VictorJuiz/thesis huggingface dataset:
Late Holocene cultural dynamics and trans-Saharan connections in Southeastern Mauritani: a remote sensing approach

This doctoral thesis investigates the prehistoric and medieval archaeological record of southeastern Mauritania (c. 2,000 BC to AD 1,100). The highlands of southeastern Mauritania present an extraordinary archaeological record for documenting the emergence, consolidation, and reorganisation of cultural dynamics. A remote sensing approach represents the most viable research methodology, politically and logistically, for this study. My work integrates quantitative methods and transdisciplinary theoretical developments to characterize and assess diachronic cultural trends in terms of regional settlement dynamics, the nature of funerary landscapes, and supra-regional connectivity. The results include the identification and spatial distribution mapping of >9,000 funerary tumuli and 1,140 settlements belonging to the Tichitt Tradition, many of which were previously unpublished or undocumented.
The Tichitt Tradition represents the growth and consolidation of a thriving agropastoral economy based on cattle-keeping and pearl millet (Pennisetum glaucum) cultivation throughout during the second millennium BC, structured around extensive, drystone settlements. I interpret these Late Holocene cultural dynamics through the lens of Complex Adaptive Systems, unfolding within the cultural milieu of pre-colonial African polities. The expansion of Tichitt Tradition communities was characterized a conservative but decentralized reproduction of material and ideological forms leading to high systemic coherence, conforming to Kopytoff’s Internal African Model. From the first millennium BC, Tichitt Tradition communities witnessed a drastic release and reorganisation of settlement patterns amidst severe aridification trends and the arrival of Lybico-Berber groups. This scenario led to migration outflows and the formation of interstitial communities with greater adaptive creativity, reflected in a greater diversity of settlement styles and the syncretism of pottery traditions described by Kevin MacDonald. The interplay between concepts of spatial and socio-political centrality and liminality—illustrated by the shifting trends of funerary monument clustering in relation to settlement centers—highlights issues of translocal resilience and landscape memorialisation among agropastoral communities in dryland ecosystems.

Keywords: satellite imagery
Mauritania
settlement patterns
Tichitt tradition
remote sensing
funerary archaeology
prehistoric archaeology
archaeology
African archaeology
Advisor: Mitchell, P
Transcription dynamics during metabolic changes

Temporal control of processes in cells such as metabolism, gene expression, and cell growth and division are ubiquitous in nature but how they are coordinated in single cells is poorly understood. The yeast Saccharomyces cerevisiae offers a tractable system in which to address these relationships, as growth rates, the number of cells in the cell division cycle (CDC), and their metabolism can be varied and linked to patterns of gene expression. Precise numbers of nascent and mature transcripts can be monitored in single cells using single-molecule RNA fluorescence in-situ hybridisation (smRNA-FISH). The Yeast Metabolic Cycle (YMC) is a model system of temporal compartmentalisation of cellular and metabolic processes in slow-growing synchronous cultures and can be compared with data from asynchronous cultures at different growth rates (exponential mid-log versus slow growth) and metabolic states.
These studies reveal that single cells from mid-log and YMC cultures possess an intrinsic metabolic and gene expression clock. Remarkably, individual cells are found to possess a high degree of variability in levels of expression of individual transcripts yet the oscillations in mean transcript levels over time are similar to those described at the population level using RNA-seq. Furthermore, although most yeast genes are proposed to show a constitutive mode of transcription initiation, the transcript distribution of oscillating transcripts along the YMC do not fit those predicted by a one-state mathematical model of constitutive transcription. Instead, the predicted “bursty” mode of expression could explain the variability in transcript levels in single cells. Cell-to-cell transcript heterogeneity was also observed for pre-rRNA transcripts during the YMC, despite population levels oscillating with periods of cell growth and ribosome biogenesis. The link to cell growth is supported by the observation that ribosomal RNA production is found to be temporally coordinated to TORC1-controlled Rps6 phosphorylation.
The examination of DNA content and cell diameters together with transcript numbers in single cells of YMC and mid-log populations indicates distinct sub-populations with different relationships between gene expression, proliferation and growth. In synchronous YMC cultures, metabolism and patterns of gene expression are proposed to alternate synchronously between phases of growth and quiescence, linked to metabolism by high or lower levels of oxygen consumption respectively. This study suggests that the organization of the culture is far more nuanced. It supports at least three distinct co-existing states in the population over each metabolic cycle, including small quiescent-like cells, slow-growing cells, and larger cells whose metabolism is remodelled, with increased oxygen consumption, to facilitate their entry and progression through the cell division cycle.

Keywords: yeast metabolic cycle
transcription dynamics
sub-populations
saccharomyces cerevisiae
RNA fluorescence in-situ hybridization
Advisor: Mellor, J
Structural studies of ER-associated protein quality control systems

ER-associated protein degradation (ERAD) is an important degradation pathway for the removal of misfolded proteins from the endoplasmic reticulum (ER). This pathway encompasses a set of evolutionary conserved mechanisms for the selection, ubiquitination and retrotranslocation of membrane and lumenal proteins from the ER to the cytosol. Recent structural studies of the yeast Hrd1 E3 ligase complex identified a possible mechanism by which ERAD substrates are retrotranslocated across the ER membrane. Yeast Hrd1 forms a heterodimer with the rhomboid pseudoprotease Der1, each of which is proposed to contribute a half-channel in the membrane for retrotranslocation. Crosslinking studies also support this hypothesis. However, the mechanisms for selection of membrane substrates are still unknown and the identity of the translocon in other ERAD pathways remains elusive. This is further hindered by a lack of structural studies, especially in mammalian systems.
This thesis presents a bottom-up screen for the identification of mammalian ERAD factors amenable to structure determination by cryo-electron microscopy (cryo-EM). High-resolution structures of the mammalian E3 ligase Hrd1 were determined and two distinct dimeric states identified. These are termed the “open” and “closed” state due to rearrangements at the dimer interface that lead to repositioning of the E3 ligase RING domains within the dimer. These structures are compared with their yeast counterpart and analysed to understand key differences that may be important in ERAD. A mammalian expression system was developed for reconstitution of Hrd1 complexes containing additional binding partners. Complexes containing Hrd1 and its core interactors were isolated and imaged by cryo-EM. Other ERAD complexes were also purified and imaged by cryo-EM. This thesis provides a foundation for future structural studies of mammalian ERAD complexes.

Advisor: Carvalho, P
Lea, S
Sex, race and power: colonial and interracial sexuality in the French Empire in Morocco, 1912-1956

This thesis examines Morocco under French rule (1912-1956) through experiences of gender, sexuality and race. It argues that colonial power was experienced intimately on a large scale through the body and through emotions. This regulation of sexuality extended from sex work into consensual relationships and through attempts to intervene into emotions and sexual desire to police racial boundaries and the limits of whiteness. This thesis outlines how French colonial authorities attempted to regulate sexuality and gender in Morocco in five chapters. The first chapter shows the exploitative sex work system introduced by French health authorities in Morocco that trapped women in brothels to protect the health of European men and women. The second chapter offers a case study of how the French military trafficked 211 Moroccan women to France to work in military brothels in 1947 to prevent interracial sexuality after brothels had been banned in France, comparing this case study to French women who moved to North Africa to sell sex in the same period and moral panics about the “white slave trade”. The third chapter examines letters from European women to their Moroccan lovers, which were used as proof that these women were “dangerous to public security” and should be expelled from Morocco for threatening racial hierarchies. The fourth chapter compares these relationships with “desert romance” novels and films from the 1920s onwards to argue that European women sought to recreate elements of fictional relationships with Moroccan men and that French authorities heavily censored films in Morocco to attempt to regulate the space of sexual fantasy. The fifth chapter looks at queerness, arguing that colonial understandings that sex between men was “traditional” to Moroccan society meant that French authorities avoided intervening when European men bought sex exploitatively from Moroccan boys, but did police gender roles and binaries.

Keywords: global history
French empire
gender
history
sexuality
North Africa
imperialism
France
Morocco
prostitution
colonialism
Advisor: McDougall, J
Carroll's regress, Bradley's regress, and the incoherence of logical consequence

§1 frames Carroll's regress as a problem of metaphysical grounding, i.e. as an instance of Bradley's regress, and attempts to provide it the strongest possible defence. §2 applies this regress to accounts of logical consequence, and argues that all such accounts ultimately fail to explain why modus ponens is valid. §3 argues that rejecting logical consequence as incoherent amounts to rejecting the analytic/synthetic distinction as incoherent, and discusses the devastating consequences of doing so. §4 shows that the self-undermining nature of such a view has its roots in the Principle of Sufficient Reason, and works towards a way of resolving the paradox that is exemplified in §5.

Keywords: Carroll's regress
Bradley's regress
logic
normativity
principle of sufficient reason
Advisor: Williamson, T
Theories of mind in international relations: why individuals' inferences about states' motives vary

In international politics, communication about motives can make the difference between bargaining and war, policies of mutual reassurance and arms races, a state of perpetual conflict and the pursuit of a shared vision for international society. However, despite its centrality, empirical research on the communication of motives has long lagged behind theoretical scholarship, and fundamental questions about the microfoundations of motives remain: how do individuals infer a state’s motives from its actions, and why do individuals’ inferences dynamically vary, sometimes converging, other times diverging, in response to a state’s signal? This thesis draws on psychology and the philosophy of mind to explore these questions. First, I examine the theoretical foundations of a recent wave of psychological research in International Rela- tions and show that this research shares with rationalism a conception of the mind as computer. In order to explain variation in belief formation and updating about motives, I argue, we must move beyond this conception and integrate rationalist and psychological approaches to information processing with constructivist insights into social facts and systems of meaning. Second, I develop a domain-specific theory of attribution to explain how individuals infer motives in international politics. Combining a cross-national survey experiment with an in-depth analysis of evolving perceptions of Soviet motives during the Carter Administration, I find support for the costly signaling hypothesis, yet also show that the way individuals infer motives is shaped by their ontological assumptions about the target. Importantly, differences in these assumptions do not always result in divergent responses to costly signals: whether or not they do depends on the signal in question. Offering novel evidence on the attributional processes that underpin costly signaling, this thesis has important implications for the risk of escalatory dynamics between states and the study of the mind in International Relations.

Keywords: experimental social science
motives
perception and misperception
attribution
signaling
international conflict
political psychology
Advisor: Johnson, D
Leader Maynard, J
"How do I make Oppa Sarang Me?": resemiotisation and reconstruction of meaning in the global anglophone K-pop fandom

The intelligibility of a mixed Korean-English phrase such as “how do I make oppa sarang me?” to a member of the global anglophone K-pop fandom is the result of dynamic and interactive processes of resemiotisation that are articulated on multiple levels. Traditional understandings of language mixing and language borrowing are no longer adequate to contextualise and understand the creative and ideological linguistic practices occurring in diverse online communities. Beyond word-for-word linguistic transfer of words frequently encountered in K-pop lyrics and Korean language media, the indexicality of certain Korean words is enhanced through the addition and subtraction of meanings as they are negotiated within a globalised fandom context.
This process of resemiotisation is a complex one, as transcultural K-pop fans operate within a cultural and linguistic convergence point in the K-pop fandom. This thesis uses three case studies of Korean cultural terms: oppa ‘older brother’, unni ‘older sister’, and skinship, to examine and evaluate how fans create meaning and ideology around the use of Korean words that carry cultural significance in Korean-speaking contexts. Much like the fans themselves, Korean cultural words now exist simultaneously in multiple semiotic contexts and using a corpus-based critical discourse analysis methodology, this thesis pays specific attention to how these words are interpreted and re-coded by English speaking fans. It will be argued that use of Korean cultural terms is read on a binary scale of ‘acceptable’ or ‘unacceptable’, mirroring intra-fandom discourse of the ‘normal’ or ‘abnormal’ fan. This thesis points to the idea that notions of authenticity, indexicality, and context inform the construction of ideology and discourse around the use of Korean cultural terms.

Keywords: Korean
K-pop
social media
fandom
online communication
Advisor: Kiaer, J
Kin and culture: clan, household and family formation in late antique Armenia

The importance of Armenia’s hereditary naxarar elite in the late antique and medieval eras has long been acknowledged by scholars, and the region’s peripheral position has made these landed aristocrats a focus of academics of the Byzantine and Sasanian Empires also. However, study of naxarar families has not been accompanied by dedicated scholarship concerning the nature of family itself as an institution within Armenia. The following thesis acts as a first step, examining how Armenian families formed, operated and what expectations were placed upon their members from the fifth century until the mid-seventh century CE.
The thesis argues the family was perhaps the most significant political entity in late antique Armenian life. Membership within a naxarar clan was more significant than official service in the Aršakuni royal court or Byzantine or Sasanian imperial administration. Indeed, monarchical and imperial courts, as well as the native Christian clerical administration, even drew on these clans to support their authority. Clan power was safeguarded from imperial interference by Armenia’s geography, strategic location and probably the institution’s deep integration at less prestigious (and less visible) levels of society, with clerics, lesser nobles and perhaps non-nobles all being arranged in clans. This was reinforced by the interlacing nature of the household, which incorporated individuals of various clans and social classes through marriage, service, slavery and dayeakut‘iwn and, in doing so, better embedded the family within the social framework.
Armenia is not unique in emphasising the family’s place as a critical institution, and Kin and Culture finds substantial parallels between Armenian and Iranian practice, most notably that of the Sasanians’ Parthian predecessors. However, Armenia is a particularly visible example of clan power. Analysis explicitly through the lens of family and family practices has implications for our understandings of late antique Armenian culture, society and law.

Keywords: household
Armenian Christianity
family
Sasanian Empire
Naxarar
Armenia
Byzantine Empire
Late Antiquity
childhood
clan
family formation
Dayeak (Wet nursing)
marriage
Advisor: Vevaina, Y
Van Lint, T
Booth, P
Nanomechanical behaviour of the monolithic framework solids: an experimental and modelling study

Metal-organic frameworks (MOFs) have established themselves as a versatile material platform for a wide variety of applications such as gas adsorption, energy conversion and storage, luminescence and chemical sensing. Over the past two decades, scientists have designed numerous MOF systems and composites that are specifically tailored for different applications, thanks to their extraordinarily large internal surface area and high tuneability. However, the integration of MOFs into real-world sensors and devices still represents a challenge. The majority of MOFs reported to date is in fact synthesised in the form of polydisperse powders, characterised by some intrinsic limitations. The aim of this thesis is to gain understanding of the mechanical behaviour of robust monolithic sol-gel MOFs, identified as a promising candidate for the transition of this class of materials from the academia to industrial deployment. The advantages and potential applications of MOF monoliths are described in Chapter 1. An overview of nanoindentation, the most used technique for the mechanical characterisation of MOFs, is provided in Chapter 2, along with a literature review of the field of MOF mechanics. Chapter 3 summarises the synthesis protocols and the material characterisation techniques utilised throughout the thesis. In Chapters 4, 5 and 6, different aspects of the mechanical response of the prototypical MOF monoliths were systematically studied by means of nanoindentation, spectroscopy, and finite element simulations. In particular, plasticity, fracture toughness and stress-strain relationships underpinning the mechanical performance of MOF monoliths are investigated, and their connections to the nanostructure and the framework architecture are established. Finally, the reported findings are critically summarised in Chapter 7, along with a personal perspective on the future development of the field.

Keywords: nanomechanics
MOFs
sol-gel
spectroscopy
FEM
monoliths
nanoporous materials
micromechanics
nanoindentation
fracture
Advisor: Tan, J
Non-parametric deep learning with applications in active learning

We challenge a common assumption underlying most supervised deep learning: that a model makes a prediction depending only on its parameters and the features of a single input. To this end, we introduce a general-purpose deep learning architecture---Non-Parametric Transformers (NPTs)---that takes as input the entire dataset instead of processing one datapoint at a time. Our approach uses self-attention to reason about relationships between datapoints explicitly, which can be seen as realizing non-parametric models using parametric attention mechanisms. However, unlike conventional non-parametric models, we let the model learn end-to-end from the data how to make use of other datapoints for prediction. Empirically, NPTs solve complex reasoning tasks unsolvable by traditional deep learning models and make use of interactions between datapoints in achieving highly competitive results on tabular data.
We then turn our attention to in-context learning, a non-parametric method for few-shot learning recently popularized as language model (LM) prompting, which conditions predictions directly on a context set of examples. Combining in-context learning with information-based active learning, we introduce Active In-Context Learning, an algorithm for designing informative context sets which minimizes labeling costs and avoids the retraining normally necessary in active learning. Next, we demonstrate that our method can tractably compute two mutual information (MI)--based acquisition functions previously deemed intractable or approximated using variational inference. Lastly, we consider active learning for downstream tasks far from LM pretraining distributions. We develop Meta-NPTs, an in-context learner meta-trained on a distribution of tasks related to the downstream task of interest. Meta-NPTs implicitly ensemble predictions over a task posterior, quantifying uncertainty over plausible task identities. In early results, Active In-Context Learning improves the few-shot learning performance of OPT-30B on BoolQ, Meta-NPTs leverage uncertainty over tasks to perform Active In-Context Learning, and our MI-based acquisition functions often outperform the established predictive entropy function.

Keywords: supervised learning
active learning
attention
non-parametric modeling
transformers
multi-task learning
meta-learning
masking
pretraining
few-shot learning
equivariance
large language models
pre-training
self-attention
tabular
invariance
prompting
Bayesian deep learning
uncertainty quantification