VictorJuiz/thesis huggingface dataset:
Robust &amp; stochastic model predictive control
Keywords: stochastic uncertainty
model predictive control
robust control
recursive feasibility
probabilistic constraint

In the thesis, two different model predictive control (MPC) strategies are investigated for linear systems with uncertainty in the presence of constraints: namely robust MPC and stochastic MPC. Firstly, a Youla Parameter is integrated into an efficient robust MPC algorithm. It is demonstrated that even in the constrained cases, the use of the Youla Parameter can desensitize the costs to the effect of uncertainty while not affecting the nominal performance, and hence it strengthens the robustness of the MPC strategy. Since the controller u = K x + c can offer many advantages and is used across the thesis, the work provides two solutions to the problem when the unconstrained nominal LQ-optimal feedback K cannot stabilise the whole class of system models.
The work develops two stochastic tube approaches to account for probabilistic constraints. By using a semi closed-loop paradigm, the nominal and the error dynamics are analyzed separately, and this makes it possible to compute the tube scalings offline. First, ellipsoidal tubes are considered. The evolution for the tube scalings is simplified to be affine and using Markov Chain model, the probabilistic tube scalings can be calculated to tighten the constraints on the nominal. The online algorithm can be formulated into a quadratic programming (QP) problem and the MPC strategy is closed-loop stable. Following that, a direct way to compute the tube scalings is studied. It makes use of the information on the distribution of the uncertainty explicitly. The tubes do not take a particular shape but are defined implicitly by tightened constraints. This stochastic MPC strategy leads to a non-conservative performance in the sense that the probability of constraint violation can be as large as is allowed. It also ensures the recursive feasibility and closed-loop stability, and is extended to the output feedback case.
The identification and characterisation of germline genetic variants that affect human cancer
Keywords: SNPs
germline
oncology
cancer

Single nucleotide polymorphisms (SNPs) have great potential to serve as important biomarkers in the clinic to identify those at increased risk for developing cancer, progressing more rapidly, and not responding to therapies. However, the clinical application of cancer-associated SNPs has proven to be more complicated than expected. One of the necessary steps will certainly be the description of the molecular and cellular mechanisms behind the observed associations. The p53 tumour suppressor pathway harbours well-described SNPs that affect p53 signalling and cancer. The aim of the work presented in this thesis was to utilise this knowledge to more efficiently characterise cancer-associated SNPs. Firstly, cancer-associated SNPs in a p53 network gene, CD44, were studied. Specifically, based on CD44’s known roles in both p53-dependent and independent signalling, it was predicted that the cancer-associated SNPs could function as biomarkers for chronic lymphocytic leukaemia progression, and for the response to anti-EGFR therapy for colorectal cancer. Indeed, supportive data is presented. Next, a methodology is presented that aims to identify cancer-associated SNPs in functional p53 binding sites using genome-wide datasets. Interestingly, a SNP is identified that dramatically influences the ability of p53 to regulate transcription of the KITLG oncogene and that associates with one of the largest risks of cancer identified to date. Intriguingly, the SNP is also shown to have undergone positive selection throughout human evolution, signifying a selective advantage, but similar SNPs are demonstrated to be rare in the genome due to negative selection, indicating that polymorphisms in p53 binding sites have been primarily detrimental to humans. Lastly, and in order to begin to explore if other polymorphic transcription factor binding motifs could be found in cancer-associated SNPs, a methodology was designed to identify SNPs in E-box transcription factor binding motifs, as they are sensitive to single base pair changes and affect cancer. Taken together, the work presented in this thesis shows how the study of how SNPs associate with, and impact upon, cancer has great potential to improve both biological knowledge and clinical outcomes.
Structural and mechanistic studies on prolyl hydroxylases
Keywords: nitric oxide
double-stranded-beta helix
2-oxoglutarate
prolyl hydroxylase
hypoxia inducible factor
transcription
crystallography

Oxygen dependent prolyl-4-hydroxylation of the alpha-subunit of the hypoxia inducible transcription factor (HIF-alpha) plays an essential role in the hypoxic response. Hydroxylation of proline residues in the N- or C-terminal oxygen dependent degradation domains (NODD or CODD) increases the affinity of HIF-alpha to the von Hippel-Lindau protein (pVHL) by approx. 1000 fold so signalling for HIF-alpha degradation. With limiting oxygen, HIF-alpha hydroxylation slows, it dimerises with HIF-beta and activates the transcription of a gene array. Prolyl-4-hydroxylation also stabilises the triple helix structure of collagen, the most abundant human protein. Both the collagen and the HIF prolyl hydroxylases (PHDs) are Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases.
Crystal structures of PHD2 in complex with CODD were determined in the current study. Together with biochemical analyses, the results demonstrate that catalysis involves a mobile region of PHD2 that encloses the hydroxylation site and stabilises the PHD2.Fe(II).2OG complex. When bound to PHD2 the pyrrolidine ring of the non-hydroxylated proline-residue adopts a C⁴-endo conformation. Evidence is provided that 4R-hydroxylation enables a stereoelectronic effect that changes the proline conformation to the C⁴-exo state, as observed when hydroxylated HIF-alpha is bound to pVHL and in collagen. The results help to rationalise NODD/CODD selectivity data for PHD isoforms and the effects of clinically observed mutations on PHD2 catalysis. Analyses on the interaction of nitric oxide with PHD2 are described and discussed with respect to regulation of the hypoxic response by nitric oxide.
Rethinking Chinese national identity. The wider context of foreign policy making during the era of Hu Jintao, 2002–2012.
Keywords: foreign policy
the United States
national identity
Japan
political psychology
public opinion
China
patriotism
nationalism

This thesis analyses China's national identity construction and its foreign policy implications especially towards Japan and the United States during the Hu Jintao period 2002-2012. The vast literature on China's rise takes “rising nationalism” in China as one of the key indicators of increased likelihood for aggressive behaviour in the future. This work problematizes some of the simplified assumptions made in this literature by emphasising the domestic context from which foreign policies rise. I argue that culture specific values deriving from national identities shape attitude structures and affect the whole thinking and conceptualisation related to foreign policy with wide-ranging consequences. Thus, in this research national identity is operationalised through values and attitudes deriving from it. With empirical evidence, I show in my thesis that most things discussed as "nationalism" in China studies literature can be analytically separated into at least two components, each with different foreign policy relevant correlates. Analysing two sets of survey material with statistical methods I show that the type of national attachment in China constrains foreign policy preferences in a different way than often assumed in the literature: "patriots" support an internationalist stance in contrast to "nationalists" who favour more assertive behaviour towards Japan and the US as well as generally protectionist economic policies. In addition to analysing the associations between core values and foreign policy preferences, I also provide other examples of cultural factors shaping Chinese foreign policy context including the role of historical legacies and their political use, and the role of the media in the formation of foreign threat perceptions and foreign policy preferences. The need to better understand these national identity dynamics is emphasised because of the ongoing pluralisation of Chinese foreign policy establishment, which gives more space to domestic input from various levels of society.
British music criticism in a new era: Studies in critical thought 1894-1945
Keywords: music criticism

The mid 1890s witnessed the start of a new era in British music criticism heralded by George Bernard Shaw. A preliminary study of the nineteenth-century critical context provides some reasons for its emergence. The new temper was defined by two critics: John F. Runciman. the self-appointed leader of the New critics. and the Rationalist Ernest Newman. Henry Hadow's Studies in Modern Music set a new standard and added impetus to discussion of critical theory. Several other critics associated with Oxford, including Parry, Tovey, Walker and Colles, formed a body of opinion that shared common values and continued a tradition stemming from Victorian writers such as Grove and Stainer. Discussions of critical theory, especially those of Newman and M. D. Calvocoressi. are given prominence.
Two new trends emerged after the First World War. The first, a reaction against the German repertoire, focused on Stravinsky and the composers associated with Diaghilev's Ballets Russes. Foremost among those who championed the aesthetic of 'objective empiricism' were Edwin Evans and Leigh Henry. A second and more conservative tendency carne predominantly from two composer-critics associated with Philip Heseltine's journal of the 1920s. The Sackbut: Cecil Gray and K. S. Sorabji. Constant Lamben continued along broadly similar lines to Gray during the 1930s, notably in his Music Ho!. and is included as a member of the Sackbut coterie. Contrast between the criticism of Eric Blom and that of the poet W. J. Turner demonstrates the range of independent thought characteristic of the new era.
Consideration of individual endeavour rather than collective trends of critical thought provides the method of documentation. The thesis attempts to elucidate the diversity of critical views without refuting a critic or entering into a polemical discourse. while in no way shirking the responsibility of arriving at an assessment of his position and achievement. Certain recurrent issues. including those surrounding Romanticism. nationalism and the rise of modernism. reflect the primary concerns of the period.
A table showing music critics of leading British newspapers and a selected chronological list of one hundred books of music criticism published in Britain between 1890 and 1950 are contained in the appendices.
Essays on the perception, representation, and categorisation of colour
Keywords: perception
colour
representation
categorisation

This thesis develops and explores a constitutive approach to colour vision, which serves as an alternative to the standard experiential view of colour vision operating in the philosophy of colour. The approach seeks to describe the nature or essence of colour vision qua psychological kind. I argue that it is constitutive of colour vision that an organism possesses the ability to achieve colour constancy. An important feature of my account is that colour constancy is characterised as the ability to discriminate differences in surface reflectance properties across changes in illumination conditions. This differs from the standard ‘appearance invariance view’, which characterises colour constancy by appealing to the phenomenology of apparent colour. I consider an important objection to the appearance invariance view posed by the argument from illumination, which might also seem to carry over to the reflectance discrimination view. The objection is based on the claim that in standard cases of colour constancy the phenomenology of apparent colour is partly illumination-dependent. I argue that the reflectance discrimination view is perfectly able to accommodate this point. As a case study in applying the constitutive approach to illuminate the distinctive nature of colour vision, I argue that a vivid feature of our ordinary experience of colour known as categorical perception should be dissociated from our colour vision abilities. Although colour ontology often is not at the forefront of discussion, these constitutive theses support the ontological view of colour known as reflectance physicalism. I critique the argument from colour similarity, which many take to pose the greatest threat to reflectance physicalism. The thrust of the argument is that colours phenomenally appear to stand in similarity relations that do not correlate with the similarities that are evident among reflectance properties. This argument lacks much force, however, as it fails to acknowledge the extreme context sensitivity of similarity and the presentation sensitivity of our knowledge of similarities.
The spatial construct of social relations: social transformation in early Kaushi, Taiwan
Keywords: GIS
Social Relations
Spatial Pattern
Settlement
Taiwan

This research attempts to extend the application of spatial analysis to the investigation of human agency in social relations. Marcos Llobera's research framework on modelling daily experience and social space showcases great potentials of utilising Geographic Information Systems (GIS) to explore the perception and behaviour of individual agents. By expanding Llobera's work and incorporating Tim Ingold's wayfaring theory to explore the human agency in the context of social relations, this research proposes a new analytical method to investigate social relations through the accumulation of intimate interactions. Exemplified with detailed analysis on two settlements of Kaushi people in Taiwan, the proposed analytical method demonstrates great strength and yields fruitful insights into their social structure and transformation. In addition, this method is particularly instrumental in unravelling specific relations between individuals, as well as between social groups. The application of this method on Kaushi settlements yielded fruitful insights of their social structure and transformation. On the other hand, the side products of this approach can be further employed to investigate the visual structure and movement intensity of a site, as well as to experiment alternative 'what if' scenarios relating to visibility, movement, and interaction. In sum, this research augments the potential of spatial analysis to explore human agency in a social context and lays out a further platform for the investigation of social relations at a settlement scale.
The role of thermal processing and protein oxidation in peanut allergy
Keywords: dendritic cells
innate immunity
peanut
protein purification
immunology
allergy
food processing
antigen uptake

Food allergies are an increasing health problem throughout the developed world. Among these, peanut allergy is particularly significant, due to its exceptional severity and frequent lifelong duration. Much of its aetiology remains unclear. In particular, it remains unknown why, unlike other food allergies, peanut allergy incidence correlates poorly with average dietary peanut consumption. A popular explanation for this discrepancy is that peanut allergy is more common in regions where predominantly dry-roasted (DR) peanuts are consumed, leading to speculation that DR-induced chemical modifications may contribute to pathological Th2 responses in humans. Yet to date, no research group has demonstrated an enhanced immunogenicity of DR peanuts relative to raw in a murine model of sensitisation.
This thesis begins with the hypothesis that dry-roasting does indeed alter the chemical composition of peanut proteins in such a way as to increase immunogenicity and allergenicity. To test this hypothesis robustly, I have first addressed flaws in previous studies by developing a methodology to thoroughly characterise samples of raw and DR peanut protein, as well as purifying samples of individual peanut allergens. Using these samples, I have demonstrated an enhanced immunogenicity of DR peanut protein relative to raw, in intragastric, subcutaneous and epicutaneous models of mouse sensitisation, and furthermore, that such enhanced responses feature a pronounced Th2 bias and functional IgE production. I will present evidence that this difference is not caused by either protein aggregation or the presence of other non-protein substances, but is due to an intrinsic property of the DR peanut proteins. I will go on to clarify candidate molecular mechanisms of this effect, examining several putative receptors and probing the effects of roasting on dendritic cell binding and interactions of peanut proteins. I conclude in light of these investigations that the dry-roasting hypothesis remains the most plausible explanation for the epidemiological distribution of peanut allergy, although many additional questions remain regarding the nature of the chemical modifications produced by roasting and the molecular basis of their recognition by the immune system.
Mating system, sex-specific selection and the evolution of the avian sex chromosomes
Keywords: Genomics
Sex chromosomes
Evolution
Biology

Sex chromosomes experience distinct evolutionary environments, due to their unusual pattern of inheritance, and studies of sex chromosome evolution can shed light on the fundamental evolutionary forces acting across the genome as a whole. Here, I combine genomic and transcriptomic data across a wide range of avian species to explore the evolutionary processes governing sex chromosome evolution. Birds are female heterogametic and therefore it is possible, via comparisons with male heterogametic species, to identify the fundamental factors driving sex chromosome evolution, versus those associated with sex.
In this thesis, I uncover a complex mosaic of recombination suppression between the Z and W chromosomes, characterized by repeated and independent divergence of gametologs, together with ongoing genetic exchange. Additionally, I highlight the role of mating system, and interplay between evolutionary forces, in driving coding and expression evolution on the Z and W chromosomes. My findings indicate that although the Z chromosome is masculinized for male-specific effects, the magnitude of genetic drift acting on Z-linked genes is elevated in promiscuous relative to monogamous mating systems. In contrast, evolution of the female-limited W chromosome is governed predominately by purifying selection. Together, my results suggest that the role of the Z chromosome in encoding sexual dimorphisms may be limited, but that W-linked genes play a significant role in female-specific fitness. In conclusion, my findings reveal the power of mating system in shaping broad patterns of genome evolution.
Machine learning in multi-frame image super-resolution
Keywords: machine learing
super-resolution
Image

Multi-frame image super-resolution is a procedure which takes several noisy low-resolution images of the same scene, acquired under different conditions, and processes them together to synthesize one or more high-quality super-resolution images, with higher spatial frequency, and less noise and image blur than any of the original images. The inputs can take the form of medical images, surveillance footage, digital video, satellite terrain imagery, or images from many other sources.
This thesis focuses on Bayesian methods for multi-frame super-resolution, which use a prior distribution over the super-resolution image. The goal is to produce outputs which are as accurate as possible, and this is achieved through three novel super-resolution schemes presented in this thesis.
Previous approaches obtained the super-resolution estimate by first computing and fixing the imaging parameters (such as image registration), and then computing the super-resolution image with this registration. In the first of the approaches taken here, superior results are obtained by optimizing over both the registrations and image pixels, creating a complete simultaneous algorithm. Additionally, parameters for the prior distribution are learnt automatically from data, rather than being set by trial and error.
In the second approach, uncertainty in the values of the imaging parameters is dealt with by marginalization. In a previous Bayesian image super-resolution approach, the marginalization was over the super-resolution image, necessitating the use of an unfavorable image prior. By integrating over the imaging parameters rather than the image, the novel method presented here allows for more realistic prior distributions, and also reduces the dimension of the integral considerably, removing the main computational bottleneck of the other algorithm.
Finally, a domain-specific image prior, based upon patches sampled from other images, is presented. For certain types of super-resolution problems where it is applicable, this sample-based prior gives a significant improvement in the super-resolution image quality.
Cellular distributed and parallel computing
Keywords: Randomised Algorithms
Time and Message Complexity
Distributed Networks
Distributed and Parallel Computing
Bio-inspired Computing

This thesis focuses on novel approaches to distributed and parallel computing that are inspired by the mechanism and functioning of biological cells. We refer to this concept as cellular distributed and parallel computing which focuses on three important principles: simplicity, parallelism, and locality.
We first give a parallel polynomial-time solution to the constraint satisfaction problem (CSP) based on a theoretical model of cellular distributed and parallel computing, which is known as neural-like P systems (or neural-like membrane systems).
We then design a class of simple neural-like P systems to solve the fundamental maximal independent set (MIS) selection problem efficiently in a distributed way, by drawing inspiration from the way that developing cells in the fruit fly become specialised.
Building on the novel bio-inspired approach to distributed MIS selection, we propose a new simple randomised algorithm for another fundamental distributed computing problem: the distributed greedy colouring (GC) problem.
We then propose an improved distributed MIS selection algorithm that incorporates for the first time another important feature of the biological system: adapting the probabilities used at each node based on local feedback from neighbouring nodes. The improved distributed MIS selection algorithm is again extended to solve the distributed greedy colouring problem. Both improved algorithms are simple and robust and work under very restrictive conditions, moreover, they both achieve state-of-the-art performance in terms of their worst-case time complexity and message complexity. Given any n-node graph with maximum degree Delta, the expected time complexity of our improved distributed MIS selection algorithm is O(log n) and the message complexity per node is O(1). The expected time complexity of our improved distributed greedy colouring algorithm is O(Delta + log n) and the message complexity per node is again O(1).
Finally, we provide some experimental results to illustrate the time and message complexity of our proposed algorithms in practice. In particular, we show experimentally that the number of colours used by our distributed greedy colouring algorithms turns out to be optimal or near-optimal for many standard graph colouring benchmarks, so they provide effective simple heuristic approaches to computing a colouring with a small number of colours.