VictorJuiz/thesis huggingface dataset:
Non-parametric probability density function estimation for medical images

The estimation of probability density functions (PDF) of intensity values plays an important role in medical image analysis. Non-parametric PDF estimation methods have the advantage of generality in their application. The two most popular estimators in image analysis methods to perform the non-parametric PDF estimation task are the histogram and the kernel density estimator. But these popular estimators crucially need to be ‘tuned’ by setting a number of parameters and may be either computationally inefficient or need a large amount of training data. In this thesis, we critically analyse and further develop a recently proposed non-parametric PDF estimation method for signals, called the NP windows method. We propose three new algorithms to compute PDF estimates using the NP windows method. One of these algorithms, called the log-basis algorithm, provides an easier and faster way to compute the NP windows estimate, and allows us to compare the NP windows method with the two existing popular estimators. Results show that the NP windows method is fast and can estimate PDFs with a significantly smaller amount of training data. Moreover, it does not require any additional parameter settings. To demonstrate utility of the NP windows method in image analysis we consider its application to image segmentation. To do this, we first describe the distribution of intensity values in the image with a mixture of non-parametric distributions. We estimate these distributions using the NP windows method. We then use this novel mixture model to evolve curves with the well-known level set framework for image segmentation. We also take into account the partial volume effect that assumes importance in medical image analysis methods. In the final part of the thesis, we apply our non-parametric mixture model (NPMM) based level set segmentation framework to segment colorectal MR images. The segmentation of colorectal MR images is made challenging due to sparsity and ambiguity of features, presence of various artifacts, and complex anatomy of the region. We propose to use the monogenic signal (local energy, phase, and orientation) to overcome the first difficulty, and the NPMM to overcome the remaining two. Results are improved substantially on those that have been reported previously. We also present various ways to visualise clinically useful information obtained with our segmentations in a 3-dimensional manner.

Keywords: probability density function
automated image analysis
Non-parametric
colorectal cancer
mixture model
level sets
Advisor: Brady, JM
The application of optimal estimation retrieval to lidar observations

Optimal estimation retrieval is a nonlinear regression scheme to determine the conditions statistically most-likely to produce a given measurement, weighted against any a priori knowledge. The technique is applied to three problems within the field of lidar data analysis.
A retrieval of the aerosol backscatter and either the extinction or lidar ratio from two-channel Raman lidar data is developed using the lidar equations as a forward model. It produces profiles consistent with existing techniques at a resolution of 10-1000 m and uncertainty of 5-20%, dependent on the quality of data. It is effective even when applied to noisy, daytime data but performs poorly in the presence of cloud.
Two of the most significant sources of uncertainty in that retrieval are the nonlinearity of the detectors and the instrument's calibration (known as the dead time and overlap function). Attempts to retrieve a nonlinear correction from a pair of lidar profiles, one attenuated by a neutral density filter, are not successful as uncertainties in the forward model eliminate any information content in the measurements. The technique of Whiteman et al. [1992] is found to be the most accurate.
More successful is a retrieval of the overlap function of a Raman channel using a forward model combining an idealised extinction profile and an adaptation of the equations presented in Halldórsson and Langerholc [1978]. After refinement, the retrieval is shown to be at least as accurate, and often superior to, existing methods of calibration from routine measurements, presenting uncertainties of 5-15%.
These techniques are then applied to observations of ash over southern England from the Eyjafjallajökull eruption of April 2010. Lidar ratios of 50-60 sr were observed when the plume first appeared, which reduced to 20-30 sr after several days within the planetary boundary layer, indicating an alteration of the particles over time.

Keywords: aerosol
Raman lidar
Optimal estimation
Advisor: Grainger, D
Vernacular Okinawa

Demand for equal rights tends to be accompanied by assimilation of ethnic subordinates while the recognition of their separate identity is liable to justify unfair segregation. When an ethnic minority is aware of this dilemma, what identity are they to claim and what ideology do they present? By looking at contemporary local activism in Okinawa, Japan, this dissertation tries to give an empirical answer to this question. In Okinawans' historical experience, both their sameness as and difference from the Japanese turned out to be disadvantageous for the people. Local activists can support neither their Japanese identity nor Okinawan identity. As a result, although they struggled against the central power of the state, their activism can not be fully embraced within the category of multiculturalist movements. The body of this dissertation consists of a historical reconstruction of citizens' movements and a sociological analysis of activists' discourse on Okinawa-Japan relations. The ethnography focuses on a particular generation of educated local people, who form the mainstream of local activists in post-reversion Okinawa, and tries to illuminate what impact the reversion movement had on them and how it shaped their thought and actions thereafter.
Chapter 1 describes the way in which Okinawan intellectuals re-contextualise obsolete religious tradition into their environmentalist or pacifist movements. Chapter 2 addresses the moral ambiguity of modern collective identities and demonstrates, with the Japanese as an example, that moral values change depending on transient international power relations. Chapter 3 focuses on the empirical historical context, the reversion movement, in which a category of Okinawan intellectuals realised this moral ambiguity. Chapter 4 examines an expression of regional identity, the Ryukyuan Arc, by which Okinawan activists tried to overcome the principle of modern social collectivity. Chapter 5 discusses how Okinawans' perception has historically changed in regard to their position in Japanese society.
The Paradise lost of liberalism

The thesis argues that the development of the New Liberalism in the late nineteenth century was opposed from the standpoint of a more "traditional" conception of liberalism by a group of political theorists who owed their inspiration to the work of Herbert Spencer. Despite the protestations of these self-styled "Individualists" that they were the true heirs of mid-century liberalism, it is argued that their political theory represented as much a transformation of Benthamite Radicalism as did that of the New Liberals. The Individualists developed raid-century liberalism in a conservative direction, arguing that social change was not to be attained by conscious design and developing an ethical justification for the actual distribution of property and power in late Victorian Britain. The thesis establishes this claim by examining six Individualist arguments derived from Spencer's Synthetic Philosophy: (1) the argument from the biological theory of evolution; (2) the argument from psychological theory; (3) the sociological conception of society as an "organism"; (4) the theory of historical development; (5) the doctrine of utility; and (6) the theory of justice and property rights.
Measurements of minor constituents which affect ozone concentrations in the stratosphere

The chemistry of stratospheric ozone is discussed and particular consideration is given to the role of chlorine compounds and to the impact of human activity on the ozone layer. An account is given of the methods used by other researchers to measure hydrogen chloride (HC1) in the stratosphere and their results are summarized.
The pressure modulator radiometer (PMR) is an instrument which can be used to make remote measurements of atmospheric temperature and composition by sensing the radiation transmitted by or emitted from an atmospheric path containing gases with absorption bands in the infra-red. A balloon-borne PMR has been used to detect the absorption of solar radiation by the fundamental vibration-rotation band of HC1 at 3.5 micrometres. Using a limb scanning technique, the mixing ratio profile of HC1 has been measured over the height range, 16 to 39 km.
It is shown that the amount of HC1 in an atmospheric path can be related to the PMR signals using a line-by-line method. The theory is developed in sufficiently general terms for it to be applicable to line-by-line calculations for many other gases with absorption bands in the infra-red. Consideration is given to the modelling of PMR measurements of transmission and emission both in the atmosphere and in the laboratory.
The instrument used to measure HC1 is described in detail. The problems associated with the interpretation of the signals are discussed and an account of the instrument's laboratory testing is given. The reduction of the balloon flight data is described and the method used to retrieve the mixing ratio profile from the PMR signals is presented.

Advisor: Houghton, J
A primary care-based intervention to improve participation in the NHS bowel cancer screening programme

Background: Currently, participation in the NHS Bowel Cancer Screening Programme (NHSBCSP) is poor, with around half of all people invited returning their (FOBT) kits. The research programme aimed to investigate whether a general practitioner’s (GP) letter encouraging participation and a detailed leaflet explaining how to complete the (FOBT) included with the invitation materials would improve uptake.
Methods: The research programme was divided into three phases which were designed to sequentially develop and evaluate the two interventions. The initial and second phases developed and refined the two interventions and the trial outcome measures with previous participants and stakeholder representatives. The final phase was a randomised 2x2 factorial trial conducted with people invited to screening in October 2009. Participants were randomised to either a GP’s endorsement letter and/or a detailed procedural leaflet with their FOBT kit. The primary outcome was verified participation in the NHSBCSP. Questionnaires were also used to evaluate participant perceptions of CRC screening and GPs views on involvement with the NHSBCSP.
Results: The factorial trial demonstrated both the GP’s endorsement letter and the detailed procedural leaflet increased participation in the NHSBCSP. In the intention-to-treat analysis, participation improved by 6% for the detailed procedural leaflet and 5.8% for the GP endorsement letter 20 weeks after receipt of the FOBT kit. The random effects logistic regression model confirmed that there was no important interaction between the two interventions, and estimated an adjusted rate ratio of 1.11 (P=0.038) for the GP’s letter and 1.12 (P=0.029) for the leaflet. The per protocol analysis indicated that the insertion of an electronic GP’s signature on the endorsement letter was associated with increased participation (P=0.039).
Conclusions: Including both an endorsement letter from each patient’s GP and a detailed procedural leaflet could increase participation in the NHSBCSP by around 10%, a relative improvement of 20% on the current participation rate. Both interventions were well-received by participants and there was minimal impact on GP workload.

Keywords: Primary Care
mass screening
faecal occult blood test
randomised trial
colorectal cancer
questionnaires
Advisor: Mant, D
Ward, A
The role of type I interferons in regulating intestinal inflammation

Intestinal homeostasis is a delicate balance between suppression of immune responses against innocuous antigens and stimulation of immune responses against pathogens. Type I interferon (IFN-1) cytokines have both immunostimulatory and immunomodulatory effects. Colon mononuclear phagocytes (MP) constitutively produced IFN-1 in a TRIFdependent manner. We explored the function of endogenous IFN-1 in the colon using the T cell adoptive transfer model of colitis. Transfer of CD4+CD45RBhi naïve T cells from wild type (WT) or IFNAR subunit 1 knockout (IFNAR1-/-) mice into RAG-/- hosts resulted in similar onset and severity of colitis. In contrast, RAG-/- x IFNAR1-/- double knockout (DKO) mice developed accelerated severe colitis compared to RAG-/- hosts when transferred WT CD4+CD45RBhi T cells. Although WT or IFNAR1-/- regulatory T (Treg) cells equally prevented disease caused by CD45RBhi naïve T cells, WT Treg cells co-transferred with naïve CD4+ T cells into DKO recipients failed to expand or maintain Foxp3 expression and gained effector functions in the colon. IFNAR signaling on host hematopoietic cells inhibited T cell-mediated colitis, but not innate colitis. MPs isolated from the colon lamina propria (cLP) required IFNAR signaling for the production of the anti-inflammatory cytokines, IL-10, IL-27, and IL-1RA, but not for the production of classic pro-inflammatory cytokines. IFN-1-dependent secretion of IL-1RA was particularly important in inhibiting the migration of inflammatory DCs with potent T cell proliferative capacity from the cLP to the mesenteric lymph nodes. Finally, preliminary results suggested that IFN-1 may shape the commensal microbiota, but is not essential for controlling specific colitis-inducing bacteria.

Keywords: type i interferons
mucosal immunology
colitis
inflammatory bowel disease
Advisor: Maloy, K
Kelsall, B
Varieties of regulation: how states pursue and set international financial standards

What explains the form and substance of international financial standards? Form refers to the legal or non-legal bindingness of an international standard. Substance refers to how significantly the standard changes the international status quo. The form and substance of international standards on bank capital adequacy, hedge funds, “bail-in” resolution, and insurance capital adequacy challenge the predictions of major rationalist, realist, and two-level perspectives. I propose a novel theory and present original evidence to test two central claims. First, the structure of domestic institutions and strategic interaction within a state incentivizes an actor from that state to prefer and pursue a certain form of international standard: legally or non-legally binding. The state actor, as a first mover, aims to propose a standard at an appropriate international institution which produces standards of its preferred form. Second, the state actor must bargain with representatives of other states according to certain decision-making rules at the international standard-setting institution. The type of decision-making rule used in bargaining—not the market power or other characteristics of key players—explains the substance of the final standard. More restrictive decision-making rules, which use majority or supermajority voting, lead to greater change than open rules, which are based on consensus or unanimity voting.
My empirical findings remove the veneer of technocratic legitimacy associated with international standard-setting to reveal intense distributional battles. In pursuing the Basel capital standards, the US Federal Reserve has been motivated more by turf wars with other US bank regulators than by its publicly stated desire to create a “level playing field” for internationally active banks. Supported by domestic collaboration between regulators and industry, French officials set a legally binding and deep de facto international standard for hedge fund managers over the vigorous objections of the City of London. By pursuing a soft standard on bail-in, the Bank of England has sought not only to protect taxpayers from costly bailouts, but also to keep Her Majesty’s Treasury at arm’s length. The lack of international insurance regulation is due not to the lack of effort by the UK Financial Services Authority and its European partners, but to open decision-making rules that allow US state regulators, albeit fragmented and under-resourced, to protect the international status quo. In each of these cases, I specify how domestic and international institutional settings provide enduring opportunities and constraints for key players in global finance.

Keywords: Resolution
Globalization
Regulation
Banking law
Insurance
International finance
Securities
Advisor: Mattli, W
Armies, politics and revolution. Chile, 1780-1826

This thesis studies the political role of the Chilean military during the years 1780-1826. Beginning with the last decades of the eighteenth century and ending immediately after the last royalist contingents were expelled from the island of Chiloé, this thesis does not seek to give a full picture of the participation of military men on the battlefield but rather to interpret their involvement in local politics. The main categories deployed in this study are 1) armies, 2) politics and 3) revolution, and the three are presented with the purpose of demonstrating that, as Peggy K. Liss has claimed, after 1810 Spanish American public life ‘became militarized; and the military, privileged’. I argue that, notwithstanding the sometimes tense relationship between civilians and the armed forces, the Chilean military became privileged because the demise of the Spanish monarchy in 1808 made them protagonists of the decision-making process. In so doing, this thesis aims to make a contribution to the understanding of Chile’s revolution of independence, as well as to discuss some recent historiographical contributions on the role of the military in the creation of the Chilean republican system. Although the focus has been placed on the career and participation of Chilean revolutionary officers, this thesis also seeks to provide an overview of both the role of royalist armies and the influence of international events in Chile.

Keywords: Chile
revolution
military
independence
Advisor: Knight, A
Bioinformatical and experimental analysis of gene expression regulation through RNAi and alternative polyadenylation

Polyadenylation signals in yeast are not very well defined and are believed to be largely degenerate. Here, we present a computational and experimental genome-wide analysis of polyadenylation signals in Schizosaccharomyces pombe (S. pombe), identifying the canonical AATAAA motif as the most frequent and functional signal. RNA-Seq data from cells grown under various physiological conditions were used to map 3’UTRs, which classify as commonly heterogenic. We have shown that many genes have alternative 3’UTRs. Our results are summarised and can be accessed in a user-friendly online database Pomb(A).
It has been shown that convergent genes require trans elements, like Cohesin, for efficient transcription termination. We demonstrate that convergent genes lacking Cohesin are generally associated with longer overlapping transcripts. Furthermore, we analysed ChIP-chip data of Rad21 and Mis4 as well as other Cohesin and loading complex subunits and show that regions of Rad21/Mis4 co-localisation are generally associated with highly transcribed genes. They are also cohesive, while sites with Rad21 only are less cohesive. Rad21/Mis4 co-localisation sites are in close proximity to annotated origins of replication, suggesting that cohesive sites may facilitate replication.
microRNAs (miRNAs) are well studies in higher eukaryotes and participate on post-transcriptional gene silencing by degrading target mRNA or blocking translation. It is believed that miRNAs do not exist in yeast. We reanalyzed miRNA presence in yeast using recently available small RNA data sets. Potential miRNA genes and targets in S. pombe were computationally predicted based on the described alternative 3’UTR data and further experimentally tested.
Dicer is an enzyme, which recognizes long dsRNA substrates and cleaves them into siRNA e↵ector molecules, essential for gene silencing. Dicer has been thought to be a purely cytoplasmic protein. However, we employed ChIP-Seq and dsRNA RNA-Seq data to show that Dicer localises in the nucleus of mammalian cells and associates with the chromatin on numerous loci. Furthermore, we present evidence that Dicer processes long dsRNA into siRNA in the nucleus and the lack of Dicer causes the accumulation of long dsRNA. This consequently induces the interferon response pathway, which ultimately leads to apoptosis and cell death.

Keywords: Human Nuclear Dicer
RNAi
Alternative Polyadenylation
Schizosaccharomyces pombe
microRNA
Cohesin
Poly(A) Signal
Advisor: Gullerova, M
Erban, R
Rasa and personhood in the Bhāgavata Purāṇa

The Bhāgavata Purāṇa is one of Hinduism's most outstanding texts composed around the 9th c. CE in south India; it is superbly written, with aesthetic sensitivity and metaphysical subtlety. In his book The Advaitic Theism of The Bhāgavata Purāṇa, Daniel Sheridan has examined the Bhāgavata Purāṇa in order to understand its religious structure, both implicit as well as explicit. This thesis aims at taking current research of the Bhāgavata Purāṇa a step forward in deciphering its doctrine, structure, and meaning.
The work first raises the question, "What are the Bhāgavata Purāṇa's literary components", and argues that the Bhāgavata Purāṇa is composed of two such groups: "Knowledge" and "Aesthetics". Knowledge is associated with direct usage of language and the conception of Impersonal Brahman, whereas aesthetics are associated with indirect usage of language and the concept of Personal Brahman. The work proceeds to look closer at the status of emotions in Indian thought, and argues that in some Indian schools, emotions are taken to possess an ontological status, and therefore are considered to reveal reality rather than obscure it. The relations of Vaiṣṇavism and dramaturgy are examined, both historically as well as theologically, and it is argued that the Bhāgavata Purāṇa has clear dramatic elements.
This thesis next proceeds to decipher the aesthetic theory underlying the Bhāgavata Purāṇa, and argues that it is Bharata's rasa theory. Two medieval positions on rasa are examined - Abhinavagupta's and Bhoja's - and it is argued that a position similar to Bhoja's underlies the text. As in Bhoja's theory it is śṛṅgāra rasa, (romantic emotions) which is considered the supreme rasa. The Bhāgavata Purāṇa's structure is highlighted, as presenting notions of personal divinity arranged in hierarchical order - from those evoking śānta rasa (tranquil emotion) to those evoking śṛṅgāra rasa. At last, four such notions are articulated; Impersonal Brahman, The Universal Person, The Person in the Heart, and the Avatāra.

Advisor: Clooney, F