VictorJuiz/thesis huggingface dataset:
Endemic forest birds of the Taita Hills

Despite intense publicity, habitat loss still remains a serious threat to biodiversity. Forest destruction is its frontrunner, both in terms of physical habitat under threat and potential for biodiversity loss. In the fragmented landscape of the Taita Hills, SE Kenya, several bird species are facing the threat of extinction from forest loss. They are absent from many of the remnant forest patches and/or are showing negative effects with increasing disturbance. Using a relatively common forest-dependent bird species - the whitestarred robin Pogonocichla stellata - as a model, the current status of this ecosystem was examined, and future patterns predicted in view of the unrelenting destruction. As expected, the robin population in the largest and most intact fragment (c35 ha) was the healthiest, suggesting that this was indeed the best quality habitat patch: it had the highest population density, highest productivity (low nest predation and high juvenile to adult ratio) and lowest turnover rates. Effects of forest deterioration were evident from the fact that the medium-sized patch (c95 ha), which is undergoing severe degradation, was a worse habitat for the robin than the tiny patches (c2-8 ha): it had the lowest population density, lowest productivity (highest nest predation rates and lowest juvenile to adult ratio), and highest turnover rates. The explanation for this is twofold. Besides the smallest patches facing lower levels of habitat loss recently, they also had high levels of dispersal between them. They occasionally operated as a finegrained system with individuals moving between them in the space of a few days. In general, the robin metapopulation is demographically (rate of change, λ = 0.996) and genetically (at migration- and mutation-drift equilibrium) stable at present. The populations in the largest and smallest patches were potential sources providing emigrants that were possibly crucial in sustaining the population in the medium-sized patch (given its low productivity and high turnover rates). Overall, these findings underscore the importance of within-patch processes, both for ensuring persistence of subpopulations and providing dispersers, as well as between-patch processes (chiefly dispersal) for ensuring metapopulation persistence. Thus, by furnishing ample sample sizes that enabled work to be carried out in all fragments throughout this landscape, the model species approach was useful for identifying the need for a two-pronged conservation strategy. First, a need to focus within fragments to reduce habitat loss and degradation, and second, to address among fragment issues relating to land-use and maintaining a forested landscape, in order to enhance connectivity between patches. Finally, based on the mechanisms by which disturbance and fragmentation are affecting bird populations e.g. predator influxes from the surrounding matrix, conservation recommendations for the Taita Hills are offered.

Advisor: Lens, L
Cresswell, W
Perrins, C
Low energy background in the NCD phase of the Sudbury Neutrino Observatory

The Sudbury Neutrino Observatory (SNO) was a 1 kilotonne heavy water Č{C}erenkov detector. Evidence for flavour changing neutrino oscillations was found by comparing the rate of Charged Current interactions with that of Neutral Current (NC) interactions.
This thesis is concerned with the accurate determination of the NC flux in the Neutral Current Detector (NCD) phase of SNO. The measurement and understanding of radioactive backgrounds arising from decays of naturally occurring 232Th and 238U chain nuclei is crucial. This is because their daughter nuclei can produce neutrons via photodisintegration of deuterium. These would be indistinguishable from those produced by NC neutrino interactions. As the probability of neutron production was dependent upon the nature and location of activity, each contribution had to be determined separately. Of particular concern were 232Th and 238U in the D2O and Neutral Current Detectors (NCDs). A maximum likelihood method was developed that exploited differences in the event isotropy and radial profile of each event class. These results were in agreement with water assay results and pre-deployment radioassays of the NCDs.
An independent measurement of the 232Th content in the D2O and H2O was made by regularly assaying the water using filters loaded with hydrous titanium oxide. The concentration of 232Th in the water was determined by coincidence counting of the final assay sample. A new counter system was designed and built and the calibration and use of this system are presented.
Two areas of increased activity were discovered on two of the NCDs deployed in the detector which would have prevented an accurate measurement of the NC flux. A method was devised to determine the composition and activity of one of these hotspots. The results were in good agreement with two independent methods and the uncertainty on the NC flux was reduced from > 7% to > 1%. The total number of neutrons produced per day by photodisintegration for 232Th and 238U in the D2O and NCDs was measured to be 0.66+0.08-0.07. This was significantly less than the expected 12.6 NC neutrino interactions per day.
In the third phase, two independent data streams existed: PMT and NCD. A Monte Carlo study was undertaken to determine whether an accurate measure of the NC flux could be obtained using only PMT data. Results showed that no improvement could be made upon results from previous phases and the best measurement of the NC flux in the final phase would be made using PMT and NCD data.

Keywords: radioactivity
assay
solar neutrinos
Advisor: Jelley, NA
Bullet hole constellations: Berlin's Neues Museum, a case study in cultural memory

This dissertation explores a shift in cultural memory theory and praxis that loosely coincides with the turn of the century. With Berlin as its focus, I trace this shift through three of its museum institutions (the Jewish Museum, the Masterplan Museumsinsel, and the Neues Museum). I specifically look at three aspects: their museum practices (how history is expressed), the main narratives embodied in their spaces (what history is being expressed), and the critical contexts in which they are embedded (what do these practices and narratives mean in the wider cultural context).
Throughout, I develop the idea of a cultural memory that emphasizes how we use the past, or what we do with our cultural inheritance. This runs counter to the cultural memory that sees remembering as a categorical imperative ('never forget' or 'lest we forget'), a memory that is clearly embodied in Libeskind's Jewish Museum and is typified in critical work that either prioritizes trauma (Caruth, LaCapra) or stresses cultivating specific empathetic responses (Landsberg's 'prosthetic memory,' Hirsch's 'postmemory'). My cultural memory hypothesis fits within the general German field of Cultural Memory Studies, as typified in the work of Jan and Aleida Assmann. The outcome of thinking about memory as use, appropriation, and transformation of cultural inheritance is the characterization of the past as an analytical tool. This notion sits well amidst current work by Dekel and Arnold-de Simine who read museum/memorial spaces as facilitators of civic engagement.
This new cultural memory can be found embodied in the architectural and curatorial framing of the Neues Museum, in its phenomenological approach to history, its narrative of fragmentary wholeness, as well as in its placing of the twentieth century in long narratives of historical continuity. These characteristics allow me to read the Neues Museum as an example of contemporary thinking about modernism, and thus as part of a discourse that looks to restore and transform crucial mythological tendencies.

Keywords: museums
20th/21st century
Neues Museum
Berlin
cultural memory
Advisor: Morgan, B
Stochastic model predictive control

The work in this thesis focuses on the development of a Stochastic Model Predictive Control (SMPC) algorithm for linear systems with additive and multiplicative stochastic uncertainty subjected to linear input/state constraints. Constraints can be in the form of hard constraints, which must be satisfied at all times, or soft constraints, which can be violated up to a pre-defined limit on the frequency of violation or the expected number of violations in a given period.
When constraints are included in the SMPC algorithm, the difficulty arising from stochastic model parameters manifests itself in the online optimization in two ways. Namely, the difficulty lies in predicting the probability distribution of future states and imposing constraints on closed loop responses through constraints on predictions. This problem is overcome through the introduction of layered tubes around a centre trajectory. These tubes are optimized online in order to produce a systematic and less conservative approach of handling constraints. The layered tubes centered around a nominal trajectory achieve soft constraint satisfaction through the imposition of constraints on the probabilities of one-step-ahead transition of the predicted state between the layered tubes and constraints on the probability of one-step-ahead constraint violations. An application in the field of Sustainable Development policy is used as an example.
With some adaptation, the algorithm is extended the case where the uncertainty is not identically and independently distributed. Also, by including linearization errors, it is extended to non-linear systems with additive uncertainty.

Keywords: Model Predictive Control
Stochastic MPC
Tube MPC
Advisor: Kouvaritakis, B
Cannon, M
Development of the cone pressuremeter

The cone pressuremeter is an in situ testing device comprising a pressuremeter mounted behind a cone penetrometer of the same diameter. Previously reported tests had indicated that the cone pressuremeter can provide measurements of soil strength, stiffness and in situ stress. The study presented in this thesis is aimed at developing methods of interpretation of the cone pressuremeter that can be applied with confidence to a variety of soil types. Carbonate sands have been the cause of significant problems associated with the design of foundations for offshore structures. A programme of cone pressuremeter testing in a carbonate sand from the west coast of Ireland is presented. Tests were carried out in a calibration chamber where conditions of vertical and horizontal stress and relative density were controlled. The influence of these parameters on measured values of cone resistance and pressuremeter limit pressure is assessed. Similar tests were also carried out in a felspathic sand, and correlations have been presented for deriving horizontal stress and relative density that are applicable to most types of sand. The influence of creep strains and of overconsolidation were other features of carbonate sand that have been assessed with the cone pressuremeter. A numerical model which accounts for the crushing characteristics of carbonate sand is presented, and is shown to improve significantly predictions of limit pressure measured in the calibration chamber. Cone pressuremeter tests were carried out in soft clay at the Bothkennar test site in Scotland. An analysis based upon cavity expansion theory was shown to provide good estimates of undrained shear strength and stiffness compared with results from other in situ and laboratory tests. Estimates of the in situ horizontal stress were found to be unrealistically high. Shear modulus in both sand and clay has been measured from unload-reload cycles carried out during pressuremeter expansion. The stress levels and strain amplitudes of these cycles have been shown to influence the shear modulus greatly. In sand, a procedure for relating these moduli to those at an extremely small reference strain is presented. In clay, shear moduli are shown to give a remarkably close agreement to others reported from Bothkennar, when due account of the strain amplitude is made. Finally, a time/cost analysis between the cone pressuremeter, the cone penetrometer and the self-boring pressuremeter is presented. The cone pressuremeter is found to be a cost-effective device bearing in mind the amount and quality of information it can provide.

Keywords: cone pressure
sand
Advisor: Houlsby, G
Analysis and Implementation of Numerical Methods for Simulating Dilute Polymeric Fluids

In this thesis we develop, analyse and implement a number of numerical methods for simulating dilute polymeric fluids. We use a well-known model in which the polymeric fluid is represented by a suspension of dumbbells in a Newtonian solvent. This model is governed by a coupled Navier–Stokes–Fokker–Planck system of partial differential equations, in which the Fokker–Planck equation is posed on a high-dimensional domain. We first thoroughly analyse a Galerkin spectral method for the Fokker–Planck equation in configuration space, before combining this method with a finite element scheme in physical space to obtain an alternating-direction method for the high-dimensional Fokker–Planck equation. Alternating-direction methods have been considered previously in the literature for this problem, but this approach has not been subject to rigorous numerical analysis before. We develop many theoretical results for our numerical algorithms, and we focus particularly on establishing stability and convergence estimates. The numerical methods we develop are fully-practical, and we present a range of numerical results demonstrating their accuracy and efficiency. We also introduce a coupled numerical algorithm for the Navier–Stokes–Fokker–Planck system, which we use to simulate polymeric fluid flow problems of physical interest. The numerical method for the high-dimensional Fokker–Planck equation is the most computationally intensive part of this coupled algorithm, but it is well suited to implementation on a parallel computer, and we exploit this fact to make large-scale computations feasible.
Working democracy

Worker co-operatives, meaning firms producing goods or services that are owned and managed by their workers, have been a marginal and problematic form of production in Britain since their first period of substantial growth in the 19th century. They have recurrent difficulties attracting capital, developing business expertise among their members, sustaining long-term commitment and growing to the size required to compete efficiently in many industries. Yet there has been a remarkable upsurge of interest in co-operatives during the past decade, and their many successes in diverse industries demonstrate that co-operatives can offer their members a powerful combination of strong business performance and a highly satisfying work life.
This thesis asks whether the weaknesses apparent in co-operatives historically, and present in many still today, are inherent in the co-operative form. Is the co-operative sector bound to remain basically marginal, or could it, with the aid of some practical reforms, come to play a significant role in the British economy? Recognising that any answer to this question is speculative, the thesis concludes that co-operatives are not inherently flawed indeed they fail at about the same rate as traditionally organised small businesses but that they do place an unusual range of demands on members which, in a legal, financial and political climate not yet geared to co-operatives, mean that democratic firms are likely to remain a small portion of the economy.
The plan of the thesis is as follows: After a brief introductory chapter, Chapter Two surveys the present state of British co-operatives and examines the external economic and legal environment in which co-operatives function. Chapter Three surveys recent research in organisational behaviour, especially about small group behaviour in traditional businesses, to assess whether the high productivity frequently asserted for co-operatives has theoretical foundation, whether co-operatives commonly violate any established principles of good organisational design and whether large co-operatives can be run efficiently and democratically. Chapter Four presents the economic status of women in the British workforce and looks at whether the attributes of co-operatives are congruent with women's needs. Two mini-case studies are presented, of a bookselling and a cleaning co-operative, each composed entirely of women.
Chapters Five, Six and Seven present the results of the field research conducted for this thesis. Each is a case study of a functioning co-operative based on extensive interviews with its members, reviews of the co-operative's files, and a brief analysis of its financial performance. The goal was to understand as much as possible about the consequences of choosing the co-operative form: for the members' job satisfaction and for the firm's productivity, market sensitivity, ability to grow, ability to employ women, and internal dynamics. Chapter Eight sets out the conclusions suggested by comparing the case studies in light of the literature examined in Chapters Two through Four.
Targeting EGFR signalling pathway in triple negative breast cancer 

Epidermal growth factor receptor (EGFR) is frequently overexpressed in the majority of triple negative breast cancer patients (TNBC). However, the molecular determinants behind their limited response to EGFR-targeted therapies are poorly understood. Here, both the acute and chronic responses of TNBC to the EGFR-targeted therapy, cetuximab (CTX), have been investigated.
The expression of EGFR has been analyzed in a cohort of 2000 breast cancer tumours from the public dataset as well as in a panel of breast cancer cell lines. Furthermore, the response of TNBC cell lines to CTX has been investigated using conventional biochemical methods. Finally, a comprehensive transcriptomic profiling of an acquired CTX-resistant TNBC model by RNA sequencing has been performed to understand the molecular determinants of acquired CTX resistance.
The results confirmed that EGFR is highly expressed in TNBC in comparison to non-TNBC breast cancer tumours and cell lines, which was associated with adverse clinical outcomes. Targeting EGFR in TNBC cell lines using CTX failed to completely inhibit the EGFR signalling pathway and was associated with an increase in ADAMs-mediated release of endogenous EGFR ligands, EGF and TGFα. Inhibition of ADAMs (ADAM10 and ADAM17) significantly enhanced the anti tumour efficacy of CTX both in vitro and in vivo. Furthermore, transcriptomic profiling of the acquired CTX-resistant TNBC cell line (MDA-MB-468CR) revealed an activation of several key oncogenic pathways and genes, including the TGFβ/BMP pathway. Blocking BMP receptors (BMPRs) restored the sensitivity of resistant cells to CTX treatment.
Collectively, current findings offer alternative strategies that could enhance the CTX response in TNBC. We further reported that simultaneous targeting of both EGFR and BMPR pathways could overcome CTX resistance, which might have important implications for the treatment of TNBC.

Keywords: Cetuximab
Triple negative breast cancer
EGFR
drug resistance
cell biology
genomics
Advisor: Ahmed, A
Kong, A
A study of tokamak energy and particle transport, based on modulated electron cyclotron resonance heating

A dynamical technique for the study of tokamak energy and particle transport has been developed. The plasma in the medium-sized DITE tokamak was perturbed by the application of modulated electron cyclotron resonance heating, with wave-launching from the high-field side. These experiments were carried out with absorption at various distances from the plasma centre, over a range of densities. Energy transport through the electron channel was dominant, and the variations in electron temperature and density were measured using the soft X-ray, electron cyclotron emission and microwave interferometer diagnostics. Analysis in the frequency domain enabled the propagation of the thermal wave to be followed. The observed behaviour was generally indicative of diffusive propagation of the thermal perturbation. Further observations indicated a modulation of the horizontal plasma shifts, diffusive propagation to the edge and a low modulation level of line-averaged density. In some atypical cases, the observed behaviour was qualitatively different; this type of behaviour was accompanied by a pronounced sawtooth oscillation locked with the modulation.
Two models have been employed for the interpretation of these results. The first model, based on the diffusive thermal transport of the perturbation, has led to results in good agreement with the experimental data. Values of the electron thermal diffusivity were deduced, in good agreement with those obtained from the alternative techniques of power balance analysis and sawtooth heat pulse propagation analysis; such agreement has not been universally obtained in similar experiments. The width of the absorption region has emerged as an important consideration in this analysis. A more complex model, including non-linear, coupled equations of particle and energy balance, has produced results in partial agreement with the experimental data, supporting, to some extent, the presence of coupled transport. It has been demonstrated how perturbation techniques can afford a useful means of testing transport models.

Advisor: Robinson, D
Understanding the nature of the faint radio-source population

This DPhil dissertation presents two new and independent samples of faint radio sources. The first sample is the 37 SXDS radio sources with flux densities at 1.4-GHz above 2 mJy, a spectroscopic completeness of 65% and a median redshift z_med ≈ 1.1. The second sample is the 47 TOOT00 radio sources with flux densities at 151 MHz above 100 mJy, a spectroscopic completeness of 85% and z_med ∼ 1.25. Optical, near- and mid-IR photometry, optical spectroscopy, and radio observations are used in the analysis and comparison of the two samples. The quasar fraction in the TOOT00 radio sources is 0.13 < f_q < 0.25 above the FRI/FRII break in radio luminosity, while use of 24 μm data reveals objects with significant but sometimes obscured accretion and gives quasar-mode fraction of 0.5 → 0.9 above the FRI/FRII break. The FRI/FRII divide seen at z < ∼ 0.5 is also observed at z ∼ 1 for FRII objects in the TOOT00 and SXDS samples, but examples of FRI radio sources above the FRI/FRII break do exist. The total number of the TOOT00 objects and their distribution are consistent with simulations based on extrapolations from previous work, while for the SXDS objects the results are only broadly similar. Based on that comparison, the redshift spikes seen at z ∼ 1.3 in TOOT00 and at z ∼ 0.65 & 2.7 in SXDS appear to be significant, and might be due to Large-Scale Structure. A V/Vmax test suggests the cosmic evolution of the TOOT00 and SXDS samples, is different. The TOOT00 radio sources are 2-times more luminous in host-galaxy starlight than the SXDS radio sources. The almost proportionality between radio luminosity at 1.4 GHz and 24 μm luminosity suggests that L_rad traces accretion luminosity and L[OII] ∝ L_rad^0.7 may reflect imperfections in the L[OII]-accretion luminosity scaling. Mid-IR 24 μm observations in the SXDS sample suggest that 30% of the light from the nucleus is absorbed by the torus and re-emitted in the mid-IR, while ∼ 1% of the light is scattered above and below the torus.

Keywords: AGN
optical
infrared
radio sources
observational cosmology
quasars
radio
Advisor: Rawlings, S