VictorJuiz/thesis huggingface dataset:
Crop residue management in oil palm plantations: soil quality, soil biota and ecosystem functions

The application of crop residues is one of the most common agricultural practices used to maintain soil ecosystems and crop productivity. This thesis focuses on the oil palm (Elaeis guineensis) agroecosystem, an important tropical crop that has expanded rapidly over the past four decades. Both land conversion and business-as-usual practices within the plantations have contributed to soil degradation. The application of oil palm residues, such as empty fruit bunches (EFB) and oil palm fronds, are thought to have positive effects on the soil ecosystem; yet there is currently a deficit of knowledge on their effectiveness. This thesis aims to examine the effects of oil palm residue application on soil physicochemical properties, soil biota, and ecosystem functions. It reports the results of extensive field trials, sample collection, and statistical analysis of crop residue applications in oil palm plantations in Central Sumatra, Indonesia.
Four key results emerged from the thesis. First, in this study site land conversion from secondary forest to oil palm does not affect litter decomposition rate, but positively influences soil fauna activity. Second, there is greater soil fauna activity following EFB application than oil palm fronds or chemical fertilizers, and the fauna activity is highly associated with changes in soil chemical properties and soil moisture conditions. Third, EFB application enhances soil ecosystem functions, through the direct provision of organic matter, and by influencing soil biota. Finally, over 15 years of application, EFB appears to be effective in maintaining or increasing annual crop yield in comparison to chemical fertiliser treatment. Temporal changes in crop yield under EFB application appear to be associated with climatic conditions and soil organic carbon. Overall, these findings improve our understanding of the potential of oil palm residue applications to increase soil quality, soil biota, and ecosystem functions. They also provide useful information for a wider audience of soil ecologists, agricultural managers, and policy makers to improve sustainable management of the oil palm ecosystem.

Keywords: EFB
soil biota
soil ecosystem function
soil quality
empty fruit bunch
crop residue management
oil palm
Advisor: Willis, K
Snaddon, J
Aspects of early hip osteoarthritis

Osteoarthritis develops secondary to the action of hostile biomechanics upon susceptible cartilage. Cam morphology describes a loss of concavity at the femoral head-neck junction resulting in femoral impaction against the acetabular rim within a functional range of movement. This impaction is termed femoroacetabular impingement and can result in pain and cause damage to adjacent articular cartilage that progresses to osteoarthritis. Cam morphology is a target for joint preservation strategies.
The first study in this thesis compares hip development in academy football players with controls from local schools. The results provide strong evidence that cam morphology can develop in response to intense sporting activity during adolescence. At present, it is not possible to recommend activity modification as the cardiovascular benefits of exercise are likely to outweigh potentially detrimental effects on hip morphology. Nevertheless, individuals participating in high-level sports during youth may represent a high risk cohort for osteoarthritis warranting surveillance.
Diagnostic tools currently available only allow identification of late joint degeneration when disease is irreversible. Advances in the field of disease biomarkers may overcome this challenge. The second study of this thesis explored the prognostic value of compositional MRI. Baseline delayed gadolinium-enhanced MRI of cartilage was able to predict the development of radiographic hip osteoarthritis in asymptomatic individuals within five years. As well as identifying individuals who are likely to benefit from intervention, compositional MRI may allow the evaluation of treatment efficacy within short timeframes.
A number of interventions aimed at joint preservation are under investigation for treating cam morphology femoroacetabular impingement. Arthroscopic surgery is increasingly performed to restore the concavity at the femoral head-neck junction and prevent impaction against the acetabular rim. A feasibility study was performed for a proposed randomised controlled study comparing operative and non-operative treatment. The study protocol was developed for the 'Femoroacetabular Impingement Trial' (FAIT).

Keywords: MRI
Osteoarthritis
Surgery
Sport
Hip
Advisor: Glyn-Jones, S
Carr, A
Modelling signalling pathways and cellular dynamics in vascular mechanobiology: a theoretical, experimental and computational study

Blood vessels are dynamic structures whose properties are continuously adapted by resident vascular cells. Existing mechanobiological models tend to ignore regulatory signalling and cell population dynamics, both key determinants of arterial growth and remodelling (G&R). In this D.Phil., a combined theoretical, experimental and computational approach is used to formulate, reﬁne and implement a novel model of the arterial wall that includes vascular mechanics, microstructure, biochemical metabolism and signalling, and cell phenotype and population dynamics.
A mathematical chemo–mechano–biological (CMB) model is formulated by coupling a biomechanical model of the arterial wall as a cylindrical nonlinear elastic membrane to a system of biologically–informed evolution laws governing ﬁbroblast cell–mediated, transforming growth factor (TGF)-β–regulated collagen metabolism. Model simulation of inﬂammatory aneurysm development suggests that increasing TGF-β levels promotes a cell–driven proﬁbrotic response leading to aneurysm stabilisation, illustrating the model’s ability to couple chemo–biological processes to tissue–level mechanical evolution.
To inform the theoretical framework experimentally, a recent mouse model of post–developmental disruption of medial smooth muscle TGF-β signalling is for the ﬁrst time subjected to hypertension, and characterised by biaxial mechanical testing and (immuno)histological staining. Increased adventitial TGF-β levels following perturbation are associated with strong proﬁbrotic responses (increased cellularity, collagen deposition, thicker walls) altering tissue mechanics (lower biaxial stress, higher structural stiffness).
Simulation of realistic arterial geometries is enabled by coupling the 1D CMB model to a three–dimensional structural solver. Heterogeneous spatial distributions of mechanical, microstructural and chemo–biological variables determining the evolution of complex saccular aneurysm geometries can be simulated with this 3D implementation.
A novel chemo–mechano–biological model of vascular cell dynamics and regulatory signalling governing arterial G&R is formulated, informed by speciﬁcally–generated experimental data, and implemented in an advanced 3D computational framework. This will allow for virtual investigation of therapies acting on chemo–biological agents of arterial G&R, with potential beneﬁts for vascular disease patients.

Keywords: vascular
collagen
TGF-beta
aneurysm
fibroblast
growth and remodelling
Advisor: Thompson, M
Watton, P
'Doppler' cooling in high-Tc superconductors

Thanks to growing capibilities in modulating the properties of materials by selectively driving a specific degree of freedom, along with recent developments in terahertz science, it has been possible to excite and probe the Josephson mode in cuprate superconductors. It is believed that in these materials, phase fluctuations in the superconducting order parameter, which are manifested by Josephson plasmonic excitations can be important in determining the critical temperature. Current efforts in finding novel ways of enhancing superconductivity are geared towards developing ways of using coherent control of this phase to reduce thermal fluctuations, hence improving the effective critical temperature in such materials.
With this in view, we propose a 'Doppler' Cooling scheme for layered superconductors having a bilayer structure and conduct a feasibility study to assess their applicability to such systems. By modelling a bilayer cuprate unit-cell as two coupled Josephson junctions, we find that it is possible to induce transitions between and interlayer and higher energy intralayer plasmonic mode via driving from an externally applied electromagnetic field only when the junction is current biased. Our study shows that the physics of the system allow such a scheme to be implemented. The low recoil imparted by photons at terahertz frequencies enables us to apply the same framework as for cooling of atomic systems. The relatively long lifetimes (&Tilde; 0.1 ns) against spontaneous decay estimated imply that cooling is not likely to be limited by inherent features of the scheme but will rather depend on other factors, such as the competition between cooling and rethermalisation. These factors need to be further studied to assess the experimental viability of the proposed scheme.

Advisor: Jaksch, D
Cavalleri, A
The mechanics of assignments: functions and form

Choses in action are valuable assets. This has compelled (and been facilitated by) the development of legal devices such as equitable assignment to allow holders of choses to deal with them, inter vivos.
This thesis makes two claims.
First, equitable assignments are best conceived as a composite of a bare trust and an atypical agency where the assignee is authorised to invoke the assignor's entitlements against the obligor to the chose assigned, as the assignee pleases.
On this conception, equitable assignments merely entail generation of a new set of jural relations as between assignor and assignee. Though these affect how the jural relations between assignor and obligor are to be discharged, those jural relations are left intact and unchanged, unless the requirements for 'statutory' assignments have been satisfied.
Second, 'statutory' assignments are regulatory in effect. Where a debt or other chose in action has been validly equitably assigned and the requirements in s 136(1) Law of Property Act 1925 are satisfied, the specific entitlements set out in sections 136(1)(a), (b) and (c) will be passed from the assignor and transferred to the assignee. But that is only true with regards entitlements falling within those provisions, and the set of entitlements listed therein is not exhaustive.
The composite model of equitable assignment, and the clarification of the nature of 'statutory' assignment, reduces confusion over their operation and effects. Accordingly, this thesis tempers the urge towards legislative reform of the law of assignment: reform may not be needed since the law is not incoherent, though it is certainly complex. And if targeted law reform to simplify the law on assignment be thought desirable, it is as well to know what one is reforming.

Keywords: intangible personalty
choses in action
Law of Property Act 1925
equitable assignment
Judicature Act 1873
statutory assignment
Common Law Procedure Act 1854
Advisor: Stevens, R
'No matter how much or how little they’ve got, they can’t settle down': A social history of Europeans on the Zambian Copperbelt, 1926-1974

This thesis traces the social history of the European community on the Zambian Copperbelt from the onset of copper mining in 1926 to the mid-1970s when a dramatic slump in the price of copper generated severe economic difficulties. There has been almost no academic work on the Copperbelt's European community and, in this respect, this thesis fills an important gap. However, a focus on the European community has a wider significance than filling this gap.
Although the Copperbelt has generally been understood in a national or regional context, this thesis argues that developments there are better understood by exploring how the Copperbelt was linked to other mining regions around the world; in Britain, South Africa, the US and Australia. The European community was largely composed of highly mobile, transient individuals, and the constant movement of people made and sustained transnational connections.
Mobility and transience are crucial to two of the main themes of this thesis: class consciousness and the importance of race. Class was a strong marker of identity for Europeans and a variant of 'white labourism' dominated life on the Copperbelt. Industrial unrest was a regular occurrence in the life of the European community as strikes and other disputes underpinned extraordinary levels of affluence. The frequency of industrial unrest diminishes the relevance of South Africa as a viable comparison, as does the relative lack of importance of race. This thesis argues that the predominant attitude of Europeans toward the African majority around them was one of indifference and that the importance of 'African advancement' has been overstated.
Archival collections in Zambia and Britain constitute the main sources for this thesis. These sources are supplemented with material from archives in South Africa and Netherlands, contemporary publications including newspapers, and interviews with former European residents of the Copperbelt.

Keywords: Zambia
Copperbelt
Mining history
Labour history
Advisor: Deutsch, J
The stratigraphical context of the Ediacaran Biota of eastern Newfoundland

Detailed geological mapping and improved understanding of the geological evolution of the siliciclastic late Ediacaran rocks of the Mistaken Point Ecological Reserve (MPER) and the Catalina Dome, both of Newfoundland, provide a new framework for improved lithostratigraphic subdivision of the successions. The lithostratigraphic correlation of the Catalina Dome with the succession at MPER is found to be incorrect, prompting the erection of the Trinity Bay North Group to classify the rocks of the Catalina Dome.
U-Pb (zircon) ages from the successions provide essential temporal constraints on the rise and fall of the Ediacara biota, and show that the Catalina Dome sections are up to 5 Myr older than previously thought. Both the MPER and Catalina Dome successions show an early fossil assemblage characterised by the presence of Trepassia and Vinlandia ; a taxonomic radiation &Tilde;575 Ma; the emergence of evidence for animals &Tilde;565 Ma; and the sudden disappearance of most forms within post-565 Ma slumped slope deposits. These points provide the basis of discussion around the potential for a biostratigraphy for the Ediacaran of Avalonia, and support the 'Ediacaran Explosion' hypothesis.
Previous research using sedimentary strucutres and geochemical proxies to assign a nonmarine deposition environment to the MPER and Catalina Dome sections is found to be flawed and without merit. There is no evidence for shallow marine or sub-aerial depositional environments. All known Avalonian rangeomorphs are found in deep-marine facies. The environmental controls on the stratigraphic distribution of taxa remain poorly constrained.
Analysis of tuffites within MPER suggests they were deposited by ashy turbidity currents, rather than as ash-falls. This prompts caution when using these tuffites for geochronological analysis, and requires the re-evaluation of the traditional taphonomic model for rangeomorph fossilisation.
'Post-fossilisation processes' are shown to bias fossil census studies, most notably through differing mechanisms of tuffite weathering and erosion. The impacts on palaeoecological studies, and geoconservation efforts are considered. The geoconservation legislative frameworks for Newfoundland and England are compared and contrasted, and recommendations made.

Advisor: Brasier, M
Variation of stellar populations and dark matter with time and environment

In this thesis, I probe the stellar and dark matter component of galaxies in order to infer their evolutionary histories. I am doing this by studying two distinct galaxy population samples: (i) a high redshift sample at z&Tilde;1, and (ii) a high density environment sample of galaxies in the nearby Coma cluster. By comparing these samples to a sample of galaxies in the local Universe in a low density environment, I infer variation in their properties as a function of time and environment.
For both samples, I create accurate dynamical models to infer the stellar Mass-to-Light ratios of the galaxies and their dark matter fractions. Furthermore, I model the stellar population of the galaxies using a full-spectrum technique while reproducing their star formation history in a non-parametric manner. In addition, I use IFS data for a subset of galaxies in the high density sample to create detailed dynamical models that strengthen the results found in that sample.
Based on the quantities derived from these analyses, I present results on the IMF normalisation and dark matter fraction of galaxies in both samples. Furthermore, I studied the scaling relations of these galaxies and compared them to that observed for the ATLAS3D sample, which serves as a low density sample of the Local Universe, to infer variation in galaxy properties as a function of time and environment.

Keywords: Galaxies
Advisor: Cappellari, M
Quasiparticle interference in strongly correlated electronic systems

We investigate the manifestation of strong electronic correlations in the quasiparticle interference (QPI), arising from the scattering of conduction electrons from defects and impurities in an otherwise translationally-invariant host. The QPI may be measured experimentally as the Fourier transform of the spatial modulations in the host surface density of states that result, which are mapped using a scanning tunnelling microscope.
We calculate the QPI for a range of physically relevant models, demonstrating the effect of strong local electronic correlations arising in systems of magnetic impurities adsorbed on the surface of non-interacting host systems. In the first instance the effect of these magnetic impurities is modelled via the single Anderson impurity model, treated via numerical renormalization group (NRG) calculations. The scattering of conduction electrons, and hence the QPI, demonstrate an array of characteristic signatures of the many-body state formed by the impurity, for example due to the Kondo effect.The effect of multiple impurities on the QPI is also investigated, with a numerically-exact treatment of the system of two Anderson impurities via state-of-the-art NRG calculations. Inter-impurity interactions are found to result in additional scattering channels and additional features in the QPI.
The QPI is then investigated for the layered transition metal oxide Sr2RuO4, for which strong interactions in the host conduction electrons give rise to an unconventional triplet superconducting state at Tc &Tilde; 1.5K. The detailed mechanism for this superconductivity is still unknown, but electron-electron or electron-phonon interactions are believed to play a central role. We simulate the QPI in Sr2RuO4, employing an effective parametrized model consisting of three conduction bands derived from the Ru 4d t2g orbitals that takes into account spin orbit coupling and the anisotropy of the Ru t2g orbitals. Signatures of such interactions in the normal state are investigated by comparing these model calculations to experimental results. We also calculate the QPI in the superconducting state, and propose how experimental measurements may provide direct evidence of the anisotropy and symmetry of the superconducting gap, and thus offer insight into the pairing mechanism and the superconducting state.

Keywords: Quasiparticle interference
Quantum impurity physics
Strongly-correlated electron systems
Computational physics
Kondo effect
Advisor: Logan, D
Naṣīr al-Dīn al-Ṭūsī and the Avicennan tradition: metaphysics and mental existence

This is a study of the metaphysics of necessary existence in the thought of the thirteenth century Persian polymath Naṣīr al-Dīn Ṭūsī (d. 672/1274). It argues that Ṭūsī is part of an important conceptualist turn within the interpretation of Avicenna's metaphysics around the thirteenth century, and that two key principles within his metaphysical scheme provide the essential means by which he defends the tenor of his predecessor's general ontology against its detractors in the aporetic tradition. These principles, each one of which is presented in their historical manifestation, are the (1) the ambiguity of existence (tashkīk al-wujūd) and (2) the being of reason (al-i'tibār al-'aqlī). The integrity of these concepts as well as the importance they have to the verification (taḥqīq) of Avicenna's metaphysics is demonstrated with reference to the single and undoubtedtly most important idea within the Avicennan metaphysic, namely, its conception of a being which is necessary of existence in itself (wājib al-wujūd bi-dhātihi). Avicenna makes two fundamental claims about the nature of such a being: that it is "sheer oneness" and that it is a being the essence of which is identical to its existence. The former establishes the unicity of the divine essence, while the latter affirms the identity of its essence and existence (māhiyyatuhu inniyyatuhu), both of which are the consequence of it being necessary in itself. Avicenna's detractors in the theological tradition rejected both of these claims by confuting the notion of divine aseity. I consider the cumulative objections raised by three of Avicenna's major critics, namely Ghazālī (d. 1111), Shahrastānī (d. 1153) and Rāzī (d. 1210)—and then demonstrate how each of these principles in Ṭūsī's thought effectively defends the Avicennan conception of the Necessary Existent.
By a gradual discovery of the fecundity of rationate beings since (at least) the time of ʿUmar Khayyām, I argue further that the concept of a being of reason (al-i'tibār al-'aqlī) is the single most important development in the mainstream post-Avicennan tradition. The second part of this thesis is therefore devoted to the notion of mental existence (al-wujūd al-dhihnī), a realm of being which ontologically grounds the subsistence of rationate being. The final part of this dissertation provides a discussion of Ṭūsī's innovative solution to the problem of correspondence; that is, how does a being of reason correspond to reality if per definiens it is a being incapable of mind-independent existence? This requires a foray into the metaphysics of truth and one of the most important philosophical ideas in the whole of post-classical Islam: 'the thing itself' (nafs al-amr). I examine the novel contributions which Ṭūsī has made for the inauguration and subsequent development of this concept in the post-Avicennan tradition. The trajectory of this dissertation may be thus be described as journey from 'being Necessary' to 'being mental' to 'being true'.

Advisor: al-Akiti, A
Pfeiffer, J