VictorJuiz/thesis huggingface dataset:
On the complexity of queries with intersection joins
Keywords: intersection joins
iota acyclicity
complexity

This thesis studies the complexity of join processing on interval data. It defines a class of queries, called Conjunctive Queries with Intersections Joins (IJQs). An IJQ is a query in which the variables range both over scalars and intervals with real-valued endpoints. The joins are expressed through intersection predicates; an intersection predicate over a multi-set that consists of both scalars and intervals is a true assertion, if the elements in the multi-set intersect; otherwise, it is false. The class of IJQs includes queries that are often asked in practice.
This thesis introduces techniques for obtaining reductions from the problem of evaluating IJQs to the problem of evaluating Conjunctive Queries with Equality Joins (CQs). The key idea is the rewriting of an intersection predicate over a set of intervals into an equivalent predicate with equality conditions. This rewriting is achieved by building a segment tree where the nodes hierarchically encode intervals using bit-strings. Given a multi-set of intervals, their intersection is captured by certain equality conditions on the encoding of the nodes. Following that, it turns out that the problem of evaluating an IJQ on an input database containing intervals can be reduced to the problem of evaluating a union of CQs on a database containing scalars and vice versa. Such reductions lead to upper and lower bounds for the data complexity of Boolean IJQs, given upper and lower bounds for the data complexity Boolean CQs. The upper bounds are obtained using a reduction called forward reduction, which reduces any Boolean IJQ to a disjunction of Boolean CQs. The lower bounds are obtained by a reduction called backward reduction, in which any Boolean CQ from the aforementioned disjunction is reduced to the input Boolean IJQ. Overall, the two findings suggest that a Boolean IJQ is as difficult as the forward disjunctions' most difficult Boolean CQ. Last but not least, this thesis identifies an interesting subclass of Boolean IJQs that admit quasi-linear time computation in data complexity. They are referred to as ι-acyclic IJQs.
Advanced deep active learning & data subset selection: unifying principles with information-theory intuitions
Keywords: active learning
uncertainty estimation
Bayesian deep learning
deep learning
information theory
active sampling
out of distribution detection
data subset selection

At its core, this thesis aims to enhance the practicality of deep learning by improving the label and training efficiency of deep learning models. To this end, we investigate data subset selection techniques, specifically active learning and active sampling, grounded in information-theoretic principles. Active learning improves label efficiency, while active sampling enhances training efficiency.
Supervised deep learning models often require extensive training with labeled data. Label acquisition can be expensive and time-consuming, and training large models is resource-intensive, hindering the adoption outside academic research and "big tech."
Existing methods for data subset selection in deep learning often rely on heuristics or lack a principled information-theoretic foundation. In contrast, this thesis examines several objectives for data subset selection and their applications within deep learning, striving for a more principled approach inspired by information theory.
We begin by disentangling epistemic and aleatoric uncertainty in single forward-pass deep neural networks, which provides helpful intuitions and insights into different forms of uncertainty and their relevance for data subset selection. We then propose and investigate various approaches for active learning and data subset selection in (Bayesian) deep learning. Finally, we relate various existing and proposed approaches to approximations of information quantities in weight or prediction space.
Underpinning this work is a principled and practical notation for information-theoretic quantities that includes both random variables and observed outcomes. This thesis demonstrates the benefits of working from a unified perspective and highlights the potential impact of our contributions to the practical application of deep learning.
Alchemical poetics in seventeenth-century women's writing
Keywords: Alchemy
Poetics
Women's writing
History of science

This thesis explores how four female poets—Aemilia Lanyer (1569-1645), Hester Pulter (1607-1678), Katherine Philips (1632-1664), and Margaret Cavendish (1623-1673)—conceptualise poetry as an alchemy of the mind that nonetheless has real, practical implications for themselves and for their readers. The ‘alchemical poetics’ of these women writers thus exhibit a lively interest in, and radical transformation of, alchemical thought that grapples variously with the saving of souls, healing of the body, and transmutation of matter. More crucially, I contend that this grouping of women writers is actively participating in the evolution of alchemical thought through poetry.
Over the course of this thesis, I present the ‘alchemical poetics’ of Lanyer, Pulter, Philips, and Cavendish as creatively engaging with, and rethinking, a wide range of alchemical authors and ideas in ways that have hitherto been underappreciated by literary critics as well as historians of science. In this regard, my thesis integrates recent shifts in the history of science and the role of women, but also fruitfully extends them into new and exciting territory. The promotion of the importance of women in histories of alchemy, now widely recognised as important to a range of scientific activities in the early modern period, has occurred alongside renewed interest in female writers of the early modern period; yet only a handful of critics have actually seen how these fields are mutually informative—a missed opportunity that this thesis aims to redress.
In four chapters, each dealing with a single author, I reveal hitherto uncovered connections between alchemical communities and draw on newly identified alchemical source material to address the deeply-rooted interconnections between alchemical practice and its poetic representation. I interrogate what this alchemical material generates in a specifically poetic context, and map how this distinctly poetic engagement shifts over the seventeenth century. The content of this thesis as well as chronological arrangement therefore seeks to reveal new perspectives not only on how these female poets engaged with the substance of early modern alchemical thought, theology, politics, and literary culture, but also how serious their contemporaries also understood that engagement to be.
A study of the cult of Guhyakālī in the medieval Kathmandu Valley through the manuscripts of the Newars

Keywords: Kaula
̐Guhyakālī
Śaivism
Tantric iconography
Śākta Tantra
Newar religion
Newar manuscripts
Hindu rituals

This thesis concerns worship in the Krama or the cult of Guhyakālī in medieval Nepal, drawing mainly on unpublished liturgical sources and Tantras for its analysis. A major part of the thesis is the edition of Vimalaprabodha’s previously unpublished Kālīkulakramārcana, the most elaborate known Krama liturgy. Beyond this edition, the thesis is the first full study of the ritual practice, rather than philosophy, of the Krama and is split into two rough sections. The first (Chapters 1 – 3) deals with the iconography of the Krama as found in the medieval Kathmandu Valley. Chapter 1 provides an analysis of the salient features of the 54-armed, ten-faced Guhyakālī as visualised in several textual and visual sources, allowing us to assess the consistency of Guhyakālī’s depiction and decipher problematic elements. This chapter also raises interesting questions on the nature of iconography and the relationship between the worshipper and worshipped in Krama visualisation. A new edition of the supreme Guhyakālī’s dhyāna from the Parātantra benefitting from these findings and new manuscript evidence accompanies the analysis. In Chapter 2, we cover the iconography of the entire Krama pantheon and note important trends concerning both central and ancillary deities. Meanwhile, Chapter 3 attempts to decode the description of some significant yet complex cakras of the Krama that warrant independent treatment.
The second section (Chapters 4 and 5) includes an extended exposition of the Kālīkulakramārcana’s entire ritual sequence. The commentary in Chapter 4 examines the ritual process of both routine and occasional rites by clarifying cryptic aspects and remarking upon distinctive elements. Chapter 5 is devoted to the last three occasional rites of the Kālīkulakramārcana, especially the Mahāśivarātrividhi. These rites find their parallel in another text by Vimalaprabodha still unknown to scholarship - the Parvatrayavidhāna – whose edition is also published as part of the thesis. The last chapter also conjectures the social context of the Krama’s rites in medieval Nepal. The non-dual theology underpinning Krama ritual is touched upon here and discussed more extensively in the conclusion.
Molecular machines for controlling transmembrane ion transport
Keywords: Anion Transport
Molecular Machines
Supramolecular Chemistry

This thesis describes the design of molecular machines for the control of transmembrane ion transport. Employing a relay transport mechanism, halogen bonding transporters with high ion selectivity and azobenzene based transporters with photo-modulated activity are reported.
Chapter 1 introduces the field of transmembrane ion transport, highlighting key examples of synthetic ion channels, mobile carriers and anchored carriers which display stimuli-responsive behaviour.
Chapter 2 identifies the dependence of membrane thickness on the therapeutically important Cl− > OH− anion transport selectivity and describes a novel highly active and selective halogen bonding relay transporter.
Chapter 3 describes a unique photo-switchable relay transport system which regulates transport activity through control of the length of a telescopic carrier arm on the relay transporter, switching with visible light within the membrane in a fully reversible manner.
Chapter 4 expands on the photo-switchable relay transport system, introducing a new anchoring ammonium group delivers transporters to both leaflets of pre-formed bilayers.
Chapter 5 outlines the experimental procedures employed in this work.
Witnessing a wounded world: a theology of ecological trauma
Keywords: suffering
trauma theology
deep incarnation
ecotheology
Christology

This thesis lies at the intersection of ecotheology and trauma theology. My basic claim is that the approach of Christian trauma theologians to cases of traumatic human suffering can be fruitfully extended and applied by ecotheologians in the context of the present ecological crisis. The category of trauma acknowledges the seemingly incomprehensible severity and scale of current ecological suffering, whilst also resisting the impulse to explain such suffering in terms of its origin or its solution. I argue that three defining characteristics of human trauma are identifiable in the ecological realm--namely, a rupture to communication, a rupture to flesh, and a rupture to time. But this ascription of trauma to nonhuman entities does not require envisaging the earth as conscious. Instead, I understand ecological trauma as an anthropomorphism of earth systems and processes that enables us to better relate to ecological suffering. Following existing work in trauma theology, I propose that the practice of bearing witness to ecological trauma constitutes a vital coping strategy. In response to the rupture of communication, I argue that Christ serves as a witness to traumas such as climate change and biodiversity loss. In response to the rupture of flesh, I expand this model of Christic witnessing by suggesting that Christ's incarnation in the flesh enables him to bear witness to the wounded flesh of the world. And in response to the rupture of time, I contend that Christ's recapitulation of creation, along with the persistence of the wounds on his resurrection and ascension flesh, allow him to witness the recurrence and permanence of contemporary ecological devastation. I conclude that a process of Christic witnessing forms one possible theology of ecological trauma. In short, Christ's permanently wounded flesh bears witness to a permanently wounded world.
Characterising the contribution of Hrd1 complex components to the UPR: Implications for cancer cell survival  
Keywords: Breast Cancer
Proteotoxic Stress
ERAD
The UPR

The Hrd1 complex is a large multiprotein complex that spans the endoplasmic reticulum (ER) membrane with Hrd1 itself functioning as an E3 ligase in the endoplasmic reticulum associate degradation (ERAD) pathway in which unfolded and misfolded proteins are cleared from the ER in order to maintain protein homeostasis. Various components of the complex are transcriptionally regulated by the unfolded protein response (UPR), a protein quality control mechanism activated upon the detection of stress, meaning the complex itself can adapt to fluctuations in levels of cellular stress.
Proteotoxic stress is often upregulated in cancer cells with this capable of manifesting as ER stress. Therefore, some cancer cells are particularly reliant on the UPR and ERAD in order to maintain the fidelity of the proteome and manage basal stress levels below a threshold that allows for survival. Much of the direct contribution of the Hrd1 complex, and specifically the role of each of its components, in this phenomenon remains unknown. This study aimed to systemically reduce the bioavailability of individual Hrd1 components to determine the resulting effect on cancer cell survival and proliferation.
Unveiling novel participants in the DNA damage response
Keywords: Interstrand crosslink (ICL)
DNA damage response (DDR)
Fanconi anaemia (FA)
Nucleolar Stress

The human genome is constantly challenged by DNA damage resulting from environmental factors and metabolic processes. To safeguard the integrity of the genome, a complex defence system known as the DNA damage response (DDR) has evolved. The DDR comprises intricate mechanisms, including DNA repair pathways, damage tolerance processes, cell cycle checkpoints and programmed cell death, together aimed at maintaining genomic stability. Among the various types of DNA lesions, interstrand crosslinks (ICLs) pose a significant threat as they impede DNA replication and transcription. Inadequate repair of ICLs is closely linked to Fanconi anaemia (FA), a genetic disorder associated with severe health consequences. Moreover, ICL-inducing agents have a broad clinical application in cancer therapy, although the emergence of drug resistance poses a challenge. Therefore, comprehending the mechanisms involved in ICL repair is critical for developing alternative treatment strategies and enhancing drug sensitivity.
The focus of this DPhil thesis is to investigate the participation and function of two novel proteins in the cellular response to ICL-induced DNA damage. Rapid accumulation of the first protein at ICL sites is observed, and its knockout results in heightened cellular sensitivity to ICL-inducing agents, indicating its positive contribution to cell survival against ICLs. Further investigations revealed that this protein operates independently of the established FA and NEIL3 pathway for ICL repair, suggesting its potential role in alternative repair mechanisms or early-stage DDR processes. The second novel protein exhibits a distinct relocation from the nucleoplasm to the peripheral nucleoli, forming a ring-shaped accumulation pattern in response to ICLs. Additional experiments demonstrate that this protein translocates into the nucleolar cap under nucleolar stress induced by various types of DNA damage and transcription inhibition. These findings support the notion that the nucleolus acts as a stress sensor, and the nucleolar translocation of this novel protein potentially contributes to cellular fate decisions or the interplay between DDR and nucleolar function. Together, the research presented in this thesis provides insights into the roles of two new protein players in preserving genomic stability. Understanding their interactions with established repair pathways and their potential therapeutic implications in FA and cancer treatment will pave the way for developing targeted interventions and improving patient outcomes.
Continuum description of living matter
Keywords: living systems
active matter
continuum theory

Living systems are one of the most complex forms of matter. Among their many different aspects, one unifying property of any living matter is activity. Active materials continually extract energy from their surroundings to move, grow, and self-replicate.
To perform these functions, active units exert forces on their environment and this raises the question of the extent to which the behaviour of biological systems can be understood by measuring forces and flows and using the generic physical theories of active matter.
At the microscale, several important aspects of the dynamics of living systems can be described by the theories of active nematics. We discuss, in the second chapter of this thesis, that long-range interactions in active suspensions at the microscale have a nematic symmetry, and this makes active nematic models a powerful tool for studying living systems.
In this thesis, we extract essential features from living systems in experiments to build continuum active nematic models that are able to capture the behaviour of the experiments. Using the continuum models, we then perform numerical simulations and linear stability analyses to explore the dynamical steady states of the model, and compare them with the ones in the experiments. We show that the conventional active nematic models need to be modified and evolved, according to the active system under study, to allow us to capture the patterns observed in different experiments.
Our results indicate that fractal-like patterns that form at the interface of bacterial droplets cannot be explained by the conventional active biphasic models. We suggest that the presence of an active layer at the bacterial interface produces the cell orientation and flow patterns in the experiments.
We then construct a continuum description for living tissues and demonstrate that introducing new continuum fields associated with cell area and aspect ratio and decoupling the direction of the active force from the cell elongation, introduces new phases to the system. Analysing experimental data on MDCK cells, we use our model to understand the misalignment in the cell shape and stress orientation in the experiments.
Finally, we extend our study to three dimensions and show that active materials with extensile activity promote formation of twist-type defects and three-dimensional flows.
Theories and programming systems for weakly consistent distributed systems
Keywords: formal proofs
blockchain consensus protocols
replicated data
distributed systems
weak consistency

Weakly consistent distributed systems are systems that provide a weak form of guarantee about the sameness of the replicated data. They allow using the replicated data from any replicas without the coordination between them and can thus enhance the performance and availability of the system. However, due to the lack of coordination, programs developed on weakly consistent distributed systems might generate counter-intuitive results.
The aim of this research is to i) address those glitches in developing programs on weakly consistent distributed systems and ii) provide formal guarantee on the executions of programs run on such systems.
In order to overcome the counter-intuitive nature of the results generated by weakly consistent distributed systems, this thesis proposes a new programming language Lasp_PC, a variant of Lasp that uses provenance and cover, and its runtime system. Optimisation techniques are also introduced for the effective execution of the programs for the language and its runtime system.
This thesis provides formal guarantee for the programs run on weakly consistent distributed systems by defining key principles for the new language and presenting proofs for the theoretical properties of the language.
The new language introduced in the thesis uses a variant of OR sets that incorporates provenance and cover, OR_PC sets. The use of provenance and cover enables the language to offer the guarantee of a new property, strong consistency in weakly consistent distributed systems. The new property ensures the exclusion of the counter-intuitive results by enabling the retrieval of computational results from the systems. There is no provision of comparable guarantees in the existing research studies on Lasp. The OR_PC sets are used to define client-level data types, which retain the guarantee of the new property. The new property is also used to extend the new language to support aggregation operations that are considered particularly difficult to be supported in weakly consistent distributed systems.
The approach taken in this research to remedy the glitches and provide the formal guarantee has been implemented, optimised and evaluated in three substantial example programs, namely, the replicated leader board, the MapReduce program and the BigBench queries.
This thesis also identifies a case study of one of the extensively-used blockchain consensus protocols, the Stellar Consensus Protocol (SCP). It is currently difficult to be adopted for the newly developed language and its runtime system but the protocol has been rigorously studied using the formal modelling and verification techniques.
The indignant middle: the middle class and the fight against corruption in contemporary Latin American politics
Keywords: corruption
scandals
grand corruption
accountability
horizontal accountability
Latin America
middle classes

Previous studies have shown a strong, negative association between income-based measures of the middle class and grand corruption. However, the causal mechanism remains undertheorized and untested. Rationalist, value-change, and socioeconomic-status participation models are useful in elucidating why the middle classes develop anti-corruption attitudes and behaviors, but we lack an empirical examination of how these attitudes and behaviors translate into grand corruption outcomes. Existing theories relying on voting behavior run against a body of literature that shows that electoral penalties for grand corruption are highly contingent and sometimes non-existent. To address these limitations, this thesis answers the question: What causal mechanism explains the negative association between middle classes and grand corruption? Leveraging cross-country, national, and individual-level quantitative data, together with in-depth process tracing of six corruption scandals in contemporary Costa Rica, Chile, and Argentina, I argue that horizontal accountability institutions mediate the relation between the middle classes and grand corruption. As middle-income sectors expand, a larger share of the population gains political resources that allow it to engage with grand corruption concerns, and to mobilize and pressure for sanctions and reforms. In highly salient episodes, the middle classes amplify the alarms set off by grand corruption revelations and spur horizontal accountability institutions to react with mediatized displays of diligence. This then draws middle-class attention to the institutional response, shielding oversight authorities from political encroachment and allowing them to convert middle-class indignation into institutional power, through enhanced resources and capabilities. The thesis contributes to our understanding of the determinants of corruption by theorizing and testing a causal mechanism that, over time and through successive iterations, builds up a country’s anti-corruption framework.