VictorJuiz/thesis huggingface dataset:
Low-precision climate computing: preserving information despite fewer bits
Keywords: shallow water model
high-performance computing
weather forecasting
climate modelling
data compression
information theory
low-precision arithmetic

Progress towards more reliable weather and climate forecasts is limited by the resolution of numerical models and the complexity of simulated processes. Performance is therefore a major bottleneck and current models are not com- putationally efficient. High precision calculations are unnecessary, despite be- ing the standard, given the uncertainties in the climate system and the errors from discretisation, data assimilation and unresolved climate processes. In this thesis, we advance several aspects of low-precision climate computing to preserve information despite fewer bits: An information-preserving com- pression is developed that distinguishes between real and false information to reduce the very large volume of climate data produced by numerical mod- els, while minimising information loss. The bitwise real information content estimates the minimum required precision in climate data, which depends on the variable and is lower than the standard precision-levels of floating-point numbers. The impact of rounding errors introduced by different low-precision arithmetics with deterministic or stochastic rounding modes is analysed in chaotic dynamical systems. Standard floating-point numbers are not the best number format for weather and climate simulations. However, alternatives, such as posits, exist, but it is unclear whether the large effort needed to de- velop the respective hardware for future supercomputers is justified given the moderate advantage they provide in our applications. A much more central issue towards 16-bit climate models is the design of low precision-resilient al- gorithms. A naive transition to 16 bits either fails or was found to cause issues like amplified gravity waves, a change in geostrophy or rounding errors that grow as quickly as discretisation errors. However, many of these issues are found to be preventable with techniques such as scaling or a compensated time integration. Combining techniques, we develop a 16-bit fluid circulation model that approaches 4x speedups on Fujitsu’s A64FX processor compared to 64 bits, despite minimal rounding errors. The result of this thesis show that there is little reason to assume that 16-bit weather and climate models are not possible. While the design of models to compute and output only the bitwise real information is challenging, it will be a major step towards computationally efficient digital twins of the Earth’s climate system.
The critical role of IL-23 receptor positive T cells in the pathogenesis of anterior uveitis associated with spondyloarthropathy
Keywords: T cells
IL-23
spondyloarthropathy
uveitis

The spondyloarthropathies (SpAs) are a group of chronic inflammatory diseases which predominantly affect the joints of the axial skeleton. However, many patients with SpA may have extra-articular manifestations within the skin and gut. Pathology of SpA in all of these tissues has been shown in recent studies to be driven by local resident populations of interleukin (IL)-23 responsive cells. The eye is also involved in these diseases, with uveitis occurring in up to 40% of patients with SpA. Therefore, it is feasible that a resident population of IL-23 responsive cells could also exist within the eye.
Recently, systemic overexpression of IL-23 in mice has shown the accumulation of a small number of γδ T cells proximal to the anterior uvea. However, although work has been done to characterize resident leukocyte populations within the anterior compartment of the eye there has been no documentation of resident lymphoid cells in these tissues and there is no evidence suggesting the presence of a sentinel cell capable of responding to IL-23.
In this study I document for the first time that a diverse population of T cells is present in the extravascular tissues of the anterior compartment of the eye in both mice and humans. I also identify the presence of a resident IL‐23R+CD3+CD4-CD8- γδ T cell in the anterior compartment of the eye, providing a potential explanation for why IL-23 is capable of affecting all of these distal sterile tissues.
I then stimulated these cells to show that they have functional IL-23R activity and that IL-23 is sufficient to drive uveitis in the absence of any pro-inflammatory mediator. I achieve this in vivo in mice through a novel mechanism enabling the sustained localized overexpression of IL-23 in the inner eye by adeno-associated virus gene transfer. Since I could not do this in humans, I instead stimulated human eye tissue with IL-23 in vitro. Here I was able to show that that IL-23 is sufficient to drive the expression of several downstream pro-inflammatory cytokines by these cells. Consistent with the concept of IL-23 being a unifying factor in SpA, I show that like the gut, skin, and joints - IL-23 can also act locally on a resident IL-23 responsive cells to drive pathology within the eye.
Presence of mind: consubstantiality and extended cognition in Montaigne's writing
Keywords: extended mind
Montaigne
consubstantiality
Renaissance thought
essays
4E cognition
authorial survival

This study investigates how the metaphysical notion of consubstantiality can be rethought fruitfully as a distinctively cognitive figure in Montaigne’s writing. It argues that the consubstantiality ‘allegory’ through which Montaigne secures his reader’s sense of authorial presence in the 'Essais' can be brought into dialogue with contemporary cognitive scientific theories of extended mind, in a way that does not foreclose the controversial sacramental implicatures of the term in its sixteenth-century French context. Using a combination of methods (close readings, philological analysis and word histories, Relevance Theory) and drawing on a range of materials from the early modern to the contemporary, the three chapters of the thesis demonstrate key affinities between i) Montaigne’s early modern sense of the mind’s ramification and extension into the material, technological and social environment, and ii) contemporary conceptions of 4E cognition. The interdisciplinary (or comparative) and transhistorical approach adopted in this study enables a reflection on consubstantiality as an ontological and discursive concept from a variety of interconnected points of view. Firstly, from the perspective of memory, which is considered within a premodern mentalité closely bound up in Humanist rhetoric and poetics, and in relation to the Essais as a technology of memory, an artificial extension of Montaigne’s biological mind and lifespan. I then explore the scope for reading Montaigne’s early modern ecological thought in tandem with contemporary theories of cognition, through the lens of ‘contexture’. By linking contexture to relevance, I explore the interpretative implications for reading consubstantiality as operating along a continuum between the literal and the metaphorical, the natural and the artificial, the secular and the sacred. The third perspective from which I consider my main topic is prosthesis. I argue that the linguistic, medical and discursive concept of prosthesis affords another means of thinking about memory, identity, extended mind and intertextuality in Montaigne’s writing; as I show, this differently-embodied perspective complements consubstantiality and sheds important light on Montaigne’s conception of how part, ‘membre’, or fragment relates to the whole. By reconceptualizing consubstantiality through extended cognition, this study not only builds on existing cognitive approaches to Montaigne, but also, in reassessing a notion at the heart of Montaigne’s writing project and pivotal to successive generations of readers’ sense of Montaigne’s enduring presence and relevance, engages a broader methodological reflection on interdisciplinary readings of texts from the past.
Outnumbered - being quantified through school grades in Germany
Keywords: numbers
ethics of quantification
Germany
quantification
ethnography
school grade

This thesis is dedicated to exploring what it means to ‘be quantified’, by investigating the lived experience of pupils with being graded. The premise underpinning the project - that grades are at their heart a form of quantification - is one which has been largely overlooked in the scholarly discourses on both of the respective concepts.
My work is built on twelve months of ethnographic fieldwork in a German comprehensive school. This context is particularly salient for the question at hand, as quantification plays a pivotal role in it: German pupils receive between 100 and 120 grades per year, and as oral participation in class constitutes 50% or more of the final grade in each subject, every day of school ‘counts’.
I investigate several effects of quantification on those at its receiving end. In their capacity as numbers, grades firstly determine the (in)visibility of different groups of students. Secondly, they shape students’ self-perceptions and mediate how pupils think about merit and justice. Thirdly, grades enact institutionally supported discipline through their visceral effects on students’ bodies and their central role in the school’s repertoire of gratification and punishment. Grades fourthly govern the distribution of credibility and can thus cause testimonial injustice where numbers and narrative are in conflict with each other. Lastly, an ethnography of being graded offers important insights into increasingly vital ethical questions around quantification and the value of the invaluable.
By joining the forces of ethnography, epistemology, and ethics, the results of this interdisciplinary anthropological-philosophical doctoral project foster a deeper understanding of a phenomenon which has a long historical legacy but has also seen an unprecedented proliferation in the recent decades of the algorithmic age: the quantification of the social.
Arctic mineral futures: tracing geoscience knowledge from field to community in the Northwest Territories, Canada
Keywords: geoscience
facilitators
public engagement
minerals
cultural geography
mining
knowledge production
mineral potential mapping
Arctic
Canada
more than human geography
ethnography
Northwest Territories
geology

This thesis explores the ‘becoming’ of mineral resources in the Northwest Territories (NWT), Canada, and the role that geoscience knowledge and bodily-material relations play in that process. Mineral resources are assembled through a diversity of practices and knowledges which enable their identification, bounding and circulation within global economies. Existing literatures have explored the circulation, valuation and demands for commodities largely from a cultural perspective. In response, this thesis presents another approach which focusses on the relations between geological materials and the bodies and emotions of scientists and citizens. This is done by drawing on literatures from cultural and resource geographies and science and technology studies.
The ‘becoming’ of resources is examined at three sites. First, this thesis follows the production of geological bedrock maps (which are the first step in finding minerals) by applying ethnographic methods of shadowing geologists working both in the office and field in the NWT. There, the movement of geologists through geological spaces and their enchantment with geological materials are shown as being crucial to the production of geoscience knowledge. This contributes to our understanding of the significance of bodily material relations in the production of geoscience knowledge, which has been unrecognised in existing resource geography literatures. Second, this thesis digs into how a mineral potential map (MPM) was created for part of the NWT with the intention of supporting an all-season road to the Arctic coast in Nunavut. There, using interviews with economic geologists and comparisons with industry best-practice guidelines, a critique about how well the MPM allows us to understand what minerals lie underground is delivered. As a result, existing literature on volume and resource accounting is developed with nuanced understanding of how geological materiality challenges resource accounting methods, and the mechanisms geoscientists use to counter this. Third, this thesis explores a site where geoscience materials are used by the Government of the Northwest Territories (GNWT) within a public engagement context to improve a community’s receptiveness to mineral resource development. There, the thesis shows how the GNWT applies a public deficit model and utilises geoscience materials to try to ‘educate’ community members and influence their emotions around the extractive industry. The GNWT is shown as siting the problem of resource development mistrust not as an issue of the government’s communication and engagement technique, but rather as one of public ignorance and mistrust in science. As a result, existing literature on public engagement, materials and emotions are developed.
An interdisciplinary approach for developing novel methods to study silks
Keywords: click-chemistry
silks
methods
mixed-effect models
interdisciplinary
fluorescence microscopy
hierarchy
multi-spectral
artificial amino acids

Silks remain objects of eternal fascination to mankind; their remarkable material properties and visual lustre attracting decades of commercial and research attention. Though much research has been conducted in the past to attempt to understand the structure of silks – as well as the highly intricate protein dynamics that occur during the spinning process – many gaps in our knowledge remain. Silks are unique in that order and hierarchy exist right from the molecular scale (primary structure of silk proteins), through to the nanoscale (secondary and tertiary silk protein structures), and right up to the microscale (microscale solid fibre). Therefore, an interdisciplinary approach must be used to understand the many facets of silk. In my thesis, I combine chemical and spectroscopic techniques, material testing techniques, and couple them with a core understanding of evolution and biology in an attempt to understand the structure-protein dynamic-mechanical property relationships of silk. I utilise unnatural amino acid incorporation to endow silks with probes for further structural and dynamic studies. I also use various fluorescence microscopy techniques to study silk structure, using silks’ natural fluorescent motifs as well as incorporated fluorophores as contrast agents. Finally, I offer a perspective piece on the highly contentious subject of nanoparticle incorporation in silks as I believe that it is important to validate various claims floating about as they are likely to guide the way for future studies, and they also have important implications in understanding how nanoparticles travel through the bodies of organisms.
A multi-method approach to understanding prehistoric bone tools
Keywords: osseous tools
bone tools
reproducibility
North African LSA
use-wear analysis
palaeolithic
basketry
perishable crafting
reflectance transformation imaging
anthropological archaeology

It is the task of archaeologists to account for a wide range of cultural practises and processes using a limited range of surviving artefacts and features. In Palaeolithic contexts, organic materials such as leather goods (bags/pouches, shoes, clothing, slings, etc.) and woven fibre artefacts (baskets, cordage, textiles, etc.) are vastly underrepresented (Croes 1997, Soffer et al. 2000, Taylor 1966). How, then, can archaeologists working in great time depths account for artefacts crafted from leather and/or plant materials? One approach is the systematic examination of osseous tools: a preferred tool material for perishable craft production in cultures around the world.
The aims of the following research were to apply new or novel inductive methods to prehistoric bone tools, in order to gain an enhanced understanding of their place(s) within the cultural repertoire of prehistoric groups, with an emphasis on perishable craft production. The basis for these analyses are bone tools from the North African Palaeolithic site of Taforalt, and ethnographic bone tools housed at the Phoebe A. Hearst Museum of Anthropology (PAHMA) and at the Pitt Rivers Museum (PRM). Investigations were organised using a chaîne opératoire approach (Leroi-Gourhan 1964, 1968). This approach encompasses the technical processes of bone tool creation and use, the tasks the bone tools were used to perform (and products they were used to produce), and ways in which information about bone tools can be shared in reproducible, high-fidelity formats.
In the broadest sense, these methods have illuminated a number of formerly unknown cultural strategies and capacities among the Palaeolithic inhabitants of Taforalt. By studying bone tools from Taforalt, it was possible to understand intentionality in raw material selection, to see an emphasis on the creation of small, thin pointed tools, and to gain proxy evidence for coiled basketry production in the absence of the baskets themselves. These baskets, in turn, likely supported the collection, processing, cooking, and storage of food resources such as acorns, pine nuts, and snails. Crafted technologies would have enabled the population at Taforalt to maintain reliable food sources irrespective of seasonality, and to support an expanding population, in turn enabling people to continue to develop specialised cultural roles and technological forms.
The ultimate goal of this research has been to understand whether bone tools can be used as proxy stand-ins for activities, technologies, and people who are otherwise archaeologically imperceptible, especially in the remote past. The following studies show that these methods, when applied to bone tools, can successfully scaffold a more nuanced understanding of prehistoric lifeways, and in particular, perishable craft production.
Moving deserts: stories of mobilities and resilience from Turkana County, a Kenyan desertscape
Keywords: pastoralism
Kenya
development
resilience
drylands
Turkana

This thesis is about resilience, drylands, and pastoralism. It aims to enhance our understanding of the meanings of resilience from the perspective of pastoral communities in drylands and in the context of their everyday lives. It draws on the case of Turkana herders living in Kenyan’s northern drylands, a place of “resilience making” for the international community. Threatened by recurrent droughts, security issues, and precarious living, Turkana County is the perfect laboratory for international organisations interested in “building resilience” to shocks and disasters, and in turn also a compelling case for a thesis which hopes to bring a more grounded, nuanced, and rooted understanding of resilience in drylands.
There is a “paradox of representation” as scholars portray pastoralists as one of the most resilient groups while practitioners see them as the most vulnerable. In this thesis, I set out to explain how there could be such divergent viewpoints and to bridge the divide. I suggest that resilience is discussed in the international development regime as a cornerstone of “pastoral development” through three dimensions: landscape, lifescape, and bodyscape. Based on 14 months of ethnographic fieldwork, I examine the local meanings of resilience across these dimensions and contrast them with outsiders’ interpretations emerging from policy documents, development interventions and scholarship.
The empirical analysis reveals the fundamental role of mobility in the lived experiences of Turkana herders. The most significant contribution of this thesis is the emergence of mobility as an integral part of everyday life, providing a new lens for the understanding of resilience which challenges dichotomous, linear, and “bouncing” views of resilience. Instead, I argue that mobility—in its many manifestations, as a quality of space, as something people do, as an aspect of identity—allows for more fluid, dynamic, and kaleidoscopic accounts of peoples’ lives. I thus propose mobility as the site where resilience takes root and where a richer grasp of resilience, drylands, and pastoralism can be found.
Molecular simulations of ion channel gating
Keywords: ion channels
molecular dynamics simulations
gating

Ion channels are membrane proteins that facilitate ion permeation across the membrane down the concentration gradient. Recently, many structures of the ion channels were solved using cryo-electron microscopy. An advancement in structural determination and computational power has enabled ion channels to be thoroughly investigated at the molecular level using molecular dynamics (MD) simulation. Here, I used a range of methods, including coarse-grained MD, free energy perturbation (FEP) and atomistic MD simulation, to study the gating mechanisms of two ion channels, the ATP- sensitive K (KATP) channel and the Transmembrane 16A (TMEM16A) channel. I used CG-FEP to determine the binding affinity of phosphatidylinositol-4,5- bisphosphate (PIP2) to the KATP channel and investigate how insulin secretory disorder effects channels PIP2 affinity. In the light of collaborative experimental studies, I have also proposed the gating mechanism of how PIP2, an activator of the channel, may compete, with ATP, an inhibitor of the KATP channel. Last, I have determined an additional gate at the outer pore of the TMEM16A channel, which is the binding site of the biphasic drug anthracene-9-carboxylate (A9C). Together, the work in this thesis has demonstrated the power of MD simulation to investigate the gating mechanisms of multiple ion channels and their interactions with the allosteric modulators.
Cannabis legalization: an ethnography of the global movement and market forces
Keywords: global supply chain
anthropology
law reform
regulated cannabis
cannabis
Bourdieu
social movement
commericalization
legal cannabis
ethnography
cannabis legalization
commodification

After decades of prohibition and advocacy for law reform, over 60 countries have legalized cannabis. Legal change has transformed cannabis as an almost wholly illicit substance into a licit one undergoing commodification. Regulations have enabled markets to emerge for an array of cannabis products, designed for medical, ‘wellness’, recreational and industrial use. But an ongoing movement for reform remains. There are campaigns for legalization, accessibility, and regulatory oversight, intertwined with demands for human rights. Meanwhile, aspects of the counterculture that surrounded illicit cannabis still linger. In this thesis, I examine the relationship between the cannabis market and movement, the people behind processes of change and commodification, and the implications of these activities.
I present an ethnographic portrait of both the market and the movement, as they move through different stages of change and development. This is based on multi-sited fieldwork in 11 countries, over 14 months, during which I attended different cannabis events and worked with different people and organizations, using participant observation and interviews. To analyze this data, I turn to Becker’s theory of deviance, Bourdieu’s discussion about ‘rules of the game’, and Abolafia’s concept of ‘markets as cultures’. I build upon, and contribute to, social movement theory, economic anthropology and organizational sociology.
The findings demonstrate parallel sets of ongoing processes – legalization, normalization and commercialization – and their complex effects, which result in processes of commodification. This reform is non-linear and dependent on people, activities, events and networks, but cannot be wholly attributable to legalization. I describe the extent to which the market has been supported by the moral norms of the ongoing advocacy movement and historical elements from the days of the counterculture. I focus on local and global processes of change and commodification to demonstrate the importance of the relationship, and sustenance, between the movement and market.