VictorJuiz/thesis huggingface dataset:
Regenerative agriculture practices and their influence on soil organic carbon and farm productivity in temperate regions
Keywords: regenerative agriculture
meta-analysis
sustainable agriculture
soil organic carbon
systematic review
RothC
agroecology

Global food production is currently contributing to numerous environmental challenges including anthropogenic climate change, biodiversity loss and widespread declines in soil health. Regenerative Agriculture (RA) is an emerging paradigm which proposes that restoring soil health, by adopting a suite of management practices that align with so-called ‘regenerative’ principles, will not only improve agricultural productivity but also contribute to climate change mitigation through increased soil organic carbon (SOC). Despite a plethora of policies and suggested practices emerging over the past decade to support the introduction of RA across the world, there is still remarkably little scientific evidence to quantify potential improvements in soil organic carbon or agricultural productivity as a result of adopting ‘holistic’ RA systems. This represents a large knowledge gap that I set out to address in my DPhil thesis using currently available evidence for individual management practices.
Research for my thesis was divided into four parts. First, I used gold-standard systematic review methods to collate the state of current knowledge and assemble datasets from published studies of management practices forming part of a RA approach. My study area was temperate oceanic regions and I examined papers that considered the following RA approaches: reduced tillage intensity, cover cropping and ley-arable rotations in arable systems, and rotational grazing, multi-species or herbal leys, and agroforestry in pasture systems. Second, using the datasets obtained from these published studies, I conducted Bayesian meta-analyses of the impact of these practices on SOC and agricultural productivity (crop yields, herbage production, livestock growth). I found that adoption of rotational grazing and herbal leys can increase herbage dry matter production and livestock growth rates in pasture systems, but there is currently insufficient evidence to determine their impact on SOC. Conversely, my results identified clear potential for RA practices in arable systems to increase SOC but no evidence of a SOC-yield win-win. Third, using this finding I simulated adoption of these arable RA practices across Great Britain using the soil carbon model RothC, and found that in the UK there is the potential to mitigate 16-27% of current agricultural emissions through soil carbon sequestration. Finally, I conducted semi-structured interviews with industry representatives and livestock farmers in England to further understand advantages and disadvantages of implementing rotational grazing, herbal leys, ley-arable rotations and trees on farms. This final part of my research highlighted potential constraints on the ability to realise the theoretical advantages demonstrated from my earlier analyses.
Computational models of assembly, structure and damage to collagen IV networks
Keywords: monte carlo
persistent homology
2d networks
collagen
molecular dynamics

Collagen IV networks play a key structural role in the human ocular lens capsule. However, their structure is not well understood, and is hypothesised to undergo significant changes over a lifetime, resulting in a loss of ability to accommodate different focal depths. In this thesis, a range of computational models and methods are developed, which aim to help better understand the properties of 2D networks of biopolymers, especially inspired by collagen IV.
The available experimental images of collagen-containing networks are assessed and an image analysis protocol is developed. A Monte Carlo method is designed, which introduces disorder into simplified graph-based networks by switching edges. In addition, Molecular Dynamics is used to simulate coarse-grained polymers which attract one another at their headgroups. These coarse-grained polymers are shown to self-assemble into a variety of interesting network structures. The coarse-grained polymer approach is combined with a Molecular Statics scheme to calculate mechanical properties of the network, and understand how the networks behave when stretched. A model that can mimic the ageing of the network over a lifetime is developed. To better understand how lens capsule motion may damage collagen IV networks, the rupturing behaviour of the polymer networks is examined by stretching ordered hexagonal networks linearly and sinusoidally until they break. This is compared to the rupturing behaviour of networks containing defects.
The MD method is used to assess the surface roughness and dimensionality of polymer networks, which is quantified by a fractal dimension. Finally, a new type of persistence diagram is used to quantify and visualise damage to ring structures in a network over time.
Pt(IV) anticancer prodrugs and liposomal encapsulation
Keywords: platinum
microbubbles
anticancer
photoactivation
prodrugs
DIPG
liposomes

This work describes the development of several photoactivatable platinum based anticancer prodrugs. The use of liposomes as a method of drug encapsulation for a known platinum complex is also explored. Finally, the synthesis of a microbubble-liposome conjugated system and the sonoluminescence effect of microbubbles are assessed. Chapter 1 discusses the fundamental properties of platinum, how it is currently utilised in chemotherapy, and the potential benefits of light-activated platinum compounds. The use of liposomes in medicine, with particular focus on drug encapsulation, is discussed in detail. The clinical applications of microbubbles are also explored. Chapter 2 describes the development and characterisation of two novel photoactivatable PtIV complexes. The solubilities, photochemical properties and pKa values of these compounds are compared to those of two previously reported complexes. Chapter 3 reviews the use of liposomes for the encapsulation of the drug iproplatin, with exploration of the best active loading method for this compound, and how the composition of the liposomes can be adapted to improve drug retention. Chapter 4 discusses the optimisation of synthesis for a conjugated microbubble-liposome drug delivery system. The phenomenom of sonoluminescence, and it’s potential use for activating photosensitive compounds is also explored. Chapter 5 describes the conclusions for this work, and what the next steps of this research would involve. Chapter 6 provides the experimental procedures and synthetic methods used in this work.
Establishment of an ex vivo precision-cut lung slice model for the evaluation of drug-radiation responses
Keywords: DNA-PK
gH2AX
lung models
ex vivo
radiation
FFR
PCLS
DNA damage response
53BP1
DDR

Background: We hypothesized that the ex vivo precision-cut lung slices could provide a novel model for studying the biological responses of normal tissue to ionizing radiation and additionally provide important mechanistic insights into drug-radiation combinations.
Aims: 1) To establish an ex vivo model of lung tissue slices from mice. 2) To evaluate DNA damage responses in ex vivo lung slices compared with in vivo responses in lungs. 3) To determine the impact of NU7441, a pharmacological inhibitor of DNA-PK, on the DNA damage response.
Methods: Left lungs from female C57BL/6 mice (6-12 weeks old) were dissected and perfused with 4% low gelling temperature agarose. Lungs were sliced (250 µm) and incubated ex vivo for up to seven days. Lung slices were irradiated (137Cs) in the presence or absence of a DNA-PK inhibitor (NU7441). Fixed tissue sections were stained for histological markers (γH2AX and 53BP1) of DNA double-strand breaks (DSBs).
Results: We established culture conditions that maintained tissue viability for up to 7 days and structural integrity for at least 3 days. We showed that DNA damage responses to ionizing radiation were similar in ex vivo lung slices and lungs irradiated in vivo. Treatment with NU7441 was associated with an increase in long-lived DNA DSBs consistent with pharmacological inhibition of DNA repair. Unexpectedly, we found that a subset of lung epithelial cells (alveolar Type II) had low levels of γH2AX and 53BP1 staining following irradiation, which may have been associated with rapid repair of DNA DSBs.
Conclusion: The DNA damage response to ionizing radiation in lung tissue is similar in ex vivo and in vivo. The ex vivo lung slice model is a novel and highly tractable experimental system for studying the biological effects of drug-radiation combinations where the ability to carefully control experimental variables gives it clear advantages over in vivo models.
The effect of domain geometry and long-range dispersal on the motion of hybrid zones
Keywords: probability
hybrid zones
population genetics
SLFV

We consider two different population models that relate to hybrid zones. In both cases individuals in the population can be of one of three types: aa which may be fitter than AA, and both fitter than the aA heterozygotes. The hybrid zone is the region separating a subpopulation consisting entirely of aa individuals from one consisting of AA individuals.
First, we investigate the interplay between the motion of the hybrid zone and the shape of the habitat, both with and without genetic drift (corresponding to stochastic and deterministic models respectively). In the deterministic model, we investigate the effect of a wide opening and provide some explicit sufficient conditions under which the spread of the advantageous type is halted, and complementary conditions under which it sweeps through the whole population. As a standing example, we are interested in the outcome of the advantageous population passing through an isthmus. We also identify rather precise conditions under which genetic drift breaks down the structure of the hybrid zone, complementing previous work that identified conditions on the strength of genetic drift under which the structure of the hybrid zone is preserved.
The second set of results regard the study of how hybrid zones are affected by long-range dispersal of the individuals in the population, assuming both homozygotes are equally fit. We ignore genetic drift and use a deterministic model, the fractional Allen-Cahn equation to study the population. We show not only that under a suitable rescaling the motion of hybrid zones converges to motion under mean curvature flow, but also that there is a family of possible rescalings that gives this result. To overcome technical difficulties arising from the heavy-tailed nature of the stable distribution, we couple ternary branching stable motions to ternary branching Brownian motions subordinated by truncated stable subordinators, and use this coupling to quantify how the large jumps of the stable motion affect our main result.
Label-free tracking and mass measurement of single protein complexes on lipid bilayers
Keywords: single molecule pull-down
optical microscopy
surface passivation
single particle tracking
lipid bilayers
mass photometry lipid
HIV

Protein-protein interactions are essential for biological processes, but can display a level of polydispersity that is difficult to study with bulk measurements. Recently, mass photometry, a label-free single molecule imaging technique, has been used to quantify protein-protein interactions by measuring the mass of single proteins. So far, however, measurements are limited to solution-based systems and nM concentrations. Here, we aim to expand the applications of mass photometry to proteins on lipid bilayers, and to increase the concentration range of solution-based measurements.
We implement a surface passivation protocol that reduces non-specific binding by up to four orders of magnitude, and apply further surface function- alisation strategies aimed at accessing measurements at μM concentrations. Next, we develop a mass photometry-based method for tracking individual protein complexes on lipid bilayers, thereby demonstrating quantification of oligomer-dependent kinetics and mobilities. We then extend this method to interactions of the HIV-1 envelope glycoprotein (Env) with broadly neutral- ising antibodies. Using our assay, we resolve polydisperse anitbody-induced cross-linking and quantify the corresponding binding affinities. We show that lipid bilayers give access to mass photometry measurements at μM protein concentrations, and demonstrate specific pull-down of target proteins from complex mixtures. Finally, we discuss aspects of the data analysis for these assays with a specific focus on systematic errors in the diffusion and mass measurements, and outline strategies for their correction.
"Working out" the relationship between informal language contact and phrasal verb development of international students in the UK
Keywords: formulaic language
informal language contact
study abroad
phrasal verb

Study abroad (SA) has long been regarded as a learning environment that is beneficial to second language acquisition (SLA), especially in competencies related to social interactions (Kinginger, 2011). However, little is known about whether SA students make actual gains in domains of English they are typically exposed to outside of classroom settings such as phrasal verbs (PVs), and whether their informal language contact contributes to such development. To explore this relationship, this study investigates students’ PV development and informal language contact, to understand how they make use of the L2 exposure during SA.
This longitudinal mixed-methods study collected data from over 250 international foundation year students studying in the UK three times in one academic year. PV data were collected through standardized tests and speech samples, while L2 contact was measured via language contact questionnaires, social network surveys, and semi-structured interviews. Paired-samples t-test revealed that there were significant gains in receptive and productive PV scores between Time 1 and Time 2, while the overall informal language contact and social networks of the participants did not see significant changes from Time 1 to Time 2. Correlation and multiple regressions analyses revealed a stronger relationship between informal language contact and PV knowledge at Time 2 than at Time 1. Mixed-effects modeling revealed that the overall English proficiency of the participants, corpus frequency of the PVs in the British National Corpus, and the amount of language contact were significant predictors of PV scores, while semantic opacity of PVs, the Chinese L1 of the participants, and L2 social networks were not.
This study underscored that the degree-oriented SA participants may have different prioritization and leisure time routines compared with summer school participants or exchange students abroad. With academic prioritization, the participants made limited gains in colloquial L2 vocabulary competency and their highly academic L2 contact did not greatly contribute to PV development.
Recasting the legality of resistance: the subaltern makings of international law
Keywords: Palestinian statehood
Palestine
international law
subaltern
Fatah
national liberation movements
Additional Protocols to the Geneva Conventions
legal epistemology
PFLP
movement building
transnational solidarity
resistance
within-system resistance
against-system resistance
marginality
laws of armed conflict
self-determination
Diplomatic Conference of 1974-1977
Article 1(4) Geneva Conventions
1970s
legal history
decolonisation
Foucauldian post-structuralism
Palestine Liberation Organisation
PLO
TWAIL

This thesis aspires to develop an epistemological understanding of international law as an outcome of ‘marginal-non-legal’ resistance. Inspired by subaltern histories of anti-colonial struggle and indigenous resistance to international law, it proposes a bottom-up, history-infused, praxis-driven framework that centres the role of marginal, non-legal resistance in constructing international law. Accordingly, it puts the disparate materials and methodologies of studying resistance prevalent in Third World Approaches to International Law (TWAIL) in conversation with critical anthropological, sociological, and historical theories of resistance. A historical account of the negotiation between Palestinian resistance and international law in the 1960s and 1970s elucidates this framework. First, the ‘within-system’ resistance of the Palestine Liberation Organisation is scrutinised through its participation and advocacy at the Diplomatic Conference of 1974-1977. At the Conference, the PLO constituted the ‘non-legal, marginal’ and was able to effect substantive changes in international law—most notably encoding the right of national liberation movements to engage in armed struggle against colonial domination, alien occupation, and racist regimes. Second, ‘against-system’ resistance of the PLO and its affiliates, including the non-legal, marginal act of revolutionary violence, is also considered constitutive of international law. Further, a study of PLO’s deradicalisation in the mid-1970s led to an internal ideological split within Palestinian resistance because of its increased collaboration with international law and its institutional processes. Thus, as subaltern resistance and international law negotiate, new marginalities emerge, which consequently necessitate a framework of law that can accommodate the incommensurable nature of subalternity. An epistemological emphasis on resistance in the historiography of international law offers a framework for law as a tool of movement. As marginal resistance evolves, international law, historically a reflective outcome of resistance, can persistently bring those at its margins into the folds of justice.
The prerogative and third source: a critical analysis
Keywords: legal history
constitutional law
capitalism
Public law
imperialism
prerogative
abuse of power
critical legal theory
state

The prerogative and ‘third source’ are two sources of authority for executive action in British law. This dissertation subjects these two sources of authority to critical analysis, examining their legal histories, conceptual foundations, doctrinal structures, normative shortcomings, and comparative equivalents. It demonstrates that the prerogative and third source are even more unsettled than is commonly acknowledged, and have been a site of struggle over giving effect to the perceived needs of the state. The prerogative does not stretch back into the mists of time, but was actively shaped and developed by judges. The third source or something like it – the notion of some further common law authority for executive action where such action is not unlawful – did not first appear in the late 1970s, and was relied upon (at least in modified form) in at least as early the nineteenth century. The prerogative and third source are often given one-sentence definitions, when mentioned in case law and commentary, but the major attempts to define the prerogative and third source are full of undesirable ambiguity. That is both a cause and consequence of significant indeterminacy in the case law on the prerogative and third source. From a normative perspective, the prerogative and third source also fall short of values supposedly upheld by the British legal order: they are not subject to structured scrutiny or circumscribed by an authoritative text. But adopting a single codified constitution does not eliminate ambiguity and indeterminacy, as the experiences of Australia and the United States demonstrate. A promising response to these problems is to seek comprehensive legislative codification of the prerogative and third source, though this will not be a panacea to the problems of executive over-reach, and will not extinguish judicial discretion in determining the limits of executive action.
Polar and dipolar contributions to collective cell motility

Keywords: Active matter
Biological physics
Collective behaviour
Cell mechanics
Phase-field simulations
Soft matter theory

Active materials take energy from their surroundings and use it to do mechanical work. The theories of active matter can describe a wide variety of living systems, such as bacterial colonies, actin-myosin networks and cell tissues. In this thesis, we investigate the collective behaviour of confluent, two-dimensional cell monolayers on a substrate, which is also one of the most common experimental systems to study collective cell motility. The cells are modelled using a computational phase field approach to study how polar and dipolar forces, the active, out-of-equilibrium force components, contribute to the cell motions.
We study the polar and dipolar contributions to collective cell motility using the phase-field model, which allows simulations of deformable cells. We study the interplay between the polar and dipolar forces in a confluent cell sheet and explore the collective behaviour emerging from different polarisation mechanisms. We find that either polar or dipolar forcing can drive the jammed-to-liquid transition. The mechanical properties, such as the cell deformation and speed, are independent of the polarisation mechanisms. However, a flocking state where most cells move in the same direction appears when the polar force of a cell aligns with its velocity as an exception.
Then we focus on studying the active inter-cellular force in a cell monolayer. We find that contractile inter-cellular forces elongate a cell and can give rise to a nematic state and active turbulence. Extensile inter-cellular forces cause frustration, where cells elongate perpendicular to their neighbours. Moreover, we show that anisotropic fluctuation in the inter-cellular forces can lead to the transition from contractile to extensile behaviour.
Finally, we investigate the interplay between the viscoelasticity of tissue and the inter-cellular forces for cells confined in a channel. We find that different collective behaviour emerges as viscoelasticity of the tissue is modulated by the cell-cell adhesion, repulsion. The transition between the jammed, nematic state, oscillation and spontaneous shear flow occurs as the cell-cell adhesion increases. The cells jam more easily with higher cell-cell repulsion, and cells of a higher aspect ratio favour steady shear.
The approaches developed in this thesis can be extended and applied to investigate other biological processes in cell mechanics, such as tissue expansion and the phase ordering of different cell types.