VictorJuiz/thesis huggingface dataset:
Accurate and precise 3D T1 mapping of the human liver at 3T using widely available magnetic resonance imaging methods
Keywords: Quantitative Imaging
T1 Mapping
MRI
Liver imaging
B1+ Mapping

Better diagnostic and treatment methods are needed to counteract the steep increase of liver diseases. A promising non-invasive biomarker for the diagnosis of liver diseases is the longitudinal relaxation time (T1) of liver tissue, measured through quantitative magnetic resonance imaging. T1 correlates with liver fibrosis and inflammation. However, non-contrast T1 mapping is currently restricted to a single slice cross sectioning the liver and uses specialist cardiac imaging sequences that are often unavailable. As such, the main questions addressed in this thesis were: Is it possible to map T1 across the whole liver using only widely available pulse sequences? If so, can one obtain an unbiased estimate of liver T1 with sufficient precision for the diagnosis of liver diseases?
To answer these questions, a set of T1-weighted sequences capable of achieving whole liver coverage was adopted. The large covariance between T1 and the transmitted magnetic field (B1+) highlighted the need for an accurate B1+ map. Slice profile effects and several off-resonance based B1+ confounders were identified and corrected. Uncorrected, the median B1+ error in a phantom was -5.2%, producing a median T1 error of 10.5%. After applying all corrections, the median T1 error decreased to -0.3% with an interquartile range of [-2.5 2.1]%.
A theoretical framework was developed to calculate the T1 variance, including the noise propagated from the B1+ map into the T1 map. This framework was validated in vivo and used to find the optimal flip angles that resulted in the highest precision across a range of T1s and B1+ factors observed in the liver at 3 T.
Using scanner-agnostic sequences together with corrections for the confounding factors, a variable flip angle 3D T1 mapping method was developed requiring 7 breath-holds. A study across 10 healthy volunteers at 3 T validated the method’s accuracy, scan/rescan repeatability and precision. The 3D T1 maps yielded mean T1 values that, on average, were 5% lower than alternative single-slice T1 maps, with a repeatability coefficient of 49 ms and a median T1 standard deviation of 31 ms, showing potential to diagnose liver fibrosis.
Characterization of nanoparticles with optical fluidic cavity
Keywords: Optical trapping
Nanoparticle Characterization
Optical microcavity
Optofluidic Microcavity

The optical trapping of nanoparticles and biomolecules has recently attracted considerable attention as a means for the manipulation and characterization of target analytes. Nano-particulate pollutants and microbiological organisms, such as viruses, have optical characteristic signatures based on their refractive index, size, and polarizability, as well as spectral signatures. By leveraging these properties, optical sensing and spectroscopy techniques have proven to be powerful tools for detecting and characterizing nanoparticles at the single-particle level. In this work, we show that the confined optical field in a Fabry-Perot style microcavity resonator can be used as a means for both trapping and measuring nanoparticle characteristics with high resolution. This characterization is performed by recording the spectral shift of the mode wavelength when the particles diffuse through the microcavity. The maximum mode displacement provides an accurate measure of the polarizability of each particle. We illustrate an accurate measurement of the distribution of polarizabilities in a solution containing a mixture of 50 nm, 75 nm, and 100 nm polystyrene particles in water. This work also studies the theory behind the behavior of particles in an optofluidic microcavity based on the particle size, the optical power, and throughput of a given instrument. Based on the developed theory, the dynamic characteristics of particle trapping in an optofluidic microcavity are further investigated by simulating a stochastic model of nanoparticle dynamics. Furthermore, this work introduces a new model for analyzing the dynamics of nanoparticles in fluidic systems and studying the optical trapping potential. This model allows to accurately design an optical microfluidic system for trapping the desired range of particles based on the flow rate and the optical power, and subsequently detect nanoparticles with high resolution. We express the trapping rate of nanoparticles as a function of the flow rate, the optical power, and the size of particles. Thus, the technique proposed in this work provides a deep understanding of the optical trapping of nanoparticles in flowing fluid, which is crucial for trapping and manipulating nanoparticles and biomolecules. We also show that similar-sized particles of different materials can be distinguished as a result of the difference in refractive indexes, which means the introduced method is sensitive to the refractive index. Therefore, it can be a powerful method to analyze nanoparticles in a solution in applications where we need high-resolution measurement at the single-particle level.
Looted letters. Book culture of Ḥafṣid Ifrīqiya (1229-1574) and Arabic manuscripts in early modern Europe after the sack of Tunis (1535)
Keywords: Tunis Expedition
Republic of Arabic Letters
Arabic Manuscript
Islamic Art
Ḥafṣid Ifrīqiya

The present thesis is based on the study of the Arabic manuscripts looted during the sack of Tunis in 1535, and then brought to Europe and sold or donated to important scholars and institutions in Italy, France, and the Habsburg Empire. The manuscript corpus examined here is thus delimited by a common provenance and collection history.
The main objective of the project is to reconstruct this corpus of Ḥafṣid manuscripts. Situated in the research field of the Material Culture of the Islamic Mediterranean, the core of the dissertation is an in-depth study of manuscripts from Ḥafṣid Ifrīqiya (1229- 1574). They are studied with regard to their aesthetic and codicological aspects, in order to understand Ḥafṣid book production. It will be argued that uncovering the visual choices behind stylistic developments helps to reveal the decisions behind the process of establishing a Ḥafṣid (imperial) identity. Furthermore, the manuscript notes – such as owner-marks and endowment deeds – help to recreate the context of the manuscripts, as well as the practices and agents involved in the book culture of Ḥafṣid Ifrīqiya.
In addition to providing an art-historical and sociohistorical interpretation of the manuscripts and contributing to the study of North African material culture, the corpus allows this research to offer new perspectives on a range of related topics. Starting with the re-evaluation of contemporary sources on a landmark event in Early Modern history, and an innovative focus on its interpretation, the project adds a missing aspect to the otherwise well-studied and important research field of Charles V and the sack of Tunis in 1535. The project brings Early Modern scholarship on Arabic texts and language into context by utilising the manuscripts from Ifrīqiya as a source to map the interest in, and scholarship on, Arabic manuscripts in Early Modern Europe.
‘What to cook and how to cook it’: Understanding the interplay of subsistence, ceramic technology, and local environments in the emergence of pottery in northeast Asia through residues
Keywords: Archaeology
Northeast China
Residues
Supercritical Fluids

Since the early 2000’s, archaeological excavations in the Nenjiang River Basin have led to the discovery of some of the oldest pottery assemblages in northeast China. The main objective of the DPhil research presented here is to understand what role vessel technology played in human lives over an extended time span regarding diets, food preferences, and human environmental interactions in this region. Pottery analysed in this thesis comes from the site of Houtaomuga 后套木嘎 located in the Lower Nen River Valley on the Song-Nen Plain, Jilin province northeast China. Using molecular and isotopic analysis, this thesis characterised lipids extracted from archaeological pottery using advanced analytical methodologies to understand pottery use at the initial implementation of the technology and over the course of the Neolithic. Results of lipid residue analysis presented as a part of this research were also described in context with other regions in northeast Asia, such as Russia’s Far East and Japan, which also have pottery bearing hunter-gather sites from the Neolithic which are contemporaneous.
Before turning to the analysis of the archaeological material from Houtaomuga, this thesis undertook a method optimisation to understand the efficiency and limitations of current techniques. This method development ensures that the method of analysis was adequate to answer proposed research questions prior to sampling and will improve upon methods for lipid residue analysis which are currently standard practice within archaeological science. As a result, this thesis presents the first extensive application of non-destructive supercritical fluid extraction (SFE) of ancient lipid residues followed by isotopic characterisation. Results indicate this novel method workflow is comparable to current methods which are highly destructive to ceramic artifacts. By using this workflow, it was determined that pottery at Houtaomuga was primarily used for cooking aquatic molluscs and C3 plant resources. While other proxies indicate that human diets at Houtaomuga were highly diverse, pottery use was highly specified for all four phases of Neolithic occupation of the site, suggesting people preferentially chose certain foods or dish types to prepare in vessels.
Joseph Brodsky and the visual arts: consumer, practitioner, interpreter
Keywords: Joseph Brodsky
Russian literature
Brodsky
Russian poetry

Joseph Brodsky (1940–1996) was a highly visual writer. This thesis looks at his poems and essays, and a range of unpublished archival documentation to argue that he was an individual sensitive to visual stimuli in his environments, whose texts are in dialogue with non-literary worlds as much as they are with literary ones. More generally, I foreground the importance of looking at literary texts from non-literary points of view.
My study is comprised of four main chapters, each dedicated to a different visual form: cinema, postcards, photography, and drawing. All were integral parts of Brodsky’s daily life and helped him express his personal experiences. These forms have been chosen as he worked directly with them all. He approached each form in a different manner and gave distinct values to each. For Brodsky, all four are united by the interdependent themes of imagination and memory.
I show how he associates cinema with imagination (Chapter One), postcards with documentation (Chapter Two), photography with perception (Chapter Three), and drawing with private dialogue (Chapter Four). As I move from Chapter One to Chapter Four, I also chart a move from forms Brodsky associates more with imagination than memory to those where memory is more prevalent. This move from imagination to memory proceeds in tandem with another development, namely one from forms that are more manufactured, and more resistant to personalisation, to those where the opposite is true. In my conclusion, I show how judgments about his treatment of visual forms, and visual experiences, more generally, can be articulated when medium-specific observations are seen comparatively.
Brodsky’s work about, and in, each of these forms gives us fresh insights into his biography and writings. The interplay between his biography, writings, and work in these visual forms, is central to each chapter. Archival documentation allows one to analyse anew each of these three components as well as the relationships between them.
Intervention evaluation and structural identifiability in compartmental models of infectious disease transmission
Keywords: African swine fever
mathematical models
structural identifiability
infectious disease
hepatitis A
transmission

This thesis concerns the principled use of mathematical models for informing control interventions in the context of an infectious disease outbreak context. We address two main related questions. First, how can interventions be evaluated and compared in a principled manner using a dynamic (time-varying), mathematical model? The second question pertains to structural identifiability, a prerequisite for successful parameter inference in dynamic models: how does the type of model output influence the structural identifiability of dynamic, mathematical models for infectious disease transmission?
We address the first question using two outbreaks of infectious disease – hepatitis A and African swine fever (ASF) – as illustrative examples, and the second question by conducting structural identifiability analysis of various ordinary differential equation (ODE) model versions. Links to all code and files needed to reproduce the results in this thesis have been provided. Our contributions are detailed in three papers: a published article and two manuscripts, now summarized.
Chapter 3: Dankwa et al. (2021) developed a dynamic, deterministic model to explain transmission in the 2017-2019 hepatitis A virus (HAV) outbreak in Louisville, Kentucky, US, among persons experiencing homelessness or who use drugs, known to be at a high risk of HAV infection. With the model, alternative vaccination scenarios were examined for effectiveness and cost, and an estimate for the critical vaccination threshold required for herd immunity in this population was derived. Prior to this study, no such estimate had been obtained for this population anywhere in the US.
Chapter 4: Dankwa et al. (2022b) developed a dynamic, stochastic, spatial model to explain ASF virus (ASFV) transmission among wild boar and domestic pig herds, and to evaluate alternative outbreak management measures. The model was developed such that it could be refined to account for more outbreak data and hence it is suitable for real- time outbreak analysis. This study is relevant, given the ongoing ASF epidemic in Europe, and the scarcity of ASFV transmission models which account for transmission at the wildlife-livestock interface, despite the evidence of such transmission in Europe.
Chapter 5: Dankwa et al. (2022a) conducted structural identifiability analysis of unknown parameters, including initial conditions, of 26 ODE model versions to demonstrate the influence of the type of model output(s) on models’ structural identifiability. Data types such as incidence and prevalence, typically encountered in disease surveillance, were studied as model outputs. This analysis emphasizes the importance of a careful consideration of model outputs prior to performing inference with transmission models.
New Mouride movements in Dakar and the diaspora
Keywords: Modou Kara
Diaspora
Gendered Violence
HIV/AIDS
Poverty
Mourdiyya
Cheikh Bethio Thioune
Youth
Street youth
Violence
Sufism
Senegal
Mourides

This thesis looks at two Mouride orders that became very popular among young people in Senegal starting in the year 2000. It focuses not only on the leaders of these two movements, known as marabouts or cheikhs, in Dakar, Senegal, but in particular on their followers, the talibés. The thesis examines the 'Thiantistes', followers of Cheikh Bethio Thioune and at the disciples of Serigne Modou Kara in order to understand why these new Mouride movements, which differ from those that have preceded them, have proven so popular with youth in Dakar. I argue that marginalised youth have impelled the creation of a new form of Sufism in Senegal, in a context whereby they are excluded from the post-colonial state and must navigate numerous difficulties daily, including violence, unemployment, and inability to attain adult status due to severe economic and political limitations. I compare and contrast the new religious movements these youth have created with those that Senegalese migrants in Belgium and France have generated, where racism and other types of exclusion lead to the desire to establish nourishing spiritual networks.
Dynamics and control of infectious disease epidemics: compartmental modelling of variations in infectiousness and symptoms during infection
Keywords: epidemic modelling
influenza
infectious disease modelling
Ebola
mathematical biology
mathematical epidemiology
mathematical modelling
COVID-19
SARS-CoV-2

Through a series of case studies, this thesis explores how changes in infectiousness and symptoms during viral infections can be represented and inferred using compartmental models, in order to provide insights on epidemics in human populations.
First, we consider a compartmental model of Ebola virus disease outbreaks which relaxes the standard assumption made in epidemiological modelling studies that all symptomatic hosts are equally likely to be detected. We show that accounting for variations in symptoms during infection can lead to significantly different projections compared to a model in which symptoms are assumed to remain constant throughout infection, demonstrating the potential importance of accounting for individual host-scale dynamics in population-scale epidemic models.
We then develop an easy-to-use framework for informing population-scale epidemic models using host-scale data and models. Our approach involves using a multi-stage compartmental population-scale model with a large number of infected compartments in order to enable variations in infectiousness during infection (reflective of individual host-scale data) to be represented. Applying our approach to the case study of influenza A, we investigate the number of individuals from whom host-scale data need to be collected in order to ensure accurate population-scale epidemic projections.
We then turn our attention to SARS-CoV-2, and develop a novel approach for inferring changes in infectiousness during infection using data from infector-infectee transmission pairs. We show that this method, which is based on compartmental modelling, provides an improved fit to data collected in the early months of the COVID-19 pandemic compared to existing approaches. Our results indicate that many transmissions occur shortly before an infector develops symptoms, highlighting the benefits of contact tracing even if contacts from a short time window before symptom onset alone are traced.
Finally, we adapt our approach for inferring changes in infectiousness during SARS-CoV-2 infection in order to obtain updated estimates of the generation time distribution (which characterises the relative expected infectiousness profile of infected hosts at each time since infection) using data from UK households. We infer a shorter mean generation time in September--November 2020 compared to earlier months, which demonstrates the importance of continued data collection and analysis in order to inform future public health policy decisions.
Ontology and iconography in Egyptian religious compositions: composite figures in the Amduat, Book of Two Ways, and apotropaic wands c. 2000-1400 BCE
Keywords: visual culture
comics studies
underworld books
iconography
Coffin Texts
visual language
multimodality
ontology
social anthropology
representation

This thesis investigates the patterns of occurrence of composite figural forms of divine beings in three categories of Egyptian pictorial–verbal religious compositions dating between 2000 and 1400 BCE: the Amduat, Book of Two Ways, and apotropaic wands. Analysis of the Amduat focuses on the burial chamber of Thutmose III (KV 34); study of the Book of Two Ways concentrates on the coffins B1C and B5C (Cairo CG 28083 and JE 37566); images on various wands are treated as selections from a repertoire. Most case studies are ophidian composites that incorporate elements of the bodies of serpents, whose cultural associations in Egypt are well-explored. The thesis argues that composite figures, which conjoin elements of human and animal bodies or parts of inanimate objects, display both ontological and semantic content, and that configurations were constrained by features of context, such as compositional format, multimodality, and decorum. Chapters 1 and 2 establish the theoretical basis of the thesis. Following the terminology of anthropologist Philippe Descola, composite figures are argued to balance interiority (subjectivity and vital force) and physicality (bodily constitution and means of action) in an analogist ontological regime, in which beings are defined and related through metaphor and symbolism. The concept of agency is treated as an aspect of interiority; its dynamics and loci are identified in the Egyptian terms sšmw and jrw. In Chapters 3 to 5, case studies from the three corpora are analysed within the frame of Neil Cohn’s notion of visual language, developed out of research on comics. This concept accommodates varied relationships between beings, images, and hieroglyphic writing by taking account of contextual features while exploiting analytical approaches deriving from art history as well as comics studies. Chapter 6 presents a typology of conceptual structures and discusses sources and transmission between corpora. The composite figure is suggested to be an emic category whose conceptual implications distinguish it from other uses of conjoined elements as a graphic schema, enabling zoomorphic composites to be related to other schemas, notably personifications. A concluding chapter extends the central ideas of the thesis to other corpora, outlines relevant theoretical considerations, and suggests how the methods developed could be extended in their application.
Detecting archaeological sites in the eastern Sahara using satellite remote sensing and digital image processing
Keywords: radar
archaeology
Sahara
Egypt
satellite
hydrology
GIS
Remote sensing

Advancements in remote sensing instrumentation are providing more detailed surveys of our planet using synoptic observations from a global, regional, and local perspective. This D.Phil. research project proposes novel techniques for detecting archaeological sites in the hyperarid desert regions and moisture-rich coastal areas of the eastern Sahara, by examining multispectral satellite imagery in the optical and microwave (radar) regions of the electromagnetic (EM) spectrum. The methodology uses sensors onboard spaceborne platforms (in contrast to airborne instruments or ground based geophysical survey) – weighted heavily towards an active radar approach. Landsat-7 ETM+, Shuttle Radar Topography Mission (SRTM), and PALSAR represent the principal imagery types used throughout this work.
Three case studies are presented, each setting out a comprehensive and well-documented protocol for archaeological site detection. The first uses Landsat ETM+ data to map and identify the distribution of ‘tell’ sites in the northwestern Nile Delta by applying a principal components transformation and a thresholding approach. The second case study produces a complete hydrologic map of the eastern Sahara from SRTM image (amplitude) and elevation data. Oases and ancient fluvial networks (palaeorivers) are mapped using the Normalized Difference Vegetation Index (NDVI) and from SRTM image data respectively. ASTER thermal infrared (TIR) is used to detect palaeolake deposits from their surface carbonate signatures. Additionally, topographic lake depressions and palaeoshoreline features are identified from SRTM DEM. The use of a DEM was found to provide a more favourable approach for mapping palaeolake systems compared to performing a spectral analysis. The final case study considers trading routes and their relationship to water sources. Imagery datasets produced over the course of the work are added to a Geographical Information System (GIS) in order to examine likely locations for new archaeological sites in Egypt’s Western Desert. Results from these investigations indicate that a fully multispectral strategy is preferred when isolating spectral signatures from archaeological materials.