VictorJuiz/thesis huggingface dataset:
Visual recognition in art using machine learning

This thesis is concerned with the problem of visual recognition in art – such as finding the objects (e.g. cars, cows and cathedrals) present in a painting, or identifying the subject of an oil portrait. Solving this problem is extremely beneficial to art historians, who are often interested in determining when an object first appeared in a painting or how the portrayal of an object has evolved over time. It allows them to avoid the unenviable task of finding paintings for study manually. However, visual recognition of art is a challenging problem, in part due to the lack of annotation in art. A solution is to train recognition models on natural, photographic images. These models have to overcome a domain shift when applied to art.
Firstly, a thorough evaluation of the domain shift problem is conducted for the task of image classification in paintings; the performance of natural image-trained and painting- trained classifiers on a fixed set of paintings are compared for both shallow (Fisher Vec- tors) and deep image representations (Convolutional Neural Networks – CNNs) to exam- ine the performance gap across domains. Then, we show that this performance gap can be ameliorated by classifying regions using detectors.
We next consider the problem of annotating gods and animals on classical Greek vases, starting from a large dataset of images of vases with associated brief text descriptions. To solve this, we develop a weakly supervised learning approach to solve the correspondence problem between the descriptions and unknown image regions.
Then, we study the problem of matching photos of a person to paintings of that person, in order to retrieve similar paintings given a query photo. We show that performance at this task can be improved substantially by learning with a combination of photos and paintings – either by learning a linear projection matrix common across facial identities, or by fine-tuning a CNN.
Finally, we present several applications of this research. These include a system that learns object classifiers on-the-fly from images crawled off the web, and uses these to find a variety of objects in very large datasets of art. We show that this research has resulted in the discovery of over 250,000 new object annotations across 93,000 paintings on the public Art UK website.

Advisor: Zisserman, A
Mechanisms of long-term presynaptic plasticity at Schaffer-collateral synapses

Synaptic plasticity is thought to be integral to learning and memory. The two most common forms of plasticity are long-term potentiation (LTP) and long-term depression (LTD), both of which can be supported either by presynaptic changes in transmitter release probability (Pr), or by postsynaptic changes in AMPA receptor number. It is generally thought that the induction of LTP and LTD at Schaffer-collateral synapses in the hippocampus depends on the activation of NMDA receptors (GluN). Recent studies, however, have demonstrated that both increases and decreases in Pr can be induced under blockade of postsynaptic GluN receptors, suggesting that the activation of postsynaptic GluN receptors by glutamate is only a strict requirement for postsynaptic plasticity. In this thesis, I therefore re-examined the role of glutamate in presynaptic plasticity. I used single synapse imaging along with electrophysiological and pharmacological techniques to independently manipulate and monitor the levels of glutamatergic signalling during synaptic activity. I discovered that glutamate is inhibitory and unnecessary for the induction of LTP at the presynaptic locus. My findings support a novel model of presynaptic plasticity in which the net activity-dependent changes in Pr at an active presynaptic terminal is jointly determined by two opposing processes that can be simultaneously active: 1) postsynaptic depolarization, which, via the activation of L-type voltage-gated Ca2+ channels, increases Pr by driving the synthesis and release of nitric oxide from neuronal dendrites and 2) glutamate release, which through the activation of presynaptic GluN receptors, decreases Pr. Computationally, this model suggests that plasticity functions to reduce prediction-errors that arise during synaptic activity, and, thereby offers a biologically plausible mechanism by which neuronal networks may optimize learning at the level of single synapses.

Keywords: calcium imaging
long-term depression
transmitter release
long-term potentiation
NMDA receptors
synaptic plasticity
L-type voltage-gated calcium channels
nitric oxide
hippocampus
Advisor: Emptage, N
Adaptive immune evasion in clinically latent HIV infection

HIV is a master of immune evasion, utilising a range of different techniques to not only survive the human immune system, but also mediate its eventual catastrophic decline. Understanding how HIV evades the adaptive immune response is paramount to developing effective treatments and vaccines. This thesis aimed to investigate three key ways in which HIV-1 and HIV-2 mediate immune evasion in the context of clinically latent infection. Chapter three summarises a study into selection pressure and mutation in the gp120 envelope gene in a narrow-source HIV-1 cohort of former plasma donors (FPDs) from China. This study further characterised the cohort, and identified specific mutations in the gene consistent with antibody and CTL-driven selection pressure. Chapter four describes an investigation into the downregulation of HLA-I mediated by primary isolates of HIV-1 and HIV-2 Nef. Nef-mediated HLA-I downregulation contributes to the evasion of CTL responses. In stark contrast to previous reports, no evidence for differential downregulation of HLA-A and HLA-B was detected, but primary isolates invariably showed reduced activity relative to laboratory-adapted and consensus variants. In performing this study, a number of limitations came to light regarding how bifurcate analyses are used to interpret flow cytometric data collected in studies of receptor modulation. A novel technique - SWARM - was therefore developed to address these limitations, and is described in chapter five. Chapter six aimed to address why CTL responses against HIV-2 Nef are rare, despite HIV-1 Nef being highly immunogenic. A series of in vitro (immuno)proteasomal processing assays revealed HIV-2 Nef is more extensively digested than HIV-1 Nef, but further experimentation is required to explain the difference in response. Finally, chapter seven briefly summarises a successful collaborative attempt to resolve the first ever crystal structure of HIV-2 Nef.

Keywords: Immune evasion
HIV
AIDS
Evolution
Advisor: Rowland-Jones, S
Dong, T
Towards a structural model of adherent knobs on the surface of Plasmodium falciparum infected erythrocytes

The Plasmodium falciparum proteome is enriched in intrinsically disordered proteins, three of which are directly linked to malaria severity; P. falciparum Erythrocyte Membrane Protein 1 (Pf EMP1), Knob-associated Histidine-rich Protein (KAHRP) and Plasmodium He- lical Interdispersed Sub-telomeric family member (PHIST) PFE1605w. Pf EMP1, KAHRP and PFE1605w all localised to protrusions (knobs) on the P. falciparum-infected erythrocyte surface, which enable pathogenic cytoadherence of infected erythrocytes to uninfected erythrocytes and endothelial cells. In this thesis, I have employed a combination of biophysical and computational methods to characterize the interactions of Pf EMP1 and KAHRP with host erythrocyte spectrin, and of Pf EMP1 with two PHIST family proteins, PFI1780w and PFE1605w. These interactions are likely to assist knob formation and, thus, promote cytoadherence. I derived atomistic structural models of complexes formed between the PHIST domain of PFI1780w and the disordered C-terminal region of the cytosolic domain of Pf EMP1, of the folded core of the Pf EMP1 cytosolic domain and domain 17 of the host erythrocyte α spectrin, and between the KAHRP 5' sequence repeat and domains 10-14 of β spectrin. Combining these structural models with previous electron microscopy information allows us to propose a detailed model as to how knobs form and how Pf EMP1, KAHRP, PFE1605w, and other possible factors could locate therein.

Keywords: pfemp1
Malaria
structural biology
Advisor: Samson, M
The volatile history of past volcanic eruptions

Volatile elements play an important role in almost every aspect of sub-volcanic systems, from the generation and storage of magma, to the timing and style of volcanic activity. Currently, the most common method for assessing pre-eruptive magmatic volatile contents is through analysis of trapped melt inclusions. However, the reliability of this record is uncertain, necessitating development of new, independent petrologic methods for determining the pre-eruptive volatile contents of past eruptions. This thesis combines physical and chemical models with empirical analyses to develop the use of apatite as a magmatic volatile 'probe'.
The first research chapter investigates well-documented difficulties in electron microprobe analysis of apatite volatile concentrations. These are found to be caused by electron-beam induced heating and electric field generation. In determining these effects, it is possible to identify optimal operating procedures for apatite analysis. The next chapter explores the theoretical evolution of apatite volatile compositions as a function of magmatic evolution, building on previous work to develop thermodynamic models that relate crystal compositions to fluid systematics during fractional crystallisation. These provide a qualitative framework for interpreting apatite compositions in natural volcanic systems.
The remainder of the thesis is dedicated to identifying new insights that can be gained from the use of apatite as a magmatic volatile 'probe'; this method is applied to constrain pre-eruptive processes at Campi Flegrei, Italy. Texturally-constrained apatite analyses are used to create a time-series of magmatic volatile evolution in the build-up to eruption. This reveals that volatile saturation occurred late in magmatic evolution, and represents a potential eruption trigger. Apatites from different eruptions show a long-term temporal variability in the H2O contents of primitive melts feeding Campi Flegrei, which correlates with different epochs of activity. Melt inclusions from all eruptions have reequilibrated post-entrapment. This study demonstrates the potential utility of apatite for investigating pre-eruptive volatile behaviour in apatite-saturated magmas.

Keywords: Petrology
Mineralogy
Geochemistry
Volcanology
Advisor: Humphreys, M
Smith, V
Pyle, D
Using student views to develop a formative assessment policy in a sixth-form History department

This project sought to explore the views of sixth-form history students concerning the efficacy of their department’s formative assessment policy, and builds on my part 2 research into student views of self and peer marking. The project first consisted of a literature review in order to provide the grounding needed to adapt the department’s current assessment policy. This policy was then implemented by all staff in the department at the start of the academic year. Questionnaires and group interviews were carried out to explore how the students responded to this policy, with the intention that their responses would then be mediated by staff to produce an adapted policy for the start of the next academic year.
One of the key findings of this project was that despite increased student confidence in self assessment, students still reported considerable reliance on the teacher. Among other conclusions drawn, it will ultimately be suggested that to further shift the balance of power in assessment away from the teacher, students need greater ownership not only over the assessment of their work, but also the assessment policy itself. Therefore, although the original aim of the project was for the staff to redraft the department’s assessment policy based on student views, instead the outcome developed into a decision to give students a role in regularly revising the policy, encouraging a more organic and embedded approach.
Although this approach to policy-making in general is far from novel, it is rarely applied specifically to formative assessment, where educationalists tend to empower students within the narrow boundaries of teacher-determined assessment activities. It is still often the teacher ultimately who ‘owns’ and ‘provides’ formative assessment activities, with students required only to play their ascribed role. Therefore, this approach contrasts considerably with some of the contemporary literature that sees formative assessment as a concern of teacher pedagogy rather than student ownership.

Keywords: MLT
MLT2016
History
Formative Assessment
Advisor: Burn, K
Hopfenbeck, T
A bridge too far? Volunteering, voluntary associations, and social cohesion

In this thesis, I seek to advance our knowledge about the factors that make people start and stop volunteer work, thus shedding light on the capacity of volunteering and voluntary associations to foster social cohesion. In particular, my goal is twofold: first, to reveal to what extent voluntary associations function as meeting places for people from different social backgrounds, and second, to assess the resilience of civic participation in the face of labor market experiences that might undermine such engagement.
I make three core contributions to the literature on voluntary association involvement. First, I pay special attention to the organizational contexts in which volunteers are embedded. Second, I adopt a dynamic approach, analyzing decisions to start and stop volunteering. Third, I attempt to disentangle alternative mechanisms that could drive the associations observed between volunteering and its potential determinants. Analyzing data from The Netherlands and the United States, my findings expose limits to the integrative capacity of voluntary association involvement.
As it turns out, the civic landscape is strongly segregated. People tend to sort into voluntary associations where they mostly meet people with similar characteristics as themselves. Such sorting occurs along multiple social dimensions, including educational attainment, religiosity, gender, and ethnicity. This constrains the opportunities for building relationships that cut across existing social boundaries. Indeed, these sorting processes can reproduce in the civic domain fault lines that dominate other spheres of life.
Furthermore, civic engagement and participation in the labor market are shown to be strongly intertwined, with the former breaking down when labor force exits occur. Voluntary association involvement is, therefore, of limited value for drawing labor force outsiders into public life. However, this chain of events does not necessarily unfold, as long as labor force outsiders retain aspirations to participate in social life.

Keywords: Civil society
Labour market
Segregation
Social capital
Integration
Volunteering
Advisor: de Graaf, N
Niemann-Pick type c disease: pathogenesis and therapy

Niemann-Pick disease Type C is a rare, lysosomal storage disorder caused by defects in either NPC1 (95% of cases) or NPC2, and characterized by progressive neurodegeneration that ultimately results in premature death. The function of the NPC1 protein still remains poorly understood and how the NPC1 or NPC2 proteins interact, or the functions of the pathways they regulate still remains unknown. We have found unexpected links between NPC and other human diseases - particularly Tangier disease, suggesting that the NPC cellular pathway is more broadly involved in human disease than previously suggested. To gain further insight into the function of NPC1 and proteins it interacts with we used the yeast orthologue, Ncr1p. I recreated the Δncr1 mutant and characterized the mutant using an array of systematic screens to identify different processes and pathways that may play a role in NPC pathogenesis. The screen implicated mitochondrial dysfunction, defects in metal ion homeostasis and lipid trafficking, cytoskeleton dysfunction and nutrient sensing deficiencies. These screens were validated in the Npc1-/- mouse model, where the effects of modulating kinases also emerged as a potential therapeutic option. In addition to kinases, we examined the therapeutic potential of the FDA-approved hypertension drug, losartan. Losartan ameliorated the acidic store Ca2+ defect, which characterizes NPC, and all downstream pathologies as well as in combination with miglustat reduced levels of neuroinflammation in the mouse model. Furthermore, the cyclodextrin analogue Crysmeb was also examined as a novel therapy for NPC, and was found to have significant survival benefits as compared to HPβCD, the cyclodextrin compound currently in clinical trials. Taken together, in this thesis I have identified novel aspects of NPC pathogenesis, as well as mechanistic links between NPC and Tangier disease – which has led to miglustat treatment options for two patients at Addenbrooke's Hostpital, Cambridge. Additionally, taking advantage of the convergent disease mechanisms I have examined treatments (losartan/Crysmeb) that take advantage of the similarities and differences between these two disorders paving the way for potential clinical studies in the future.

Advisor: Platt, F
Single-walled carbon nanotubes as charge extraction layer for perovskite solar cells

This thesis describes the development of a charge-extraction layer for perovskite solar cells based on a network of polymer-functionalized single-walled carbon nanotubes (SWNTs). The starting point is the addition of SWNTs as additives to improve the charge trans- port characteristics of a solid-state hole-transporting material - 2,2,7,7-tetrakis-(N,N-di-p- methoxyphenylamine)9,9-spirobifluorene (spiro-OMeTAD). In a double-layer structure this is shown to perform comparably well to devices in which the charge transport of spiro-OMeTAD is enhanced by conventional doping. By means of photo-induced absorption spectroscopy, it could be shown that a significant fraction of photogenerated charges are transferred to the SWNTs. This finding demonstrates that the nanotubes act as charge selective contacts in their own right without requiring the presence of dedicated hole transporter material. In- stead, they can be embedded in a matrix of an inert polymer, which can be chosen according to characteristics related to stability rather than their electronic properties. Such an SWNT- PMMA composite structure is shown to outperform conventional hole-transporter systems during and after thermal stressing cycles. Finally, the issue of hysteresis is addressed. The additive 4-tert-butylpyridine (tBP) is shown to significantly improve the steady-state performance of devices with the SWNT-PMMA composite structure. In order to understand the mechanism and underlying interactions of the additive, the possible interaction interfaces are investigated one by one, leading to the conclusion that a direct interaction between tBP and the perovskite absorber must be responsible for the observed effect. The work in this thesis opens the avenue for SWNT-based hole transporter systems which provide a chemically stable and mechanically resilient charge-selective contact, and show particular promise for improving the overall stability of perovskite devices.

Advisor: Nicholas, R
Impedance-based battery temperature monitoring

Accurate on-board temperature monitoring of lithium-ion batteries is important for safety and control purposes. Impedance temperature detection (ITD) is a promising approach for temperature estimation, whereby the internal cell temperature is directly inferred from online electrochemical impedance spectroscopy (EIS) measurements at a single frequency. Previously, ITD was used to infer the volume-average cell temperature; the present work focuses on extending ITD to enable estimation of the spatially-resolved temperature distribution of cells with internal temperature gradients.
Two novel hybrid methods for temperature monitoring are introduced, based on combining impedance measurements with (i) an additional surface temperature measurement, and (ii) a thermal model. These methods predict the temperature distribution of the cell in either 1-D or 2-D, and can therefore identify localised hot spots, and hence the global maximum cell temperature. In each case, the methods are experimentally validated using cylindrical LiFePO4 cells (26650 for the 1-D experiments, 32113 for the 2-D experiments) monitored with periodic 215 Hz impedance measurements, and fitted with an internal thermocouple and one or more surface thermocouples for validation. Method (i) is shown to be more accurate than a standard ITD method based on impedance measurement only: ε = 0.6◦C vs. 2.6◦C respectively, over a 3500 s drive cycle. In method (ii), the impedance measurement forms part of a state/parameter estimation algorithm; in this case, the performance of an extended Kalman filter using impedance measurement is shown to be comparable - although slightly inferior - to an equivalent Kalman Filter using a conventional surface temperature measurement.
This work also presents a novel low-order 2-D thermal model based on the spectral-Galerkin (SG) method. The model can be used in conjunction with the proposed hybrid methods or in a conventional temperature monitoring scheme. Time- and frequency domain simulations show that the SG model using as few as 4 states is capable of accurately modelling the thermal dynamics of a large format cylindrical cell with a highly transient heat generation input. The model can account for different external temperatures and/or convection coefficients at each surface - a generality which makes it suitable for simulating various battery cooling configurations.

Advisor: Howey, D
Digital era local government in England

Local governments have been developing online services, aiming to better serve the public and reduce administrative costs. However, the impact of this work, and the links between governments' online and offline activities, remain uncertain.
Using a new full-population dataset of the UK government web, this thesis directly analyses the structure and content of government online. It argues that recent digital-centric public administration theories, typified by the Digital Era Governance quasi-paradigm, are not empirically supported by the UK local government experience. Instead, it argues for a positive but critical attitude to the value of technology in public administration.
New methods are developed for full-text empirical analysis of government web crawl data and the use of machine learning approaches for adding attributes to full-population data. Webometric and content analyses of the .gov.uk web are conducted, together with a time-series panel regression of English local government cost, service quality, satisfaction, and an expert assessment of web provision.
English local government online is highly heterogeneous and there is remarkably little intrinsic structure to the .gov.uk web. Geography is weakly visible in online government structures, but there is little evidence that online structures closely reflect the offline activities of government.
Empirically, English local governments' web development levels are found not to be associated with improvement in the cost of, quality of, or satisfaction with council services, challenging the merit of online approaches to service improvement.
Overall, the importance of digital-centric approaches to local government service improvement is challenged. A more nuanced theoretical approach to online service delivery is advocated, which discards utopian enthusiasm and focuses on concrete service improvements.
It is recommended that full-population quantitative analyses be used more broadly in political science, with awareness of both the opportunities and the challenges associated with them.

Keywords: Big data
Web crawling
Webometrics
Network analysis
Digital Era Governance
Local government
Methodology
Internet
e-government
Advisor: Margetts, H
Nash, V