VictorJuiz/thesis huggingface dataset:
Tumour vessel structural analysis and Its application in image analysis
Keywords: computer simulation on GPU
vessel image segmentation and skeletonization
vessel structure quantification
spatiotemporal pharmacokinetic modelling

Abnormal vascular structure has been identified as one of the major characteristics of tumours. In this thesis, we carry out quantitative analysis on different tumour vascular structures and research the relationship between vascular structure and its transportation efficiency.
We first study segmentation methods to extract the binary vessel representations from microscope images. We found that local phase-hysteresis thresholding is able to segment vessel objects from noisy microscope images. We also study methods to extract the centre lines of segmented vessel objects, a process termed as skeletonization. We modified the conventional thinning method to regularize the extremely asymmetrical structure found in the segmented vessel objects. We found this method is capable to produce vessel skeletons with satisfactory accuracy.
We have developed a software for 3D vessel structural analysis. This software is consisted of four major parts: image segmentation, vessel skeletonization, skeleton modification and structure quantification. This software has implemented local phase-hysteresis thresholding and structure regularization-thinning methods. A GUI was introduced to enable users to alter the skeleton structures based on their subjective judgements. Radius and inter branch length quantification can be conducted based on the segmentation and skeletonization results. The accuracy of segmentation, skeletonization and quantification methods have been tested on several synthesized data sets.
The change of tumour vascular structure after drug treatment was then investigated. We proposed metrics to quantify tumour vascular geometry and statistically analysed the effect of tested drugs on normalizing tumour vascular structure.
finally, we developed a spatio-temporal model to simulate the delivery of oxygen and 3-18 F-fluoro-1-(2-nitro-1-imidazolyl)-2-propanol (Fmiso), which is the hypoxia tracer that gives out PET signal in an Fmiso PET scanning. This model is based on compartmental models, but also considers the spatial diffusion of oxygen and Fmiso. We validated our model on in vitro spheroid data and simulated the oxygen and Fmiso distribution on the segmented vessel images.
We contend that the tumour Fmiso distribution (as observed in Fmiso PET imaging) is caused by the abnormal tumour vascular structure which is further aroused from tumour angiogenesis process. We depicted a modelling framework to research the relationships between tumour angiogenesis, vessel structure and Fmiso distribution, which is going to be the focus of our future work.
The road not taken?: a longitudinal and interdisciplinary examination of energy behaviours
Keywords: behaviour Change
environment
energy

Albert Einstein believed “we can't solve problems by using the same kind of thinking we used when we created them.” This quote, in my opinion, is particularly relevant for the academic literature that examines individual energy use. I believe that we have historically taken a categorized approach towards looking at individual energy use. Instead of thinking about multiple behaviours widely, we tend to look at individual behaviours deeply - focusing on electricity use, gas use, or travel behaviour in isolation instead of examining them simultaneously. For this reason, this thesis explores if and how an intervention aimed at one energy behaviour may influence or have untargeted effects on other energy behaviours across household energy use and personal travel behaviour from an interdisciplinary research perspective. The relevant literature is reviewed and an innovative methodology is devised to answer the research questions. By examining quantitative and qualitative data, the thesis evaluates the targeted and untargeted effects of an electricity display study across household energy and travel behaviours, assesses the influence that social and technical experiences with the display may have on behaviour, and explores how individuals conceptualize their energy usage to better understand untargeted effects. The findings indicate that 1) in a sample of 19 participants, 15 had untargeted effects in gas and 4 had untargeted effects in gas and travel, 2) the combined effect of social and technical experiences with the display can explain why an untargeted effect did or did not take place, and 3) participants perceived household energy as a resource but perceived travel as a means to move from one place to another. These findings lead to the development of a novel contribution of this research, known as the tangential effect. Contributions to theory and policy, an assessment of the methodological approach, and future research areas are given.
The anthropological construction of Czech identity: academic and popular discourses of identity in 20th century Bohemia
Keywords: Fojtik
Skalnikova
Central and Eastern Europe
Roma
narodopis
Holy
ethnology
Hubinger
folklorism
Nahodil
Niederle
etnografie

Through close textual analysis of 20th century Czech anthropological texts from the Revivalist and Socialist periods and contemporary social research conducted after the Velvet Revolution, I demonstrate certain prominent discourses of identity developed in early Bohemian anthropology and their continuities in present day popular discourses. In each period, identity is deeply intertwined with teleological theories of history with Czech populations at the apex of cultural evolutionary development. In the Revivalist period this apex was believed to be the democratic nation state, transitioning to a Marxist nation state in the Socialist period, and in the contemporary period is conceived of as a neoliberal nation state. A major function of anthropology in the Revivalist and Socialist periods was to legitimate either period’s respective teleological theory and Czech possession of relevant values as 'objective' and 'natural' fact, a general mode of discourse which continued in the contemporary period in numerous editorials in the 1990s on the advantages of capitalism. The contemporary manifestation has particularly noteworthy consequences for the Roma minority, which I argue has provided Czech discourses with an ethnic category 'anti-thetical' to their own identity, providing a 'repository' for negative Czech self-stereotypes emerging from collaboration in the Socialist period.
The profits of the past: nostalgic white writing of post-apartheid South Africa
Keywords: South African literature (English) -- White authors -- History and criticism
South African literature (English) -- 21st century -- History and criticism
Post-apartheid era -- South Africa
South African literature (English) -- 20th century -- History and criticism
Nostalgia -- South Africa
Nostalgia -- Literature

Drawing on relevant theory from memory studies, literary criticism, sociology, reception studies and book history, this thesis examines the prevalence of nostalgia in white South African writing of the post-apartheid period. It identifies the numerous and remarkably conventional texts by white authors that proliferated in this time which might be described as nostalgic, arguing that these constitute a key genre of post-apartheid South African literature. In seeking to offer an explanation for why these nostalgic forms predominated in this period, this study takes into consideration the full "communications circuit" of a book i.e. the life-cycle of a book from production to consumption. Consequently, it employs an interdisciplinary framework to examine nostalgic literature from the perspectives of both the producers and consumers of texts. It is argued, ultimately, that post-apartheid nostalgic writing was particularly involved in the protection of certain formulations and structures of whiteness at individual, collective and institutional levels.
The argument unfolds in three phases, each of which explores the value of nostalgia and nostalgic white writing in a different but related sphere: namely, literature, memory, and the market. The first phase of the argument provides a literary critical reading of the generic hallmarks of these novels, considering a range of representative texts, including works by Mark Behr, André Brink, Justin Cartwright, J. M. Coetzee, Lisa Fugard, Christopher Hope, Jo-Anne Richards, and Rachel Zadok. The second examines the allure of nostalgia and nostalgic books for the writers and readers of this literature, drawing on sociological studies of post-apartheid white South African identity and reader-response theory to analyse a selection of online and print reviews by readers. In the third phase, the thesis utilises a book historical approach to investigate the influence of various literary markets and the publishing industry, both local and global, in shaping the nostalgia trend.
Planning and exploring under uncertainty
Keywords: path planning
robotics
Gaussian processes
exploration

Scalable autonomy requires a robot to be able to recognize and contend with the uncertainty in its knowledge of the world stemming from its noisy sensors and actu- ators. The regions it chooses to explore, and the paths it takes to get there, must take this uncertainty into account. In this thesis we outline probabilistic approaches to represent that world; to construct plans over it; and to determine which part of it to explore next.
We present a new technique to create probabilistic cost maps from overhead im- agery, taking into account the uncertainty in terrain classification and allowing for spatial variation in terrain cost. A probabilistic cost function combines the output of a multi-class classifier and a spatial probabilistic regressor to produce a probability density function over terrain for each grid cell in the map. The resultant cost map facilitates the discovery of not only the shortest path between points on the map, but also a distribution of likely paths between the points.
These cost maps are used in a path planning technique which allows the user to trade-off the risk of returning a suboptimal path for substantial increases in search speed. We precompute a probability distribution which precisely approximates the true distance between any grid cell in the map and goal cell. This distribution under- pins a number of A* search heuristics we present, which can characterize and bound the risk we are prepared to take in gaining search efficiency while sacrificing optimal path length. Empirically, we report efficiency increases in excess of 70% over standard heuristic search methods.
Finally, we present a global approach to the problem of robotic exploration, uti- lizing a hybrid of a topological data structure and an underlying metric mapping process. A ‘Gap Navigation Tree’ is used to motivate global target selection and occluded regions of the environment (‘gaps’) are tracked probabilistically using the metric map. In pursuing these gaps we are provided with goals to feed to the path planning process en route to a complete exploration of the environment.
The combination of these three techniques represents a framework to facilitate robust exploration in a-priori unknown environments.
Parents' time with children: micro and macro perspectives
Keywords: Childcare
family policy
time use
parental investment

This thesis studies the dynamics of parents’ time with children. It uses self-reported time diary data to empirically document discrepancies between high- and low-educated parents’ time spent in various childcare activities. By doing so, the study considers one important but under-researched form of childhood inequality, namely inequality in parental time investment. The thesis is among the first to provide an extensive and detailed empirical documentation of variations in parents’ time use with children and to examine the effect of macro-structure and policy context on parenting behaviour. Using the American Time Use Survey (2003-2008), the thesis first investigates variations in parents’ time spent in different types of childcare among white parents in the US. Then, the American Heritage Time Use Survey (1965-2010) is employed to examine whether differences between high-and low-educated parents’ time spent with children have been growing or diminishing over time. Finally, the Multinational Time Use Survey (1965-2008) is used to explore the relationship between specific policies, macro-economic structure and childcare across time and across countries.
The results can be summarized as follows. High-educated parents provide more primary childcare for their children compared to low-educated parents. The difference is particularly acute during the early years of childhood, and the gap is particularly wide for childcare activities which are fundamentally important for the social and cognitive development of children. This parental investment gap, most notably between high-and low-educated mothers, has been widening in the US. The main source of this widening phenomenon is the steady increase in high-educated mothers’ time spent in interactive and developmental childcare activities, rather than in routine and physical childcare activities. The analysis of cross-national data shows that the strong positive effect of education on childcare is a cross-national occurrence. However, the strength of this association varies considerably across time and across countries: universal paid leave for mothers and a gender egalitarian labour market structure help alleviate the education and gender gap in childcare. Mothers provide more primary childcare as the number of available paid leave weeks increases, while fathers increase their contribution to primary childcare as the percentage of women in the labour market increases. The provision of paid leave for mothers decreases the effect of education on primary childcare, and specific family policies as well as gender egalitarian socio-economic contexts can help alleviate inequalities in parental time investment in children.
Transcranial stimulation to enhance cortical plasticity in the healthy and stroke-affected motor system
Keywords: Stroke
Transcranial magnetic stimulation
motor
resting state networks
Transcranial direct current stimulation

This thesis investigated transcranial direct current stimulation (tDCS) as applied to the motor system, and its ability to modulate underlying cortical processes and resultant motor behaviours. Functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) were employed to assess the extent to which tDCS induces quantifiable changes in neural structure and function in controls and stroke patients.
Modifications in the connectivity of intrinsic functional networks following tDCS application were examined using resting state fMRI. Polarity-specific changes were found: cathodal (inhibitory) tDCS increased the strength of the default mode network and increased functional coupling between major nodes within the motor network. No significant effects were found following anodal (excitatory) tDCS.
Although anodal tDCS elicited only subtle changes in resting activity, it is known to produce robust modifications of behaviour. Single and paired-pulse TMS were used to investigate the neurophysiological underpinnings of these changes. Consistent with the theory of homeostatic plasticity, anodal tDCS applied prior to task performance increased GABAA-mediated cortical inhibition and worsened behaviour. The specificity of these changes suggests a central role for the mechanism of surround inhibition.
A longitudinal clinical trial in chronic stroke patients was conducted to determine the utility of tDCS as an adjunct in motor rehabilitation. Serial MRI scans revealed that, when combined with motor training, anodal tDCS increased functional activity and grey matter in primarily ipsilesional motor areas. These brain changes were correlated with behavioural improvements in the stroke-affected upper limb.
The laterality of connectivity at baseline, as measured by resting state activity and corticospinal tract integrity, was predictive of response to the rehabilitation program, particularly in those stroke patients who received tDCS. Asymmetry favouring the contralesional hemisphere predicted greater behavioural gains. Such results underscore the importance of re-normalisation of structure and functional activity toward the lesioned hemisphere in stroke rehabilitation.
The magnetoencephalographic signature of catechol-O-methyltransferase
Keywords: magnetoencephalography
neuroscience
catechol-o-methyltransferase

Catechol-O-methyltransferase (COMT) metabolizes catechols, notably dopamine. The COMT Val158Met polymorphism influences its enzyme activity, and multiple neural correlates of this genotype on dopaminergic phenotypes have been reported, particularly with regards to working memory. COMT activity can also be regulated pharmacologically by COMT inhibitors. The ‘inverted-U’ relationship between dopamine signalling and cognitive performance predicts that the effects of COMT inhibition will differ according to COMT genotype. The goal of this thesis was to better understand COMT’s impact on brain function and behaviour. Here, 33 subjects homozygous for COMT Val158 (‘Val homozygotes’) and 34 homozygous for COMT Met158 (‘Met homozygotes’) were randomly assigned, double-blind, to a single dose of the brain-penetrant COMT inhibitor tolcapone (200mg) or placebo. They completed the N-back task of working memory, an emotional face processing task, and a gambling task, in a magnetoencephalography (MEG) scanner, allowing both behavioural performance and neural activity to be investigated. The data presented in this thesis confirm that COMT activity influences performance on, and neural activity during, the N-back task, in a way consistent with the inverted-U model of dopamine function. The effect on risky decision making is novel, and indicates that COMT plays roles in domains beyond working memory, and that such domains may also follow an inverted-U. Neural activity during the faces task and the gambling task also show COMT-modulated differences. The behavioural results show that the direction of effect of a drug can be influenced by sequence variation in its target gene. They are of translational relevance, since COMT inhibitors are used in the adjunctive treatment of Parkinson’s disease and are under evaluation in schizophrenia and other disorders. The MEG data show that for the three tasks, there are effects of Val158Met genotype, of tolcapone, and their interaction, on neural activity (for example, the P300 during N-back), revealing a complex temporal and spatial pattern which sheds some light on the neural processing underlying these tasks and their previously reported fMRI correlates.
Human layout estimation using structured output learning
Keywords: structured output learning
multiclass classification
computer vision
structured ranking
machine vision
human layout
hand detection
machine learning
artificial intelligence

In this thesis, we investigate the problem of human layout estimation in unconstrained still images. This involves predicting the spatial configuration of body parts.
We start our investigation with pictorial structure models and propose an efficient method of model fitting using skin regions. To detect the skin, we learn a colour model locally from the image by detecting the facial region. The resulting skin detections are also used for hand localisation.
Our next contribution is a comprehensive dataset of 2D hand images. We collected this dataset from publicly available image sources, and annotated images with hand bounding boxes. The bounding boxes are not axis aligned, but are rather oriented with respect to the wrist. Our dataset is quite exhaustive as it includes images of different hand shapes and layout configurations.
Using our dataset, we train a hand detector that is robust to background clutter and lighting variations. Our hand detector is implemented as a two-stage system. The first stage involves proposing hand hypotheses using complementary image features, which are then evaluated by the second stage classifier. This improves both precision and recall and results in a state-of-the-art hand detection method. In addition we develop a new method of non-maximum suppression based on super-pixels.
We also contribute an efficient training algorithm for structured output ranking. In our algorithm, we reduce the time complexity of an expensive training component from quadratic to linear. This algorithm has a broad applicability and we use it for solving human layout estimation and taxonomic multiclass classification problems.
For human layout, we use different body part detectors to propose part candidates. These candidates are then combined and scored using our ranking algorithm. By applying this bottom-up approach, we achieve accurate human layout estimation despite variations in viewpoint and layout configuration. In the multiclass classification problem, we define the misclassification error using a class taxonomy. The problem then reduces to a structured output ranking problem and we use our ranking method to optimise it. This allows inclusion of semantic knowledge about the classes and results in a more meaningful classification system.
Lastly, we substantiate our ranking algorithm with theoretical proofs and derive the generalisation bounds for it. These bounds prove that the training error reduces to the lowest possible error asymptotically.