VictorJuiz/thesis huggingface dataset:
Characterisation of a mouse gene-phenotype network

Following advancements in the "omics" fields of molecular biology and genetics, much attention has been focused on categorising and annotating the large volume of data that has been produced since the sequencing of human and model genomes. With high-throughput data generated from these "omics" experiments and the increasing deposition of information from genetics experiments in biological databases, our understanding of the mechanisms that bridge the gap from genotype to phenotype can be explored in a holistic context. This is one of the aims of the relatively new field of systems biology, which aims to understand the complexity of biological systems in a holistic manner by studying the system as an ensemble of interacting parts. With increased volume and comprehensiveness of biological data, prediction of gene function and automatic identification of potential models for human diseases have become important aspects of systems-level analysis for wet-lab geneticists and clinicians.
Here, I describe an integrated analysis of mouse phenotype data with high-throughput experiments to give genome-wide information about gene relationships and their function in a systems biology context. I show a functional dissection of mouse gene and phenotype networks and investigate the potential that ontology-compliant phenotype annotations can offer for functional classification of genes. The mouse genome and phenome show modularity at higher levels of cellular, physiological and organismal function. Using high-throughput protein-protein interaction data, the mouse proteome was dissected and computationally extracted communities were used to predict phenotypes of mouse gene ablation. Precision and recall curves show comparable performance for higher levels of the MP ontology to those undertaken by comprehensive mouse gene function prediction such as the Mouse Function Project which predicted Gene Ontology terms. I also developed and tested an automatic procedure that relates mouse phenotypes to human diseases and demonstrate its application to the use cases of identifying mouse models given a query consisting of a set of mouse phenotypes and breaking down human diseases into mouse phenotypes.
Taken together, my results may be useful as a map for candidate gene discovery, finding how mouse networks relate to human networks and investigating the evolutionary origins of their components at higher levels of gene function.

Keywords: gene network
phenotype network
bioinformatics
biochemistry
ontology
Advisor: Hancock, J
Hodgkin, J
Towards the study of cold chemical reactions using Zeeman decelerated supersonic beams

Zeeman deceleration is an experimental technique which allows for the manipulation of open-shell atoms and molecules in a supersonic beam thus producing mK-cold, velocity-tunable beams of particles in selected quantum states. The method relies on the Zeeman interaction between paramagnetic particles and time-varying, inhomogeneous magnetic fields generated by pulsing high currents through an array of solenoid coils.
This thesis describes the construction and implementation of a supersonic beam setup including a 12-stage Zeeman decelerator. The Zeeman decelerator follows an original design that makes it possible to replace individual deceleration coils. Using ground-state hydrogen atoms as a test system, it is shown that the transverse acceptance in a Zeeman decelerator can be significantly increased by generating a rather low, temporally varying quadrupole field in one of the solenoid coils.
An electron-impact source was constructed and optimised enabling, for the first time, the Zeeman deceleration of metastable helium atoms in the 23S1 state, with an up to 40 % decrease in the kinetic energy of the beam. It is shown that the pulse duration for electron-impact excitation needs to be matched to the acceptance of the decelerator in order to attain a good contrast between the decelerated and undecelerated parts of the beam.
Experimental results are rigorously analysed and interpreted using three-dimensional numerical particle trajectory simulations. A phase-space model provides, for the first time, a means to estimate the six-dimensional phase-space acceptance in a Zeeman decelerator and to find optimum parameter sets for improved Zeeman deceleration schemes. The approach also reveals a hitherto unconsidered velocity dependence of the phase stability which is ascribed mainly to the rise and fall times of the current pulses that generate the magnetic fields inside the deceleration coils.
In the future, it is planned to combine the Zeeman decelerator with a source of cold atomic and molecular ions to study chemical collisions at low temperatures. A hybrid magnetic guide consisting of permanent magnet assemblies (Halbach arrays) in hexapole configuration and a set of current-carrying wires is proposed and simulated as an interface between these setups. The design promises very efficient velocity selection, a high degree of quantum-state selection and a nearly complete removal of residual carrier gas. Prospects for using magnetic hexapole focusing in front of the Zeeman decelerator are discussed.
The work represents a major step towards the study and control of chemical reactivity of paramagnetic species in the low-temperature regime and it will help in the testing of fundamental chemical reaction theories.

Keywords: magnetic fields
supersonic beam
hydrogen atoms
Zeeman effect
cold molecules
metastable helium
Advisor: Softley, T
Imperial longings and promised lands

This thesis concentrates on two discrete contexts in which Jewish and imperial concerns converged: the Boer War and the British Mandate for Palestine. For Britain's Jews, the Boer War represented a rare and uncomfortable moment in which the Jewish Question achieved relative prominence. However the war also generated a different set of 'Jewish questions', leading the Anglo-Jewish establishment to refine its own understanding of patriotic and imperial duty. The case of Palestine, by contrast produced less straightforward and predictable outcomes. Ottoman entry into World War I, which prompted both British and Zionist considerations into the merits of a Jewish homeland as part of the imperial system, created an acute conflict for British Jewry's communal leadership. Although not negating the advantages of a British-Jewish Palestine either to the Empire or to Jews in need of refuge, its decision to oppose the Balfour Declaration privileged at some cost a distinctive reading of Jewish interests over a more obvious synthesis of national and sectarian goals.
Despite continued objections to Zionism's ideological outlook and its pursuit of statehood, the Anglo-Jewish establishment located in the interwar development of a British-Jewish Palestine a means to advance both Jewish communal and imperial agendas. As the alliance between the Zionists and Britain unravelled in the final decade of the Mandate, British Jews eager to safeguard their position as well as their vision of Palestine's future would persist in defending this relationship.
In its exploration of the evolution of Anglo-Jewish attitudes towards Britain, the Empire and Mandatory Palestine, this thesis aims to address both thematic and chronological gaps in the historiography of Anglo-Jewry. By drawing attention to the uniqueness of Anglo-Jewry's imperial connection to Palestine and to the domestic impact of British involvement, my work also contributes to scholarship on Zionism and the Mandate Finally, it offers a framework for considering the impact of, and relationship to, Empire of minority groups residing in Britain.

Advisor: Rechter, D
State and labour in the U.S

The thesis examines the National Accord undertaking between the American central labour federation (AFL-CIO) and the Carter White House, in the light of their respective political strategies. The Accord provides a focal point and a point of departure for the study of the evolving political organization and activity of organized labour nationally, within the changing contours of American national government and politics. The study is placed in the context of broader theories of state-labour relations in the advanced industrialized democracies of the West.
The thesis explains the changing character and role of the AFL-CIO as the broadest level of representative aggregation within the labour sector, and labour's changing ties to the Democratic Party, role in presidential politics and special status within Congress. Also examined are selected characteristics of the Carter presidency and the changing policypolitical strategy of the Carter White House toward organized labour, from a relatively isolated mode of policymaking to extensive consultation and policy concessions through the Accord negotiations.
The Accord was a political exchange whereby the labour leadership participated in the wage restraint programme in return for consultative rights and specific quid pro quo policies, including countercyclical measures to offset fiscal austerity. The President subsequently sustained a policy of fiscal and monetary restraint despite the approaching election and the increasing protests of organized labour. However, in the face of strong opposition from some of Carter's senior economists, the labour leaders secured significant modifications to the second year of the pay standard. The 1980 presidential election renewed incentives for continuing cooperation when economic policy otherwise jeopardized relations.
Theoretical studies of underscreened Kondo physics in quantum dots

We study correlated two-level quantum impurity models coupled to a metallic conduction band in the hope of gaining insight into the physics of nanoscale quantum dot systems. We focus on the possibility of formation of a spin-1 impurity local moment which, on coupling to the band, generates an underscreened (USC) singular Fermi liquid state. By employing physical arguments and the numerical renormalization group (NRG) technique, we analyse such systems in detail examining in particular both the thermodynamic and dynamic properties, including the differential conductance.
The quantum phase transitions occurring between the USC phase and a more ordinary Fermi liquid (FL) phase are analysed in detail. They are generically found to be of Kosterlitz-Thouless type; exceptions occur along lines of high symmetry where first-order transitions are found. A `Friedel-Luttinger sum rule' is derived and, together with a generalization of Luttinger's theorem to the USC phase, is used to obtain general results for the T=0
zero-bias conductance --- it is expressed solely in terms of the number of electrons present on the impurity and applicable in both the USC and FL phases. Relatedly, dynamical signatures of the quantum phase transition show two broad classes of behaviour corresponding to the collapse of either a resonance or antiresonance in the single-particle density of states. Evidence of both of these behaviours is seen in experimental devices.
We study also the effect of a local magnetic field on both single- and two-level quantum impurities. In the former case we attempt to resolve some points of contention that remain in the literature. Specifically we show that the position of the maximum in the spin resolved density of states (and related peaks in the differential conductance) is not linear in the applied field, showing a more complicated form than a simple `Zeeman splitting'. The analytic result for the low-field asymptote is recovered. For two-level impurities we illustrate the manner in which the USC state is destroyed: due to two cancelling effects an abrupt change in the zero-bias conductance does not occur as one might expect. Comparison with experiment is made in both cases and used to interpret experimental findings in a manner contrary to previous suggestions. We find that experiments are very rarely in the limit of strong impurity-host coupling. Further, features in the differential conductance as a function of bias voltage should not be simply interpreted in terms of isolated quantum dot states. The many-body nature of such systems is crucially important to their observed properties.

Keywords: quantum dot
Kondo physics
conductance
underscreened
Luttinger
magnetic field
numerical renormalization group
Advisor: Logan, D
Pictures of processes

This work is about diagrammatic languages, how they can be represented, and what they in turn can be used to represent. More specifically, it focuses on representations and applications of string diagrams. String diagrams are used to represent a collection of processes, depicted as "boxes" with multiple (typed) inputs and outputs, depicted as "wires". If we allow plugging input and output wires together, we can intuitively represent complex compositions of processes, formalised as morphisms in a monoidal category.
While string diagrams are very intuitive, existing methods for defining them rigorously rely on topological notions that do not extend naturally to automated computation. The first major contribution of this dissertation is the introduction of a discretised version of a string diagram called a string graph. String graphs form a partial adhesive category, so they can be manipulated using double-pushout graph rewriting. Furthermore, we show how string graphs modulo a rewrite system can be used to construct free symmetric traced and compact closed categories on a monoidal signature.
The second contribution is in the application of graphical languages to quantum information theory. We use a mixture of diagrammatic and algebraic techniques to prove a new classification result for strongly complementary observables. Namely, maximal sets of strongly complementary observables of dimension D must be of size no larger than 2, and are in 1-to-1 correspondence with the Abelian groups of order D. We also introduce a graphical language for multipartite entanglement and illustrate a simple graphical axiom that distinguishes the two maximally-entangled tripartite qubit states: GHZ and W. Notably, we illustrate how the algebraic structures induced by these operations correspond to the (partial) arithmetic operations of addition and multiplication on the complex projective line.
The third contribution is a description of two software tools developed in part by the author to implement much of the theoretical content described here. The first tool is Quantomatic, a desktop application for building string graphs and graphical theories, as well as performing automated graph rewriting visually. The second is QuantoCoSy, which performs fully automated, model-driven theory creation using a procedure called conjecture synthesis.

Keywords: graph rewriting
quantum computing
quantum information
automated reasoning
category theory
Advisor: Coecke, B
Abramsky, S
Enforcing the GNU general public licence: copyright or contract?

The GNU General Public Licence (GPL) is one of the most widely used licences in the field of Free and Open Source Software (FOSS). Principally a legal document drafted to facilitate the development, use and transfer of software, the licence also embodies a strong ideological character that seeks to challenge the paradigmatic representation of software as property. At its core, the GPL places great emphasis on the licensee’s freedom to view, use, modify and distribute a covered work. However, for all its claims to openness and freedom, the GPL functions by way of restrictions. These restrictions are primarily designed to prohibit privatisation of the work by downstream licensees, but they also restrict other forms of conduct deemed contrary to the established practices of FOSS development.
This paper asks a seemingly simple legal question, yet it is one that is deeply entangled in the ideological and strategic complexities of a field that has received little in the way of judicial clarification. The question is whether the GPL’s restrictive provisions are contractual in nature or merely property-based restrictions that act unilaterally to define the scope of the granted rights. Focusing almost exclusively on Anglo-American jurisprudence, this paper will consider a variety of licensing issues relating to formalities, the nature and scope of rights, and remedies in order to determine on which side of the property/contract divide the GPL's restrictive provisions reside, or perhaps should reside.

Keywords: Free Software
Contract
Licensing
GPL
Copyright
Open-Source Software
Advisor: Dinwoodie, G
Refugees and underdevelopment in Africa

Using an empirical study of the Barundi refugee settlements of Ulyankulu, Mishamo, and particularly Katumba in Western Tanzania, this study argues that the causes and consequences of the African refugee problem must be examined outside the normative humanitarian framework. It postulates that the refugee problem can be understood only in the historical context of the integration of African communities into the capitalist system and their resultant underdevelopment. Furthermore, that the neo-colonial state, its class character, and ethnic divisions, aggravated by economic crisis, fosters a climate of repression - prompting forced migration.
The unequal relationship between western capital and Tanzania is exemplified in the microcosm of the refugee phenomenon, where international/ regional policy, legislation, security considerations, and aid not only demobilize a potential political force, but usurp the authority of the national and local state. Donor/state/refugee relationships are further discussed in the context of the settlements.
The schemes, located in remote areas and with tight restrictions on mobility, while providing a humanitarian solution, act as mechanisms for the control of the Barundi refugees. Utilization of their labour is intentionally part of Tanzania's development strategy. Settlement and integration are discussed in relation to the contribution of Barundi people to the development of commodity production in Tanzania both historically and with regard to their current potential. While dismissing the notion of an undifferentiated mass of refugees, this study reveals how donor activities and the objective material conditions of the rural areas contribute to commodity production and mercantilist activities with increasing inequalities.
It concludes that large groups of refugees in rural areas will inevitably heighten local tensions, and that only through greater x political liberalization' - removal of restrictions on mobility and political representation, will Barundi refugees gain control of their lives, and Tanzania's long-standing goal of the liberation of African peoples be realized.
Electron and hadronic recoil calibration for the first measurement of the mass of the W boson by the ATLAS experiment at the Large Hadron Collider

This thesis presents work towards the first measurement of the mass of the W boson (mW) at ATLAS at the Large Hadron Collider using √—s = 7 TeV collision data taken in 2011. The electron energy calibration is presented, including a detailed study of the linearity of the ATLAS electromagnetic calorimeter. Separately, the measurement of the W boson recoil is calibrated using Z boson events. Recoil corrections for the underlying event, pileup, recoil magnitude resolution, recoil angular resolution and recoil response mismodelling are determined, with statistical uncertainties on these corrections corresponding to an estimated uncertainty on mW of 3.9 MeV. The corrections for calorimeter non-linearity and recoil modelling improve the description of the data, though systematic biases remain. To achieve a precision commensurate with the statistics of the data, these biases will need to be understood.

Keywords: ATLAS
Large Hadron Collider
Advisor: Hays, C
Haywood, S
Versatile synthetic strategies towards the development of novel neuroblastoma inhibitors and their analogues

The aim of this thesis was to identify and develop anti-neuroblastoma agents via two strategies. The first involves a targeted therapy approach towards the synthesis of new drug-like PTP inhibitors (Chapter 2 and 3) and the second involved devising a new versatile synthetic route to the recently established anti-tumour natural-product lead, methyl jasmonates and its analogues (Chapter 4).
From a unique proprietary screening library of 5000 drug-like compounds targeted towards PTPs, three compounds from two distinct chemical series, tetrahydroquinolines P00104 and P00341, and thiobarbituric acid P00337, were identified as PTPN22 inhibitors (IC50 = 5 μM) with moderate potency in vitro. A synthetic route to each chemical series was established and optimised and the procedure was used to synthesize a series of rationally-designed analogues for detailed structure-activity relationship (SAR) studies. The compounds were tested for PTP inhibitory activity against PTPN22 via two experimentally optimised protein assays and were tested for cytotoxicity in a number of neuroblastoma cell lines. However, none of the compounds including the resynthesized hits displayed any promising biological activity, and further investigation on these chemical series was abandoned and another strategy for developing anti-neuroblastoma agents was pursued.
During the last decade, many studies have reported the cytotoxic effects of methyl jasmonate, a plant stress hormone, against various tumours both in vitro and in vivo. As the research on the anti-tumour properties of methyl jasmonate is still at early stages, and also due to the lack of a versatile synthetic procedure for the preparation of its structural derivatives, detailed SAR studies of this compound have not yet been conducted. In the course of this project, a novel versatile synthetic route to methyl jasmonate and its analogues has been developed, which allows substituents to be readily introduced at the α- and β-position of cyclopentenone. This synthetic procedure will facilitate future extensive SAR studies of methyl jasmonate in tumour cells. The cytotoxic activity of the synthesized methyl jasmonate was confirmed against a range of neuroblastoma cell lines including SK-N-SH, SHSY5Y, LAN5 and the Kelly cells, and a further study on the mechanism by which methyl jasmonate induces neuroblastoma cell death is currently underway.

Keywords: Medicinal Chemistry
Methyl Jasmonate
Oncology
Advisor: Russell, A