VictorJuiz/thesis huggingface dataset:
Vision-based legged robot navigation: localisation, local planning, learning

The recent advances in legged locomotion control have made legged robots walk up staircases, go deep into underground caves, and walk in the forest. Nevertheless, autonomously achieving this task is still a challenge. Navigating and acomplishing missions in the wild relies not only on robust low-level controllers but also higher-level representations and perceptual systems that are aware of the robot's capabilities.
This thesis addresses the navigation problem for legged robots. The contributions are four systems designed to exploit unique characteristics of these platforms, from the sensing setup to their advanced mobility skills over different terrain. The systems address localisation, scene understanding, and local planning, and advance the capabilities of legged robots in challenging environments.
The first contribution tackles localisation with multi-camera setups available on legged platforms. It proposes a strategy to actively switch between the cameras and stay localised while operating in a visual teach and repeat context---in spite of transient changes in the environment. The second contribution focuses on local planning, effectively adding a safety layer for robot navigation. The approach uses a local map built on-the-fly to generate efficient vector field representations that enable fast and reactive navigation. The third contribution demonstrates how to improve local planning in natural environments by learning robot-specific traversability from demonstrations. The approach leverages classical and learning-based methods to enable online, onboard traversability learning. These systems are demonstrated via different robot deployments on industrial facilities, underground mines, and parklands.
The thesis concludes by presenting a real-world application: an autonomous forest inventory system with legged robots. This last contribution presents a mission planning system for autonomous surveying as well as a data analysis pipeline to extract forestry attributes. The approach was experimentally validated in a field campaign in Finland, evidencing the potential that legged platforms offer for future applications in the wild.

Keywords: self-supervised learning
robot navigation
field robotics
local planning
localisation
collision avoidance
visual teach and repeat
traversability estimation
state estimation
forestry applications
robotics
autonomous systems
visual navigation
Advisor: Fallon, M
The evolving role of the judge in digitally assisted adjudication

The thesis analyses the evolving role of the judge in digitally assisted adjudication. It proposes two novel roles and one adapted role for the human judge, named co-designer, integrator, and overseer or quality controller respectively. To conceive of these roles the thesis builds on insights from computer and data sciences, philosophy of information and of design, sociotechnical theory, jurisprudence, and law.
From sociotechnical theory it borrowed and adapted the concept of cognitive assemblage, bridging the classical object-subject divide. A cognitive assemblage is defined as an assembly of digital infrastructures, legal technologies and human beings, and their practices to make meaning of legal information in adjudication. It is argued that the human judge has lost the monopoly over judicial decision-making to now adjudicate in a cognitive assemblage together with other humans and legal technologies.
Furthermore, the thesis introduces a concept derived from the cognitive assemblage: the programmatic level of law-making, operating in addition to the general level of statute and precedent and the specific level of the court case. It acknowledges the extra abstraction and layer of treatment digital technologies add to other technologies and to reality. It also assists with conceptualising legal implications.
The thesis then explores some possible enhancements and challenges for the rule of law of the cognitive assemblage of human judges and legal technology and of the programmatic level of law-making for adjudication.
Finally, the three evolving roles of the human judge are conceived with the concepts of the cognitive assemblage, of the programmatic level of law-making, and with essential aspects of the rule of law that must be maintained. It is argued that the judge should participate as a co-designer in the design of legal technologies that are used to decide on specific court cases; must integrate the output of legal technologies in the individual legal case whilst respecting the narrative of the parties; and oversee or control the quality of digital technologies. The thesis thus aims at contributing to a theory of judicial decision-making transformed by digital technologies.

Keywords: Rule of law
Role of the judge
Expert systems / machine learning
Digitally assisted judicial decision-making
Legal Tech
Adjudication
Cognitive ensemble/assemblage
Advisor: Armour, J
Understanding the physical processes causing surface creep on faults

Since the 1960s, we have observed creep events along the central San Andreas Fault. Despite this, we still do not know (1) when they occur, (2) where they occur, (3) how they grow spatially, (4) how much moment they release, or (5) the driving physics behind them. To address these questions, I use creepmeter and strainmeter data from along the central San Andreas Fault.
Using a cross-correlation approach, I examine 18 USGS creepmeter records between 1985 and 2020 and identify 2120 creep events. I correlate these events between creepmeters and identify many large (> few km long) creep events. Next, I combine creepmeter and strainmeter observations at the northern end of the central San Andreas Fault to identify the along-strike location, depth, and magnitude of creep events. Strainmeters record strain offsets associated with creep events, which I reproduce by modelling the strain produced by a rectangular patch of slip at various fault locations and magnitudes. I find that creep events are not the repeated rupture of a single fault patch but arise from a range of along-strike locations at depths >4 km, with a magnitude of 3–4.
Finally, I use displacement-time evolution of creep events to discriminate between five rheological models for creep events: (1) rate and state friction at a constant state rate near steady state, (2) rate and state friction above steady state, and (3) rate and state friction below steady state (4) power-law flow, and (5) linear flow. Using a basin￾hopping approach, I minimise the misfit between the observed creep event and the predicted displacement from each model. Most creep events have their displacement evolution best described by power-law flow or rate and state friction below steady state. These surprising results suggest that additional work is required to understand the driving physics behind creep events.

Keywords: San Andreas fault
geophysics
shallow creep events
aseismic fault slip
creepmeters
Advisor: Hawthorne, J
Cartwright, J
Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2

Retroviruses, a type of RNA virus, have a unique life cycle wherein they reverse transcribe their viral RNA genome and integrate as a provirus into the host’s DNA. When retroviruses integrate into the germ line of humans, they can form human endogenous retroviruses (HERVs), which make up approximately 8% of the human genome. HERV-K (HML-2) is the most recently acquired HERV but mutations have rendered it mostly silent except in many cancers, neurological diseases, and during the aging process.
To better understand HERV-K, I expressed its main structural protein Gag and determined its structure in the immature CA lattice of virus-like particles (VLPs). HERV-K VLPs have a greater distance between the membrane and the immature capsid (CA) lattice than other retroviruses, which correlates with the presence of small proteins SP1 and p15 between CA and MA. Using cryo-electron tomography (cryoET) and subtomogram averaging (STA), we resolved the immature lattice of HERV-K CA to 3.2A. The resulting map allowed me to build a hexameric atomic model with most side chains well resolved. I confirmed the trimeric and dimeric interactions between hexamers using site-directed mutagenesis and molecular dynamics simulations. A large conformational change in the lattice must occur during maturation, which is driven by the linker between the N-terminal and C-terminal domain, similar to HIV-1. A structure-based phylogenetic analysis with corresponding CA structures of other retroviruses revealed highly conserved assembly patterns across genera and evolutionary time.
SARS-CoV-2, another RNA virus, caused a worldwide pandemic in 2020. We analyzed the structure of the spike (S) protein derived from the ChAdOx1 nCoV-19 vaccine using subtomogram averaging. We found S to be in its prefusion conformation, which can elicit an immune response for protection. We also used a multimodal, multiscalar approach of frozen, infected cells to study assembly and egress of SARS-CoV-2. Our approach can now be applied to a wide range of viruses to understand different viral life cycles.

Keywords: HERV-K
Retroviruses
SARS-CoV-2
cryoEM
Structural biology
Advisor: Zhang, P
Bowden, T
Rocking the boat: maritime humanitarianism and responses to displacement at sea, 1978-2022



This thesis examines the history of humanitarian aid at sea from the 1970s to the present day. It focuses on humanitarian projects that locate, support and transport people in distress at sea, most often refugees and migrants who are seeking safety and opportunity across borders. I argue that maritime humanitarianism is a rebellious form of assistance, which has frequently ‘rocked the boat’ within the relief industry by putting forward distinctive arguments about aid. The thesis identifies three main manifestations of this rebelliousness. First, maritime humanitarianism has resisted processes of professionalisation, opposing the bureaucratisation of relief efforts. Second, it has embraced political debates over immigration and border control, posing a challenge to the humanitarian principle of neutrality. Third, it has promoted advocacy as a central means of intervening in crisis, complicating classical understandings of impartiality. In these ways, maritime aid agencies have pushed against conventional approaches to relief. I argue that their ‘rebellions’ stem from the specific operational frictions that arise at sea, where care is provided on the move beyond territorial borders. In maritime settings, aid workers’ obligations towards stranded migrants, and the duty to uphold the right to free movement and asylum, have a traction that frequently overrides classical humanitarian protocol.
The thesis makes this argument by looking at three maritime projects. The first was launched by two ‘Boat for Vietnam’ committees in the South China Sea in the 1970s; the second by a Cuban-American organisation named Hermanos al Rescate in the Florida Straits in the 1990s. The third project was kickstarted by the German aid agency Sea-Watch in the Central Mediterranean in 2015. Each of these ventures took humanitarians into unusual operational territory and together they highlight the problems and politics of providing aid ‘without borders’. By looking at the details of maritime relief, the thesis raises themes relevant to humanitarian and refugee history, including the politics of migration and displacement, the recurring ethical dilemmas of aid, and the tension between humanitarian intervention and state sovereignty. At the same time, it prompts us to reflect on how humanitarianism looks different when it is carried out in the specific setting of the sea, instead of in landed contexts ‘in the field’.

Keywords: search and rescue
humanitarianism
maritime aid
forced migration
Advisor: Scott-Smith, T
Panhellenism and local tradition in early Greek epos

Early Greek epos encompasses a wide range of characters who are each given a local origin: for example, Akhilleus of Phthia, Helen of Sparta, Nestor of Pylos. The surviving poems of the epic tradition, however, do not focus on single locations, but strikingly combine characters and places from all across the Greek-speaking world and beyond, a feature often referred to as 'Panhellenism'.
This thesis critically examines 'local' and 'Panhellenic' aspects of early epos through a variety of different methodologies. The first chapter sets out previous scholarship on the question and my working assumptions about the poetic tradition. I give a brief survey of the corpus as a whole in comparison to archaic lyric. The first part of the thesis then consists of a series of general studies, treating evidence from patterns of material culture during the period in which the tradition developed; iconography; the dialectal basis of the poetic language; and the importance of the catalogue to epic composition. The second part of the thesis provides a number of case studies of particular characters or places, examining the interaction between epic and local tradition. These case studies are: Akhilleus and Odysseus; the city of Thebes; Helen of Sparta; and the family of Oineus.
In general, I argue against the idea - prominent in previous scholarship - that early epos results from an 8th century fusion of distinct local poetic traditions that formed independently in the Early Iron Age (EIA). Instead, I propose an alternative model in which the inclusion of different places and characters is an inherent aspect of the epic tradition. Incorporation of local material is likely to have occurred at many different points in the development of hexameter poetry, stretching back into the EIA. This long and gradual process results in the rich, complex tapestry of stories and people that characterises archaic Greek epos.

Keywords: local tradition
Catalogue Poetry
epic dialect
Thebes
archaic Greece
archaic Greek literature
Achilles
Panhellenism
Greek epos
oral tradition
Meleager
Helen of Sparta
Odysseus
regionalism in the Early Iron Age Aegean
Oineus
Advisor: Kelly, A
Entertainment, propriety, transgression: the ‘unorthodox’ Greeks of Istanbul in the late Ottoman Empire

This doctoral thesis aims to look into the ways in which Greek Orthodox Christians in the entertainment sector, as well as the clientele, transgressed social, moral, political, and legal boundaries in the perspectives of the Ottoman state, the Greek Orthodox lay and clergy, and the broader society in Istanbul in the late Ottoman Empire, approximately from the mid-nineteenth century to the First World War. In order to fulfil its aim, the thesis focuses on entertainment practices primarily taken up by Greek Orthodox Christians and analyses them through the lens of transgression under the themes of prostitution, alcohol trade and consumption, live music venues, religious festivities, and merchandise with visual features. It questions what transgression meant to the conceptual parties in the empire and how they interpreted it as definers of transgression. It also proposes to show where transgressors stood during an era when the Greek Orthodox community was manifesting signs of a move towards a more tight-knit community life as Ottoman Istanbul was experiencing organisational and urban transformations. It argues that transgressions linked to entertainment generated different concerns for the different parties even when their perspectives on the features of these transgressions overlapped. Furthermore, it claims that neither the Greek Orthodox community nor the entertainment sector under study, in which Greek Orthodox Christians were highly noticeable, manifested themselves as homogenous formations. By shedding light on the network linked to entertainment, the thesis also intends to reconsider who ‘the black sheep of the family’ were and tries to bring new perspectives to the reading of non-Muslim communities in the late Ottoman Empire.

Keywords: Constantinople
19th century
alcohol
transgression
brothel
prostitution
entertainment
Ottoman Greek
photography
Apokria
early 20th century
tavern
music hall
Orthodox Christian
carnival
Istanbul
printed merchandise
postcard
Ottoman Empire
Advisor: Mignon, L
The development of non-β-lactam inhibitors of bacterial transpeptidases

β-Lactams, which inhibit bacterial transpeptidases, are currently the most widely used antibacterials globally. The emergence of bacterial resistance, conferred by β- lactamases in particular, which degrade β-lactam antibiotics, poses a perilous threat to human health. In conjunction with the development of β-lactamase inhibitors (BLIs), new antibiotics are needed that are stable to β-lactamase degradation. As β- lactamases provide bacterial resistance against β-lactam-containing antibiotics, the development of non-β-lactam transpeptidases inhibitors may be a promising strategy.
Chapter 1 provides a review of non-β-lactam analogues synthesised as potential antibacterial inhibitors, from which several promising molecular scaffolds such as the lactivicins and the benzisothiazolinones were identified. Chapter 2 describes the design and synthesis of non-β-lactam analogues using both reported and novel synthetic methodologies. In Chapter 3, synthesised compounds were evaluated for antibacterial and inhibitory activity against transpeptidases produced by Mycobacterium tuberculosis. In Chapter 4, synthetic methods for the modification of 2- oxoglutarate (2-OG), originally conceived for the synthesis of γ-lactone-functionalised lactivicin analogues, were repurposed for the synthesis of 2-OG analogues as inhibitors of isocitrate dehydrogenase (IDH) variants. In response to the coronavirus pandemic, Chapter 5 details the development of benzisothiazolinones as inhibitors of SARS-CoV-2 main protease.
The work described in this thesis made substantial progress in developing strategies for the synthesis of non-β-lactam transpeptidase inhibitors, which will be used to combat antimicrobial resistance, and pioneered facile methodology for the synthesis of functionalised 2-OG analogues for biological studies.

Keywords: bacterial resistance
2-oxoglutarate
SARS-CoV-2
Antimicrobial resistance
organic synthesis
lactivicin
covalent inhibitors
medicinal chemistry
Antibiotics
SAR studies
tuberculosis
Advisor: Schofield, C
Single cell analysis of the developing and adult uveal tract reveals stromal and immune populations of relevance to the spectrum of uveal diseases

The eye is a highly complex organ, in which miniscule deviations from baseline homeostasis can have profound impacts on vision. The uveal tract is a pigmented layer within the eye, with vital supportive roles for the function of the eye. Perturbations of the tissue microenvironment of the uvea occur in several pathologies of the eye such as inflammatory and degenerative eye diseases.
Single cell RNA sequencing has been transforming the understanding of cellular subtypes across organs, and the eye is no exception. However, the uveal tract has so far not been investigated in detail using single cell techniques either in development or in adult life. Here, I use single cell RNA sequencing to produce a single cell ‘atlas’ of the developing and adult uveal tract. I identify novel cell subtypes not previously documented within the uveal tract. Further, I identify subtypes of fibroblast within the uveal tract and demonstrate that there is heterogeneity of the fibroblast populations both within individual uveal regions, but also between the separate tissues that make up the uveal tract as a whole. Finally, I show that fibroblasts can be polarised towards specific phenotypes by exogenous signals, and demonstrate that fibroblast responses to some external mediators may play a role in pathologies of the uveal tract.

Keywords: iris
uveitis
choroidal neovascularization
choroid
ciliary body
uvea
Advisor: Buckley, C
Coles, M
Sherlock, J
Transitional shock wave/boundary-layer interaction unsteadiness on a cone-flare in hypersonic flow

The causes of unsteadiness in hypersonic, axisymmetric, and transitional shock wave/boundary-layer interactions (SWBLIs) are investigated experimentally using a cone-flare model in the Oxford High Density Tunnel (HDT). The motivation of this research was to provide accurate measurements of the unsteadiness of transitional SWBLIs and provide a technique for studying such unsteadiness experimentally and numerically. Increasing the field’s understanding of these interactions will improve our ability to predict the large thermal and aerodynamic loading caused by transitional SWBLIs, i.e., SWBLIs in which the boundary layer is transitional. In turn, the design of the thermal protection systems and aerodynamic surfaces of hypersonic vehicles, which inevitably come in contact with SWBLIs in this flight regime, can be refined.
Although the time-averaged characteristics of hypersonic SWBLIs have been studied in detail, transient measurements of transitional SWBLIs are rare in the literature. Similarly, recent studies at hypersonic Mach numbers have considered the boundary-layer and shear-layer disturbances which are amplified within the separation region of transitional SWBLIs. They found that a disturbance was amplified in the shear layers of these interactions which was distinct from the disturbance which dominates the transition process in axisymmetric, hypersonic boundary layers, the second-mode instability. However, there are gaps in the literature between the amplification of shear-layer instabilities, their breakdown to turbulent spots within the interaction region, and the resulting effects on the flowfields of these SWBLIs. The present thesis aims to bridge these gaps by linking the measurement of shear-layer instabilities, observations of turbulent spot formation, and movement of the separation region. A technique was also developed and implemented experimentally to confirm the link between turbulent spot formation and SWBLI unsteadiness. This technique can be used in future numerical work to reproduce such results without needing computationally-expensive simulations of the shear-layer transition process.

Keywords: hypersonics
boundary-layer transition
shock wave/boundary-layer interactions
aerodynamics
Advisor: McGilvray, M
Wylie, S
Development of macrocyclic peptides as multifunctional probes in chemical biology

Multifunctional probes combine a target engagement motif with at least one additional application, and have been used in a myriad of ways in chemical biology to identify the roles of their target in normal and disease settings. In this thesis, multifunctionality is installed to selective cyclic peptide inhibitors of epigenetic proteins: CP2 which inhibits histone demethylases 4A-C (KDM4A-C), and TiP1 which inhibits ten eleven translocation enzymes (TETs).
Multifunctional peptide probes were synthesised for epigenetic targets by addition of unnatural amino acids as click chemistry handles, or through installing photoreactive groups. Cu(I)-catalysed azide-alkyne cycloaddition click chemistry was used to synthesise peptide conjugates. Both CP2- and TiP1-based affinity peptide probes were produced by conjugating biotin to the peptides, and target engagement of biotinylated peptides was tested in cell lysates. Photoreactive multifunctional peptides were also assessed, for both KDM4A and TET activity, however these did not specifically crosslink their targets under the conditions tested.
E3 ligase binders were also installed to produce cyclic peptide proteolysis recruiting chimeras (PROTACs), to promote target protein degradation through the ubiquitin-proteasome system. A panel of ten CP2-based PROTACs was synthesised, using different linkers, recruiting either von Hippel Lindau (VHL) or cereblon (CRBN) E3 ligases. KDM4A protein degradation was established in cells transiently overexpressing HaloTagged and Flag tagged KDM4A (HaloFlagKDM4A) using HaloTag targeting PROTACs. Conditions established using HaloPROTACs were used to test the panel of CP2-PROTACs.

Advisor: Llobet, AI
Kawamura, A