VictorJuiz/thesis huggingface dataset:
Reliable and spectrally efficient encoding and modulation techniques
Keywords: spectral efficiency
reliability
encoding
maximum distance separable codes
orthogonal frequency division multiplexing (OFDM)
index modulation
modulation

Due to remarkable growth in mobile data traffic, intelligent devices, and connectivity, the need for spectrally/energy efficient and reliable communication systems increases day by day. Moreover, to meet the fast-growing demand for data communication and massive connectivity, next-generation networks will require to deploy more advanced modulation techniques than the existing ones. In this respect, index modulation (IM) and its combinatorial encoding structure have gained considerable popularity thanks to their attractive advantages, including low-complexity implementation, better error performance, and improved energy/spectral efficiency over conventional modulation and multiplexing schemes. Although IM is a potential candidate for the next-generation networks due to its beneficial properties, one needs to design more reliable and spectrally efficient modulation techniques to satisfy the requirements of the next-generation networks. Therefore, this thesis investigates reliable and spectrally efficient encoding and modulation techniques, proposing novel designs based on combinatorial and well-known encoding mechanisms. Our designs uncover novel applications of combinatorial tools such as set partitioning and composition in encoding. The resulting concepts are general modulation methods, which comprehend the classical and IM techniques as particular cases. They also exhibit a better error performance and higher achievable rate than the IM and classical modulation techniques, making them a better candidate for future wireless networks. Apart from the combinatorial framework, we exploit a simple maximum distance separable code to show the actual potential of the IM and related schemes as well as design a modulation concept that achieves better error and achievable rate performance than the classical and combinatorial methods while exhibiting a low-complexity structure.
Theory and application of PBPK modelling in drug development: the double-edged sword of complexity
Keywords: compartment lumping
secondary lymphoid tissue
model reduction
cell-based therapy
PBPK modelling
monoclonal antibody
model simplification
physiology

Physiologically-based pharmacokinetic modelling has become an integral part of model-informed drug development. However, the extensive structure and parameterisation of such models may give rise to issues with model identifiability, parameter estimation and model analysis techniques. In this thesis, we examine the strengths and limitations of whole-body physiologically-based pharmacokinetic models in regard to their complexity by investigating methods of extracting information from such models in clinically relevant applications with limited or no data, as well as how the complexity may be managed in practice. We first address the gaps in the quantitative understanding of the immunological role of the spleen. We do this by assessing how in silico splenectomy affects T cell distribution and bioavailability of T cells in the secondary lymphoid tissue in human. Based on the predicted lack of significant difference in the T cell concentration in secondary lymphoid tissue, we conclude that the remaining tissue is predicted to have insufficient cellular and trafficking capacity to compensate for immune functions normally mediated by the spleen. We then discuss the potential limitations of single versus multiple lymph node compartment models in the development of immunotherapeutic modalities. Illustrating the concept by comparing two models with different lymph node compartmentalisation, we show how the choice of the number of lymph node compartments affects the model predictions and, thus, how its application dictates the necessary level of detail in the model. Finally, we propose a model describing the deposition, pharmacokinetics and pharmacodynamics of anti-CD20 monoclonal antibodies administered intravenously and subcutaneously, and analyse the model’s identifiability in the context of clinical data format. We fit the model to antibody blood data and show that the model predictions are consistent with the current knowledge on the mechanism of action of anti-CD20 antibodies. We further discuss the data needed for the framework to facilitate consideration of efficacy- and safety-related problems. The thesis concludes with a discussion of the results in the context of model-based drug development, regulatory perspective and the extent to which physiologically-based mathematical models can contribute toward insight and decision support for therapeutic development.
Quantitative histology for assessing organ health
Keywords: histopathology
transplant
computer vision
histology
machine learning
image analysis
deep learning

This thesis aims to take the first step in developing a quantitative analysis workflow for characterising histological changes in pre-implantation renal biopsies. Solving this is highly beneficial as there is a significant disparity between organ supply and demand worldwide. It can also help to alleviate the workload caused by a shortage of pathologists. This work would allow quantitative measurement of histological features related to chronic and acute injuries in pre-implantation biopsies. These features can then be linked to scores given by pathologists, post-transplant clinical endpoints, and proteomic biomarkers to help researchers better understand the mechanisms of organ injury and repair.
First, we build the main feature extraction workflow based on convolutional neural networks (CNN) to automatically segment different tissue compartments in renal biopsies. We design handcrafted features and qualitatively show that some of these features can capture visual changes related to chronic and acute injuries.
Then, we find that many tissue compartments in the primary dataset have artefacts not present in the training data. We discuss Bayesian Neural Networks (BNNs) to quantify uncertainties in segmentation and propose a way to improve histological estimates.
Next, we propose using tissue compartment-based features to improve classification and interpretability in a multi-instance learning setting. In addition to learned attention, tissue compartments are weighted by segmentation quality to reduce the impact of instances that bear little resemblance to the training data.
Finally, we combine techniques developed in this project to detect acute injuries from biopsies. We propose an algorithmic score consisting of models trained on pathologists’ assessments and donors’ clinical states. The score is significantly associated with Delayed Graft Function (DGF) in the test data.
These findings suggest that our workflow can facilitate research in kidney transplant where pathologist time is limited. It also shows histology has great potential in predicting post-transplant complications.
Animals in Vedic prose
Keywords: Vedic prose
animals
mr̥ga
paśu
Vedic
human-animal relationship
Veda

This thesis examines a well-known axiom of ancient Indian thought: the human being is classified as one of the five domestic animals, paśu. Although this notion is well-known, often mentioned in secondary literature, it has not yet received a comprehensive, scholarly treatment. Drawing on the detailed philological and textual-historical study of the Vedic poetry and prose, this thesis explores the classification of the human as a domestic animal, as well as the categories of “animality” and “humanity” more broadly.
The thesis is composed of three core chapters. The first discusses the semantic history of the three most common Vedic animal terms: paśu, mṛga, and the antonymic dyad, grāmya and āraṇya paśu. As well as introducing the terms in a broad context, it argues that their evolution documents the transition of Vedic lifestyle from semi-nomadic pastoralism to agricultural sedentism.
Building on this, the second and third chapters explore the position of the human being within the paśu group. The second chapter discusses similarities and differences between the human and the rest of the group, in terms of both body and behaviour. The Vedic corpus suggests, however, that in the mythical past, people and domestic animals used to look and behave alike: just like people, domestic animals walked on two-feet, exercised agency, and sacrificed. I argue that this common history indicates that the species of paśus are mutually “related”. There is a sense of what I call “ontological proximity”: an entangled existence driven by a shared history and mutual care. The third chapter further investigates the notion of “ontological proximity” by way of detailed reading of two mythical narratives from the Vedic Brāhmaṇas, arguing that this idea is clearly present and used creatively in Vedic animal imagery.
Singularity formation, existence and regularity for degenerate Cahn-Hilliard equations
Keywords: singularity
partial differential equations
asymptotic expansions
nonlinear equation
touchdown
pinch-off

Cahn-Hilliard models are central for describing the evolution of interfaces in phase separation processes and free boundary problems. In general, they have non-constant and often degenerate mobilities. However, in the latter case, the spontaneous appearance of regions of vanishing mobility and their impact on the solution are not well understood. In this work, we study the axially symmetric 2-dimensional setting, and develop a singular perturbation theory to identify a range of degenerate mobilities for which the solution forms a singularity in infinite time. Moreover, we obtain two different approximate self-similar profiles which divide this range of degeneracies into two. We complement this approach by adapting the known theory for degenerate parabolic partial differential equations and Sobolev spaces of radial functions to obtain the existence and regularity of a weak radially symmetric solution. This is an improvement from the weak existence for the degenerate Cahn-Hilliard equation obtained previously, which does not ensure symmetry. Finally, we raise conjectures on the strict boundedness of the solution, which would restrict the formation of singularities.
Mathematical modelling of platelet production
Keywords: bioreactor
asymptotics
proplatelets
mathematical modelling
fluid dynamics
platelets

Hospitals sometimes experience shortages of donor blood platelet supplies, motivating research into in vitro production of platelets. We use mathematical modelling to study platelet production.
First, we model the flow in a novel platelet bioreactor described by our collaborators in Shepherd et al. The bioreactor consists of an upper channel, a lower channel, and a cell-seeded porous collagen scaffold situated between the two. Flow is driven by gravity, and controlled by valves on the four inlets and outlets. The bioreactor is long relative to its width, a feature which we exploit to derive a lubrication reduction of the Navier-Stokes equations in the channels coupled to Darcy flow in the scaffold.
We first consider the quasi-steady regime, with slowly-moving valves, before incorporating inertia in two regimes: one to study small amplitude valve oscillations, and one to study order one amplitude valve oscillations. The former is a systematic reduction; the latter incorporates a phenomenological approximation for the cross-sectional flow profile. To achieve clinically and commercially viable yields of platelets, our collaborators will need to be able to finely control the fluxes and shear stresses in the bioreactor. Thus we use our model to predict how fluxes and shear stresses may be controlled using bioreactor valve dynamics and geometrical parameters.
Next, we study platelet production at the cellular level, modelling an intermediate stage of proplatelet formation. During this stage, pseudopodia (called proplatelets) elongate from the body of the platelet-producing cell, and platelets form along the proplatelets. Shear stress from external flow enhances both the proplatelet elongation and platelet formation rates, though it is unknown whether this enhancement is due to purely mechanical effects, or whether mechanotransductive effects are involved. We construct two models to investigate the dynamics of proplatelet elongation and to compare these two possible mechanisms, by assessing their effects on the shape and elongation rate of a single proplatelet. The first model uses active gel theory to model the cytoskeleton-powered proplatelet elongation, and resistive force theory to model the drag between external flow and the proplatelet. The second model uses the method of regularised Stokeslets to characterise the flow around proplatelets tethered to a wall in a half-space, with each proplatelet described as an inextensible elastic rod. The models provide computationally-light bases into which future experimental hypotheses may be incorporated.
Be fruitful and multiply? Anglican efforts to control fertility in interwar England
Keywords: Secularization
Birth control
Eugenics
Birthrate
Church of England
Neo-Malthusianism

This thesis examines the moral justification offered by Anglican leaders for their support for eugenic, pronatalist, and neo-Malthusian schemes between the First and Second World Wars. It argues that Anglican leaders comprehended their widespread efforts to control fertility within the context of a broader struggle over competing conceptions of human purpose in English society, and that these women and men regularly justified their efforts on the grounds that fertility-manipulation schemes served to align procreative behaviours with ‘Christian’ conceptions of human purpose. Additionally, this thesis argues that key aspects of the shared moral logic of Anglican leaders can help to explain the pervasive interest in birthrate patterns, along with the enduring appeal of fertility-manipulation schemes, amongst middle- and upper-class men and women of varying religious and political persuasions in England, as well as across Europe and North America, during the first half of the twentieth century. Furthermore, it sheds light on how population concerns led to the liberalization of Church of England teachings on marriage, sexuality, and procreation, and also provides a qualitative contribution to the historiography on secularization by illuminating how Anglican leaders sought to maintain moral influence in the face of perceived large-scale rejection of Christian moral teachings.
Set against a backdrop of rapidly declining birthrates, this thesis has five main chapters, and it is arranged chronologically and thematically. Chapter One explains why Anglican leaders believed procreative behaviours fell under the purview of the Church of England, which functioned as one of the leading moral voices in English society, and Chapter Two elucidates why Anglican leaders believed married couples were having an ‘incorrect’ number of children. The final three chapters explore, in order, the moral justification for various efforts aimed at controlling the fertility of specific socio-economic classes, the ‘mentally unfit,’ and the vast majority of the English populace.
Perceptions of Paraguayan teachers from different socio-economic contexts about the use of technology in the classroom to foster critical thinking skills
Keywords: low SES
high SES
Paraguay
CTS
Critical Thinking
low-income schools
Educational technologies
Critical Thinking Skills
high-income schools
EdTech
Paraguayan education

Critical thinking has become a required and highly valuable skill in the academic and professional environment. For that reason, the development of this ability is nowadays a major topic of discussion in the academic and educational sphere. New educational policies mainly focused on the enhancement of critical thinking skills (CTS) are being elaborated for schools and universities. These policies include the use of EdTech since studies suggest that its use helps to foster CTS in the classroom. However, this data is not definitive because many other variables can influence or interfere. Scholars have emphasised the importance of the context-specific study, and there is relatively little research evidence that focuses specifically on the Paraguayan context. Therefore, to contribute to the literature, this study focused on the perceptions of Paraguayan teachers from different contexts about the relationship between EdTech and CTS. One group of teachers work in ICT well-equipped classrooms (Smartboard, surrounding sound system, Wi-Fi, and more) and the other in a traditional setting (classroom with chairs and whiteboard). These teachers were interviewed individually to know what their thoughts are regarding the use of EdTech and Critical thinking development according to their experience. The findings suggest teachers from the low-SES context are more optimistic about the use of technology to improve the learning experience and foster CTS, while teachers from the high-SES context have a more critical and neutral approach toward the use of technology in the classroom.
Instruction, devotion, meditation, sermon : a critical edition of selected English religious texts in Oxford, University College 97 with a codicological examination of some related manuscripts
Keywords: codicological
sermons
critical edition
University College 97
meditation
devotion
Oxford
Christian literature
English religious texts
sermon
religious literature
religious texts
manuscripts
Middle English

The thesis is comprised of an edition of thirteen Middle English religious texts found in the three earlier 'booklets' of Oxford, University College 97. The texts cover a range of genres including instructional, devotional, meditational and homiletic texts. Each text has been critically edited withfull apparatus, including a textual analysis of the manuscripts edited.
The texts edited from the first booklet are: 'An Exposition on The Ten Commandments', 'The Seven Commandments of the New Testament', 'The Visitation of the Sick', and 'An Exposition on the Diliges Dominum Deum Tuum'. Texts from the second booklet edited are: 'A Treatise on the Two Ways by Sir John Clanvowe' and 'An Exposition on the Pater Noster in Short.' The remaining texts edited come from the third booklet: 'The Twelve Articles of the Faith', 'The Mirror of Sinners', 'A Meditation of the Five Wounds of Jesus Christ', 'A Good Meditation for One to say Alone', 'The Meditation of St Anselm', 'Of Three Arrows that shall be shot on Domesday', and finally, 'A Sermon by John Gregory, Austin Friar of Newport.'
The introductory chapter to the critical edition examines the availability of exemplars, the dissemination of texts via booklets, the personal tastes of the compiler and the utility of the texts, all factors which may have influenced the compiler/owner in his choice of texts for each booklet and for the entire manuscript. The first portion discusses the dissemination patterns for the texts based on the textual analyses from the critical edition and a codicological examination of the other manuscripts involved. The second portion examines the literary content and practical function of the texts, the thematic coherence of the texts within each booklet and within the three booklets as a whole.
The thesis also includes a detailed description of Oxford, University College 97, a selective catalogue from the 54 manuscripts collated and a glossary.
Autocratic legacies and immunisation against extremism: a rational choice approach
Keywords: authoritarianism
political economy

Why do some post-transitional democracies have extremist parties associated with the former regime, while others have mainstream parties associated with the former regime, and yet others have no parties associated with the former regime?
Using a rational choice theoretical approach, in this dissertation I show that the “self-interested” relationship between the general population and autocratic incumbents, operating through a top-down logic of reception of various kinds of material benefits provided by autocratic policy outputs, are crucial factors in shaping post-transitional attitudes towards the regimes’ policies and consequently, voting preferences. Popular support has been shown to be a crucial element for the long-term stability of dictatorships. In order to increase it, autocratic leaders may produce general policy outputs, that will benefit virtually all the population, or particularistic policy outputs, that will only benefit specific groups. The top-down provision of these two policy outcomes will create distinct relations of self-interested dependence with the population, culminating in two different kinds of support.
But what happens to this stock of popular support after transitions to democracy? Rational voters will have incentives to vote in a way that allows them to keep, or minimise the loss of the material benefits distributed during the former regime, in the new uncertain democratic context. Consequentially, in regimes that created general support, newly formed parties will utilise the positive inheritance of the former regime, having incentives to become mainstream in order to maximise their electoral success. This is possible because the majority of the population benefited from general outputs. Conversely, regimes that exclusively created particularistic support only benefited a niche segment of the general population, being unfavourable to the great majority. Therefore, unable to become mainstream, in order to utilise this legacy, associated parties are more likely to become extremist.
Preparative mass spectrometry instrumentation for large native protein deposition
Keywords: electron microscopy
RF power switch
mobility filter
electrospray-ion-beam deposition
effective potential
preparative mass spectrometry
ES-IBD
soft landing
native protein complex
IMS
enzymatic activity
preparative ion mobility spectrometry
native MS
ion funnel

Electrospray-ion-beam deposition (ES-IBD) is a preparative mass spectrometry technique which produces highly purified samples of non-volatile molecules adsorbed on a surface. An ES-IBD mass spectrometer (MS) ionises the analyte, transfers it into the gas phase, removes contaminations with a mass filter in vacuum and deposits it with a controlled landing energy onto a substrate. ES-IBD coupled to microscopy can elucidate the structure of biomolecules and their assemblies. In conjunction with scanning tunnelling microscopy, glycan connectivity of oligosaccharides was revealed. For larger molecules, such as native protein complexes, efforts are underway to determine their structure and conformation by coupling ES-IBD to cryo-electron microscopy or low-energy electron holography. However, there are no instruments available dedicated to depositing large, native protein complexes controlled and efficiently. In this thesis, I have modified a commercial MS designed for the analysis of large, native protein complexes (Thermo ScientificTM Q ExactiveTM UHMR) for deposition. The modified instrument has adequate beam intensity and good landing energy control. In conjunction with electron microscopy, it was shown that the native shape of protein assemblies is retained after dehydration and deposition. I used an enzymatic assay to quantify the activity of the non-covalent protein complex alcohol dehydrogenase after deposition on a dry surface. Moreover, I developed another instrument for mass- and mobility-filtered deposition of both small and large molecules. Its atmosphere-pressure interface, the ion funnel, is optimised for high transmission and it has a continuous parallel flow ion mobility filter to enable conformation-selected deposition. Radio-frequency power switches with a flexible operation frequency permit to transmit any ion with a mass-to-charge range > 50 Th, in particular heavy ions. The basis for the development of the second MS was the detailed investigation of the transport processes within an ion funnel. I formulate a 4-step ion funnel transmission model underpinned by transmission measurements of a conventional ion funnel and ion trajectory simulations taking into account the gas flow field.