VictorJuiz/thesis huggingface dataset:
Investigating nonlinear integrable optics with a Paul trap
Keywords: high-intensity accelerators
landau damping
quasi-integrable optics
coherent resonances
Paul trap
nonlinear integrable optics

Designing high-intensity accelerators has traditionally relied on using computer simulations to study the beam dynamics. As intense beams are comprised of large numbers of particles, all interacting via Coulomb forces, such simulations require significant computational power in order to numerically predict these interactions. The Intense Beams Experiment (IBEX) is a linear Paul trap that can replicate the transverse beam dynamics in accelerators by trapping low-energy ions using RF electric fields that emulate the magnetic focusing elements of particle accelerators. IBEX’s flexibility allows different lattice designs and beam intensities to be tested with ease, which means that it can be used to test novel lattice configurations for high-intensity accelerators. Examples of such lattices arise from the theory of Nonlinear Integrable Optics, and, as discussed in this thesis, the related theory of Quasi-Integrable Optics (QIO). These theories suggest techniques for introducing nonlinear elements such as octupoles into an accelerator lattice, while keeping the system integrable and hence maintaining stable particle motion.
In this work, an upgrade to the original IBEX trap was designed, manufactured, and commissioned with the aim of experimentally testing the principles of QIO. Simulations were used to test the ability of a quasi-integrable lattice to damp a space-charge-driven coherent resonance without exciting the 4th order incoherent resonance in the vicinity. This lattice was then compared to a lattice which broke the integrability conditions, which was shown to excite the 4th order resonance. Using the newly-commissioned IBEX-2 trap, we were then able to test the quasi-integrable lattice experimentally and verify the results from simulations. This thesis demonstrates the first ions successfully trapped in a quasi-integrable lattice in a Paul trap, and discusses the benefits of introducing octupole elements according to the method prescribed by the theory of QIO. The experimental results presented here show the potential value of QIO to research on high-intensity beams in accelerators.
Inertial learning and haptics for legged robot state estimation in visually challenging environments
Keywords: legged robots
inertial navigation systems
state estimation

Legged robots have enormous potential to automate dangerous or dirty jobs because they are capable of traversing a wide range of difficult terrains such as up stairs or through mud. However, a significant challenge preventing widespread deployment of legged robots is a lack of robust state estimation, particularly in visually challenging conditions such as darkness or smoke.
In this thesis, I address these challenges by exploiting proprioceptive sensing from inertial, kinematic and haptic sensors to provide more accurate state estimation when visual sensors fail. Four different methods are presented, including the use of haptic localisation, terrain semantic localisation, learned inertial odometry, and deep learning to infer the evolution of IMU biases.
The first approach exploits haptics as a source of proprioceptive localisation by comparing geometric information to a prior map. The second method expands on this concept by fusing both semantic and geometric information, allowing for accurate localisation on diverse terrain.
Next, I combine new techniques in inertial learning with classical IMU integration and legged robot kinematics to provide more robust state estimation. This is further developed to use only IMU data, for an application entirely different from robotics: 3D reconstruction of bone with a handheld ultrasound scanner. Finally, I present the novel idea of using deep learning to infer the evolution of IMU biases, improving state estimation in exteroceptive systems where vision fails.
Legged robots have the potential to benefit society by automating dangerous, dull, or dirty jobs and by assisting first responders in emergency situations. However, there remain many unsolved challenges to the real-world deployment of legged robots, including accurate state estimation in vision-denied environments. The work presented in this thesis takes a step towards solving these challenges and enabling the deployment of legged robots in a variety of applications.
To what extent are formative assessment strategies used in schools contributing to student learning? A systematic review and meta-analysis
Keywords: publication bias
holistic learning
heterogeneity

Objective: To determine the effects of formative assessment interventions and strategies aimed at optimising the learning outcomes in children and adolescents.
Design: A systematic review and meta-analysis.
Data sources: After searching PsycInfo, ERIC, Education Research Complete, A+ Education and Scopus electronic university databases, there were 3689 potentially eligible studies published between January 1, 2002 to December 31, 2022.
Eligibility criteria for selecting studies: This study includes randomised controlled trials, quasi-experimental studies, and controlled trials that assessed the effect of a formative assessment-based strategy or intervention against learning outcomes in students attending either primary or secondary years of schooling (i.e., aged 5–18 years).
Results: Thirty-eight (38) studies with over 16,000 participants and 43 calculated effect sizes were included in the final analysis. The sample size adjusted mean effect across all the learning and development outcomes was of a small to medium magnitude (Hedges’ g=0.31), 95% confidence interval [CI] (0.29 to 0.39). After applying the Duval and Tweedie (2000) Trim and Fill Method to account for publication bias, the average effect size was adjusted to g=0.16. Effect sizes also varied significantly based on whether they targeted cognitive, psychomotor, or affective learning outcomes. Only a small proportion (less than 10%) of formative assessment interventions examined in this systematic review indicated a detrimental impact on student learning and development.
Conclusion: Formative assessment interventions consistently have a positive effect on student learning in both primary and secondary school settings across psychomotor, affective, and cognitive learning domains. However, the reported effect of formative assessment interventions in previous meta-analytic studies appears to have been inflated by the inclusion of studies that suffer from weaker study designs. Furthermore, the scope of studies included in this systematic review and meta-analysis showed even studies with stronger study designs were plagued with poor methodological quality and substantial publication bias. Moreover, the evidence reported is limited by consistency in intervention dosage, study design, and data collection instruments.
Pulsed electron paramagnetic resonance investigation of molecular magnetic systems
Keywords: molecular magnetic system
EPR
quantum information processing

Porphyrins, consisting of four pyrroles connected by methine bridges, can accommodate different types of metal ions or groups in the centre, because the four nitrogen atoms in the molecule function as outstanding ligands. In this thesis, a vanadyl group is incorporated in the centre in order to investigate the electron spin–spin interactions and coherence properties, because the vanadyl group in the nuclear spin-free carbon−sulfide ligands has been found to have a long coherence time. Graphenoids, composed of annulated benzene rings, have the same basic unit of graphene. Because of the delocalisation of electrons in π-conjugation structure, graphenoids have many interesting electronic properties, and therefore have obtained attention from researchers in different fields. Through introducing different defects and side groups in the structures and adjusting the size and shape of the molecules, it is possible to tune the magnetic and coherence properties of graphenoids.
In this thesis, we use electron paramagnetic resonance spectroscopy to investigate the magnetic and coherence properties of an ensemble of isolated paramagnetic molecules. Vanadyl porphyrin dimers with different spacers are discussed, and we especially focus on the electron spin–spin interactions in these molecules. We use strongly and weakly coupled representations to describe the spin systems of triply linked dimers and all other dimers, respectively, because of different strengths of isotropic exchange coupling, compared with both the hyperfine coupling and the electron Zeeman anisotropy. The noncoincidence effects of different interaction tensors play an important role in the CW-EPR spectra and need to be considered in simulations. We also investigated the coherence properties dependence on different exchange coupling strengths and attached side groups. Furthermore, we discuss the temperature dependence of the coherence properties and structural effects on the magnetic properties by studying two types of graphenoids with two different defects, including two neighbouring five- and seven-membered rings and two disjoint five-membered rings.
Modelling the dynamic flight behaviour of birds in different frames of reference
Keywords: shearwater
reference frame
guidance
animal-borne camera
flight
soaring
motion capture
biomechanics
energetics
bird-of-prey
hawk
GPS
albatross
pursuit
animal behaviour
dynamic soaring

In this thesis I consider two aspects – energetics and guidance – of two dynamic flight behaviours performed by birds – dynamic soaring and prey pursuit. Uniting the thesis is the collection and modelling of bird trajectory data in different frames of reference to make inferences on dynamic flight behaviour. In particular, I collect data in a camera-fixed reference frame to model the dynamic soaring flight trajectories of Manx shearwater in an aerodynamic reference frame, whereas I model the attack trajectories of Harris’ hawks in both an inertial and a background frame of reference using data collected in an Earth-fixed frame of reference. The output of my investigation into the energetics of dynamic soaring is the first empirical demonstration of dynamic soaring outside the albatrosses, the formulation of a new metric for identifying and quantifying dynamic soaring, and the demonstration that the large-scale distribution of the Manx shearwater is affected by their dynamic soaring behaviour. The output of my investigation into the guidance of prey pursuit is the finding that Harris’ hawk attack trajectories are well modelled by the proportional navigation (PN) guidance law commonly used by homing missiles. However, I also show that a guidance law that can be mechanised using only visual information – rather than the inertial and visual information required by PN – also successfully fits attack trajectory data. Finally, I propose a method for analysing eye-in-head movements during dynamic flight in birds, and I find that Harris’ hawks limit eye-in-head movement during terminal pursuit, a necessary condition to implement PN guidance. In being reflective about the reference frames in which I model bird behaviour and, in cases, by modelling the same data in different reference frames, I expose the utility of the reference frame concept in analysing biological systems.
Understanding and improving disability training for health workers in sub-Saharan Africa
Keywords: sub-Saharan Africa
disability
health worker training

The World Health Organization estimates that 16% of the world’s population is disabled. Health worker training in many countries has been described as limited, ineffective, and unsystematic with regard to disability. This insufficiency is likely to be detrimental to the quality of health care that disabled people receive across health systems globally and understanding the training and other mechanisms that help health workers to improve their care for disabled patients could improve health outcomes.
To date, there has been limited research on disability training to health workers in sub-Saharan Africa. Pilot programmes in countries like Ghana have shown promise, but there remain substantial gaps in the literature. This aim of this thesis is to understand how to improve health worker training in sub-Saharan Africa by exploring the current state of health worker training on disability in sub-Saharan Africa and makes recommendations to improve it. The thesis explores these topics through i) a systematic literature review to characterise existing health worker training on disability globally; ii) a document analysis of disability laws and policies in selected countries in sub-Saharan Africa; iii) secondary analysis of regional data to understand how disabled people use health services; and iv) qualitative interviews to explore health workers’ perspectives of training on disability in Ghana.
The systematic review found that there are numerous individual interventions to train health workers about disability, but these are usually one-off trainings, with limited evaluation, follow-up, or consistency across settings. Similarly, the document analysis showed some laws and policies required training, but did not provide further details (i.e., curriculum, budget, timing, etc.) necessary for implementation. Furthermore, secondary analysis showed that there were no substantial differences in where disabled people seek care, which emphasized the importance of training every health worker. Finally, the qualitative data demonstrated that training interventions were acceptable and effective in changing the attitudes and behaviour of health workers. However, these interviews, together with the other results of the thesis, show that health worker training must be more robust in its frequency, formality, and follow-up to ensure health workers are all trained to improve health equity for disabled people.
Differential DNA hydroxy/methylation analyses for improving prognostic accuracy in localised PDAC and a better understanding of PDAC progression
Keywords: patient stratification
PDAC
cancer research
differential DNA hydroxymethylation analyses
differential DNA methylation analyses

Despite immense efforts, the prognosis of pancreatic ductal adenocarcinoma (PDAC) remained very poor. The main reasons include the lack of early-stage symptoms and effective screening programmes, leading to delayed clinical presentations, with only 15-20% of patients being diagnosed with localised resectable tumours. However, ~40% of these patients develop distant recurrence within 12 months, suggesting that while clinically identified as localised, a subset of the patients likely had micro-metastatic lesions and neoadjuvant chemotherapies might have been the better option. There are strong demands for improving prognostic accuracy and this project aims to distinguish PDAC patients with metastasis-prone tumours from those with truly localised resectable tumours via DNA methylation (5mC) and hydroxymethylation (5hmC) signatures.
Starting with raw 5hmC & 5mC data, pairwise differential analyses were performed to identify significantly differentially hydroxy/methylated CpGs - D(h)MPs and significantly differentially hydroxy/methylated regions - D(h)MRs. ChAMP detected 3 DhMPs being significantly hypo-hydroxymethylated in patients with distant recurrence, whereas 21 DhMRs were significantly differentially hydroxymethylated. Similarly, 35459 DMPs and 551 DMRs were detected. Scorings were performed for subsequent unsupervised hierarchical clustering analyses to check how well the identified signatures distinguish between the two groups. The results showed that 5(h)mC profiles indeed have the power to separate patients into their prognostic groups. To gain a better understanding of the underlying mechanisms, functional enrichment analysis was performed for the top signatures. As validation, RT qPCR of selected genes in classical & squamous PDAC cell lines were performed; in which 6 of the candidate genes have a profound transcription pattern, suggesting an overlap between our hydroxy/methylomic-driven stratification and the transcriptomic-driven classical/squamous stratification.
In conclusion, this preliminary study showed that 5(h)mC signatures have the potential to improve prognostic accuracy. Most importantly, this approach can be adapted for other scientific questions, bringing new opportunities to combat PDAC and different diseases.
A mixed-methods study of antibiotics use and prescribing dynamics in Indonesian hospitals: implications for antimicrobial stewardship
Keywords: antibiotic use
antimicrobial stewardship
antimicrobial resistance

Antimicrobial resistance (AMR) is an accelerating public health problem, with antimicrobial agents, including their inappropriate use, being one of the key drivers. In Indonesian hospitals, there is a fragmented picture of antibiotic use and of the drivers of prescribing patterns. This thesis aimed to fill this knowledge gap by assessing patterns and quality indicators of antibiotic prescribing for hospitalised patients, mapping their drivers and dynamics, and exploring the factors influencing the implementation of antimicrobial stewardship (AMS) programmes.
Using an explanatory sequential mixed-method approach, data collection was conducted in six hospitals in Jakarta, between March 2019 and October 2020.
A quantitative survey found high proportions of hospitalised patients receiving systemic antibiotics, that guideline compliance was poor, use of blood cultures was low, and that prolonged surgical prophylaxis was common.
The qualitative findings revealed multidimensional social-cultural factors influenced antibiotic prescribing, such as disjunctions between drivers of AMR and day-to-day clinical practice, antibiotic prescribing as risk aversion vis-à-vis concerns of poor clinical outcomes, the ‘pull’ of conformity to normative, suboptimal group prescribing practices, and suboptimal operations of microbiology and surgical facilities. Effective AMS programme implementation was challenged by ineffective resourcing and institutional buy-in, cost-prohibitive culture testing, entangled hospital priorities to generate profits, and a non-collegial communication approach to AMS execution.
Three identified areas of improvement are addressing hierarchical cultural norms in the medical profession, encouraging ownership of the AMR problem and solution among all stakeholders, and developing sustainable context-specific AMS strategies. Based on the complex adaptive system (CAS) concept, I formulated four recommendations: 1) identifying the agents of influence; 2) evaluating the problem using a CAS lens; 3) developing health system resilience; and 4) identifying leverage points.
In conclusion, this thesis contributed to the development of a conceptual framework showing how multilevel and multidimensional social-cultural factors interact to influence antibiotic prescribing and AMS implementation.
Two-dimensional conformal field theories: the irrational, the rational and the celestial
Keywords: string theory
holographic correspondence
celestial holography
rational CFTs
quantum gravity
ADS/CFT correspondence
conformal bootstrap
conformal field theories

The aim of this thesis is to explore the world of two-dimensional Conformal Field Theories via bootstrap techniques. The thesis is divided in three central chapters, where we will study Irrational, Rational and Celestial CFTs.
The holographic dual to a theory of pure higher-spin gravity in AdS3 is an Irrational CFT with WN algebra, where N corresponds to the highest-spin field present in the theory. Our aim in chapter 3 will be to study the spectrum of such a theory of gravity by constructing the density of states via the Poincar ́e and Rademacher constructions, which both exploit the modular invariance of the torus partition function. When studying the densities, we encounter exponentially large amounts of negative-norm states in the near-extremal region, which would render the theory non-unitary. We propose to cure these negativities by adding operators of low twist, which can be interpreted naturally from the gravity perspective as orbifolds with conical defects and can be added without losing unitarity.
The classification of Rational CFTs will occupy our attention in chapter 4. Our goal is to understand the spectral decomposition of the torus partition function of several RCFTs, and see how it can aid in the efforts to explore the space of such theories. We begin by introducing the basics of harmonic analysis on the fundamental domain of the modular group. Afterwards, we study the Rankin-Selberg transform of one-character RCFTs’ partition function and find an interesting relation between different central charges. From there, we start investigating multi-character RCFTs, and make a proposal to build families of multi-character RCFTs from one-character theories via their Rankin-Selberg transforms.
The duality between scattering amplitudes of massless particles in R(2,2) space and the correlation functions of a Celestial CFT living on the celestial torus will be the subject of Chapter 5. The goal of this chapter is to provide a prescription that allows us to go from momentum-space amplitudes to the ambidextrous basis, where the celestial amplitudes take the form of a two-dimensional CFT correlation function, via an improved light transform. We explicitly build 2-, 3- and 4-point amplitudes of massless external particles, and show how the ambidextrous prescription maintains conformal covariance in all scattering channels whilst ridding the amplitude of its distributional factors. We then move onto an explicit tree-level four-gluon, where we will use alpha space decomposition, an inversion formula method specific to SL(2, R) primaries, to obtain data from the Celestial CFT’s spectrum.
Exploring multiple efficacies through sensory relatedness at Restore, an Oxfordshire mental health charity
Keywords: medical anthropology
multiple efficacies
treatment evaluation
sensory relatedness
community mental health

This thesis responds to the demand for an anthropological evaluation of the service at Restore. It is an exploration of the multiple efficacies in this community mental health charity. Empirically, I work with archival materials about the hospital and community spaces where Restore was incubated and founded. I also present ethnographic accounts of the gardening, craftwork, and catering work at Restore’s three recovery groups in Oxford and Banbury. I use a diversity of research methods to study these empirical materials, including participant learning and experience, visual archives analysis, spoken discourse analysis, photo-elicitation and semi-structured interviews.
Guided by the approach of Sensory Medical Anthropology, I emphasise the therapeutic efficacies generated through the restoration of the body’s orientation to others, a problem identifiable from the lived experiences of mental illness. I propose that the gardening, craftwork, and catering work at Restore’s recovery groups are intrinsically intercorporeal, and the processes for members (service users) to learn the body techniques and collaborate in groups cultivate vital and productive relations.
Moreover, the transmission of body techniques and the collaboration in groups cultivate care, which enables many members to transit into volunteering roles within Restore. Many members become empotted and emplaced as skilful workers for Restore’s shops and cafes that cater for the local community. Providing the multiple trajectories for a service member to become ‘better’ at Restore, the Oxfordshire Mental Health Parnership (OMHP)’s monitor of the ‘discharges’ of service users into paid employment, which is the most valued outcome that directly informs the statutory funding for Restore, needs to be re-considered. The definition of ‘moving on’ within the charity could also include more diverse possibilities to enable creative and long-term recoveries.