and TGIF1.
Climate-related disaster risk in mountain areas: the Guatemalan highlands at the start of the 21st Century
Keywords: social vulnerability
extreme rainfall
disaster risk
Guatemala
hazards
mountains
landslides

Mountains are hazardous places. Framed in political ecology and disaster theory in geography, this research set out to answer the overarching question of how the risk of climate-related disasters has changed in mountain areas of Guatemala at the start of the century. It involved four main related activities that examined key elements of disaster risk: 1) the trigger, assessing extreme rainfall trends based on daily records; 2) the hazards, through an evaluation of the relevance of land use and cover (LUC) to slope failure; 3) elements of social vulnerability, looking at its geography and trend at the turn of the century, and also exploring the role of globalisation in specific communities; and 4) an assessment and mapping of disaster risk in two sites, including an estimation of exposure levels to hazards. Methods range from statistical analysis of quantitative data (rainfall, landslide, and vulnerability chapters), GIS-based modelling (risk mapping), and qualitative analysis including interviews.
The main findings state that: increasing annual and extreme rainfall has contributed to higher disaster risk only in a few areas; LUC change from forest to annual crops has increased risk in a few locations but it has not done so in most of the volcanic highlands either because there has been only minor LUC change or because LUC does not seem to have an effect on slope failure in certain types of geology. Disaster risk has decreased overall because vulnerability has become lower in the vast majority of mountain areas but risk may be higher as a result of increased exposure to hazards either in mountain communities or in marginal areas of the capital and surrounding municipios. The analysis of risk helped identify four mountain zones where risk is very likely to have increased. Further research questions are mostly related to studying the evolution of climate-related disaster risk in those areas.
Signal processing methods for cerebral autoregulation
Keywords: maximal overlap discrete wavelet transform
signal processing
cerebral autoregulation
near infrared spectroscopy
hilbert wavelet
non-parametric correlation analysis
gaussian copula analysis

Cerebral autoregulation describes the clinically observed phenomenon that cerebral blood flow remains relatively constant in healthy human subjects despite large systemic changes in blood pressure, dissolved blood gas concentrations, heart rate and other systemic variables. Cerebral autoregulation is known to be impaired post ischaemic stroke, after severe head injury, in patients suffering from autonomic dysfunction and under the action of various drugs. Cerebral auto-regulation is a dynamic, multivariate phenomenon. Sensitive techniques are required to monitor cerebral auto-regulation in a clinical setting. This thesis presents 4 related signal processing studies of cerebral autoregulation. The first study shows how consideration of changes in blood gas concentrations simultaneously with changes in blood pressure can improve the accuracy of an existing frequency domain technique for monitoring cerebral autoregulation from spontaneous fluctuations in blood pressure and a transcranial doppler measure of cerebral blood flow velocity. The second study shows how the continuous wavelet transform can be used to investigate coupling between blood pressure and near infrared spectroscopy measures of cerebral haemodynamics in patients with autonomic failure. This introduces time information into the frequency based assessment, however neglects the contribution of blood gas concentrations. The third study shows how this limitation can be resolved by introducing a new time-varying multivariate system identification algorithm based around the dual tree undecimated wavelet transform. All frequency and time-frequency domain methods of monitoring cerebral autoregulation assume linear coupling between the variables under consideration. The fourth study therefore considers nonlinear techniques of monitoring cerebral autoregulation, and illustrates some of the difficulties inherent in this form of analysis. The general approach taken in this thesis is to formulate a simple system model; usually in the form of an ODE or a stochastic process. The form of the model is adapted to encapsulate a hypothesis about features of cerebral autoregulation, particularly those features that may be difficult to recover using existing methods of analysis. The performance of the proposed method of analysis is then evaluated under these conditions. After this testing, the techniques are then applied to data provided by the Laboratory of Human Cerebrovascular Physiology in Alberta, Canada, and the National Hospital for Neurology and Neurosurgery in London, UK.
Creation and manipulation of quantum states in nanostructures
Keywords: entanglement
crystal defect
NMR
magnetic sensor

Nanostructures are promising building blocks for quantum technologies due to their reproducible nature and ability to self-assemble into complex structures. However, the need to control these nanostructures represents a key challenge. Hence, this thesis investigates the manipulation and creation of quantum states in certain nanostructures. The results of this thesis can be applied to quantum information processing and to extremely sensitive magnetic-field measurements.
In the first research chapter, we propose and examine methods for entangling two (remote) nuclear spins through their mutual coupling to a transient optically excited electron spin. From our calculations we identify the specific molecular properties that permit high entangling power gates for different protocols.
In the next research chapter, we investigate another method to create entanglement; this time between two remote electronic spins. This method uses a very sensitive magnetic-field sensor based on a crystal defect that allows the detection of single magnetic moments. The act of sensing the local field constitutes a two-qubit projective measurement. This entangling operation is remarkably robust to imperfections occurring in an experiment.
The third research chapter presents an augmented sensor consisting of a nitrogen-vacancy centre for readout and an `amplifier' spin system that directly senses tiny local magnetic fields. Our calculations show that this hybrid structure has the potential to detect magnetic moments with a sensitivity and spatial resolution far beyond that of a sensor based on only a nitrogen-vacancy centre, and indeed this may be the physical limit for sensors of this class.
Finally, the last research chapter investigates measurements of magnetic-field strength using an ensemble of spin-active molecules. Here, we describe a quantum strategy that can beat the common standard strategy. We identify the conditions for which this is possible and find that this crucially depends on the decoherence present in the system.
Understanding the link between interleukin 17 and vaccine-induced protection in tuberculosis
Keywords: T cells
interleukin 17
cytokines
cholera toxin
tuberculosis
immunology

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M.tb), remains a global health problem and although BCG offers some protection against childhood disseminated disease and other mycobacterial infections, its efficacy against pulmonary TB varies between 0 and 80%. Modified Vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel TB vaccine designed to boost mycobacterium-specific CD4+ T cell response primed by BCG. MVA85A induces strong interferon (IFN)-γ responses, a cytokine known to be essential for protection following M.tb infection. A strong IFN-γ response is not a correlate of protection and in terms of the adaptive response, interleukin (IL)-17 is emerging as an important cytokine following vaccination as it is thought to help boost IFN-γ production by CD4+ T cells. This thesis shows that MVA85A induces IL-17 in PBMC and whole blood of human BCG – MVA85A vaccinees. This is replicated in mice receiving BCG – MVA85A intranasally. The administration of cholera toxin (CT) with BCG enhances IL-17 and confers improved protection following M.tb challenge, which is partially dependent on IL-17 and on the mucosal route of administration. Since CT is not a suitable adjuvant in humans, an alternative IL-17-inducing pathway was investigated. In human BCG – MVA85A-vaccinated volunteers, blocking the hydrolysing ability of the CD39, an apyrase responsible for hydrolysing pro-inflammatory ATP, enhances IL-17 production. Challenge of BCG – MVA85A-vaccinated CD39-/- mice with M.tb slightly improved the protective capacity of the vaccine, suggesting that a pathway dependent on ATP-driven inflammation may be a target for improving the immunogenicity of a vaccine against M.tb disease. Overall, this thesis has confirmed the important role of IL-17 in vaccine-induced protection against TB disease and identifies a possible target pathway for improvement of a novel vaccine.
Two-channel Kondo phases in coupled quantum dots
Keywords: two-channel Kondo
quantum dots
numerical renormalization group
NFL
NRG
Kondo
non-Fermi liquid
Anderson model

We investigate systems comprising chains and rings of quantum dots, coupled to two metallic leads. Such systems allow to study the competition between orbital and spin degrees of freedom in a nanodevice, and the effect this subtle interplay has on two-channel Kondo (2CK) physics. We demonstrate that a rich range of strongly correlated electron behaviour results, with non-Fermi liquid 2CK phases and non-trivial phase transitions accessible. We employ physical arguments and the numerical renormalization group (NRG) technique to analyse these systems in detail, examining in particular both thermodynamic and dynamical properties.
When leads are coupled to either end of a chain of dots, we show that the resulting behaviour on low temperature/energy scales can be understood in terms of simpler paradigmatic quantum impurity′⊨.Aneffectivelow-e≠rgysing≤-sπn2CKmodelisderivedforallodd-≤n>hcha∈s,whi≤thebehaviourofeven-≤n>hcha∈sisrelatedfundamentally→t
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In particular, for small interdot coupling, we show that an effective coupling mediated though incipient single-channel Kondo states drives all odd chains to the 2CK fixed point (FP) on the lowest temperature/energy scales. A theory is also developed to describe a phase transition in even chains. We derive an effective channel-anisotropic 2CK model, which indicates that the critical FP of such models must be the 2CK FP. This physical picture is confirmed using NRG for various chain systems.
We also examine the effect of local frustration on 2CK physics in mirror-symmetric ring systems. The importance of geometry and symmetry is demonstrated clearly in the markedly different physical behaviour that arises in systems where two leads are either connected to the same dot, or to neighbouring dots. In the latter case, we show for all odd-membered rings that two distinct 2CK phases, with different ground state parities, arise on tuning the interdot couplings. A frustration-induced phase transition thus occurs, the 2CK phases being separated by a novel critical point for which an effective low-energy model is derived. Precisely at the transition, parity mixing of the quasidegenerate local trimer states acts to destabilise the 2CK FPs, and the critical FP is shown to consist of a free pseudospin together with effective single-channel spin quenching. While connecting both leads to the same dot again results in two parity-distinct phases, a simple level-crossing transition now results due to the symmetry of the setup. The proposed geometry also allows access to a novel ferromagnetically-coupled two-channel local moment phase.
Driven by varying the interdot couplings and occurring at the point of inherent magnetic frustration, such transitions in ring structures provide a striking example of the subtle interplay between internal spin and orbital degrees of freedom in coupled quantum dot systems, and the resulting effect on Kondo physics.