VictorJuiz/thesis huggingface dataset:
Knowing and understanding

The avowed aim of the thesis is to show that there are some synthetic necessary truths, or that synthetic apriori knowledge is possible. This is really a pretext for an investigation into the general connection between meaning and truth, or between understanding and knowing, which, as pointed out in the preface, is really the first stage in a more general enquiry concerning meaning. (Not all kinds of meaning are concerned with truth.) After the preliminaries (chapter one), in which the problem is stated and some methodological remarks made, the investigation proceeds in two stages. First there is a detailed inquiry into the manner in which the meanings or functions of words occurring in a statement help to determine the conditions in which that statement would be true (or false). This prepares the way for the second stage, which is an inquiry concerning the connection between meaning and necessary truth (between understanding and knowing apriori).
The first stage occupies Part Two of the thesis, the second stage Part Three. In all this, only a restricted class of statements is discussed, namely those which contain nothing but logical words and descriptive words, such as "Not all round tables are scarlet" and "Every three-sided figure is three-angled". (The reasons for not discussing proper names and other singular definite referring expressions are given in Appendix I.)

Keywords: Functions vs rogators
Synthetic necessary truth
Gottlob Frege
Immanuel Kant
Synthetic apriori knowledge
Advisor: Pears, D
The theology of violence

This thesis investigates the theology of violence in early modern England. It finds that violence had an important place in the theology of the English Revolution, which is at variance with many twentieth-century perceptions of Christianity. After introducing these ideas in the first chapter, chapter two begins with an outline of the general conceptions of the relationship between the Divine and violence, contrasting the image of a God of peace with a God of war. It also outlines just war theory, which was central to early modern English views of legitimate violence. Additional aspects of contemporaries' conceptions involved ideas of authorisation, violence as punishment, and a hierarchy of legitimate violence. These ideas are further developed in chapter three, first with reference to the Elizabethan Homilies and then in relation to theologians during the civil wars. This discussion of theologies of obedience anticipates chapter four's analysis of the theologies of resistance in relation to the theology of violence. Chapter four addresses a variety of themes concerning the illegitimacy of suicide and the corresponding legitimacy of self defence. The chapter concludes by addressing the idea of direct divine authorisation for violence, which is modelled by the biblical Book of Joshua and developed by examining Calvin's commentaries on the text. Direct authorisation lays the groundwork for chapter five, which addresses the apocalyptic perspective in relation to the theology of violence. The three interrelated themes of anti-Catholicism, anti-idolatry, and a new dispensation are examined. In chapter six, the previous themes are considered in an analysis of the regicide. The discussion of the regicide not only draws on the preceding discussion of the theology of violence but also examines the "scapegoating" dimension of the execution of the king. The final chapter offers reflections on the importance of the theology of violence for the view of the English civil wars as "wars of religion."

Advisor: Dr Felicity Heal, C
A site-directed spin labelling study of the human alpha-lactalbumin molten globule

The human α-lactalbumin (α-LA) molten globule formed at low pH is a model for the study of protein folding intermediates. The molten globule lacks native-like side-chain interactions, resulting in a fluctuating ensemble of tertiary structures, characterisation of which has been precluded by severe line-broadening in NMR spectra and a lack of long-range NOEs. Paramagnetic relaxation enhancements (PREs) have been measured in a variant of α-LA in which all native cysteines have been mutated to alanine (all-Ala α-LA). Cysteine residues have been mutated into regions of interest and spin labelled with MTSL. These measurements have confirmed that all-Ala α-LA forms a compact molten globule. Transient, long-range interactions that are stabilising the compact fold have also been identified using PREs measured in urea-denatured states. This has identified several interactions formed by hydrophobic residues from both the α- and β-domain, which could be important for initiating and driving folding. The molten globule’s 3D topology has been probed by measuring long-range distances between MTSL pairs using Double Electron-Electron Resonance (DEER). Broad distance distributions have been identified between elements of secondary structure, indicative of a fluctuating but compact fold. By contrast, a narrower distance distribution has been measured within one of the major helices, indicative of native-like secondary structure. The surface accessibility of all-Ala α-LA and that of two other variants ([28-111] α-LA and 4SS α-LA) has been probed using solvent PREs obtained using TEMPOL, a paramagnetic co-solute. This has revealed differences in the solvent-exposure of hydrophobic residues due to the removal of disulphide bonds. This method has also identified buried hydrophobic residues that contribute to forming the molten globule’s stable, native-like core.

Keywords: nuclear magnetic resonance spectroscopy
paramagnetic relaxation enhancement
human alpha-lactalbumin
TEMPOL
molten globule
double electron-electron resonance
electron paramagnetic resonance spectroscopy
MTSL
Advisor: Redfield, C
Disorder and defects in functional molecular frameworks

This Thesis explores the role of structural defects and disorder and their relationship to experimental data, with a particular emphasis on molecular framework materials. The question of how we can build atomistic models of amorphous materials from experimental data without needing to make system-specific assumptions is addressed. The role of 'structural invariance', i.e. the limited range of distinct local atomic environments within a material, as a restraint within reverse Monte Carlo refinement (RMC) is investigated. The operation of these invariance restraints operate is shown to be system-dependent and the challenges associated with effective refinement, e.g. configurational 'jamming', are also investigated. A generalisation to the 'structural simplicity', i.e. the simplest model, holding all else constant, is most likely to be correct. Three new metrics of structural simplicity are proposed: two intrinsically three-dimensional measures of local geometric invariance and one measure of local symmetry. These metrics are shown to robustly quantify the configurational quality. The ability of these metrics to act as effective restraints for the RMC refinement of amorphous materials is demonstrated by the construction of the first data-driven tetrahedral models of amorphous silicon. The role of defects and disorder within metal–organic frameworks (MOFs) is investigated through the canonical MOF UiO-66(Hf). Through a combination of techniques, including X-ray diffuse scattering, anomalous diffraction, total scattering and electron diffraction measurements, the existence of correlated metal-cluster absences in UiO-66(Hf) is demonstrated. Furthermore the ability to synthetically tune both the interactions and concentration of defects is shown. The thermomechanical properties of defective UiO-66(Hf) are also examined. UiO-66(Hf) is shown to rapidly densify by up to 5% (ΔV/V ) on ligand elimination. The resultant densified phase exhibits colossal (≥100MK-1) volumetric negative thermal expansion (NTE); the largest reported value for any MOF. Finally, the capability to tune the physical properties of MOFs through defect incorporation is demonstrated through the defect-dependence of both the densification and the NTE.

Keywords: metal-organic frameworks
molecular frameworks
defects
crystallography
disorder
Advisor: Goodwin, A
Evaluation of volume holographic optical elements in dichromated gelatin

The use of dichromated gelatin (DCG) for the formation of holographic optical elements is investigated. In particular, a study is made of the possible sources of spurious recording and replay in such diffracting media. The formation of spurious gratings due to boundary mismatch, when recording a transmission grating in air, is investigated. Experimental results are treated using a simple linear theory which is capable of predicting the relative modulation strengths of each of six recorded gratings. The efficiencies of each of these gratings is related to Fresnel's Laws of reflection and therefore the beam ratio. A brief experimental study of the beam ratio is made. It is found that linear theories do not explain replay of gratings recorded at high exposure energies. This is because DCG exhibits a saturating recording characteristic. A theoretical model is developed to verify experimental results of modulation versus exposure energy for the recording of single and double exposure transmission gratings and their subsequent harmonics. This gives good agreement for most cases, however, it does not explain fully the replay of a difference grating formed due to nonlinearities in the double exposure hologram. A coupled wave theory is therefore developed to take account of both multiple grating interactions between the two primary recordings and the recording of a third grating with a spatial frequency equal to the difference of the two fundamental frequencies. The model gives good agreement with experimental results for varying replay angles and wavelengths. DCG is finally used as a tool to investigate the formation of noise gratings in silver halide emulsions. In particular, results are presented for experiments which were performed to study the effect of high angular scatter upon the selectivity of the noise grating and the recording of reflection noise gratings.

Advisor: Solymar, L
Context Based Querying of Dynamic and Heterogeneous Information Sources

The proliferation of freely-accessible data-intensive websites, the growing availability of pervasive and mobile applications, as well as initiatives for open-accessible linked data in the Web, provided the users with potential sources of valuable information. These data also represent new business opportunities for industries, while their processing and management is a rich research field for academics. In addition, pervasiveness and mobility make information available everywhere and at any time; therefore, user-centred, dynamic and on-the-fly integration of heterogeneous becomes extremely useful in practical situations such as mobile data management, in particular with devices as tablets, pads and smartphones. We present a methodology and a set of technologies for ontology-driven, context-aware data-integration systems capable of seamlessly handling heterogeneous and dynamic data sources in a dynamic environment where the possibly mobile, transient and evolving data sources are not known in advance. In such Nomadic Data-Integration Systems (N-DIS), query answering is driven by an ontology and the context is used to formally represent the situations in which the users or the applications need to operate. In our work, we re-think query-answering techniques coming from description logics and database theory, and we apply them to an evolving scenario, composed by heterogeneous data sources with the additional constraint of the context-based personalisation of queries and, as a consequence, of their answers. The concept of N-DIS and the corresponding design methodology has been applied to various application fields such as decision support for medical-emergency situations, Semantic-Web meta-data management, Semantic Search and pervasive advertisement, with promising results.
Tractable query answering for description logics via query rewriting

We consider the problem of answering conjunctive queries over description logic knowledge bases via query rewriting. Given a conjunctive query Q and a TBox T, we compute a new query Q′ that incorporates the semantic consequences of T such that, for any ABox A, evaluating Q over T and A can be done by evaluating the new query Q′ over A alone. We present RQR—a novel resolution-based rewriting algorithm for the description logic ELHIO¬ that generalizes and extends existing approaches. RQR not only handles a spectrum of logics ranging from DL-Lite_core up to ELHIO¬, but it is worst-case optimal with respect to data complexity for all of these logics; moreover, given the form of the rewritten queries, their evaluation can be delegated to off-the-shelf (deductive) database systems. We use RQR to derive the novel complexity results that conjunctive query answering for ELHIO¬ and DL-Lite+ are, respectively, PTime and NLogSpace complete with respect to data complexity. In order to show the practicality of our approach, we present the results of an empirical evaluation. Our evaluation suggests that RQR, enhanced with various straightforward optimizations, can be successfully used in conjunction with a (deductive) database system in order to answer queries over knowledge bases in practice. Moreover, in spite of being a more general procedure, RQR will often produce significantly smaller rewritings than the standard query rewriting algorithm for the DL-Lite family of logics.

Keywords: Query Rewriting
OWL
Query Answering
Description Logics
Advisor: Horrocks, I
Motik, B
In aid of conflict: a study of citizen activism and American medical relief to Spain and China

The outbreak of the Spanish Civil War in 1936 and the Second Sino-Japanese War in 1937 triggered many responses amongst the American public, including a number of private initiatives in medical aid that occupied a borderland between traditional humanitarian relief and political activism. This study is interested in the stories of three organisations arising in this tradition: the American Medical Bureau to Aid Spanish Democracy (AMBASD), the American Bureau for Medical Aid to China (ABMAC), and the China Aid Council (CAC). While three separate initiatives in terms of who was responsible for their creation in the United States, and the communities they sought to help abroad, all three demonstrate parallels in their foundation and development that merit a joint historical consideration.
Emerging from the backdrop of isolationism in U.S. foreign policy, the AMBASD, ABMAC, and CAC became a means of voicing both political and humanitarian ideals through the medium of medicine. In many ways, this thesis becomes a study of lost causes. As political campaigns, none of the organisations in this study succeeded in changing U.S. policy, although the ABMAC and CAC benefitted from interests that overlapped with larger changes in U.S. military alliances. As humanitarian organisations, only one (the ABMAC) lived past the conflict to which it owed its foundation. Their story, however, retains its historical interest in challenging both the way in which we examine the mythology of humanitarian idealism, and our understanding of the balance between internationalism and isolationism in the 1930’s United States. For the medical activists of these organizations, medical aid offered both a tangible outlet for personal ethical and political beliefs, but also promised an alternative means of diplomacy that brought greater agency to more popular levels.

Keywords: medical relief
Second Sino-Japanese War
humanitarianism
medical activism
Spanish Civil War
medical volunteer
American Red Cross
international aid
Advisor: Harrison, M
Davies, G
Stochastic models of ion channel dynamics and their role in short-term repolarisation variability in cardiac cells

Sudden cardiac death due to the development of lethal arrhythmias is the dominant cause of mortality in the UK, yet the mechanisms underlying their onset, maintenance and termination are still poorly understood. Therefore biomarkers are used to determine arrhythmic risk within patients and of new drug compounds. In recent years, the magnitude of variations in the length of successive beats, measured over a short period of time, has been shown to be a powerful predictor of arrhythmic risk. This beat-to-beat variability is thought to be the manifestation of the random opening and closing dynamics of individual ion channels that lie within the membrane of cardiac cells. Computational models have become an important tool in understanding the electrophysiology of the heart. However, current state-of-the-art electrophysiology models do not incorporate this intrinsic stochastic behaviour of ion channels. Those that do use computationally costly methods, restricting their use in complex tissue scale simulations, or employ stochastic simulation methods that result in negative numbers of channels and so are inaccurate. Therefore, using current stochastic modelling techniques to investigate the role of stochastic ion channel behaviour in beat-to-beat variability presents difficulties.
In this thesis we take a mathematically rigorous and novel approach to develop accurate and computationally efficient models of stochastic ion channel dynamics that can be incorporated into existing electrophysiology models. Two different models of stochastic ion channel behaviour, both based on a system of stochastic differential equations (SDEs), are developed and compared. The first model is based on an existing SDE model from population dynamics called the Wright-Fisher model. The second approach incorporates boundary conditions into the SDE model of ion channel dynamics that is obtained in the limit from the discrete-state Markov chain model, and is called a reflected SDE. Of these two methods, the reflected SDE is found to more accurately capture the stochastic dynamics of the discrete-stateMarkov chain, seen as the ‘gold-standard’ model and also provides substantial computational speed up. Thus the reflected SDE is an accurate and efficient model of stochastic ion channel dynamics and so allows for detailed investigation into beat-to-beat variability using complex computational electrophysiology models. We illustrate the potential power of this method by incorporating it into a state-of-the-art canine cardiac cell electrophsyiology model so as to explore the effects of stochastic ion channel behaviour on beat-to-beat variability. The stochastic models presented in this thesis fulfil an important role in elucidating the effects of stochastic ion channel behaviour on beat-to-beat variability, a potentially important biomarker of arrhythmic risk.

Keywords: cardiac electrophysiology
ion channels
Langevin equation
stochastic
Advisor: Burrage, K
Kay, D
Rodriguez, B
An SEM EBIC study of the electronic properties of dislocations in silicon

Individual, well structurally characterised dislocations present in n-type silicon have been studied using the electron beam induced current (EBIC) mode of an SEM.
An EBIC system has been designed and constructed which includes i) phase sensitive detection, ii) computerised control of the experimental equipment and data capture and iii) a variable temperature SEM specimen stage.
With this system measurements have been made of the EBIC contrast of individual segments of deformation induced dislocations produced by two stage compressive deformation at 850°C and 420°C.
An experimental and theoretical analysis of EBIC signal generation in the Schottky barrier specimens used in this work is presented. This shows that the EBIC contrast measurements made may be directly correlated to the dislocation recombination strength.
Contrast measurements have been made at temperatures in the range 120K to 370K and for electron beam currents from 6 x 10-12A to 2 x 10-9A. Several new effects have been observed. Minority carrier diffusion length measurements have also been performed in silicon containing dislocations. These show that the value obtained may depend upon experimental parameters used in a hitherto undetected manner.
A new theory describing recombination of carriers at charged dislocations has been developed and this has been extended to provide a description of the variation of the EBIC contrast of dislocations with temperature, electron beam current and also the transient response of the EBIC contrast. Comparison of the theoretical predictions with the results gained experimentally shows full agreement for low temperatures or large beam currents. At high temperatures and small beam currents the theory shows the EBIC contrast will behave differently depending on the density of dislocation states present.
Interpretation of the experimental results in terms of this theory allows some new insight to be gained for recombination at dislocations, and values for some of the parameters controlling recombination have been obtained.

Advisor: Ourmazd, A
Booker, G
The development of functional hyaluronan hydrogels for neural tissue engineering

Tissue engineers – in order to develop therapies for the treatment of complex neurological injuries and diseases – attempt to recreate elaborate developmental mechanisms in vitro. Neuronal precursor cells are excellent candidates for the study of developmental operations such as cell adhesion, differentiation, and axonal pathfinding. Hyaluronan (HA) is a common polysaccharide that is found extensively throughout the neuronal extracellular matrix (ECM), and can be functionalised and crosslinked to form stable hydrogels that support growing neuronal cells. Hyaluronan hydrogels can be modified chemically and mechanically to mimic the ECM of the developing brain, awarding control over mechanisms such as differentiation and axonal pathfinding. This thesis is concerned with the functionalisation and characterisation of HA hydrogels, ultimately in order to simulate vital properties of the developing brain. Here we show that HA hydrogels can be finely tuned mechanically (by modulating stiffness and viscosity), and chemically, by the conjugation of peptides that mimic the neural cell adhesion molecule (NCAM). NCAM mimics and novel mimics of sialylated NCAM significantly influence the differentiation of NSPCs in 2D and 3D. HA hydrogels successfully support long term culture of neural cells in 3D, and encourage the formation and extension of neurites of several cell types including human, mouse and rat neuronal precursor and stem cells. These results demonstrate for the first time that novel NCAM mimicking peptides can be conjugated to well defined hydrogel matrices that influence intricate developmental behaviours in 3D. Understanding how neural cells form functional networks is essential for the development of clinical approaches that attempt to address the injuries and diseases that affect these systems.

Keywords: biomimetics
trauma
hydrogel
stem cell
hyaluronan
hyaluronic acid
SANS
traumatic
neural
regenerative medicine
neuronal
neural network
tissue engineering
brain injury
Advisor: Cui, Z