VictorJuiz/thesis huggingface dataset:
Reinforcement learning based mapless robot navigation

Navigation is the one of the most fundamental capabilities required for mobile robots, allowing them to traverse from a source to a destination. Conventional approaches rely heavily on the existence of a predefined map which is costly both in time and labour to acquire. In addition, maps are only accurate at the time of acquisition and due to environmental changes degrade over time. We argue that this strict requirement of having access to a high-quality map fundamentally limits the realisability of robotic systems in our dynamic world. In this thesis, we investigate how to develop practical robotic navigation, motivated by the paradigm of mapless navigation and inspired by recent developments in Deep Reinforcement Learning (DRL).
One of the major issues for DRL is the requirement of a diverse experimental setup with millions of repeated trials. This clearly is not feasible to acquire from a real robot through trial and error, so instead we learn from a simulated environment. This leads to the first fundamental problem which is that of bridging the reality gap from simulated to real environments, tackled in Chapter 3. We focus on the particular challenge of monocular visual obstacle avoidance as a low-level navigation primitive. We develop a DRL approach that is trained within a simulated world yet can generalise well to the real world.
Another issue which limits the adoption of DRL techniques for mobile robotics in the real world is the high variance of the trained policies. This leads to poor convergence and low overall reward, due to the complex and high dimensional search space. In Chapter 4, we leverage simple classical controllers to provide guidance to the task of local navigation with DRL, avoiding purely random initial exploration. We demonstrate that this novel accelerated approach greatly reduces sample variance and significantly increases achievable average reward.
The last challenge we consider is that of sparse visual guidance for mapless navigation. In Chapter 5, we present an innovative approach to navigate based on a few waypoint images, in contrast to traditional video based teach and repeat. We demonstrate that the policy learnt in simulation can be directly transferred to the real world and has ability to generalise well to unseen scenarios with minimal description of the environment.
We develop and test novel approaches towards the key issues of obstacle avoidance, local guidance and global navigation, towards our vision of enabling practical robotic navigation. We show how DRL can be used as a powerful model-free approach to tackle these issues.

Advisor: Markham, AC
Trigoni, A
Capacity and culpability

How should the criminal law account for defendants’ incapacities? It’s often claimed that some incapacities make individuals less culpable for wrongdoing. But what follows if this is true? Like many others, I claim that the criminal law ought not to convict offenders disproportionately to their culpability. Thus, if incapacities render individuals less culpable, then the criminal law ought to account for that lowered culpability. But rather than accepting this ‘culpability principle’ under the guise of non-instrumentalist retributivism, I instead derive it from instrumental considerations regarding fair labelling.
Next, I survey how the law accounts for incapacities. I generate and populate a novel threefold taxonomy of incapacity rules, comprising what I call incapacity doctrines, incapacity relativisations, and counterfactual incapacity relativisations. I then defend the use of these incapacity rules from certain critiques, including from those who argue for the abolition of some incapacity rules. Many incapacity rules are formulated not (only) by reference to their target incapacities, but (also) by reference to certain proxy attributes, and in particular to the relevant incapacity’s aetiology. I defend the use of such proxies but critique those rules which require proof of aetiological proxies in addition to proof of the underlying incapacity.
The final chapters ask why and how incapacities exculpate. I defend the widely accepted view that incapacities exculpate if they make defendants less able to conform to the requirements of a norm. Finally, I ask what it means for one to be incapable of something. I argue that we cannot rely only on metaphysical considerations when ascribing incapacities for the attribution culpability.

Keywords: Capacity
Crime
Incapacities
Advisor: Edwards, J
Stable isotopes as tracers of copper corrosion in the atmosphere and soil environment: a geographic study on brochantite and malachite formations on historic and archaeological material using δ18O, δ13C and δ2H

A refined methodology using light stable isotopes in precipitation to determine the formation location of copper minerals is tested, for the eventual use on archaeological bronzes that corroded in the soil environment. To do this, δ18O in historic brochantite and archaeological malachite is used to determine whether the region in which these common minerals formed may be identified when the δ18O is a function of the δ18O in meteoric water and temperature. The waters in each phase of the hydrologic cycle have distinct isotopic compositions and can yield information on climate or water provenance. The possibility that this δ18O study can be supplemented by including the hydroxyl-δ2H in brochantite or δ13C in malachite is explored as sub-studies.
This study shows no significant difference between the δ18OSO4 in brochantite, and the δ18OSO4 variances are about equal among the cities considered. Furthermore, there is no statistically significant correlation between δ18OSO4 or hydroxyl-2H and the δ18O in precipitation, precipitation amount, pH, surface temperature, latitude, or age of deposit. About 50% of brochantite’s δ18OSO4 is sourced from local meteoric water. Of the three SO2 → SO4 pathways that contribute oxygen in brochantite, oxygen percentages can be calculated for two pathways at a time.
The malachite data shows significant difference between the geographic groups surveyed, but does not suggest a statistically significant relationship between the δ18O or δ13C in malachite and the δ18O in local precipitation or surface temperature. A significant relationship is apparent between δ18O and δ13C with some clustering within sample sites. Therefore, a comprehensive study into the δ13C of malachite would be worthwhile. Climate-focused research also shows potential.
This work can be used to advise on authenticity issues or guide in provenance studies when choosing between suspected sites. Further refinement is necessary before it may be adopted for cases without suspected formation sites.

Advisor: Pollard, M
Sun Yat-sen on China's place in international society

This thesis argues that Sun Yat-sen's intellectual engagement with China’s entry into international society should be seen through the prism of tianxia wei gong (all-under- heaven is shared by all), the crown jewel in his ideas on international relations. While the literature on the expansion of international society essentially frames China as a passive recipient of the standard of civilization, Sun’s conceptualization of tianxia shows an active in-depth engagement with worldviews emanating from aspiring entrant nations which have hitherto been neglected. His conceptualization of tianxia rests on his belief in the possibility of equality and justice between nations, including those yet to attain full membership in international society, anchored by a moral hierarchy centered around wangdao and self-rectification. The analysis of Sun’s tianxia presented here suggests that standards of civilization are far more multi-dimensional and nuanced than the existing literature portrays. In essence, the standard of civilization should not be seen merely as a one-dimensional checklist of objective and discrete items to be checked off one by one. Sun’s ideas on tianxia and international relations suggest that there is more agency on the part of new entrants than commonly assumed. However, Sun’s privileging of the moral over the political dimension of self-rectification, while being the defining characteristic of his ideas, is also its key weakness, because Sun never effectively addresses the issue of what happens in the event that countries start prioritizing their immediate political or economic interests over morality. Finally, it is open to question whether nations not rooted in Confucian culture or familiar with the concept of wangdao could ever self-rectify and center themselves in Sun’s tianxia.

Keywords: Sun Yat-sen
Standard of Civilization
Tianxia
Expansion
International Society
Advisor: Khong, Y
Caplan, R
Responses to deaths in custody: the politics of prisons and immigration removal centres

My DPhil thesis explores responses to deaths in custody. Specifically, it is concerned with how a range of different actors respond to suicidal behaviour – including self-harm, attempted suicide and completed suicide – in prisons and immigration removal centres (IRCs).
It is a theoretical and empirical work, with two overarching aims. The first is to engage with theoretical accounts of imprisonment and immigration detention, as exemplified by literature on the sociology of punishment, and the politics of criminal justice and migration control. Throughout the thesis, I treat prisons and IRCs as social and political institutions, and analyse responses to the problems within them, including suicidal behaviour, as partly political in nature. The theoretical sections of the thesis are found mainly in Chapters 2 and 3, which review a wide range of relevant literature and develop an original argument about responses to deaths in custody. The theoretical claims made in these chapters are substantiated in later empirical sections.
The second aim is to make an original empirical contribution to the study of responses to suicidal behaviour in custody. There are three different types of ‘response’ that I discuss in the thesis, each of which corresponds to an empirical chapter. These are: prevention work inside immigration detention that is carried out by detainee custody officers and managers (Chapter 5); investigations into deaths in prisons and IRCs that are carried out by independent professionals (Chapter 6); policy efforts by political elites and expert bodies to reduce the number and rate of deaths in custody (Chapter 7). In each case, I set out the distinctive dynamics of the field, whether it is the internal life of an immigration detention centre, the bureaucratic process of a death investigation, or the bewildering world of government policymaking. The final chapter connects the theoretical and empirical sections of the thesis.

Keywords: Deaths in custody
Politics of punishment
Prisons
Punishment
Suicide
Immigration removal centres
Immigration control
Advisor: Bosworth, M
An integrated metagenomic approach to investigating disease heterogeneity in sepsis due to community-acquired pneumonia

Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. There is an increasing global burden of disease and it is associated with high mortality, long-term disability and shortened life expectancy. Clinical management of sepsis remains supportive rather than curative and progress in sepsis research has been severely constrained by a heterogeneous disease phenotype, limiting the interpretation of clinical trials and the development of effective therapeutic interventions. One source of heterogeneity is the pathogen but the frequent failure of clinical microbiology to identify the infecting organism in sepsis has limited efforts to understand the effect of disease heterogeneity involving the pathogen. Community-acquired pneumonia (CAP) is the most common cause of sepsis and clinical microbiology is unable to provide a diagnosis in 47% of such cases, suggesting that alternative methods such as clinical metagenomics may enable improved diagnostics.
Clinical metagenomics involves the application of next-generation sequencing technologies to characterise all the DNA and/or RNA present in a sample, enabling analysis of the entire microbiome as well as the human host genome or transcriptome from patient samples. This thesis presents the development and validation of Castanet, a method for targeted metagenomic sequencing using probe-based enrichment. Clinical metagenomic data is presented for 573 patients admitted to intensive care with sepsis due to CAP, including 447 patients for whom clinical microbiology did not identify a pathogen. In addition, digital droplet PCR data is presented for the most frequently identified causative bacteria (Streptococcus pneumoniae) and reactivated virus (Epstein-Barr virus) in the metagenomic cohort. Finally, this thesis explores how improved resolution of microbiology in the sepsis cohort can be applied to transcriptomic and genomic-based approaches to understand the host response in sepsis. This includes exploration of Epstein-Barr virus reactivation, differential gene expression analysis for different pathogens, and analysis of the association between specific HLA alleles and susceptibility to different pathogens.
This thesis demonstrates the utility of integrating metagenomic data with other omic methods to enable improved understanding of the heterogeneous host response in sepsis, with opportunities for a precision medicine approach.

Keywords: Metagenomics
Sepsis
Community-acquired pneumonia
Advisor: Knight, JC
Barnes, E
Putting English to work: a qualitative study of students at American universities

Employability has become a function of the university in recent decades following a shift in societal, economic, and political discourses. Employability’s importance has led the liberal arts to come under challenge because of their apparent lack of labor market utility. English, which has experienced steep declines in graduate numbers, has been perceived as lacking labor market connections and utility. As employability has been studied from a variety of perspectives – including numerous studies on the liberal arts and employer perspectives – this study chose to look at a single academic major from the student perspective.
The aim of this study was to explore the how students understood the connection between their academic course and post-graduation plans. Using a constructivist case study, data was collected from nine English majors at two mid-sized American universities through semi-structured interviews.
Thematic analysis of the data revealed that participants understood their English degree as being clearly connected to their future career plans. Although students perceived this connection through aspects like passion, employable skills, and the availability of widespread opportunities, they were explicit in noting the challenges and complexities of connecting the English degree to the labor market. This was expressed as a perceived lack of institutional and career support and the belief that no clear path exists to link English to a specific occupational industry.
The findings highlight the link between the English degree and the labor market as well as revealing student perceptions that their degree will influence and support their future career plans. Findings of this study may have policy and programmatic implications for English departments and institutions as they work to produce employable English graduates with strong connections to an academic field.

Advisor: Keep, E
Iron controls the adaptive immune response

Adaptive immune responses require dynamic cellular reconfigurations as antigen-specific lymphocytes proliferate, acquire effector functions and generate immunological memory. Several metabolic pathways are co-opted during this process, but specific metabolites identified as important substrates are rarely systemically limiting. Iron deficiency affects a billion people worldwide and a mutation in transferrin receptor that disrupts the ability of lymphocytes to acquire iron causes immunodeficiency. However, to date if and how serum iron deficiency disrupts adaptive immunity has not been investigated. Here we demonstrate that genetic defects in iron homeostasis, such as the TfrcY20H/Y20H mutation and IRP1/2 deficiency, cell-intrinsically disrupt adaptive immunity. We find that T-cell metabolic activity including mitochondrial ATP generation is impaired by limiting iron acquisition in vitro, concomitant with reduced proliferation, suggesting that iron is a key ‘immunometabolite’. We then provide in vivo evidence that transient and physiological serum iron deficiency caused by increased activity of the iron regulatory hormone hepcidin profoundly reduces the magnitude of the primary antigen specific CD8, CD4 and B-cell responses to multiple immunisation platforms, and alters the differentiation trajectory of CD8 T-cells such that memory and secondary recall responses are impaired even after iron status has been normalised. Low serum iron levels also disrupt protective T- and B-cell responses to experimental influenza virus infection, increasing lung viral load, inflammation and neutrophil infiltration, and prolonging weight loss in infected animals. Overall, these findings reveal an unexpected sensitivity of adaptive immunity to serum iron availability and may have implications for control of infections and vaccination programmes in developing-world populations where iron deficiency is highly prevalent and the infectious burden is considerable.
More generally we suggest that manipulating iron availability may provide a tool to control the amplitude and quality of adaptive immune responses.

Advisor: Drakesmith, H
BRCA2 loss induces an innate immune response via activation of the cGAS-STING pathway

Heterozygous germline mutations in BRCA2 predispose to cancer. Such BRCA2-deficient tumours are sensitive to PARP inhibitors. Yet, tumours acquire resistance and, eventually, relapse. The tumour suppressor BRCA2 plays key roles in genome maintenance. Chromosome instability upon loss of BRCA2 induces senescence and apoptosis. However, it can promote tumourigenesis, if p53 signalling is defective. Still, a p53-deficient tumour cell remains confronted with accumulating chromosome instability even though cell death is evaded.
Here, we investigated how p53-deficient tumour cells react to BRCA2 depletion on a transcriptional level. Expression of BRCA2 was inhibited for 4 or 28 days and differential gene expression was characterised. As an early response to loss of BRCA2 (4 days), genes involved in cell cycle, organelle fission, chromosome segregation, DNA replication and DNA repair were downregulated. Furthermore, cell cycle progression was perturbed which was associated with cell cycle arrest in G1. On the other hand, chronic loss of BRCA2 (28 days) resulted in upregulation of genes associated with an innate immune response. We confirmed that loss of BRCA2 instigated formation of micronuclei activating the cGAS-STING pathway which, in turn, cascaded into a type I IFN response. Moreover, treatment with PARP inhibitors further stimulated the activation of the type I IFN response in cells and tumours lacking BRCA2.
These findings demonstrate that genomic instability upon loss of BRCA2 inflicts a cell-intrinsic typeI IFN response which can be further stimulated pharmacologically by treatment with PARP inhibitors.

Keywords: cGAS-STING
innate immune response
BRCA
oncology
DDR
cancer
DNA damage response
Advisor: Tarsounas, M
Blackford, A
Sørensen, C
Amortized inference and model learning for probabilistic programming

Probabilistic modeling lets us infer, predict and make decisions based on incomplete or noisy data. The goal of probabilistic programming is to automate inference in probabilistic models that are expressed as probabilistic programs---programs that can draw random values and condition the resulting stochastic execution on data. The ability to define models using programming constructs such as recursion, stochastic branching, higher-order functions, and highly-developed simulation libraries allows us to more easily express and perform inference in models that have simulators, a dynamic number of latent variables, highly structured latent variables or nested probabilistic models. The key to success of probabilistic programming is efficient inference and model learning in such models. The most powerful black-box approximate inference algorithms for probabilistic programs are either sampling-based (Monte Carlo simulations) or optimization-based (variational methods). In both cases, one must re-run the inference algorithm for new data. Hence, our first goal is developing algorithms for amortized inference which, here, refers to reducing the run-time cost of inference by pre-training a neural network that maps from observed data to efficient parameters for performing fast, repeated inference. Our second goal is developing algorithms for model learning that are advantageous for two classes of models that one might typically want to write as probabilistic programs: models of sequential data and models that contain discrete latent variables. In this thesis, we discuss the general topic of Bayesian machine learning and probabilistic programming before moving on to our methodological contributions in amortized inference and model learning.

Advisor: Wood, F
Teh, Y
Improving wellbeing in student paramedics: targeting risk factors and predictors of PTSD

Student paramedics are at an increased risk of developing mental health problems compared to the general population due to the nature of their work. They are especially at high risk of developing posttraumatic stress disorder (PTSD), a severe stress reaction that can occur after exposure to traumatic events. To date, interventions aimed at reducing poor mental health or preventing the risk of PTSD in this population have not been very effective. Evidence-based interventions are urgently needed.
This thesis aims to address poor mental health in student paramedics. First, by evaluating a tool to improve wellbeing and reduce psychological distress (Study 1). Second, by targeting factors relevant to the development of PTSD with a specific focus on assessing and understanding rumination, a risk factor for PTSD, characterised by abstract thinking, and modifying responses to intrusive memories, a predictor of PTSD (Chapters 2, 3 and 4). No previous studies have looked at these factors in a population of student paramedics.
Study 1 showed that daily planning ahead can improve wellbeing in student paramedics significantly better than reading about mental health. Planning ahead also reduced psychological distress and increased the experience of mindfulness in student paramedics as did reading about how to cope with stress. Study 2 developed and validated a new measure of concrete and abstract thinking (CAT). The CAT fills a gap in the literature by providing a user-friendly, valid, reliable and population-specific measure of concrete and abstract thinking. A ‘Best Version CAT’ is recommended for further use. Abstract thinking measured by the CAT was associated with established measures of rumination, worry and PTSD. Study 3 builds on this by assessing abstract thinking (using the CAT) as a predictor of PTSD symptom severity, at 6-week and 6-month follow-up in a large sample of student paramedics. Findings revealed that abstract thinking predicts PTSD symptom severity over and above established measures of rumination at 6-weeks but not at 6-months. Finally, Study 4 aimed to reduce intrusive memories and maladaptive responses to intrusions after an analogue trauma film. The study failed to show superiority of a stimulus discrimination technique over a counting intrusions technique, both of which seemed to help student paramedics disengage from trauma memories.
The results of this thesis contribute to our understanding of factors that may influence the wellbeing and mental health of student paramedics. A better understanding of these factors may, in the future, help to inform targeted PTSD prevention for student paramedics and emergency workers more broadly.

Keywords: PTSD
Student Paramedics
Emergency workers
posttraumatic stress disorder
Advisor: Wild, J
Ehlers, A