VictorJuiz/thesis huggingface dataset:
The political economy of internal displacement in Colombia : the case of African palm oil

Some 5 million people were classified as internally displaced in Colombia at the end of 2012, which represented about 10 per cent of the population and the highest number in the world at the time. Colombia differs from other countries with high levels of displacement in that it is comparatively politically stable, has effective national institutions, a relatively strong formal economy, and can by no means be described as a ‘failed’ or ‘failing’ state. The displacement literature tends to characterise the phenomenon as a humanitarian crisis and a side effect of the long-running civil war. But Colombians continue to be displaced in very large numbers despite the formal demobilization of the paramilitaries in 2006 and the diminished military capacity and engagement of the guerrillas since about the same period: the same groups that are widely regarded as being the main perpetrators of displacement.
This thesis contends that displacement of the civilian population in Colombia is frequently not a consequence of violence, but rather the primary objective, where violence plays a facilitatory role. Moreover, the thesis asserts that these massive levels of displacement are substantively linked to predominantly economically-motivated logics and are regionally specific. By examining an agricultural commodity that has significantly expanded relatively recently in Colombia - African palm oil - this research examines if and how expanded cultivation may be linked to displacement. Using a political economy framework of analysis combined with empirical fieldwork, it explores the ‘localised displacement logics’ whereby land is coercively acquired by powerful local groups.
The thesis concludes that the abandonment and dispossession of land from poor and marginalised groups constitutes part of an ongoing process of capitalist expansion and statebuilding in Colombia. Contrary to assertions that it is the intra-state conflict that constitutes the central obstacle to development, Colombia’s current trajectory of capitalist development may actually be a central obstacle to sustainable peace and not lead to an end to displacement.

Keywords: Colombia
internally displaced persons
political economy
African palm oil
Advisor: Chatty, D
Pearce, J
Protein fold evolution on completed genomes: distinguishing between young and old folds

We review fold usage on completed genomes in order to explore protein structure evolution and assess the evolutionary relevance of current structural classification systems (SCOP and CATH). We assign folds on a set of 150 completed genomes using fold recognition methods (PSI-BLAST, SUPERFAMILY and Gene3D). The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds and how we have arrived at the set of folds we see today. In particular, we develop a technique to estimate the relative ages of a protein fold based on genomic occurrence patterns in a phylogeny. We find that SCOP's
α
β
′classhasrelativelyfewerdist∈ctfoldsonlar≥≥nomes,andt
ˆ
f
oldsofthisclasstend→beolder;foldsofSCOP′s
small protein' class follow opposite trends. Usage patterns show that folds with many copies on a genome are generally old, but that old folds do not necessarily have many copies. In addition, longer domains tend to be older and hydrophobic amino acids have high propensities for older folds whereas, polar - but non-charged - amino acids are associated with younger folds. Generally domains with stabilising features tend to be older. We also show that the reliability of fold recognition methods may be assessed using occurrence patterns. We develop a method, that detects false positives by identifying isolated occurrences in a phylogeny of species, and is able to improve genome wide fold recognition assignment sets. We use a structural fragment library to investigate evolutionary links between protein folds. We show that 'older' folds have relatively more such links than 'younger' folds. This correlation becomes stronger for longer fragment lengths suggesting that such links may reflect evolutionary relatedness.

Keywords: protein folding
protein evolution
protein structure
Advisor: Deane, C
A  multi-centre study of the impact of endometriosis on health-related quality of life and work productivity

Background: Endometriosis is a common condition in women of reproductive age, causing pelvic pain and subfertility, but little is known about its impact on health-related quality of life (HRQoL) and work productivity worldwide.
Methods: In 10 countries across five continents, this study recruited 1,418 women, aged 18-45, without a previous surgical diagnosis of endometriosis, scheduled to undergo a laparoscopy to investigate symptoms suggestive of endometriosis or to be sterilised. Pre-operatively, women completed a standardised questionnaire assessing symptoms, diagnostic delay, HRQoL and work productivity using validated instruments. Surgeons completed a standardised questionnaire incorporating findings at laparoscopy including endometriosis stage according to revised American Fertility Society criteria.
Results: There was a mean delay of 9.2 years (SD 8.8), principally in primary care, between the onset of symptoms and diagnostic laparoscopy. This diagnostic delay was longer in centres where healthcare was predominantly state-funded (12.8 vs. 7.6 years; p<0.001). In multivariate analyses, the delay was positively associated with the number of pelvic symptoms (chronic pelvic pain, dysmenorrhoea, dyspareunia and heavy periods; p<0.001) and a higher body mass index (p<0.001). Physical HRQoL was significantly reduced in affected women compared to those with similar symptoms and no endometriosis (p=0.012). Not being in paid employment, severe pelvic pain and moderate-severe disease were associated with reduced physical HRQoL (all p<0.001). Each affected woman lost on average 10.0 hours (SD 10.6) of work weekly, due mainly to reduced effectiveness while working. The annual indirect cost of endometriosis associated with work productivity loss ranged from US399perwomaninIbadan(Nigeria)toUS18,586 per woman in Boston (USA).
Conclusions: Endometriosis significantly impairs HRQoL and work productivity across countries and ethnicities, yet women continue to experience diagnostic delays in primary care. A higher index of suspicion is needed to expedite specialist assessment of symptomatic women. Future research should seek to clarify pain mechanisms in relation to endometriosis severity.

Keywords: endometriosis
quality of life
work productivity
diagnostic delay
Advisor: Zondervan, K
Kennedy, S
Webster, P
Rare earth metal boryl and gallyl compounds: synthesis and reactivity

This Thesis describes the syntheses, characterisation and reactivity of rare earth metal boryl and gallyl compounds. Experimental and computational studies were performed to investigate the structure and bonding in these compounds.
Chapter 1 introduces key metal-boryl and metal-gallyl compounds of the s, p, d and f-blocks via literature review.
Chapter 2 describes the syntheses, structures and bonding analyses of rare earth metal boryl compounds. A short introduction to rare earth metal cations is given.
Chapter 3 describes the syntheses, structures and bonding analyses of rare earth metal gallyl compounds. The preparation of a new class of rare earth metal cations will also be reported. A short introduction to rare earth metal amidinates is given.
Chapter 4 presents reactivity studies of the rare earth metal gallyl compounds described in Chapter 3. To facilitate a direct structure and reactivity comparison, the corresponding boryl compounds were also synthesised. The results of a comprehensive DFT computational study to investigate the structure and bonding in these compounds are also presented. A short introduction to metal-element and metal-metal bond reactivity is given.
Chapter 5 presents full experimental procedures and characterising data for the new compounds reported.

Keywords: Main Group
Rare Earth Metals
Inorganic
Organometallic
Advisor: Mountford, P
Investigation of Portfolio Choice that Tracks a Continuously Moving Target

We investigate the problem of tracking a moving target, specifically a given continuously compounded, deterministic growth rate by using linear quadratic control theory. We first present some preliminaries and then derive and solve the corresponding Riccati equations for our problem. We then implement our findings in MATLAB by using one stock from the FTSE100 and a risk-less asset and analyze the results. Furthermore, we focus on situations when the performance of our tracking is not the expected and highlight when this can happen and what the risks involved are. We also present situations when we would need to borrow or short sell, like in the case of aggressively tracking a target. We then briefly present the extension to multi asset portfolios. Finally, we discuss the case of tracking a market index.
Enhancing motor performance in the healthy and Parkinsonian brain: adaptation, oscillations, and electrical stimulation

Parkinson's disease (PD) is characterized by debilitating impairments in motor control arising from pathophysiological alterations in basal ganglia circuitry and function. In this research thesis two main approaches, namely electrical recording and stimulation, are combined in order to better understand motor performance in Parkinson's disease and ways it might be improved. Three main types of motor behaviors are studied: discrete ballistic movement, repetitive movement, and motor adaptation.
First, deep brain stimulation (DBS) of the subthalamic nucleus (STN) was shown to improve the velocity of discrete, ballistic movements in PD. The neural correlates of ballistic movements were then studied by recording from the STN of PD patients, revealing onset of beta-range desynchronization prior to, and gamma-range frequency synchronization during, performance of fast arm reaches. To determine a causal role for these oscillatory frequencies in motor behavior, the motor cortex of healthy humans was stimulated at either beta or gamma frequency during a 'go/no-go' grip force task. Beta stimulation resulted in slower force generation on 'go' trials but enhanced inhibition during 'no-go' trials, whereas gamma stimulation resulted in faster force generation on 'go' trials.
Second, STN DBS resulted in improved repetitive tapping performance in PD patients through a reduction in variability. Recordings from the STN demonstrated that repetitive movement was accompanied by a substantial and persistent suppression of beta oscillatory activity.
Third, Parkinson's patients were tested on a motor adaptation task, revealing intact learning but impaired retention of a visuomotor rotation. Application of direct current stimulation of the motor cortex resulted in enhanced adaptation during both learning and retention in PD patients and healthy controls.
These results causally implicate the basal ganglia and oscillatory activity in motor control, provide insight into the neuronal mechanisms of motor performance and adaptation, and demonstrate promising new avenues for enhancing motor control in Parkinson's disease.

Keywords: Subthalamic Nucleus
Motor Learning
Basal Ganglia
Oscillations
Deep Brain Stimulation
Parkinson's
Neurophysiology
Advisor: Jenkinson, N
Brown, P
Aziz, T
Predictability of a laboratory analogue for planetary atmospheres

The thermally-driven rotating annulus is a laboratory experiment used to study the dynamics of planetary atmospheres under controlled and reproducible conditions. The predictability of this experiment is studied by applying the same principles used to predict the atmosphere. A forecasting system for the annulus is built using the analysis correction method for data assimilation and the breeding method for ensemble generation. The results show that a range of flow regimes with varying complexity can be accurately assimilated, predicted, and studied in this experiment. This framework is also intended to demonstrate a proof-of-concept: that the annulus could be used as a testbed for meteorological techniques under laboratory conditions.
First, a regime diagram is created using numerical simulations in order to select points in parameter space to forecast, and a new chaotic flow regime is discovered within it. The two components of the framework are then used as standalone algorithms to measure predictability in the perfect model scenario and to demonstrate data assimilation. With a perfect model, regular flow regimes are found to be predictable until the end of the forecasts, and chaotic regimes are predictable over hundreds of seconds. There is a difference in the way predictability is lost between low-order chaotic regimes and high-order chaos. Analysis correction is shown to be accurate in both regular and chaotic regimes, with residual velocity errors about 3-8 times the observational error. Specific assimilation scenarios studied include information propagation from data-rich to data-poor areas, assimilation of vortex shedding observations, and assimilation over regime and rotation rate transitions.
The full framework is used to predict regular and chaotic flow, verifying the forecasts against laboratory data. The steady wave forecasts perform well, and are predictable until the end of the available data. The amplitude and structural vacillation forecasts lose quality and skill by a combination of wave drift and wavenumber transition. Amplitude vacillation is predictable up to several hundred seconds ahead, and structural vacillation is predictable for a few hundred seconds.

Keywords: ensemble prediction
rotating annulus
47.10.ad
96.12.Jt
imperfect model
47.32.Ef
47.11.Bc
data assimilation
47.55.pb
vacillation
breeding
instability
forecast
Chaos
predictability
92.60.Bh
92.60.Wc
47.52.+j
baroclinic
perfect model
47.20.-k
Advisor: Read, P
New main group and rare earth complexes and their applications in the ring-opening polymerisation of cyclic esters

This Thesis describes the synthesis and characterisation of new Main Group and Rare Earth alkyl, amide, alkoxide and borohydride complexes and their use as catalysts for the ring-opening polymerisation (ROP) of ε-caprolactone and rac-lactide.
Chapter 1 introduces ROP from an industrial and academic perspective, as well as polymer characterisation techniques. A literature review is given, with an emphasis placed on Main Group catalysts.
Chapter 2 describes the synthesis and characterisation of new homo- and hetero-scorpionate Main Group complexes. An introduction to homo- and hetero-scorpionate ligands is given, as well as a discussion of the ε-caprolactone and rac-lactide ROP activity displayed by the new complexes.
Chapter 3 describes the synthesis and characterisation of new neutral and cationic Main Group borohydride complexes supported by the tris(pyrazolyl)methane and tris(pyrazolyl)hydroborate ligands. A review of borohydride complexes is also given. The ε-caprolactone and rac-lactide ROP activity shown by the complexes presented is also discussed.
Chapter 4 describes the synthesis and characterisation of new mono- and di-cationic yttrium complexes supported by the tris(pyrazolyl)methane and triazacyclononane ligands. An introduction to the synthesis of neutral and cationic Rare Earth complexes is given. An overview of immortal ROP is also provided. The activity of the new complexes towards the immortal ROP of rac-lactide is also discussed.
Chapter 5 contains experimental details and characterising data for the new complexes reported in this thesis.
CD Appendix
contains .cif files for all of the new crystallographically characterised complexes.

Keywords: Cyclic Esters
Ring-Opening Polymerisation
Alkaline Earth
Cationic
Lactide
Caprolactone
amide
alkoxide
Tris(pyrazolyl) hydroborate
Main Group
Rare Earth
Tris(pyrazolyl) methanide
alkyl
Borohydride
Advisor: Mountford, P
The dynamical stereochemistry of photon–initiated bimolecular reactions

The product state specific stereodynamics of the photon–initiated reaction of O(¹D₂) with H₂ has been investigated by polarised Doppler–resolved laser induced fluorescence, under room temperature bulb conditions. Product state resolved differential cross sections, excitation functions and rotational angular momentum alignments are reported for the following product channels,
O(¹D₂) + H₂(¹Σ+g ; v = 0) -> OH(X²Pi; v' = 0;N' = 14; f) + H(²S).
at a mean collision energy of 12 kJ mol-1. The data are compared with extensive state resolved quasi–classical trajectory (QCT) calculations of the linear and angular momentum distributions and excitation functions conducted on the Schinke–Lester (SL1) and K ab initio ground state (1¹A') potential energy surfaces. Overall, good agreement is obtained between the QCT calculated and experimentally determined stereodynamical features. The results are discussed in light of other recent work on this prototypical insertion reaction, and on the related systems of O(¹D₂) + HD and CH₄.

Keywords: insertion reaction
bimolecular reaction
polarization
OH
O + H2
stereodynamics
Advisor: Simons, J
Time Series Model for Forecasting Intraday Volatilities

The aim of this dissertation is to construct different intraday volatility forecasting techniques for the future contracts and to evaluate their accuracies in terms of the forecasting errors. In order to achieve these goals the intraday volatility levels are assumed to be reflected by the absolute values of the intraday returns. The periodic intraday volatility factor is modelled by different regression methods and the future intraday absolute returns are forecasted. Since the intraday returns depend on the overall volatility of the particular day, Exponential Weighted Moving Average and GARCH(1,1) techniques are implemented to predict these quantities. Finally, the results reveal that the most accurate method for the intraday volatility forecasting is based on modelling each 5 min interval during the day as an independent variable in the periodic intraday component and this holds not only for the next day forecasting but also for the longer time horizon.
Niche segregation by cheetah (Acinonyx jubatus) as a mechanism for co-existence with lion (Panthera leo) and spotted hyaena (Crocuta crocuta)

Intraguild competition and predation have been recognised as important ecological factors influencing the population dynamics of carnivores. The effects of these interactions are often asymmetrical due to a size-related dominancy hierarchy. However, it has been suggested that competitively subordinate carnivores can minimise the costs of predation and competition through spatial and temporal avoidance. Here I investigate the ecological and behavioural mechanisms by which cheetahs (Acinonyx jubatus) coexist with competitively stronger lions (Panthera leo) and spotted hyaenas (Crocuta crocuta). Fieldwork was carried out in the Okavango Delta, northern Botswana, between October 2008 and August 2011. A total of 20 Global Positioning System (GPS) radio-collars were fitted on all known cheetahs (n=6), lion prides (n=5) and spotted hyaena clans (n=6) in the study area (approx. 3 000 km2). Pre-programmed radio-collars recorded locations and activity continuously for each individual and these data were complemented with direct behavioural observations. Cheetah data were analysed with respect to the temporal and spatial likelihood of encountering lions and spotted hyaenas. Results suggest that the response to the risks posed by other predators is species-specific, habitat-specific and dependent on the immediacy of the risk. Resource partitioning was not the main mechanism for coexistence as cheetahs overlapped extensively with lions and spotted hyaenas in time, space and habitat use. Instead, cheetahs adjusted their spatial distribution in response to immediate risks or adapted their habitat use depending on their vulnerability (e.g. behaviours such as feeding or with differing levels of moonlight at night). In general, cheetah temporal and spatial distribution is a hierarchal process, firstly driven by resource acquisition and thereafter fine-tuned by predator avoidance. In addition, habitat heterogeneity seemed to be key in facilitating coexistence. Understanding the behavioural mechanisms that interacting apex predators adopt to regulate these negative interactions could be crucial to carnivore conservation, especially as human-related habitat loss is forcing species into ever smaller areas.

Keywords: African lion
wildlife
spatial segregation
coexistence
carnivore conservation
cheetah
large carnivores
temporal segregation
niche overlap
avoidance behaviour
animal behaviour
intraguild
spotted hyaena
machine learning
felids
Botswana
landscape of risk
Okavango Delta
GPS collars
competition
African carnivores
Advisor: Macdonald, D
RASSF1A regulation of transcription factors in tumourigenesis and stem cell fate determination

RASSF1A silencing is the most widely reported epigenetic event in sporadic human malignancies and is increasingly observed to be associated with poorer prognosis and outcome in lung, breast and bladder cancers amongst others. By performing a genetic screen in mice using Sleeping Beauty (SB) transposon-mediated insertional mutagenesis, we identified candidate genes associated with tumourigenesis in the absence of Rassf1a. A top hit in our screen was the terminal differentiation transcription factor Runx2. In this study, we describe how together loss of RASSF1A and RUNX2 exacerbate oncogenic YAP1-TEAD complexes and how RUNX2, p73 and TEAD effectively compete for YAP1 association. Interestingly, YAP1-TEAD complexes, as well as RUNX factors have been known to be important regulators of embryonic development by affecting cell fate. We show that RASSF1A is a novel regulator of stem cell pluripotency by introducing a cross link between the Hippo and Wnt signalling pathways, via TEAD and &beta;-catenin. More specifically, we demonstrate that RASSF1A is a barrier to somatic cell reprogramming by activating differentiation circuits, but its loss results in upregulation of the core stem cell marker network (NANOG, OCT4 and SOX2) in embryonic stem cells and the pre-implantation mouse embryo. In addition, we find that deregulation of the Hippo pathway in the absence of RASSF1A also leads to increased prevalence of stem cell characteristics in cancer and higher proportion of 'cancer stem cells'. This effect is mediated through both YAP and its paralog TAZ. Finally, we show that a second isoform of RASSF1, RASSF1C, the expression of which is maintained in cancers, contributes to cancer stem cell generation through a similar mechanism. This work concentrates on establishing the biology of RASSF1A in normal tissue and answering whether the broad prognostic value in tumours from biologically distinct tissues is due to a fundamental control of stem cell pluripotency.

Advisor: O'Neill, E