VictorJuiz/thesis huggingface dataset:
Tectonics of the western Mediterranean

The evolution of the Western Mediterranean takes place between the converging African and Eurasian plates, therefore the motion between them cannot be determined directly. The motion between them is the finite difference between the independent seafloor spreading systems in the Central and North Atlantic Oceans.
Primary magnetic anomaly data from the North and Central Atlantic was reexamined. All Late Cretaceous and Cenozoic anomalies (Anomaly 34 - Anomaly 2) were remapped. Fracture zones were remapped using bathymetic maps, topographic profiles from ship tracks, SEASAT altimetry (geoid deflection) data, and SEASAT derived gravity images. Fracture zones were used as the primary control for the determination of rotation parameters.
Finite difference solutions were computed between matched anomalies using the newly determined rotation parameters for each ocean with parameters of Pindell et al. (1988) used for Early Cretaceous and Jurassic spreading in the Central Atlantic. The product was a kinematic model describing the motion of Africa with respect to Europe from 175 Ma to the present.
The motion of Africa was seen to be much smoother and not marked by the sharp, unusual direction changes that characterized previous work. On a gross scale the motion could be divided into phases that correlated with major geological events, but on a smaller scale it was clear that relative motion between Africa and Eurasia did little more than set very broad boundary conditions within which a variety of geological events occurred.
Africa's motion is divisible into several distince phases. From the Jurassic start of seafloor spreading until the Late Cretaceous Quiet Zone (KQZ) the motion between the plates was sinistral strike-slip. During the KQZ, but prior to Anomaly 34 (84 Ma, Campanian) Africa's motion changed to northeasterly directed compression. Shortly after Anomaly 30 (68 Ma), close to the Cretaceous-Tertiary boundary, until after Anomaly 24 (55 Ma, mid-Eocene) there was a period of little relative motion between the two plates.
After Anomaly 24 strong relative motion recommenced between Africa and Eurasia. Africa continued on a trajectory between N and NNE until the Middle Miocene (Anomalies 5A - 5D) when motion became directed to the NW.
Within the relative motion framework a model for the geological evolution of the Western Mediterranean Sea is evolved. Although the Western Mediterranean is a Neogene phenomena the history of the region prior to this time is also examined, albeit in less detail. Among the major problems for which solutions are suggested is the convergence direction of Iberia with respect to Europe and the reason extension initiated in the Tyrrhenian Sea.

Advisor: Dewey, J
Long term appearance-based mapping with vision and laser

This thesis is about appearance-based topological mapping for mobile robots using vision and laser. Our goal is life-long continual operation in outdoor unstruc- tured workspaces.
We present a new probabilistic framework for appearance-based mapping and navigation incorporating spatial and visual appearance. Locations are encoded prob- abilistically as random graphs possessing latent distributions over visual features and pair-wise euclidean distances generating observations modeled as 3D constellations of features observed via noisy range and visual detectors. Multi-modal distributions over inter-feature distances are learnt using non-parametric kernel density estima- tion. Inference is accelerated by executing a Delaunay tessellation of the observed graph with minimal loss in performance, scaling log-linearly with scene complexity.
Next, we demonstrate how a robot can, through introspection and then targeted data retrieval, improve its own place recognition performance. We introduce the idea of a dynamic sampling set, the onboard workspace representation, that adapts with increasing visual experience of continually operating robot. Based on a topic based probabilistic model of images, we use a measure of perplexity to evaluate how well a working set of background images explains the robot’s online view of the world. O/ine, the robot then searches an external resource to seek additional background images that bolster its ability to localize in its environment when used next.
Finally, we present an online and incremental approach allowing an exploring robot to generate apt and compact summaries of its life experience using canon- ical images that capture the essence of the robot’s visual experience-illustrating both what was ordinary and what was extraordinary. Leveraging probabilistic topic models and an incremental graph clustering technique we present an algorithm that scales well with time and variation of experience, generating a summary that evolves incrementally with the novelty of data.

Keywords: computer vision
mobile robotics
autonomous systems
machine learning
Advisor: Newman, P
The role of calnexin, calreticulin and heavy chain glycosylation in MHC class I assembly

Class I heavy chain (HC) must assemble with β-microglobulin (β2m) and acquire optimal peptide in order to be presented to cytotoxic T cells (CTLs). Calnexin is involved in the initial folding of class I HC and subsequent assembly with β2m. Incorporation of "empty" or suboptimally loaded class I molecules into the multimolecular loading complex is essential for them to acquire optimal peptides. The loading complex consists of several cofactors: TAP, tapasin, ERp57 and calreticulin. The precise role of calnexin and calreticulin in the regulated assembly and peptide loading and the significance of their physical interaction with other cofactors of the loading as well as preloading complex still remains unclear.
Using mouse fibroblasts that lack calreticulin, I have studied the role of calreticulin in the assembly and loading of H2-Kb and H2-Db expressed in these cells. MHC class I molecules in calreticulin-deficient cells are able to assemble with β2m normally, but their subsequent loading with optimal, stabilising peptides is defective despite their ability to interact with the TAP complex. The "empty" or suboptimally loaded class I molecules exit the ER rapidly. Reflecting the loading defect, presentation of endogenously processed antigens by class I molecules in calreticulin-deficient cells is impaired.
I have used a human calnexin-deficient cell line CEM.NKR to study assembly of class I in the absence of calnexin. The results demonstrate that contrary to current understanding, calnexin has an important role in class I HC assembly with (32- microglobulin.
The role of heavy chain glycosylation in class I biogenesis is still controversial. My findings suggest asparagine (N)-linked glycosylation of human class I heavy chain at position 86 is optimal and any deviations from "normal" glycosylation results in poor loading with peptides and some defect in the assembly with β2m. Despite affecting the loading function, glycosylation did not have significant effect on presentation of a high affinity binding epitope to HLA-A*0201 specific CTLs.
Finally, I show that co-operation from all domains of calreticulin is essential in order to generate a fully functional calreticulin. Interestingly, proline-rich (P) -domain of calreticulin downregulated expression of a number of cellular proteins including MHC class I HC, despite restoring the cytosolic calcium levels in calreticulindeficient cells. The effect of P-domain on class I expression was at the level of transcription.

Advisor: Elliott, T
A critical study of the life of the 13th-century Tibetan monk U rgyan pa Rin chen dpal based on his biographies

U rgyan pa Rin chen dpal (1230-1309) was a great adept of the bKa' brgyud school of Tibetan Buddhism, particularly renowned for his knowledge of the Kālacakra tantra and the unique teaching known as the Approach and Attainment of the Three Vajras (rDo rje gsum gyi bsnyen sgrub), said to have been given to him in his vision by Vajrayoginī (rDo rje rnal 'byor ma) in the Miraculous Land (sprul pa'i zhing) of U rgyan. He was the student of the 2nd Karma pa, who entrusted him with the Black Hat, which he passed to the 3rd Karma pa. He was also a great traveller who journeyed widely across and beyond Tibet. He met Qubilai Khan in the capital of Yuan China and visited sacred Buddhist sites in South India. He has been aptly described by van der Kuijp as "the great Tibetan yogi, thaumaturge, scholar, alchemist, and traveler".
Thanks to the availability of a large amount of hitherto unknown materials from eleven biographies, the thesis has put considerable weight on the bibliographical comparison and analysis of the different works in an attempt to establish the possible relationship between them. This is supplemented by summaries of the biographies, to give an overview of the protagonist's life in Part One of the thesis. Part Two consists of a critical study of the different phases and aspects of U rgyan pa's life in the unique historical, political and religious context of each phase, drawing materials from the corpus of biographies and in the light of other primary and secondary sources in Tibetan, Chinese and Western languages. In Chapter I, U rgyan pa's family lineage, childhood and early studies are discussed in order to find out how his innate propensities and early studies are represented as having influenced his character. In Chapter II, the account of U rgyan pa's journey to West Tibet and U rgyan is studied. A sixteen-stanza song in his own words epitomising this journey, supplemented by route maps, will be used as a framework to illustrate and reconstruct his journey to the Land of the Ḍākinīs. In Chapter III, the teachings he received and the subsequent transformation of his character and status, are explored. In Chapter IV, his career as a tantric master, his other pilgrimages and benediction trips, and his conflicts with various religious and political authorities, are examined. The materials will be scrutinised in the hope of separating as far as possible fact from fiction.

Keywords: Tibetan history
U rgyan pa Rin chen dpal
Tibetan biography
Advisor: Ramble, C
Genetic, socio-ecological and fitness correlates of extra-group paternity in the European badger (Meles meles)

The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles).
To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit.
I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers.
In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.

Keywords: extra-group paternity
heterozygosity-fitness correlations
inbreeding depression
pairwise relatedness
capture-mark-recapture survival analysis
european badger
Meles meles
lifetime reproductive success
paternal effects
sexually antagonistic genetic effects
local density effects
Advisor: Macdonald, D
Structural and functional magnetic resonance imaging (MRI) in the prediction and characterization of mild cognitive impairment (MCI) and Alzheimer's disease (AD)

The aim of the research presented in this thesis was to improve the characterisation of the changes in brain structure and function that occur at different stages of Alzheimer’s disease (AD) progression, from pre-symptomatic AD, to mild cognitive impairment (MCI), to clinically evident dementia, using magnetic resonance imaging (MRI) techniques.
Baseline structural MRI data from a cohort of healthy older adults who were followed prospectively for ten years, during which time some developed MCI and some AD, were analysed. It was found that structural MRI could detect volume loss in medial-temporal lobes up to 7-10 years before clinical symptoms of AD appear. In addition, volumetric variability of medial-temporal regions detected by structural MRI across cognitively healthy older adults correlated with their performance on a task of visuospatial associative memory, and functional activation of the same regions occurred during successful performance of the same task on functional MRI (fMRI).
Three groups of participants - cognitively healthy controls, people with MCI, and patients with probable AD - were then recruited and underwent a multimodal MRI protocol, which included functional sequences acquired at rest and during the execution of two different cognitive tasks (visuospatial associative memory and self-appraisal). Cross-sectional comparisons showed: (i) that successful visuospatial associative memory performance was associated with increased functional activity (measured with task fMRI) in lateral prefrontal regions in AD patients relative to controls and (ii) that increased functional activity overlapped with frontal brain networks showing increased functional connectivity (measured with resting fMRI) in the same AD patients. Further, by demonstrating group- and condition-specific decreased frontal activity in AD patients relative to controls during a self-appraisal fMRI task, it was shown the specific utility of fMRI to unravel cognitive mechanisms underlying specific neuropsychological symptoms such as unawareness of cognitive impairment (anosognosia) in MCI and AD.
In conclusion, structural MRI can detect morphological changes in the preclinical stage of AD, possibly earlier than previously described, and these reliably match cognitive functioning in older adults. In the MCI and AD stages, once symptoms of cognitive impairment are clinically evident and measurable, task-related and resting functional MRI can inform on residual brain function detectable over and above the known changes in brain morphology and cognitive performance that have already occurred at these stages, emerging as a sensitive marker of residual ability that could potentially be used to measure the effect of new treatments.

Keywords: imaging
MRI
Alzheimer's disease
mild cognitive impairment
Advisor: Wilcock, G
Tracey, I
Modelling divisive inhibition in the primary visual cortex from optogenetic circuit mapping data

Recurrent networks are abundant in the neocortex and are recognised as a means of amplifying feedforward thalamic sensory inputs. However, when operating at high gain, which is necessary for this signal amplification, the standard recurrent network firing rate model suffers from increased reaction times to rapidly changing stimuli. Divisive inhibition has been proposed as a means of bypassing this coupling of system gain and time constant. In my thesis I focus on the importance of inhibition in recurrent networks in visual information processing. This was motivated by a recent study where the presence and absence of translaminar inhibition distinguished cells in the primary visual cortex. I apply several divisive inhibition schemes to an existing recurrent network model of simple and complex cells. The schemes are studied analytically and also simulated to assess how well they can be integrated into this existing model whilst simultaneously solving the coupled system gain and time constant problem. Though each scheme has its benefits, I propose that a mixture of schemes is likely in real physiology.

Keywords: Divisive Inhibition
Optogenetics
Vision
Advisor: Miesenboeck, G
Nanostructured thin film pseudocapacitive electrodes for enhanced electrochemical energy storage

This thesis presents work relating to the fabrication of novel thin film electrodes for energy storage applications, with a focus on low cost, nanostructured transition metal oxides, and electrode manufacture by atomised spray deposition.
Iron oxide (FeOx) nanowires were synthesised hydrothermally and combined with multi-walled carbon nanotubes (MWNT) in sprayed electrodes, which provided the necessary conductivity enhancement for effective energy storage. The spray processing technique allowed for facile control over the relative fraction of MWNTs in the sprayed electrodes. Optimised electrodes were investigated in a range of aqueous electrolytes, and the best energy storage behaviour occurred in Na2SO3 with a maximum capacitance from cyclic voltammetry of 312 Fg-1 at a scan rate of 2 mVs-1. The FeOx/MWNT electrodes were investigated for their suitability as lithium-ion battery anodes and showed reasonable energy storage behaviour.
Nickel oxide (NiO) electrodes were manufactured by hydrothermal synthesis and annealing followed atomised spray deposition. The performance of the NiO electrodes was enhanced though combination with aqueous graphene suspensions, produced in-house by ultrasonic exfoliation of graphite. The processing route used to combine the nanomaterials was considered and a co-synthesis route resulted in the best performing electrodes. Different substrates were investigated, as the most commonly used Ni-foam substrate reacted with the basic electrolytes necessary for electrochemical activity of NiO.
NiO/graphene electrodes showed charge/discharge capacitances of up to 571 Fg-1 at a current density of 10 Ag-1, which was maintained at over 300 F/g at a very high current density of 100 Ag-1.
Asymmetric supercapacitor devices were constructed using various combinations of FeOx, NiO, and commercial carbon black electrodes to extend the operating potential window beyond the ~1.23 V limit of symmetric aqueous-electrolyte devices. Power densities of over 20 kWkg-1 were achieved for an FeOx/MWNT-carbon device, which was comparable with current commercial carbon-only supercapacitors.

Keywords: Electrode fabrication
Pseudocapacitor
Supercapacity
Spray deposition
Advisor: Grant, P
Aspects of supersymmetric phenomenology

The current state of supersymmetric models of elementary particle physics is reviewed. Full calculations of the differential cross sections for the production of squarks and gluinos are performed, and the results folded with parton distributions to give total cross sections for pp and pp processes. The gluino production rate is used together with an analysis of its decay, taking proper account of the transverse momentum distribution of the decay products, to derive limits on the gluino mass from existing beam dump experiments; this limit is rather weak, typically mg > 3 GeV (the exact results depend on the details of the supersymmetric model).
The production of squarks and sleptons in ep processes is considered, allowing for gaugino-Higgsino mixing, and the prospects for using these processes to extract information about the gaugino-Higgsino mixing parameters are discussed. Finally we consider the production of squarks or sleptons in association with a photino; although of order of ϰ3 in perturbation theory, this process has a characteristic signature and may be where squarks or sleptons are first discovered if they are too heavy to be pair produced at LEP.

Advisor: Smith, C
Characterisation of T cells induced by candidate conserved region HIV-1 vaccines in healthy HIV-1/2 negative volunteers

HIV-1 has claimed the lives of millions of people globally and continues to spread despite development of highly active antiretroviral therapy. In 2013, 2.1 million new infections occurred and over 35 million people were living with HIV-1 infection. A prophylactic HIV-1 vaccine that can prevent infection or reduce viremia and subsequent transmission will always be an important part of the solution to bring this epidemic under control.
In this thesis, the first HIV-1 vaccine candidate to focus on conserved regions of the virus (HIVconsv) was assessed in a phase I clinical trial conducted in healthy HIV-1/2 negative volunteers in Oxford. The HIVconsv T-cell immunogen was delivered using three leading vaccine modalities (DNA (D), modified vaccinia virus Ankara (M) and chimpanzee adenovirus serotype 63 (C)), in several novel heterologous prime-boost regimens.
The frequency of T cells elicited through HIVconsv vaccination in the CM and DDDCM regimens surpassed that of previous HIV-1 cell-mediated vaccines. A large proportion of these T cells produced multiple cytokines and proliferated in response to recall peptides. The breadth of T-cell responses were also greater than the non-efficacious STEP study vaccine, with an average of 10 T-cell epitopes per vaccine recipient recognised across CM and DDDCM regimens. In vitro HIV-1 control mediated by CD8&plus; T cells was demonstrated for all vaccinees receiving the CM regimen, mainly against clade A (U455) and clade B (IIIB) isolates. Two vaccinees, demonstrated superior control of 6/8 and 7/8 viruses from the panel. The CM regimen induced significantly higher magnitudes of viral inhibition compared to the DDDCM or DDDMC regimens, with this regimen showing potential to overcome the disadvantage for subjects of carrying non-protective HLA alleles.
Investigation of T-cell specificities revealed that the frequencies of T cells specific for conserved Gag but more so Pol regions significantly correlated with in vitro virus control. Direct examination of peptide expanded T-cell lines showed that all Pol pool- and limited Gag pool-specific cell lines reduced HIV-1 replication in vitro. In most individuals, targeting multiple HIV-1 epitopes concomitantly resulted in higher levels of virus inhibition than targeting a single viral epitope and two T-cell specificities showed enhanced control of HIV-1; the first within Pol (TAFTIPSI) and second from Gag (TERQANFL). These data support further development of the conserved region strategy for T-cell vaccines against HIV-1.

Keywords: HIVconsv
HIV Vaccines
conserved regions
Advisor: Hanke, T