VictorJuiz/thesis huggingface dataset:
A system-level approach to single-molecule live-cell fluorescence microscopy

In this work a system-level approach was taken to the single-molecule fluorescence microscopy of living cells. This primarily involved the unification of relevant information within appropriately structured artefacts that were used to inform and enhance experimentation.
Initially the diversity of emerging single-molecule techniques was reviewed and presented with a novel article structure to suit the purpose of designing an experiment (Harriman and Leake 2011). Techniques were grouped by the type of information they could access, rather than the standard organisation centred on the techniques themselves.
A bespoke microscope was conceived and built with reference to knowledge and tools from the fields of Architecture and Systems-Engineering. The microscope layout would enable multiple experiment types through independent control of multiple illumination beams. A technique was developed enabling the prescription of evanescent field penetration depth for each incident beam.
The various empirical and theoretical results that are used to understand and modify a microscopy experiment were integrated into an internally consistent simulation model (Harriman and Leake. 2013). This was used to inform the selection of experimental components and parameters and ultimately acquire higher data quality as measured by functions such as signal-to-noise ratio (SNR).
The combined experimental system of microscope and simulation model was applied in two live-cell investigations. In Escherichia coli, the spatial distribution of membrane bound proteins was investigated and a novel technique was applied to the analysis of colocalisation. Results indicate that NADH dehydrogenase and ATP synthase follow uncorrelated trajectories. This supports the hypothesis of spatial decoupling of molecules that energise the membrane and molecules that use membrane energy.
In human carcinoma cells, the mechanism of ligand-receptor binding was investigated. Data was collected prior to and periodically after the addition of ligands, and fluorescence images were acquired of both ligands and receptors. Analyses based on single particle tracking are currently being carried out by a collaborator to extract information on stoichiometry and dynamics at the single-molecule level.

Keywords: single-molecule
fluorescence
optics
colocalisation
Advisor: Leake, M
Outcome reporting bias in randomised trials

Background
Selective reporting of outcomes within a published study based on their nature or direction can result in systematic differences between reported and unreported data. Direct evidence of outcome reporting bias is limited to case reports.
Objective
To study empirically the nature of outcome reporting bias in randomised controlled trials (RCTs).
Methods
Three cohorts of RCTs were identified: PubMed-indexed RCTs published in December 2000; trial protocols approved by a Danish ethics committee from 1994-95; and trial protocols funded by a government agency in Canada from 1990-98. Data on reported and unreported outcomes were recorded from all trial publications and a survey of authors. An outcome was considered incompletely reported if insufficient data were presented for meta-analysis. Odds ratios relating the completeness of outcome reporting to statistical significance were calculated for each trial, and then pooled using a random effects meta-analysis. Protocols and publications were also reviewed for discrepancies in primary outcome reporting.
Results
519 trials with 10,557 outcomes, 102 trials with 3613 outcomes, and 48 trials with 1390 outcomes were identified for the PubMed, ethics committee, and funding agency cohorts respectively. 22%-35% of outcomes per parallel group study were, on average, incompletely reported for meta-analysis. Fully reported outcomes had a two- to three-fold higher odds of being statistically significant compared to incompletely reported outcomes. The most common reasons given for omitting outcomes included a lack of clinical importance, lack of statistical significance, and space constraints. Major discrepancies between primary outcomes in protocols and publications were found in one half of trials.
Discussion and conclusions
The reporting of trial outcomes is frequently inadequate for meta-analysis; is biased to favour statistical significance; and is inconsistent with pre-specified protocol outcomes. Unacknowledged modifications to outcomes specified in trial protocols constitute scientific misconduct. Meta-analyses may therefore produce inflated and unreliable estimates of treatment effect.

Advisor: Altman, D
Models for adaptive feeding and population dynamics in plankton

Traditionally, differential-equation models for population dynamics have considered organisms as "fixed" entities in terms of their behaviour and characteristics. However, there have been many observations of adaptivity in organisms, both at the level of behaviour and as an evolutionary change of traits, in response to the environmental conditions. Taking such adaptiveness into account alters the qualitative dynamics of traditional models and is an important factor to be included, for example, when developing reliable model predictions under changing environmental conditions. In this thesis, we consider piecewise-smooth and smooth dynamical systems to represent adaptive change in a 1 predator-2 prey system.
First, we derive a novel piecewise-smooth dynamical system for a predator switching between its preferred and alternative prey type in response to prey abundance. We consider a linear ecological trade-off and discover a novel bifurcation as we change the slope of the trade-off. Second, we reformulate the piecewise-smooth system as two novel 1 predator-2 prey smooth dynamical systems. As opposed to the piecewise-smooth system that includes a discontinuity in the vector fields and assumes that a predator switches its feeding strategy instantaneously, we relax this assumption in these systems and consider continuous change in a predator trait.
We use plankton as our reference organism because they serve as an important model system. We compare the model simulations with data from Lake Constance on the German-Swiss-Austrian border and suggest possible mechanistic explanations for cycles in plankton concentrations in spring.

Keywords: population dynamics
dynamical systems in biology
Filippov systems
bifurcations of limit cycles and periodic orbits
planktonic protozoa-algae dynamics
Lotka-Volterra interaction
Advisor: Porter, M
Maini, P
Theoretical investigations of polyhedral inorganic molecules

This Thesis describes some theoretical studies on cluster compounds of the main group and transition metal elements.
Chapter 1 presents a review of the theoretical aspects of cluster chemistry. Three major theoretical approaches are identified, namely the localised, delocalised and free electron models and their historical development is described.
The research described in this Thesis is based on extensions of Stone's Tensor Surface Harmonic (TSH) methodology, supported by Extended Huckel molecular orbital calculations. In Chapter 2, the TSH approach is used to describe the skeletal bonding in 3- and 4-connected polyhedral clusters. Like the deltahedral clusters, 4-connected molecules are generally characterised by (n+1) Skeletal Electron Pairs (SEP's). 3- connected clusters, however, possess 3n/2 SEP's. This difference is attributed to the occurrence of additional non-bonding orbitals in the 3-connected case.
In Chapter 3, the bonding in a novel class of deltahedral metallaborane clusters is discussed. These hyper-closo or iso-closo species are studied from a fragment orbital viewpoint, regarding the structures as metal-capped fragments of a borane icosahedron. In this way, the problem of whether these clusters possess n or (n+1) SEP's is studied for n=9, 10 and 11.
Although most deltahedral clusters conform to the (n+1) SEP rule, there are a significant number which do not. In Chapter 4, these deviations are rationalised from a group theoretical/topological viewpoint. A group theoretical paradigm is developed which simplifies the derivation of the frontier orbitals for these molecules.
Chapter 5 extends the TSH methodology to clusters with bispherical topologies. To discuss these clusters, the TSH wavefunctions are modified to include radial, as well as angular nodes. The methodology is also applied to clusters with toroidal topologies, where the capping atoms form a ring around the equator of the inner cluster sphere.
The bonding in π-donor- and π-acceptor-bridged clusters of the transition metals are compared in Chapter 6. Although the symmetry aspects are identical and lead to similar bonding patterns, the ir-donor clusters are characterised by a number of unoccupied dδ-based orbitals. The bonding in a series of closo, nido and arachno π-donor clusters, based on edge- and face-bridged octahedral molecules is considered and a relationship between the cluster electron count and the number of unavailable dδ-based orbitals is identified.

Advisor: Mingos, D
Mingos, M
Controlled synthesis and properties of layered double hydroxides

The aims of this thesis are concerned with the synthesis of layered double hydroxide nanoparticles with controlled morphology and particle size distribution and an investigation of their physical properties. An introduction of layer double hydroxide chemistry, especially existing synthetic approaches, is reviewed in Chapter 1. Structural investigations, characterisation techniques, the properties and the applications of LDHs are discussed consecutively.
The first successful synthesis of lithium aluminium nanorods using the hydrothermal treatment of a gibbsite precursor with a rod-like morphology is described in Chapter 2. The rod morphology is depicted using electron microscopy and confirmed by comparing refined X-ray diffraction patterns to a standard sample.
Chapter 3 describes the application of reverse microemulsion method to prepare Co-Al and Ni-Al LDH nanoplatelets. The LDH particle sizes can be effectively controlled, and the structures of the nanoplatelets are investigated. The magnetic properties of the LDH nanoplatelets are dependent on the size of the nanoplatelets.
A novel single component microemulsion system for the synthesis of LDHs is developed in Chapter 4. Mg-Al LDH nanoplatelets were successfully synthesised with precise particle size control. The factors affecting the formation of the microemulsions and the mechanism of the synthesis are discussed.
Chapter 5 focuses on the applications of the novel single component microemulsion methods to prepare a range of LDHs with different metal combinations including Co-Al, Ni-Al, Zn-Al, Li-Al, Ca-Al, and Ni-Fe. This method proves very effective at controlling the particle sizes. The magnetic properties of the LDHs containing paramagnetic transition metal centres have been studied in detail.
In Chapter 6, the DIFFaX program has been used to simulate the XRD patterns of layered structures. The factors influencing the XRD patterns in these materials have been systematically investigated including the effects of particle size, stacking faults, and disorder. The XRD patterns of materials described in previous chapters are simulated using the latest DIFFaX+ code in order to estimate the particle sizes and stacking sequences.
The characterising techniques and the experimental details are listed in Chapter 7.

Keywords: DIFFaX
reverse micelle/microemulsion
LDH
Advisor: O'Hare, D
Segmentation and sizing of breast cancer masses with ultrasound elasticity imaging

Uncertainty in the sizing of breast cancer masses is a major issue in breast screening programs, as there is a tendency to severely underestimate the sizing of malignant masses, especially with ultrasound imaging as part of the standard triple assessment. Due to this issue about 20% of all surgically treated women have to undergo a second resection, therefore the aim of this thesis is to address this issue by developing novel image analysis methods. Ultrasound elasticity imaging has been proven to have a better ability to differentiate soft tissues compared to standard B-mode. Thus a novel segmentation algorithm is presented, employing elasticity imaging to improve the sizing of malignant breast masses in ultrasound. The main contributions of this work are the introduction of a novel filtering technique to significantly improve the quality of the B-mode image, the development of a segmentation algorithm and their application to an ongoing clinical trial. Due to the limitations of the employed ultrasound device, the development of a method to improve the contrast and signal to noise ratio of B-mode images was required. Thus, an autoregressive model based filter on the radio-frequency signal is presented which is able to reduce the misclassification error on a phantom by up to 90% compared to the employed device, achieving similar results to a state-of-the art ultrasound system. By combining the output of this filter with elasticity data into a region based segmentation framework, a computationally highly efficient segmentation algorithm using Graph-cuts is presented. This method is shown to successfully and reliably segment objects on which previous highly cited methods have failed. Employing this method on 18 cases from a clinical trial, it is shown that the mean absolute error is reduced by 2 mm, and the bias of the B-Mode sizing to underestimate the size was overcome. Furthermore, the ability to detect widespread DCIS is demonstrated.

Keywords: medical image analysis
ultrasound
breast cancer
elasticity imaging
Advisor: Noble, JA
The invention of the new culture movement in 1919

The expression ‘New Culture Movement’ was born in summer 1919, in the intersections of academic debate, political activism, media coverage and intellectual marketing strategies. I have traced the emergence of the phrase and the discourses around it, using sources like journals, newspapers, student essays, advertisements and conference protocols.
The New Culture Movement was a buzzword, deployed by practically-minded but lesser-known intellectuals to promote agendas they had held long before its invention. Many notions we associate with the Movement until today already surrounded it in 1919: for example, that it was connected to the political protests of ‘May Fourth,’ and driven by star intellectuals such as Hu Shi and Chen Duxiu. But closer scrutiny reveals that the New Culture Movement and its network of associations were a construct, an amalgam of newspaper stories and intellectual marketing ploys: the connection to May Fourth was created by newspapers; the intellectuals at the periphery drew upon Hu Shi’s and Chen Duxiu’s prestige to add glamour to their own agendas. Nevertheless, the New Culture Movement shaped China’s 20th century. As only some agendas could credibly be sold as the Movement, it catalysed the plethora of competing agendas that had emerged since the 19th century to tackle the challenges of a changed world order.
The New Culture Movement later became a founding myth of ‘Modern China’ and was regarded as the obvious result of global trends towards ‘modernisation,’ which visionary intellectuals recognised. But more recent literature has decentred the Movement, noted a longer history of its ideas and the careerism of its participants. I drive this point further by showing that, at the Movement’s very core, were practically-minded business and marketing strategies, deployed by numerous, lesser-known actors. It was in this way that the course for 20th-century China and one of its founding myths was set.

Keywords: Chinese newspapers
1919
baihua
May Fourth Movement
Chinese history
New Culture Movement
Republican Period
Advisor: Ditmanson, P
Renewable natural resources planning for regional development with special reference to Kashmir

Natural resources are part of the social capital. It is useful to classify them in relation to their use by man. Renewable resources can be used and yet perpetuated at a given Isvel of quantity and quality. They include the attributes of soil and landscape, the btotic and water resources. Minerals and fossil fuels, on the other hand are depleted through use. They are non-renewable resources.
Renewable resources, together with man, comprise a dynamic bio-system. Any usage of resources affects the system and, in turn, society and vice versa. The resource uses considered here are agriculture, horticulture, forestry, grazing, and watershed protection. These uses embrace an area's rural sector. This includes that part of the output of goods and services and of employment in the economy which depends on the use of land conceived as a natural resource. A conjoint consideration of all the above uses is required to adapt an area's resource-use pattern to society's needs. For this, case studies are needed. This Investigation pertains to Kashmir valley in north India.
The role of renewable resources in development is analysed in chapter II. This provides a conceptual background.
In a poor region like Kashmir, renewable resources have an important place in catalysing development. This involves the transformation of the available renewable resource capital, such as forests, into more productive forms. Additionally, the effects of the increasing man/land ratio can be offset through an intensification of land-use.
A conservationist policy, which impedes the above process, is unhelpful to economic development. The policy should be to economizeon scares man-made capital and skills. They may be combined with larger doses of underutilized renewable resources and unskilled labour. The question in development is not of locking up the social capital for posterity or of canalising society's limited resources into one or the other sector. It is of allocating resources to most productive opportunities.
The planning method evolved here consists of synthesising biotechnical, economic and institutional analyses. The analytical stages do not rigidly follow this order; for, in practice, one analysis has feed-back effects on another.[See text for remainder of abstract].
Clash of organisational cultures?  A comparative analysis of American and British approaches to the coordination of defence, diplomacy and development in stability operations, 2001-2010

This thesis examines the challenge of coordinating civilian and military efforts within a so-called ‘whole-of-government’ approach to stability operations. The empirical analysis focuses on British and American attempts to implement an integrated civilian-military strategy in Afghanistan and Iraq between 2001 and 2010. Unlike many existing analyses, the thesis consciously avoids jumping to the search for solutions to fix the problem of coordination and instead offers a nuanced explanation of why it arises in the first instance. Empirical data was gathered through personal interviews with a wide range of civilian and military practitioners between 2007 and 2011. Together with the in-depth study of official documents released by, and on, the defence, diplomatic and development components of the British and American governments, they provide the basis for a fine-grained analysis of obstacles to interagency coordination.
The thesis offers a framework for analysis that is grounded in organisation theory and distinguishes between material, bureaucratic and cultural dimensions of obstacles to interagency coordination. It identifies organisational cultures as a crucial force behind government agencies’ reluctance to participate and invest in an integrated approach. The empirical chapters cover interagency dynamics within the government bureaucracy and in operations on the ground, including the role of specialised coordination units and Provincial Reconstruction Teams in the pursuit of coordination. The thesis concludes that stabilisation remains an inherently contested endeavour for all organisations involved and that the roles and expectations implied by contemporary templates for coordination clash with prevailing organisational identities and self-perceptions. These findings caution against the procedural and technocratic approach to interagency coordination that permeates the existing literature on the subject and many proposals for reform. While the thesis examines a specific empirical context, its conclusions have broader implications for civilian-military coordination and the quest for an integrated approach to security in the twenty-first century.

Keywords: post-conflict reconstruction
civil-military relations
state-building
Advisor: Caplan, R
Scheipers, S
Vital sign monitoring and data fusion for paediatric triage

Accurate assessment of a child’s health is critical for appropriate allocation of medical resources and timely delivery of healthcare in both primary care (GP consultations) and secondary care (ED consultations). Serious illnesses such as meningitis and pneumonia account for 20% of deaths in childhood and require early recognition and treatment in order to maximize the chances of survival of affected children. Due to time constraints, poorly defined normal ranges, difficulty in achieving accurate readings and the difficulties faced by clinicians in interpreting combinations of vital signs, vital signs are rarely measured in primary care and their utility is limited in emergency departments.
This thesis aims to develop a monitoring and data fusion system, to be used in both primary care and emergency department settings during the initial assessment of children suspected of having a serious infection. The proposed system relies on the photoplethysmogram (PPG) which is routinely recorded in different clinical settings with a pulse oximeter using a small finger probe. The most difficult vital sign to measure accurately is respiratory rate which has been found to be predictive of serious infection. An automated method is developed to estimate the respiratory rate from the PPG waveform using both the amplitude modulation caused by changes in thoracic pressure during the respiratory cycle and the phenomenon of respiratory sinus arrhythmia, the heart rate variability associated with respiration. The performance of such automated methods deteriorates when monitoring children as a result of frequent motion artefact. A method is developed that automatically identifies high-quality PPG segments mitigating the effects of motion on the estimation of respiratory rate.
In the final part of the thesis, the four vital signs (heart rate, temperature, oxygen saturation and respiratory rate) are combined using a probabilistic framework to provide a novelty score for ranking various diagnostic groups, and predicting the severity of infection in two independent data sets from two different clinical settings.

Keywords: Photoplethysmogram
Novelty Detection
Vital Signs
Breathing Rate
Pulse Oximeter
Respiratory Rate
Paediatric Triage
Physiological Monitoring
Advisor: Tarassenko, L