VictorJuiz/thesis huggingface dataset:
Exploiting the physical in cyber-physical systems

This thesis argues that cyber-physical systems are, by their very nature, at risk from physical-layer attacks as well as cyber attacks. The proliferation of cheap and easy-to-use sensing and actuation technologies has drastically lowered the bar for attackers to conduct physical-layer attacks, even with only limited resources. As our reliance upon cyber-physical systems grows, so too does the impact of attacks.
It is argued that the same easy accessibility of technology that equips attackers, also enables the use of physical-layer security techniques in developing defences. A series of work is presented, exploring the practical use of physical phenomena to secure real-world cyber-physical systems.
Timing constraints are used for the verification of aircraft location claims, to inhibit spoofing. This demonstrates a straightforward application of physical-layer techniques, enhanced with mobility, to drastically limit an attacker’s capabilities.
Wireless propagation measurements are used to determine the presence of a drone and track it during a privacy-invasion attack; where traffic itself does not provide sufficient insight. The successful results highlight the potential for using even simple, ubiquitous metrics to gain detailed insight into the physical world.
Leaked electromagnetic signals are then used to detect a class of malicious network; exploiting the wireless propagation mode to achieve better performance and more convenient deployment characteristics than are possible with the original signal. This demonstrates the scope for incorporating unconventional physical effects to improve a security design.
The combined results are drawn on to argue that the use of physical-layer features is practical in real systems, even those that were not originally designed with due consideration for their tacit physical dependencies.
An eavesdropping attack is also presented against a state-of-the-art electric-vehicle charging system. This attack builds upon the electromagnetic leakage used defensively earlier, which is exacerbated by design choices made in the charging system. The eavesdropping attack is shown to be widely effective against real deployments, with results that suggest various active attacks would also be effective.
Observations from the attack are used to argue that as well as being practical, it is also necessary to incorporate physical-layer features in security design, as even emerging modern systems with detailed security models are vulnerable to critical physical-layer attacks.

Keywords: software-defined radio
wireless
security
physical-layer
Advisor: Martinovic, I
The first count of Gondomar's library and diplomatic practice (1613-1622)

This thesis offers the first detailed study on the intersection between diplomacy and Spanish libraries during the early modern period. It focuses on the library of Diego Sarmiento de Acuña, first count of Gondomar (1567-1626). Once deemed by John Elliott as the ‘greatest specialist in English affairs’ of Spain, Gondomar oversaw a very notable embassy in London from 1613 to 1622. He also became one of the main conduits of English information to Madrid during the Anglo-Spanish peace of the early 17th century (1604-1625).
Through a detailed analysis of Gondomar’s library, my thesis explores the political value behind the various types of English sources acquired during his embassies: books, printed portraits, maps, manuscript reports, pamphlets and other such items. As shown by recent historiography, the procurement of local sources was important to premodern diplomats, as they endeavoured to share in the period's bid for ‘information mastery’ about other polities, such as England. However, as this study illustrates, the mechanics that gave life to such ambitious ideals are often difficult to reconstruct with the records of a personal repository like Gondomar's. Thus, even though the evidence connecting Gondomar's library with his diplomatic strategy is often suggestive, it is no less true that the information unearthed in this thesis seldom leads to a straightforward interpretation on the Spanish ambassador's wider policies.
Nevertheless, by studying the documentary practices carried out by premodern agents like Gondomar, this project casts some light into the ways in which local sources could become an important concern for a diplomatic manoeuvre or turn into one of the main subjects of a diplomatic report. In the process, this thesis also offers suggestive evidence on how a personal library could be shaped by state affairs, and influenced by a series of social, religious and linguistic contexts outside the repository's walls.

Keywords: England
Spain
Information Management
Early Modern
Political History
Diplomacy
History of Communications
Cultural History
Renaissance
History of the Book
Libraries
Europe
The role of chromodomain helicase DNA binding protein 6 (CHD6) in thymic epithelial cell development and function

Thymic epithelial cells (TECs) uniquely have broad transcriptional ability to express over 90% of all protein-coding genes, including those which are tissue-restricted, through a process referred to as promiscuous gene expression (PGE). PGE is in part under the control of the autoimmune regulator (AIRE) in TECs, although the precise molecular mechanisms by which AIRE operates to enable PGE, are not fully understood. Chromodomain helicase DNA binding protein 6 (CHD6) is a DNAdependent ATPase, which plays a role in chromatin remodeling, and it has been proposed as one of the AIRE partners. The overall aim of this doctoral thesis is to define and understand the role of CHD6 in thymus biology. A mouse model, which is conditionally deficient of CHD6 in TECs (designated as Chd6TEC-/- ), was generated to investigate the proposed objective. Phenotypic analyses of Chd6TEC-/- mice demonstrated no differences in the qualitative and quantitative measures of TECs, thymocytes and peripheral T cells compartment, indicating non-essential role of CHD6 in the development of thymic epithelial cells and thymocytes maturation in general. Interestingly, genome-wide transcriptomic data and analysis of tissue-specific-antigen in TECs revealed that CHD6 is a positive regulator of PGE, predominantly among genes decorated with repressive histone marks. CHD6 is proposed to regulate PGE by: i) localising and recruiting AIRE protein complexes to specific loci possessing DNA strand breaks and decorated with specific repressive histone marks, and ii) changing the chromatin accessibility of the particular loci. Confocal imaging confirmed the physical proximity of CHD6 and AIRE in medullary TEC which corroborates the proposed functional interaction. Additionally, Chd6TEC-/- mice are observed to be more susceptible to organ-specific-autoimmunity. In summary, this study has demonstrated CHD6 as a novel regulator of PGE and its crucial role in central tolerance induction.

Advisor: Hollander, G
Network clearing algorithms and statistical methods for risk assessment

This thesis presents methodological contributions for the quantification of systemic risk in financial systems. Clearing algorithms that can be used for computing financial contagion effects are presented and their relation to network centrality measures is discussed. An algorithm that allows computing clearing solutions for networks of financial contracts including debt of multiple seniority classes, equity participations as well as contingent convertible debt and bail-in-able debt is presented. We present a valuation function that allows computing network-based valuations of contingent convertible and bail-in-able debt instruments. An application to systemic risk assessment for bail-in decisions using real-world data is presented, showing that bail-ins have the potential to reduce systemic risk in some crisis situations. An alternative approach to systemic risk assessment based on a metamodel of clearing algorithms is presented. We use quantile panel regression for learning the metamodel and present statistical tests for deciding between different quantile panel estimators as well as goodness-of-fit measures. An application with real-world-data shows how regulators could improve their identification of systemically important banks.

Keywords: mathematical finance
networks
machine learning
systemic risk
Identity and identities: the metaphysics and semantics of 'qua'

One of the most fundamental principles in the logic of identity is Leibniz’s Law: if a and b are identical, then any property had by a is also had by b. But this logical notion of identity would appear to be in tension with our ordinary understanding of the multifaceted identities of individuals. For it is quite common for a single individual to have multiple functions, roles, or identities and have different, even incompatible properties in these different roles or capacities. For instance, when a judge is also the referee of a football club, it is possible for the judge to be corrupt while the referee is uncorrupt. When a father is also a literary critic, it is possible for the father to be kind while the critic is cruel. And when, like Duchamp’s piece Fountain, a urinal is also an artwork, it is possible for the urinal to be ordinary while the artwork is extraordinary. Cases with this structure are not uncommon, yet they would appear to provide counterexamples to Leibniz’s Law. A standard response amongst philosophers is to invoke qualifications with ‘as’ or ‘qua’: The person is corrupt qua judge but uncorrupt qua referee. The person is kind as a father but cruel as a critic. Fountain is ordinary qua urinal, but extraordinary qua work of art. Despite the prominence of this response, there is next to no systematic literature on how such qualifications work and how precisely they help reconciling cases such as the above with Leibniz’s Law. To fill this lacuna, this dissertation investigates the metaphysics, semantics, and logic of qualification. I develop and assess four initially plausible proposals for how a satisfactory solution to the puzzle cases can be reconciled with (some version of) Leibniz’s Law using qualifications with ‘as’ or ‘qua’, and I argue that all but one are unsatisfactory. I go on to develop the remaining approach to qualification into a detailed theory, and I show that my theory of qualification affords an illuminating way of negotiating the tensions between identity, the simple well-behaved relation everything bears to itself and only itself, and identities, the categories we live by.

Keywords: 'as' phrases
identity
constitution
qualification
qua
Leibniz's law
Molecular genetic approaches for the determination of embryo viability

Since its first application in the 1990s, genetic testing of preimplantation embryos has undergone a major transformation and its utilisation continues to grow. While in preimplantation genetic screening, euploid embryos are identified and prioritised for uterine transfer, preimplantation genetic diagnosis identifies embryos free of genetic disease to avoid transmission of hereditary genetic disorders from parents to offspring.
This study aimed to deliver a novel preimplantation genetic screening protocol, which is capable of high accuracy aneuploidy detection utilising array-based, nano-scale quantitative real-time polymerase chain reaction. Furthermore, it focused on the development of a preimplantation genetic diagnosis protocol, which is capable of accurate detection of maternally inherited mitochondrial DNA mutations and which is fully compatible with comprehensive chromosome screening.
After extensive validation, the novel preimplantation genetic screening technique was successfully implemented clinically for testing of blastocyst-stage embryos and now offers a valuable option for couples undergoing in vitro fertilisation combined with preimplantation genetic screening. It is a unique method in that it is streamlined, rapid, versatile and less labour intensive compared to other conventional methods for aneuploidy screening. Furthermore, it has the potential to become an in-house component of an in vitro fertilisation laboratory, thereby reducing the processing time and eliminating the need for embryo cryopreservation. This in turn will help reduce the cost of in vitro fertilisation cycles with preimplantation genetic screening.
In addition, a new preimplantation genetic diagnosis protocol for detection of mitochondrial DNA diseases in conjunction with comprehensive chromosome screening using a next-generation sequencing technology was developed and delivered. The new method was successfully applied in four in vitro fertilisation patients transmitting different mutations causing mitochondrial DNA disease. In one patient, the transfer of an unaffected embryo resulted in the birth of a healthy child.
In summary, two novel methods were successfully developed, validated and clinically implemented for preimplantation genetic screening and preimplantation genetic diagnosis of mitochondrial DNA diseases.

Keywords: Preimplantation genetic diagnosis, PGD
Preimplantation genetic testing for mitochondrial DNA disease, PGT for mtDNA disease
Preimplantation genetic screening, PGS
Preimplantation genetic testing for aneuploidy, PGT-A
Advisor: Wells, D
Learning probabilistic representations for inference, training and interpretability

For decades, the holy grail of many fields of science, mathematics and statistics has been the ability to predict the future or, more quantitatively, to forecast the behaviours of quantities of interest. Examples range from predicting the value of financial products to forecasting energy consumption and several other applications.
While historically practitioners have focused on designing handcrafted methods for specific prediction tasks, the tools of Machine Learning (ML) promise to automate data analyses that extract patterns and structures and leverage this information in future forecasts. The addition of the probabilistic framework of Bayesian Machine Learning enables the inclusion of useful prior knowledge and provides predictive uncertainty quantification.
This thesis focuses on generative modeling, an important class of algorithms that stands at the core of Bayesian ML: by making structural assumptions on the generative processes that produced the data, generative models intend to explain the observed variability and yield a deep, interpretable understanding of data.
We present three original contributions, which leverage model-based machine learning to gain insights about the data-generating process and subsequently leverage them to provide reliable predictions. First, we propose a novel probabilistic framework based on constrained Gaussian Processes that incorporates derivative information in the form of ordinary differential equations. Second, we propose a novel noise model for Gaussian Processes that, in conjunction with state-of-the-art moment matching and adversarial techniques, addresses the problem of parameter inference in systems of stochastic differential equations. Finally, we move our attention to the optimization and sampling algorithms employed for Bayesian inference. In particular, we use Gaussian Process latent variable models to learn lower-dimensional space embeddings wherein optimizers and samplers can operate more effectively, thereby producing a meta-algorithm that can be applied to these inference methods to improve efficiency.

Keywords: bayesian
machine learning
probabilistic
gaussian processes
training
inference
Advisor: Osborne, M
Rainforth, T
Designing boron nitride nanotubes and their macroscopic assemblies via sacrificial templating

Hexagonal boron nitride nanotubes (BNNTs) have properties advantageous for the development of next generation materials and advanced composites that exhibit improved mechanical strength, high temperature resistance and thermal conductivity.
The future exploitation of BNNTs depends on the development of economically accessible and safe production methods. These should also present a scope for BNNT structural tunability, and output a high purity of BNNTs versus other possible hexagonal boron nitride (h-BN) structures. In this thesis, a novel synthesis technique is validated that is primarily motivated by a demand to address these issues.
Here, atmospheric pressure chemical vapour deposition (APCVD) is employed in conjunction with a safe and easy-to-handle compound, ammonia borane (H3N−BH3),to deposit h-BN coaxially onto the surface of multi-wall carbon nanotubes (MWCNTs). Subsequently, thermal oxidation is demonstrated to remove/sacrifice the MWCNTs, thereby leaving BNNTs as shells that exhibit diameter dependence on their MWCNT templates. By this method, BNNTs with walls 2-3 nm thick are synthesised, and nanotube outer diameters 16±2 nm and 40±16 nm are obtained using separate grades of MWCNT templates. The achieved BNNT diameter control exemplifies the versatility of MWCNT as a template material, which is justified by its structural compatibility to BNNTs, commercial scale availability and established morphological diversity. It is also argued here that use of H3N−BH3 precursor favours the van der Waals isolation of the deposited h-BN from the MWCNT template, which is advantageous for the h-BN purity of the BNNT shell.
The work presented here also establishes that the proposed APCVD and sacrificial templating method, when implemented in combination with vacuum filtration, is a novel and adaptable means of fabricating macroscopic assemblies of BNNTs. This is achieved at the cm-scale for BNNTs randomly entangled within a low density, self-supporting and sheet-like architecture with thicknesses <100µm. Furthermore, platelet crystals discovered on the surface of these BNNT assemblies, revealed to be boric acid, provide evidence in support of a new theory on the oxidation behaviour and moisture sensitivity of BNNTs.
Throughout this work, newly synthesised nanomaterials (non-assembled and assembled) are characterised by multiple techniques including electron microscopy, spectroscopy and thermogravimetry, in order to determine their qualities such as dimensionality, crystallinity, chemical composition and thermal stability.

Keywords: BNNTs
atmospheric pressure CVD
buckypapers
nanotube assemblies
CNTs
carbon nanotubes
nanotube synthesis
boron nitride nanotubes
heteronanotubes
ammonia borane
boric acid
sacrificial templating
Advisor: Grobert, N
The repair mechanisms of DNA damage induced by G-quadruplexes stabilisation in BRCA1/2-deficient cells

Mutations in the breast cancer type 1 or 2 susceptibility protein (BRCA1 or BRCA2 respectively) predispose to the onset of breast and ovarian cancer. Indeed, cells lacking homologous recombination (HR) rely mainly on error-prone mechanisms to repair DNA double-strand breaks (DSBs) and have an inherently increased sensitivity to replication stress. These defects can be exploited therapeutically with chemicals such as poly [ADP-ribose] polymerase (PARP) inhibitors. Among this family of inhibitors, olaparib has been approved by the Food and Drug Administration (FDA) in January 2018 as a maintenance treatment for breast cancer patients with BRCA defects. However, tumours ultimately develop resistance to olaparib treatment, stressing the need to develop new pproaches to target resistant tumours. G-quadruplexes (G4s) are thermodynamically stable secondary DNA structures resulting from the folding of guanine-rich DNA sequences. During replication, unresolved G4s due to small molecules stabilisation,can induce fork stalling, ultimately leading to DSBs formation. Among these small molecules, pyridostatin (PDS) has been shown to effectively stabilise G4 structures. In BRCA-deficient cells HR is impaired, thus PDS leads to DSBs accumulation and genomic instability. Surprisingly, we observed that DSBs induced by PDS could be repaired in BRCA2-deficient cells. We identified classical non-homologous end joining (cNHEJ) as a repair mechanism for PDS-induced DNA damage in our cell models including those with HR-deficient background using two chemical inhibitors of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a protein ensuring effective cNHEJ functions. Indeed, we described that PDS and DNA-PKcs inhibitors have a synergistic effect in BRCA-deficient cells. Furthermore, we showed that PDS-induced lesions seem retained longer in BRCA-deficient cells that have acquired resistance to PARP inhibitors via the loss of the p53 binding protein 1 (53BP1). Whether this is due to the roles of 53BP1 in regulating cNHEJ activity or end resection remains to be elucidated. In summary, our results provide new insights into G4 ligands-induced DNA damage and their repair in HR-defective models. This knowledge could be further exploited towards a new therapeutic approach to treat mutated BRCA carriers with breast cancer that have developed PARP inhibitors resistance.

Keywords: small molecules
BRCA1/2
pyridostatin
G4s
DNA damage
olaparib
NHEJ
HR
DSBs
DNA-PKcs inhibitors
PARP inhibitors
G-quadruplexes
Advisor: Tarsounas, M
Ryan, A
Ramadan, K
The roles of BRCA2 in chromosome integrity

High frequency of fork stalling and fork degradation are associated with DNA damage accumulation and represent key replication pathologies in cells lacking BRCA2. As a consequence, these cells enter mitosis with under-replicated DNA, which leads to interlinks between sister chromatids in anaphase. Failure to resolve these interlinks causes chromosome mis-segregation, aneuploidy and micronuclei. Here we show that BRCA2 loss leads to micronuclei formation, which triggers an innate immune response signalling via activation of the cGAS- STING pathway. However, cleavage of these interlinks by the MUS81 endonuclease activates mitotic DNA synthesis (MiDAS), thereby completing genome replication and ensuring correct chromosome segregation. Which genomic loci require BRCA2 for their replication and therefore become unstable upon BRCA2 inactivation remains unknown. Here we label mitotic nascent DNA and perform EdU-seq to monitor at high-resolution sites where MiDAS occurs in absence of BRCA2. Our findings reveal that loss of BRCA2 triggers MiDAS at 150 genomic loci, which map within regions replicating in early S phase and are therefore distinct from aphidicolin-induced common fragile sites. Our results suggest that BRCA2 inactivation causes replication failure at early-replicating genomic regions, a subset of which completes replication during mitosis.

Keywords: BRCA2
cancer biology
DNA damage