VictorJuiz/thesis huggingface dataset:
Trapping ultracold atoms in time-averaged adiabatic potentials

This thesis describes the trapping and manipulation of ultracold atoms in time-averaged adiabatic potentials (TAAP). The time-averaged adiabatic potential, proposed in [Phys. Rev. Lett. 99, 083001 (2007)], uses resonant radio frequency (rf) radiation to couple the different magnetic substates of a hyperfine level manifold. The resultant dressed states are time-averaged and produce smooth and versatile trapping geometries. More specifically, we apply rf-radiation (MHz) to a quadrupole magnetic field, which results in an ellipsoidal trapping potential for rubidium-87 atoms in the F=1 manifold. This geometry is time-averaged with the help of oscillating (kHz) Helmholtz fields.
We develop a convenient loading scheme for the TAAP which uses a standard TOP trap and suffers negligible atom losses and heating. Subsequently we characterize the TAAP trap itself and observe low heating rates and sufficient lifetimes (>3s). Furthermore it is possible to use a second, weaker rf-field to evaporatively cool the atoms to quantum degeneracy [Phys. Rev. A. 81, 031402 (2010)]. This opens up a route for further experiments in this potential: we show how atoms can be trapped in a double well potential and a ring trap geometry. Additionally a process to instigate rotation in these potentials by rotating the polarization of the rf-radiation is developed and implemented. This allows us to impart angular momentum onto the atomic cloud and spin it into a ring.

Keywords: TAAP
adiabatic potential
BEC
Advisor: Foot, C
"All Conflict is Local"

Previous civil war analyses have approached conflict as a single category with limited exceptions, and this thesis project assesses whether differentiating conflicts by their type and intensity using a local-level geo-referenced analytical approach produces differing results for sub-groups of conflicts. The conflicts are divided into 1) governmental hostilities, where the aim of the armed non-state group is to capture the state, and 2) territorial hostilities, where the aim of the armed non-state group is to capture increased autonomy or secession for a territorial claim. The conflicts are also differentiated by intensity into 1) low-intensity conflicts, with fewer than 1000 battle-related deaths per year, and 2) civil wars, with 1000 or more battle-related deaths per year. The results demonstrate that conflicts with differing insurgent goals and intensities of battle are correlated with markedly different factors. There are three factors – local population density, change in local rainfall, and statewide GDP growth – that are significant to both governmental and territorial hostilities but have opposite signs for the two sets. Only one variable – Polity IV scores – showed a consistently significant correlation for governmental and territorial hostilities. There are no factors that are significant to both low-intensity conflict and higher-intensity civil war. These findings suggest that approaching all conflicts as a single class, particularly at the local level, may not reveal significant differences in factors correlated with conflict. Modeling of local conflict will require differentiation of conflicts into salient sub-groups. For policymakers and practitioners, this research suggests that there is not a one-size-fits-all approach for conflict prevention but that strategies need to be targeted to specific types of conflict.

Keywords: violence
civil conflict
civil war
Advisor: Duch, R
Designing a 3.8-GeV/c muon-decay ring and experiment sensitive to electronvolt-scale sterile neutrinos

The liquid-scintillator neutrino-detector (LSND) and mini booster neutrino experiment (MiniBooNE) experiments claim to observe the oscillation ῡµ→ ῡe, which can only be explained by additional neutrinos and is a claim that must be further tested. This thesis proposes a new accelerator and experiment called νSTORM to refute or confirm the oscillation these claims by studying the CPT-equivalent channel νe→νµ. A 3.8-GeV/c muon decay ring is proposed with neutrino detectors placed 20 m and 2000 m from the decay ring. The detector technology would be a magnetized iron sampling calorimeter, where the magnetic field is induced by a superconducting transmission line. In a frequentist study, the sensitivity of this experiment after 5 years would be >10σ. The range of the thesis discussion starts with the proton front-end design and ends with neutrino parameter estimation. After describing the phenomenology of sterile neutrinos, the facility and detector performance work is presented. Finally, the systematics are explained before the sensitivity and parameter-estimation works are explained.

Keywords: neutrino factory
sterile neutrino
nuSTORM
Advisor: Cobb, J
Complaint in Scotland c. 1424 - c. 1500

This thesis provides the first account of complaint in Older Scots literature. It argues for the coherent development of a distinctively Scottish complaining voice across the fifteenth century, characterised by an interest in the relationship between amatory and ethical concerns, between stasis and narrative movement, and between male and female voices.
Chapter 1 examines the literary contexts of Older Scots complaint, and identifies three paradigmatic texts for the Scottish complaint tradition: Ovid’s Heroides; Boethius’s De Consolatione Philosophiae; and Alan of Lille’s De Planctu Naturae.
Chapter 2 concentrates on the complaints in Oxford, Bodleian Library MS Arch. Selden. B. 24 (c. 1489-c. 1513). It considers afresh the Scottish reception of Lydgate’s Complaint of the Black Knight and Chaucer’s Anelida and Arcite, and also offers original readings of three Scottish complaints preserved uniquely in this manuscript: the Lay of Sorrow, the Lufaris Complaynt, and the Quare of Jelusy.
Chapter 3 focuses on the relationship between complaint and narrative, arguing that the complaints included in the Buik of Alexander (c. 1438), Lancelot of the Laik (c. 1460), Hary’s Wallace (c. 1476-8), and The Buik of King Alexander the Conquerour (c. 1460-99) act as catalysts for narrative movement and subvert the complaint’s traditional identity as a static form.
Chapter 4 is a study of complaint in Robert Henryson’s three major works: the Morall Fabillis (c. 1480s); the Testament of Cresseid (c. 1480-92); and Orpheus and Eurydice (c. 1490-2), and argues that Henryson consistently connects the complaint form with the concept of self-knowledge as part of wider discourses on effective governance.
Chapter 5 presents the evidence that a text’s identity as a complaint influenced its presentation in both manuscript and print witnesses. The witnesses under discussion date predominantly from the sixteenth century; the chapter thus also uses them to explore the complaints’ later reception history.

Keywords: Complaint
Lament
Chaucer
Book History
Medieval Literature
Older Scots Literature
Advisor: Mapstone, S
Quantifying regional left ventricular function using spatio-temporal tracking techniques

Increasingly, diagnosis of cardiac disease, relies on computer processing of images to aid decision making. In this thesis, we use echocardiography, which is the most widely used cardiac imaging modality to study the motion of the left ventricle.
Currently, clinical reporting of echocardiography examinations is operator-dependent and largely qualitative. Commercially available software does not track the left ven- tricle. Also, it does not provide quantification of regional function.
This thesis establishes a framework for the quantitative regional analysis of left ven- tricular function. The endocardial and epicardial contours are automatically tracked during the cardiac cycle. A quantitative measure of regional endocardial wall excur- sion and myocardial thickening, based on a 16-segment model of the heart, is then obtained based on these boundaries.
The new tracking framework is based on Kalman filtering which makes a single pre- diction as to the position of the boundary on the next frame. We develop a mea- surement model for the endocardial border, the tissue/blood interface, and the epi- cardium, the tissue/tissue interface. Having tracked the endocardial and epicardial boundaries, we introduce an interpretational space which provides clinically mean- ingful regional quantitative measures of left ventricular function. We illustrate all the concepts on one example.
We apply the ideas developed to stress echocardiography, in a small retrospective clinical test.

Advisor: Noble, A
Dynamic mechanical properties of fibre reinforced plastics

A small gas gun, capable of accelerating a projectile 1m long by 25.4mm diameter to about 50 m/s, and an extended split Hopklnson bar apparatus have been designed and constructed for the tensile impact testing of fibre reinforced composite specimens at strain rates of the order of 1000/s. Elastic strain measurements derived from the Hopkinson bar analysis are checked, using strain gauges attached directly to the specimen and the validity of the elastic moduli determined under tensile impact is confirmed.
Epoxy specimens reinforced with plain-weave fabrics of either carbon or glass or with several hybrid combinations of the two in various lay-ups, giving five different weight fractions of reinforcement from all-carbon to all-glass, have been tested in tension at three strain rates, nominally, ~10-3/s, ~10/s and ~103/s. The effect of both hybrid composition (volume fraction of carbon reinforced plies) and applied strain rate on the tensile modulus, the tensile strength and the strain to fracture is determined and a limited hybrid effect is observed in specimens with a carbon volume fraction in the approximate range 0.6 to 0.7 where, at all three strain rates there is an enhancement of the failure strain over that for the all-carbon plies and an increased failure strength, most marked in the impact tests, over that predicted by the rule of mixtures. The fracture surfaces of specimens are examined by optical and scanning electron microscopy and the failure process in the hybrid composites is related to that found in the all-carbon and the all-glass specimens.
The classical laminated plate theory and the Tsai-Wu strength criterion are used to predict the stiffness and strength of the hybrid composites from the elastic and strength properties of the constituent plies. Analytical predictions are in good agreement with experimental measurements.

Advisor: Harding, J
Design and synthesis of small molecule chemical probes for bromodomain-containing proteins.

Bromodomains (BRDs) are protein modules which bind to acetylated lysines on histones and transcriptional regulating proteins. BRD-containing proteins are involved in a large variety of critical cellular processes and their misregulation, or mutation of the genes encoding for them, has been linked to pathogenesis in humans. The generation of chemical probes (potent, selective and cell permeable small molecules) in cellular experiments to investigate the biological role of the BRDs is thus desirable.
A chemical probe for the CREB (cyclic-AMP response element binding protein) binding-protein (CBP) and E1A binding protein (p300) BRDs was developed, starting from a low molecular weight, weak and non-selective dimethylisoxazole benzimidazole compound. Parallel synthesis was used to optimise the initial hit into a weak, but selective CBP inhibitor. Further modification of the two N-1 and C-2 moieties of the benzimidazole scaffold, led to highly potent and selective CBP inhibitors. Structure-guided design was then applied to optimise the selectivity of the series for CBP over the first domain of bromodomain-containing protein 4 BRD4(1). A strategy to reduce the flexibility of the N-1 and C-2 ethylene linker groups through the incorporation of conformational constraints led to inhibitors with increased selectivity. The optimal compound was highly potent for the CBP and p300 BRDs (Kd 21 nM and 32 nM, respectively) and selective over BRD4(1) (40-fold and 27-fold, respectively). On-target cellular activity was observed in a fluorescence recovery after photobleaching (FRAP) assay (0.1 μM), a p53 reporter gene assay (IC50 1.5 μM) and a Förster resonance energy transfer (FRET) assay (5 μM).
A weak indolizine bromodomain-containing protein 9 (BRD9) inhibitor was used as the starting point for the development of a BRD9/BRD7 chemical probe. Analogues were synthesised via [3+2] cycloadditions. An optimised compound was found to be highly potent (68 nM) and selective over BRD4(1) (34-fold). On-target cellular activity was observed in a FRAP assay (5 μM). Efforts were made to improve the cellular activity through the introduction of an ionisable centre to aid solubility. A selection of piperazine analogues were shown to be potent and selective, and these compounds warrant further investigation of their selectivity and cellular activity.
Overall, the work has led to the first potent and selective inhibitors of the CBP/p300 and BRD9 BRDs. It also highlights the role of structural analysis in the development of inhibitors that modulate protein-protein interactions.

Keywords: organic chemistry
medicinal chemistry
structure-based drug design
epigenetics
bromodomains
Advisor: Schofield, C
Brennan, P
Further results on Gram's Law

This thesis shows that Gram's Law and the Rosser Rule (methods for locating zeroes of the Riemann zeta-function) fail in a positive proportion of cases. A weaker version of Gram's Law is shown to be true in a positive proportion of cases. Also included are theorems on Turing's Method and its extensions to Dirichlet L-functions and Dedekind zeta-functions.

Keywords: Turing's Method
Gram's Law
zeta function
Rosser Rule
Advisor: Heath-Brown, DR
Magnetotransport in Graphene: A study of Quantum Hall Breakdown, Energy Loss Rates, and Weak Localization

This thesis reports magnetotransport measurements in graphene Hall bar devices. Graphene samples fabricated from different techniques (epitaxial growth on silicon carbide, exfoliation, and CVD) are measured and compared. Measurements are taken primarily using a 21T magnet, at liquid Helium 4 temperatures.
The first three chapters present the background for the work. Chapter One details the motivation for the thesis, and gives a general background to carbon and the state of carbon research. Chapter Two covers the theoretical background of graphene, including the anomalous quantum Hall effect and weak localization. Chapter Three covers the synthesis of graphene and a typical procedure undertaken for device fabrication.
The next three chapters report experimental results. Chapter Four presents measurements of the energy loss rates in exfoliated graphene. The mechanism of carrier energy loss is investigated, and compared to theory. Further, the breakdown of the quantum Hall effect in the device is investigated, demonstrating peak current densities far in excess of those found in the literature for exfoliated graphene. Chapter Five shows measurements comparing the carrier energy loss rates in graphene derived from the epitaxial, exfoliated and CVD fabrication techniques. An unconventional method for measuring the energy loss rate based on measuring the weak localization peak is developed, and trends in the energy loss rates with carrier density are investigated for a wide range of devices. Chapter Six reports a comparison of the decomposed weak localization scattering lengths from graphene devices derived from the epitaxial and CVD methods, and compares these to measurements from the literature. Further, a previously reported saturation of the weak localization in graphene is investigated, and demonstrated to be an experimental artefact.
This thesis provides a development of the understanding, and an experimental verification, of several aspects of heat transfer in graphene. An understanding of heat transfer is of critical importance to proposed high-density nano-electronics, and bolometry applications. The high breakdown currents and observed trends in carrier density are also of significant assistance in the design of low-cost resistance metrology devices based on graphene.

Keywords: Nanotechnology
Magnetotransport
Carbon
Advisor: Nicholas, R
Coordination of frontline workers for improving the health of children in Rajasthan (India) : a case study

All governments aim to ensure better health and nutrition to children. The Rajasthan state (India) has implemented a unique frontline coordination model where Accredited Health Social Activist (ASHA) Sahyoginis are expected to support two other frontline workers (FLWs) i.e. the Anganwadi Workers from the Integrated Child Development Services and the Auxiliary Nurse Midwives from the Health department to improve child health. This thesis focuses on examining the existing coordination between the three groups of FLWs in Rajasthan by exploring FLWs' participation in child immunisation and Vitamin A supplementation (two common activities), service coverage and beneficiary's' knowledge (expected outcomes), and the challenges faced and areas that need improvement for better frontline coordination.
A mixed methods design was used. Sixteen villages from two blocks (tribal and non-tribal) of Udaipur district (Rajasthan) were selected using multistage purposive sampling. The formative stage included 12 FLWs' in-depth interviews (IDIs) as well as a review of FLWs' job descriptions to understand the process and government expectations on their participation in routine childhood immunisation, polio camps, routine Vitamin A supplementation and Vitamin A campaigns. The next stage included data collection from the 16 selected villages i.e. structured questionnaire survey of FLWs (46), observations of Maternal and Child Health and Nutrition Day (16), review of FLWs' immunisation and Vitamin A registers (32) and a structured questionnaire survey of registered infants' mothers (321)-all to ascertain the actual participation of FLWs in these four activities and the outcomes. IDIs with FLWs (46) and FLWs' line managers (17) were conducted to understand their experience, issues and solutions for better frontline coordination.
The participation of FLWs in three of the four activities (except Polio Camps) was found to be limited. The FLWs and their line managers were also dissatisfied with coordination between FLWs. Poor outcomes also indicated unsatisfactory coordination. Overall, frontline participation and outcomes were better in tribal than non-tribal villages. A variety of factors (i.e. personal, professional, organisational, and geo-socio-cultural) appeared to affect coordination between FLWs.
Appropriate recruitment, training, monitoring and supervision and rewards to the FLWs along with greater political commitment for coordinated approached and addressing intra-departmental challenges are proposed to improve frontline coordination and child health in Rajasthan.

Keywords: Integration
Community Health Workers
India
Coordination
Frontline Workers
Convergence
ASHA
Cooperation
NRHM
Advisor: Webster, P
Bhattacharyya, S
How does the chromatin remodeler ATRX identify its targets in the genome?

ATRX is a chromatin remodeling protein associated with X-linked Alpha-Thalassemia Mental Retardation syndrome and cancers that use the Alternative Lengthening of Telomere pathway. In the absence of ATRX there is a DNA damage response associated with telomeres and the expression of certain genes are perturbed. Recent findings (Law et al, 2010 Cell) have shown that ATRX is preferentially enriched at GC-rich tandem repeats in the genome. The mechanism for this localisation is unknown but may be related to the potential for these GC-rich tandem repeats to adopt non-B form DNA structures; ATRX has been shown to bind such structures (G4) in vitro. This study aims to understand the specific factors of the repeats that signal ATRX targeting.
To address the research questions, an experimental system was developed, in which known targets, the ψζ VNTR and telomere repeats, were inserted into an inducible ectopic gene in the 293T-Rex cell line by site-directed recombination.
ATRX was found to be enriched at the ectopic repeats compared to an endogenous negative control suggesting that it is recruited by the repeats independent of its original context. Furthermore, ATRX enrichment increased upon transcription of the ectopic gene, and this was dependent on the orientation of the repeat with the non-template strand being G-rich. Interestingly, when the repeat was transcribed, the distribution of ATRX across the repeats was asymmetrical with most ATRX binding downstream of the repeat. Moreover, there was a direct correlation between the repeat size and level of ATRX bound: the longer the repeat the higher the increase in ATRX enrichment.
To determine the signal for ATRX binding, assays were performed to look for features which reflected the distribution of ATRX including H3K9me3, RNA polII, G4, R loops and DNA supercoiling. R loops look to be a strong candidate for the signaling of ATRX binding.

Keywords: non-B DNA structures
ATR-X syndrome
G-quadruplexes
chromatin remodelling factors
G4
GC-rich tandem repeats
R-loops
ATRX
Advisor: Gibbons, R
The role of inflammasomes in intestinal inflammation

Single Nucleotide Polymorphisms (SNPs) in the intracellular pattern recognition receptor gene NLRP3 are associated with susceptibility to Crohn’s disease, a form of inflammatory bowel disease (IBD). Following cell damage or infection, NLRP3 triggers the formation of inflammasomes, a multimolecular protein complex containing NLRP3, ASC and caspase-1, which mediate secretion of IL-1β and IL-18. NLRP3 inflammasome activation in macrophages has been implicated in protection against several pathogens, but whether NLRP3 activation in tissue cells contributes to protective immunity against bacterial pathogens is unknown. We show that upon infection with the attaching/effacing (A/E) intestinal pathogen Citrobacter rodentium, Nlrp3-/- and Asc-/- mice displayed higher bacterial colonization, more weight loss and exacerbated intestinal inflammation. We further show that Nlrp3 inflammasome activation in intestinal epithelial cells (IECs) acts rapidly after infection to limit bacterial replication and penetration, and inhibits the development of inflammatory pathology in the gut. We also show that epithelial Nlrp3-mediated protection is independent of the classical inflammasome cytokines IL-1β and IL-18. Thus an Nlrp3-Asc circuit in IECs regulates early defense against a mucosal pathogen and limits inflammation in the intestine. Nlrp3 inflammasome activation has also been implicated in protection in acute models of experimental colitis, but its role in chronic models of colitis is unknown. We found that Asc signaling is necessary for the development of innate chronic intestinal inflammation driven by Helicobacter hepaticus. Thus while deficient inflammasome signaling in tissue cells increases susceptibility towards enteric pathogens, excessive inflammasome activation can drive chronic intestinal inflammation.

Keywords: mucosal immunity
Inflammasome
intestinal inflammation
Advisor: Maloy, K