VictorJuiz/thesis huggingface dataset:
Security and privacy in location-aware mobile systems
Keywords: VANET
cyber security
vehicular network

For centuries, methods to obtain location information were crucial for our economic success. While initially requiring expert training and cumbersome tools like astrolabes and compasses, advances in material and engineering sciences have brought the ability to determine one’s position on Earth to our fingertips. Devices as small and mobile as smart phones can now acquire and process location information.
Fuelled by this new data source, social media companies immediately realised the potential to enhance their users’ experience and embedded location-based features into their products. Simultaneously, platforms which allow users to use location information as triggers for automation tasks emerged.
Beyond these use cases for entertainment and convenience, recent advances in academic and industrial research have started to leverage location information for security and safety purposes. While the advantages of location-aware mobile systems to improve security are undisputed, methods to ensure the reliability of location information and minimise the impact on user privacy still require further research.
In this dissertation, we aim to extend the knowledge about security and privacy implications of location information. To achieve this, we first analyse the different paths a mobile system can come in contact with this type of information. Based on these insights, we identify threats associated with the acquisition and processing of location claims. We recognise that in many cases, the absolute location of mobile devices is not needed but rather their constellation is sufficient. For example, the proximity of two devices can aid to validate location claims before relying on them for security or safety critical applications. We propose to use the trajectory a device takes to approach a location as that location’s fingerprint. To show the feasibility of this idea and its potential applications, we evaluate two scenarios: user authentication and collective awareness in future intelligent transportation systems.
Finally, we analyse the consequences of data sharing for user privacy. More specifically, we investigate Vehicular Ad-hoc Networks (VANETs) as an open network where location information is essential to ensure its safe operation but also vastly available to malicious actors. We develop solutions to improve passenger privacy while providing more fine grained accountability in these networks which are a cornerstone in the future of intelligent transportation systems.
The ice-water interface and its interactions with colloidal monolayers
Keywords: Colloids
Colloidal monolayer
Ice-water interface

We investigate the interaction of colloidal particles with the ice-water interface using a combination of a directional solidification stage, a light microscope and thin sample cells. Firstly, we focus on separating the contributions of colloids from that of salt in inducing the Mullins- Sekerka instability of the ice-water interface. We show that while the instabilities more quickly develop at higher freezing velocities, the presence of the particles enhances the development of the perturbations. Consequently, we observe fully developed instabilities as ‘ice-fingers’ only when particles are present and at high freezing velocities. Secondly, we study the structures formed by the colloidal particles accumulating in front of the ice-water interface during the unidirectional freezing. By using di↵erent image analysis methods, we find that despite the slow freezing velocity, the increase of the particle concentration in front of the interface is still too quick for the formation of a crystal structure. However, once the particles have been entrapped by the ice, they form linear or zig-zag structures between the ice fingers. Thirdly, we look at the event of ‘thermal regelation’, specifically the movement of single particles in ice towards the ice-water interface. This is possible due to the presence of a premelted liquid film, surrounding the particle. Particle movement is measured by using tracking algorithms, and fitted to theoretical predictions, which capture a thermomolecular and a viscous force to describe the motion. From this we are able to determine that non-retarded van der Waals interactions dominate this premelting for our particle-ice system. In the last chapter, we study the 3D shape of the interface, and show how it is curved between the two walls. An earlier theory describing the typical curvature is shown not to work, and by varying material properties, we show that thermal conductivities of the different materials likely need to be accounted for. We finish the thesis with a conclusion and outlook.
Power at the margins of post-colonial states in Africa: remaking authority on fast track resettlement farms in Zimbabwe
Keywords: AFRICA
JAMBANJA
LAND REFORM
STATE POWER

I use the case of the rapid displacement and remaking of authority on resettlement farms during the Fast Track Land Reform Programme (FTLRP) in Zimbabwe to engage with and contribute to scholarly debates on the making and unmaking of power and authority on the margins of post-colonial states in Africa. The FTLRP resulted in 170,000 black smallholder households being resettled on close to 11 million hectares of land previously held by approximately 4,500 white large-scale farmers from 2000 to 2004, a process that repeatedly remade authority in unexpected and difficult to explain ways. I use the FTLRP to build on and challenge Christian Lund’s twilight institution approach. This approach focuses on non-state organizations that exercise public authority by mimicking “stateness”, usually in contexts where states and ruling parties are weak. Twilight institutions proliferated under FLTRP in efforts to control land access, conduct and order, but they were directly shaped by complex interactions with a historically strong bureaucratic state, which was itself increasingly conflated with the ruling party, Zanu PF. I argue that it is through an ethnographic approach to the logics, languages and practices of authority at the state’s margins that we can best understand these processes and re-evaluate the concept of twilight institutions. I found that twilight institutions were used to enforce order and govern conduct by a powerful ruling party whose political agenda was incompatible with long-established state bureaucratic ideas and practices, yet the twilight institutions remained, to an important extent, subordinate to those same state bureaucracies. Nonetheless, twilight institutions shaped rural authority in significant ways by elaborating a coherent set of ideas, symbols and practices of authority, which they used to mediate struggles for justice and survival at the state’s margins.
Division of labour and the evolution of complex groups
Keywords: Complexity
Division of labour
Evolution

Division of labour occurs when cooperating individuals specialise to perform different roles. This kind of behaviour is encountered widely across the tree of life, from the separate functions of distinct genes within a genome to the specialised castes of eusocial insect societies. However, division of labour is not simply a ubiquitous social behaviour across the natural world. Instead, it has also been a critical factor in the evolution of more and more complex forms of life.
When individuals divide labour, they become more dependent upon the cooperation of others. When the mutual dependence scales tip such that individuals can no longer survive and reproduce outside the group, then a transition in individuality may occur such that the group itself begins to act as an evolutionary individual in its own right. For example, the division of labour between reproductive germ cells and sterile somatic cells facilitated the evolution of obligate multicellular organisms. A similar division between reproductive queens and sterile workers underlies the evolution of eusocial insect societies. As a consequence, the study of division of labour not only provides explanations for a diverse behaviour but can also help us to understand why some forms of life have become so complex.
In this thesis, I have employed kin-selection theory to explain the evolution of division of labour between helpers and reproductives. I first show when such division of labour is favoured over uniform behaviour and draw conclusions about the degree of specialisation that is expected to evolve. I next consider the biological factors that can lead to the evolution of social groups comprised predominantly of sterile helpers. I then develop evolutionary theory to explain why labour dividers may employ environmental information to optimally coordinate their allocation of labour. In much of this work, I consider the effect of relatedness on the evolution of division and its various forms. I finish the thesis with an opinion piece on the different ways that relatedness may be modelled in social evolution theory.
Techniques for high repetition rate laser wakefield acceleration
Keywords: Laser Wakefield Acceleration
Laser Guiding
Plasma Diagnostics
Spectral Interferometry
Resonant Excitation

I present work on three different techniques in order to contribute towards laser wakefield acceleration (LWFA) experiments which could operate at multi-kHz repetition rates and at low plasma densities ne ~ 1017 cm-3, enabling the acceleration of higher energy electrons in a single stage. Together, these techniques would help to make the next generation of LWFA facilities substantially more competitive with conventional accelerators.
Firstly, I consider the accuracy required to resonantly excite plasma wakefields with trains of many laser pulses, produced by high average-power but lower peak-power laser systems. Through theory, simulations and experimental results, I show a strong constraint on the systematic error acceptable in the separation of pulses. However, I also explore using chirped trains of laser pulses, where the pulse separation increases over time, to increase the efficacy of resonant excitation when the pulse spacing cannot be perfectly matched to the plasma.
Secondly, I describe a recent technique which can measure plasma waves rapidly and sensitively, using temporally encoded spectral shifting (TESS). I generalise the technique to probe pulses with non-Gaussian profiles and demonstrate that it can be extended to measure quasi-linear wakefields which are not sinusoidal. I detail how a TESS analysis can be conducted in practice and present results from a recent experiment using the technique.
Thirdly, I outline a proposed all-optical method of creating plasma waveguides which would be capable of operating at low densities and high repetition rates and are in principle immune to damage from laser pulses. Start to end simulations demonstrate that these hydrodynamic optical-field-ionized plasma channels could meet all of the requirements for next generation laser wakefield acceleration experiments and are used to propose some optimum experimental parameters.
Visual guidance of target-oriented flight behaviours in birds
Keywords: Flight
Vision
Inertial Measurements
Birds

Birds are highly dependent on vision to guide their flight during goal-directed tasks. They shift their visual attention primarily through head reorientation, with limited eye movement; however, measuring head orientation in free-flying birds is a significant technical challenge. While the gaze strategies of some birds have been studied in considerable detail in laboratory environments, studies of visual guidance in natural environments have largely been limited to inferences based on GPS-derived flight trajectories. This thesis aims to advance our understanding of how birds use their visual system to guide target-directed flight, using novel instrumentation to measure the gaze strategy of homing pigeons (Columba livia) and peregrine falcons (Falco peregrinus) flying in their natural environments.
We use GPS-derived flight tracks to explore the visual mechanisms available to pigeons to compensate for wind drift, finding that they partially compensate for lateral displacement caused by the wind performing better than a naive strategy requiring no knowledge of the wind. We then describe the development of a custom-built sensor, incorporating a GPS receiver and head-mounted inertial measurement unit (IMU), which measures bird position and head orientation. Using this instrumentation, we find that pigeons coordinate angular head saccades with their wingbeats. Our results also reveal that vertical head stabilisation is enhanced when flying with flock companions, largely via increased wingbeat frequency. The focus of pigeons’ visual attention during homing flight is measured with the sensor, allowing specific points of interest to be identified in the landscape that do not lie on the bird’s track. Finally, we find that in the closing phases of predatory pursuit, peregrine falcons continuously track their target position using either their frontally or laterally facing fovea. Refined iterations of the exploratory technique developed here have the potential to revolutionise our understanding of large-scale spatial cognition and short-range guidance in birds and may, in turn, lead to applications in the design of visually-guided unmanned aerial systems.
Novel protein modification strategies
Keywords: dehydroalanine
carbohydrate
DBHDA
Protein
Sirt2
radical

Site-directed mutagenesis allows the ready variation of proteinogenic amino acids; genetic code expansion permit the incorporation of a few more. The widespread use of these genetic techniques has caused a revolution in molecular biology. A crucial limitation of genetic techniques is the ‘ribosomal filter’, where an amino acid has to be processed by the ribosome or other translational enzymes.
I have developed a chemical technique for the direct modification of proteins allowing the incorporation of a large scope of amino acid side-chains. Notably, this technique is independent of the ribosome. Radical addition to protein backbone dehydroalanine (Dha) forms C(sp3)-C(sp3) bonds directly onto a protein to facilitate “chemical mutagenesis”.
Protein glycosylation is difficult to study due to mixtures associated with biological glycosylation machinery. In Chapter 1: I have employed the above chemical mutagenesis method to create homogenous glycoproteins which retain a native bond. During this study, I have demonstrated the biological relevance of these transformations by showing reactivity with glycosidases and glycosyl transferases, found interesting reactivity of an extremely polarised amide substrate, and have used the method on an aggregation prone periplasmic protein.
In Chapter 2: I used techniques developed in Chapter 1 to create intermediate mimics of the Sirt2 catalysed deacetylation of Histones. I used the mimics of Sirt2 intermediate 2 to determine the geometry around an unstable reaction intermediate. Having atomic control over the amino acid allowed us to create mimics of both the R and S diastereomers. Using analyitical size exclusion chromatography I have obtained qualitative results which show the R isomer is bound by Sirt2 much stronger than the S, hinting that the R isomer is that which is present in biology.
In Chapter 3: I demonstrated a green synthesis of 2,5-dibromohexadiamide (DBHDA); which has been used extensively in the prior two chapters to modify protein Cys residues into Dha. The developed method of producing DBHDA replaces CCl4 with cyclohexane and gives a yield of 31 % over 3 steps and 6 functional group interconversions. The DBHDA produced was found to be of extremely high purity (99.7 % ± 1.21), which was determined by the use of quantitative 13C NMR spectroscopy.
Investigating the role of IGF-1R in the cellular response to DNA damage
Keywords: IGF-1R signalling and the response to radiotherapy
Generating IGF-1R mutants clones
Type I insulin-like growth factor receptor
Growth factor receptor signalling and DNA damage
Growth factor receptor kinases and the response to irradiation
IGF-1R and DNA damage
CRISPR-genome editing the IGF-1R gene

IGF-1R plays an important role in regulating cell proliferation, survival and migration. Its overexpression in a number of cancers has been associated with radio-resistance. Previous studies from our group and others have confirmed that depletion or inhibition of IGF 1R can sensitise cancer cells to ionising radiation. However, the underlying mechanisms remain elusive. Our study aimed to uncover the mechanisms of radio-sensitisation associated with the IGF-1R signalling pathway. This was achieved by investigating changes at the proteome, transcriptome and metabolome levels using siRNA-mediated gene silencing and also IGF-1R mutant isogenic models which we generated from p53 wild-type osteosarcoma U2OS cells using the CRISPR/Cas9 genome editing technique.
We confirmed that suppressing the IGF-1R function through either transient or permanent depletion of the protein enhances U2OS sensitivity to γ-irradiation with average dose enhancement ratios of 3.5 and 3 respectively at 5Gy. Double-strand break induction and resolution were not impaired in IGF1R-deficient cells as determined by γH2AX foci tracking and there was no evidence that the activation of the DNA damage response was compromised in the mutant with evidence of ATM, CHK1 and RPA phosphorylation along with p53 accumulation. Moreover, we did not find defects in cell cycle checkpoint integrity which prompted us to evaluate intrinsic properties associated with IGF 1R deficiency that may affect cell survival following exposure to γ-irradiation.
Transcriptome and metabolome profiling revealed significant differences in genes and metabolites associated with various cellular pathways, particularly the cellular response to stress, intracellular metabolism and, cell motility and migration. The interplay of molecular changes affecting these cellular processes might account for the radio-sensitisation of IGF 1R deficient cells. Future investigations should attempt to explore this possibility given that previous research on this same topic have hinted at the likelihood that the cellular response to ionising radiation is governed by complex multiple factors.
Immunogenicity of vaccines for malaria-exposed populations
Keywords: Ebola
flow cytometry
T follicular helper cells
malaria
controlled human malaria infection
antibody responses
clinical vaccine trials
vaccine immunogenicity

An efficacious malaria vaccine will be a necessary tool for malaria eradication, however current vaccine candidates have only demonstrated a moderate level of short-term efficacy. Additionally, these vaccines often display reduced immunogenicity and efficacy in the malaria-exposed target populations compared with the malaria-naïve populations in which they are initially tested. Reduced vaccine immunogenicity in malaria-exposed populations may affect vaccines for diseases other than malaria. The 2014-2016 Ebola outbreak in West Africa highlighted the need to produce effective vaccines against emerging infectious diseases. Many of the outbreak pathogens for which such vaccines are being developed have geographical distributions that overlap with areas of malaria transmission. Therefore being able to effectively vaccinate malaria-exposed individuals is a key requirement for this new generation of vaccines. This thesis aims to characterise the immunogenicity of candidate malaria and Ebola vaccines in detail and explores potential mechanisms of reduced immunogenicity in malaria-exposed populations. Experiments demonstrated that concomitant administration of viral vectored and VLP-based malaria vaccines caused a Th1-skewed cytokine response that was associated with reduced antibody titres and efficacy, similar to the immunosuppressive effect of acute malaria infection. Humoral, but not cellular, responses to malaria and Ebola vaccines were reduced in malaria-exposed adults and children but not in infants. Although this reduction was associated with malaria exposure in some cases, it was clear that other factors were involved. Further experiments revealed a role for cytomegalovirus infection in the reduction of vaccine immunogenicity in both malaria-naïve and malaria-exposed young adults. Overall this thesis highlights the importance of understanding what impacts immunogenicity in order to optimise vaccines for the target populations.
The role of subchondral circulation in the physiology of load transmission
Keywords: Intraosseous pressure
Microangiogram
Subchondral anatomy
Vascular oclusion
Subchondral vessels
Osteoarthritis
Osteonecrosis
Steroids
Kellgren-Lawrence
MRI
Bone flexibility
Choke valve
Loading
Subtraction
Hydraulic
Bone pain

Although the blood supply of bone at rest is well defined, the way in which skeletal activity might affect perfusion under active joints has received little attention. Intraosseous pressure (IOP) has been studied for several decades and was thought to be raised in osteonecrosis, arthritis and bone pain but there has been difficulty in defining IOP and using it for clinical purposes. This work aims to explore subchondral physiology during loading and to seek supporting evidence for a specialised subchondral circulation adapted to load transmission.
Originally in 1985 IOP was studied in an animal model. IOP at rest was found to be variable and sensitive to measurement technique. It had underlying cardiac, respiratory and circulation waves. It was correlated with blood pressure and had a proportionate pulse pressure (PP). Subchondral IOP was raised by proximal venous occlusion and loading. Steroid treatment increased IOP, probably by reducing intraosseous fat volume.
For this thesis in 2014 an in vitro calf foot model was developed and used to further investigate IOP at rest and with combinations of perfusion. The model was then used to study different patterns of loading. Load was found to be transferred partly by hydraulic forces from subchondral to cortical bone through high pressure tolerant tissues. There appeared to be a one way valve within the bone.
Previously undescribed upper tibial vascular marks were found on MRI scans. 60 pairs of scans were scored against osteoarthritis (OA) by Kellgren-Lawrence grade on plain x-rays. Vessels were reduced or lost in early OA. A second study of 200 paired X-ray and MRI scans confirmed the initial results and examined the femoral subchondral vascular marks.
Axial subchondral histology in animal and human tissue showed the presence of subchondral vessels. The subchondral vascular network was found to be present in healthy bone but absent in osteoarthritis. A subcortical valve like structure appears to exist that might allow high pressure hydraulic force transmission without vascular damage. Finally, other evidence in support of the thesis is advanced.
IOP measurement is only a reflection of perfusion conditions in the blood pool at the needle tip. A new understanding of IOP and its use in exploring bone perfusion by a subtraction technique is offered. Load is transferred partly by hydraulic force from the subchondral bone to the cortical shaft. Histologically there are subchondral vessels with possible valves in the subcortical region. A fine subchondral capillary plexus exists under healthy cartilage. Subchondral tissues support hydraulic pressure transmission during weight bearing. Vessels are lost in early OA. Osteoarthritis may be due to failure of vasculo-mechanical circulation in the subchondral region.