VictorJuiz/thesis huggingface dataset:
From the LHC to IceCube, a melange of particle phenomenology

Three topics in particle phenomenology are independently considered: (1) the flux of prompt atmospheric neutrinos at terrestrial observatories, (2) the resummation of dijet event shapes in Soft-Collinear Effective Theory, and (3) aspects of non-abelian discrete symmetries of flavour. The thesis thus decomposes into three chapters addressing each point in a self-contained way, including short introductions and concluding remarks. Regarding (1), we calculate the neutrino flux arising from the decay of charmed mesons produced in cosmic ray collisions in the atmosphere, with the charm cross-section being evaluated using NLO QCD techniques and input into a series of equations describing particle cascades. In (2) we present a NNLL' resummation of e+e− angularities, a class of observables generalizing thrust. This resummation necessarily includes the calculation of two-loop soft anomalous dimensions and matching corrections, which we also detail in generality. Finally, in (3), we develop a novel ‘bottom-up’ procedure to search for symmetries capable of predicting elements of fermionic mixing matrices and then apply it to both the quark and lepton sectors, finding numerous finite groups of interest.

Advisor: Bell, G
Sarkar, S
Novel applications for hierarchical natural move Monte Carlo simulations: from proteins to nucleic acids

Biological molecules often undergo large structural changes to perform their function. Computational methods can provide a fine-grained description at the atomistic scale. Without sufficient approximations to accelerate the simulations, however, the time-scale on which functional motions often occur is out of reach for many traditional methods. Natural Move Monte Carlo belongs to a class of methods that were introduced to bridge this gap. I present three novel applications for Natural Move Monte Carlo, two on proteins and one on DNA epigenetics. In the second part of this thesis I introduce a new protocol for the testing of hypotheses regarding the functional motions of biological systems, named customised Natural Move Monte Carlo. Two different case studies are presented aimed at demonstrating the feasibility of customised Natural Move Monte Carlo.

Keywords: Functional Motions
epigenetic marks
Hypothesis-testing
Advisor: Minary, P
Deane, C
Knapp, B
Driven by data: city-scale localisation at night

This thesis is about facilitating the use of vast quantities of data for robotics applications, particularly for the tasks of mapping and localisation in the context of lifelong learning. Further, we tackle the specific problem of localising an autonomous vehicle at night, in urban environments, using vision.
In general, robotics applications have some unique and unusual data requirements. The curation and management of such data are often overlooked. An emerging theme is the use of large corpora of spatiotemporally indexed sensor data which must be searched and leveraged both offline and online. Without careful thought to their organisation, however, this leads to vast quantities of data which quickly become unmanageable. The current paradigm of collecting data for specific purposes and storing them in ad-hoc ways will not scale to meet this challenge. In the first part of this thesis, we present the design and implementation of a data management framework that is capable of dealing with large datasets, and provides functionality required by many offline and online robotics applications. We systematically identify the data requirements of these applications and design a relational database that is capable of meeting their demands.
This database framework is then used to facilitate the storage and retrieval of maps in our visual nighttime navigation system, a problem which has its own unique set of challenges. Despite it being dark exactly half of the time, surprisingly little work has addressed these challenges. A defining aspect of nighttime urban scenes is the presence and effect of artificial lighting. By building a model of the environment which includes a representation of the spatial location of every light source, localisation becomes possible using monocular cameras. One major challenge we face is the gross change in light appearance as a function of distance, due to flare, saturation, and bleeding. To overcome this, we model the appearance of each light as a function of vehicle location, using this to inform our data association decisions and to regularise the cost function which is used to infer vehicle pose. We demonstrate that our system is able to localise successfully at night, over 40km, in situations where a traditional point feature based system fails.

Advisor: Newman, P
Magnetic resonance spectroscopy of the in vivo brain with semi-LASER

Changes in the metabolic state of the brain can occur, for example, as a result of neuronal activity or in pathologies such as cancer. In these cases, an altered energy demand can lead to changes in neurochemical concentrations detectable using proton magnetic resonance spectroscopy (1H-MRS). This thesis explores in vivo 1H-MRS methods for detection of such changes in the healthy and diseased brain. Specifically, this thesis aims to develop methods with semi-LASER localisation, thereby minimising the negative effects of chemical shift displacement and field inhomogeneity on spectral acquisition.
Firstly, a Hadamard-encoded semi-LASER method for simultaneous measurement from two regions was developed at 7 T. Slice profiles, with low chemical shift displacement and small amounts of signal overlap, were revealed in phantom and in vivo. This was then implemented in a study of neurochemical change during positive and negative blood oxygen level-dependent (BOLD) responses. Negative BOLD responses are thought to reflect regions of neuronal suppression. A small decrease in ascorbate, as well as the T2*-induced linebroadening of several spectra, were observed in these regions. Furthermore, increases in glutamate and lactate were detected in positive BOLD regions. These findings suggested that negative BOLD may not be generated by an increase in local GABA concentration.
Secondly, an optimised semi-LASER sequence (TE = 110 ms) at 3 T was shown to improve localisation of the oncometabolite 2-hydroxyglutarate (2-HG) – a product of IDH-mutation found in the majority of gliomas. This resulted in improved detection of 2-HG in patients compared to an existing technique. The method was also compared to 7 T, where benefits of an increased spectral resolution resulted in significantly better detection of 2-HG along with associated metabolites.
This thesis highlights the importance of robust localisation for performing sensitive in vivo 1H-MRS neurochemical measurement in the human brain.

Keywords: MRS
2-hydroxyglutarate
negative BOLD
semi-LASER
Advisor: Emir, U
Jezzard, P
Fundamentals of property law: possession, title and relativity

This thesis is concerned with the doctrine of title by possession and the doctrine of relative title. Many property lawyers believe that these doctrines are elementary, important and interesting. But, while virtually everyone accepts that possession of land or chattels is a source of title and that titles are relative, the doctrines have long been a focus of debate. The nature of possession, the nature of the possessor’s title, and the relationships between possession, relative title and ownership have been particularly contentious. Accordingly, this thesis seeks to provide sound answers to the following questions: (1) what, in this context, is possession? (2) What is the nature of the title that is acquired by taking possession of land or chattels? (3) Does English law recognise landownership and chattel-ownership?—and, if it does, is a person who acquires, by virtue of his or her possession, a title to land or chattels the (or an) owner of the land or chattels? It is argued in Chapter 2 that, for the purposes of the doctrine of title by possession, the general rule is that a person is in possession of land or chattels if and only if she has: (i) a sufficient degree of exclusive physical control; and (ii) an intention to possess. Chapters 3–5 are concerned with the second question. It is argued that, upon obtaining possession, a person acquires, in cases involving land, an estate in fee simple absolute in possession and, in cases involving chattels, a general property interest. Chapter 6 is concerned with the third question. It is argued that English law does recognise landownership and chattel-ownership; and that a person who acquires a title by obtaining possession of land or chattels owns the land or chattels if her title is supreme but not if it is inferior.

Keywords: Ownership
Possession
Property Law
Relative title
Advisor: McFarlane, B
Swadling, W
Josephus on the servile origins of the Jews in Egypt

The Exodus story of the Israelites’ slavery in Egypt and subsequent redemption was central to Jewish accounts of their national origins and was an important component of Jewish self-identification in antiquity. Although Greek and Latin sources appear ignorant of the Exodus story, ancient ethnographies of the Jews in non-Jewish sources claim that the Jews were originally Egyptian. This thesis examines how Josephus presents the Exodus story of the Jews’ servile national origins in Egypt to a Roman audience who had biases against slaves, freedmen, and Egyptians, and little knowledge of Jewish origins apart from reports that they were Egyptian by origin.
Josephus’s first work Jewish War, a politico-military history, includes tangential remarks about Jewish origins, but implies in the proem that the Jews were originally Egyptian. Jewish Antiquities, which rewrites the biblical account of Jewish origins, explicitly denies that the Jews were originally Egyptian and deliberately omits mention of the Jews’ servitude in Egypt at important points in the narrative where it would have been expected. In Against Apion, an apologia, Josephus subtly uses keywords and the rhetorical technique of insinuatio to prove that the Jews were not originally Egyptian without stating openly that this is a goal of the work.
Several factors explain these results. Aristotle’s theory of natural slavery, which posits that slaves are innately defective, was part of the ideological assumptions of first century CE Roman elites. Romans were also ambivalent about their own partly-servile origins in Romulus’s asylum. Influenced by Augustan propaganda about Actium, first-century Roman sources deride Egyptians with a range of negative stereotypes. Josephus denies that the Jews were Egyptian and omits their servile origins at important points in the narrative where the Bible mentions it in order to portray the Jews as favorably as possible.

Keywords: Natural slavery
Exodus
Josephus
Ancient ethnography
Ancient historiography
Ancient Judaism
Jewish Origins
Advisor: Goodman, M
Characterisation of the histone acetyltransferase KAT7 as a novel target for radiosensitisation

Radiotherapy is one of the pillars of modern cancer therapy. However, side effects associated with normal tissue toxicity limit the effectiveness of this treatment. It is therefore desirable to develop tumour-specific radiosensitising agents, which can increase tumour cell kill without increasing the radiosensitivity of the surrounding normal tissue.
This project aimed at validating the radiosensitising potential of depletion of the histone acetyltransferase KAT7, and elucidating the underlying mechanism of action. My results showed a radiosensitising effect of KAT7 depletion in seven tumour cell lines. At the same time, a panel of normal tissue cell lines was not radiosensitised. The depletion of KAT7 caused general cell cycle changes, most notably a twofold increase in the proportion of mitotic cells. At the same time, the G2M checkpoint governing entry into mitosis appeared to be impaired. Livecell imaging confirmed a more than threefold increase in mitotic catastrophe following irradiation in KAT7-depleted cells. An oligonucleotide microarray also showed the downregulation of key members of the mitotic pathway, and patient data demonstrated higher expression of KAT7 to be associated with worse prognosis.
In summary, this project supports the tumour-specific radiosensitising potential of KAT7 depletion. This novel target for radiosensitisation seems to exert its effects through altering entry into and progression through mitosis.

Advisor: Higgins, G
McKenna, G
Structural and functional study of picornaviruses

Picornaviruses are responsible for a variety of human and animal diseases, ranging from hepatitis A, foot and mouth disease, through polio to hand-foot-and-mouth disease and the common cold. In addition to their importance in causing diseases, they also serve as models for understanding the basic mechanisms of host-pathogen interactions, virus entry and viral genome release.
Although the structure of a number of picornaviruses from the Entero, Cardio, Aphtho and Senecavirus genera have been determined at close to atomic resolution with X-ray crystallography, structural and functional studies on Parecho, Kobu and Hepatovirus are very limited. I have thus studied members of these genera: Ljungan virus, Aichi virus and hepatitis A virus to further understanding of the molecular basis of pathogenesis, viral entry, assembly and stability for these viruses in particular and for picornaviruses in general. In addition I have studied the VLPs of CVA16 as potential vaccine candidates.
The atomic structure of Ljungan virus determined by cryo-EM, shows remarkable features, including an extended VP1 C-terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N-terminus of VP3, which orders some 12% of the viral genome. This charge-driven RNA attachment suggests that this branch of the picornaviruses use a different mechanism of genome encapsidation.
The cryo-EM structure of Aichi virus at 3.7 Å resolution is intermediate between the enteroviruses and cardioviruses. On the outer surface a polyproline helix structure, not seen previously in picornaviruses is present at the C-terminus of VP1, corresponding to the position where integrin binding motifs are found in some other picornaviruses. A peptide corresponding to this polyproline motif somewhat attenuates virus infectivity suggesting a role in attachment to a cellular receptor.
The cryo-EM structure of a complex between hepatitis A virus and a potent neutralizing antibody, together with other data suggest that this antibody mimics receptor binding.
2A proteins from Ljungan virus, Sebokele virus and human parechovirus play a different role in these viruses compared to other members of the picornavirus family and the X-ray structures of these proteins reveal incredible plasticity and an H-box motif that may not be catalytically active.
In summary, this thesis provides an insight into some important aspects of host-virus interactions especially the events occurring during viral assembly and receptor recognition.

Advisor: Stuart, D
Fry, E
Illuminating the deep: an exploration of deep-sea benthic macrofaunal ecology in the Northwest Atlantic Ocean

Understanding of the fundamental ecology of deep-sea ecosystems remains immature relative to more familiar shallow-water and terrestrial habitats, despite more than two hundred years of scientific investigation. This thesis aims to progress knowledge of deep-sea benthic ecology by the analysis of over three hundred box core samples collected from the Northwest Atlantic continental slope as part of the international NEREIDA programme. Aspects of the ecology of Peracarida (Crustacea) are studied, and this is facilitated by the coupling of a large faunal dataset with extensive environmental information. To further enhance the power of this dataset, phylogenetic and functional characteristics of assemblages are investigated. Using community phylogenetic methodology, it is demonstrated that the peracarid assemblages studied are structured more strongly by variation in environmental parameters than they are by competitive interactions. Analyses demonstrate that the intensity of bottom trawling, seafloor temperature, current speed, food availability, sediment characteristics and physical habitat heterogeneity all influence deep-sea peracarid assemblage biodiversity metrics. Further, the importance of high poriferan biomass for the promotion of peracarid assemblages of high density, biomass, richness and diversity is highlighted. Of relevance to the management of deep-sea ecosystems, the results of this thesis suggest that caution should be exercised when applying species distribution models to data-deficient environments, whilst the location of spatial closures in the NAFO Regulatory Area may not be fully optimal for the protection of all components of diverse benthic assemblages against the impacts of bottom trawling. The importance of deep-sea diversity is demonstrated by the finding of positive biodiversity – ecosystem functioning relationships. However, the form of these relationships is found to be dependent on the biodiversity and ecosystem functioning metrics employed, and a hypothesis for a generalised form of biodiversity – ecosystem functioning relationships is proposed. Finally, this thesis calls for more ambitious deep-sea ecological investigations, and it is hoped that its findings will encourage future research initiatives, helping to further illuminate this enigmatic and fascinating environment.

Keywords: Benthic ecology
deep-sea
Peracarida
Advisor: Rogers, A
Input-output analysis and growth theory

This thesis studies a theory for the amplification of technological improvement by the production network structure of the economy.
The theory is motivated by the idea that, to the extent that inputs and outputs of industries form a chain, improvements are passed down the chain and accumulate multiplicatively. Under a simple model for technological improvement it is possible to compute the overall improvement factor for the general case where the production network has a complicated structure containing cycles. We call this the trophic depth by analogy with ecology.
This leads to testable predictions about GDP growth and its variance. We analyse data for 40 countries and 35 industries from 1995 to 2009 and demonstrate that trophic depths are strongly correlated with economic growth. A regression of GDP growth of countries against their trophic depths has a highly statistically significant R-squared equal to 0.38, and when other standard explanatory variables are added to the regression, the trophic depth remains a robust and statistically significant contributor.
We perform some statistical analysis to understand the evolution of trophic depths at different stage of the economic development. We identify two growth paths. Along the first growth path, countries are catching up frontier economies while along the second growth path countries are falling behind. This approach allows us to make some forecasts about the evolution of trophic depths and of the wealth of countries. This provides a comprehensive framework to understand the acceleration and deceleration of economic growth.
Then, we study another type of technological progress that corresponds to the adoption of new goods in the production chain. This mechanism is related to the dynamic of the production network and for this purpose we perform a link prediction analysis to determine some key factors for new adoptions.
Finally, we analyse the relation between stock return comovement and institutional preferences across stocks of various size. A growing literature highlights the role of investors' common asset holdings on market dynamics. While previous studies focused on large stocks we also include small stocks in the sample in order to acknowledge the shift in institutional preferences towards small stocks over the last decades. Moreover, we add the input-output linkages between firms from different industries to our set of explanatory variables.

Advisor: Farmer, D
Temperature and density measurements of plasmas

Diagnosing the temperatures and densities of plasmas is critical to the understanding of a wide variety of phenomena. Everything from equations of state for warm dense matter (WDM) found in Jovian planets and inertial confinement fusion (ICF) to turbulent and dissipative processes in laser-produced plasmas, rely on accurate and precise measurements of temperature and density. This work presents improvements on two distinct techniques for measuring temperatures and densities in plasmas: x-ray Thomson scattering (XRTS), and Langmuir probes (LPs).
At the OMEGA laser facility, experiments on warm dense matter were performed by firing lasers at an ablator foil and driving a planar shock into cryogenically cooled liquid deuterium. XRTS in the collective scattering regime was implemented to probe the matter, measuring densities of ne ~ 4.3 × 1023 cm−3, temperatures of Te ~ 12 eV and ionizations of Z ~ 1.0. Through an extension to XRTS theory for inhomogeneous systems, it was possible to extract an additional parameter, the length scale of the shock, whose value of Λ ~ 1.33 nm was consistent with the predicted mean free path, and therefore the thickness of the shock.
A unique triple Langmuir probe prototype was designed and tested at the Gregori group’s lab at the University of Oxford. This probe was designed for a high temporal resolution of ~ 200 MHz for probing laser-produced shocks. The probes were used to measure the shock formed from ablating carbon rods in an argon gas fill. The probe yielded plasma parameters of ne ~ 1.0 × 1017 cm−3 , and Te ~ 1.5 eV, consistent with measurements from interferometry and emission spectroscopy.

Keywords: HEDP
Plasma
Langmuir Probes
Lab Astro
XRTS
X-ray Thomson Scattering
Laboratory Astrophysics
Astrophysics
High Energy Density Physics
Physics
Advisor: Gregori, G