VictorJuiz/thesis huggingface dataset:
Identifying the mechanisms driving pancreatic ductal adenocarcinoma stem cell characteristics using single-cell RNA-sequencing
Keywords: Bioinformatics
Single-cell RNA-sequencing
Pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest human malignancies. Surgery, the only curative treatment, is precluded by the late stage at diagnosis in 80% of cases. Recurrence after surgery is common, and the disease does not respond well to chemotherapy and radiotherapy. Resistance to therapy and recurrence are thought to be driven by pancreatic cancer stem cells (PCSCs), a subset of cells with self-renewal and differentiation capacities. Annihilating these cells is therefore of paramount importance for treating PDAC. Identifying these cells, however, has proven challenging. Currently, there is no gene signature able to identify PCSCs. In this thesis, I employed single-cell RNA-sequencing to integrate multiple approaches towards the identification of PCSCs (experimentally-derived markers, bioinformatics-based gene sets, and computational tools to infer developmental potential from expression data), to uncover the genes and processes characterizing PCSCs, and to assess the effects of I-BRD9, an inhibitor of BRD9, a bromodomain-containing protein involved in chromatin remodelling upon the PCSCs, using two single-cell RNA-sequencing PDAC datasets. The results evidenced cell cycle abnormalities as crucial to cancer stemness in PDAC, with multiple lines of evidence converging towards the identification of clusters whose markers significantly overlapped with cell cycle-related stemness-associated gene sets as PCSCs. Traditionally-derived PCSC markers were found to be largely of low reliability. A transitional cell population distinct from both PCSCs and the bulk of the cells, and one with an advanced stage of differentiation which however regained partial stemness-like characteristics, were identified as highly drug-resistant, suggesting that greater than previously believed PDAC cell heterogeneity, not merely PCSCs, is involved in chemoresistance. I-BRD9 achieves a ~6-fold reduction of PCSCs in one dataset, likely mediated by the demonstrated downregulation of key G2/M DNA replication checkpoint-linked genes such as TOP2A and CDK1, but the effects are partially reversed by the addition of PDAC drug gemcitabine.
Re-presenting dislocation: the poetics of exile and diaspora in ancient Jewish texts
Keywords: diaspora
exile
Hebrew Bible
poetics

This thesis considers examples of ancient Jewish literature that present open-ended poetics concerning exile and diaspora. Part I of the thesis focuses on the book of Lamentations, Second Isaiah, and 1QS to demonstrate that these examples present the resolve of exile as deferred, and do not focus solely on physical homecoming. Part II considers how the diaspora narratives of Esther and Joseph also reflect an open-ended poetics towards exile and diaspora by the way in which they characterise the diaspora heroes/heroines. Moreover, the interpretations of Esther in antiquity present an open-ended poetics by portraying the exile and diaspora as part of a larger history of displacement that is neither inherently negative nor absent of divine providence.
The language of “opened-endedness” is inspired from the work of Sidra DeKoven Ezrahi, who discusses how some Jewish texts offer “closure” to the “narrative of exile,” whereas others are more “open-ended.”1 In terms of biblical scholarship, and scholarship on Second Temple, Hellenistic literature and beyond, ancient Jewish literature is often regarded as containing closed poetic expressions concerning exile and diaspora. In the case of texts such as Second Isaiah, this literature is largely portrayed as a body of work that failed as prophecy because its idealized imagery of homecoming did not historically come to pass. Moreover, the diaspora narratives of Esther and Joseph, and the interpretations of Esther in antiquity, are often regarded as apologising for aspects of diaspora life, or as viewing the state of exile and diaspora as a burden. However, this thesis argues that these examples belong to a larger history of ancient Jewish texts that reflect upon displacement, suffering, and its impact on the divine’s relationship with the people in poetically nuanced ways.
Administrative jurisdiction
Keywords: judicial review
administrative law
jurisdiction

Jurisdiction is the extent of a power. This gives rise to an important distinction. Jurisdictional errors take an authority outside the scope of its power. Nonjurisdictional errors do not, even if they render the ensuing exercise of power unlawful. Unwelcome baggage has made the task of arriving at a coherent account of jurisdiction needlessly difficult. That baggage is the common assumption that lack of jurisdiction is the sole basis for judicial review. This is wrong. Abandoning it makes space for an attractive account of when an error is jurisdictional. An error is jurisdictional if (i) it is an instance of a kind of error, in the sense of ground of review, which could arise at the outset of proceedings, but (ii) it does not pertain to a collateral matter, the purpose of which is tangential to the purpose of the inquiry. I shall call this the revised temporal view of jurisdiction. It accepts the possibility of judicial review on both jurisdictional and nonjurisdictional grounds. But the distinction has practical significance for at least three reasons. First, only acts with a jurisdictional flaw are nullities. Second, jurisdictional questions take analytical priority over nonjurisdictional ones. Third, post hoc explanations are only acceptable for jurisdictional issues.
High-fidelity, near-field microwave gates in a cryogenic surface trap
Keywords: laser free gates
microwave gates
two-qubit gates
quantum computing
calcium 43
ion transport
surface trap
dynamical decoupling
trapped ions

We present a novel dynamical decoupling strategy for near field microwave gradient driven, Mølmer-Sørensen style, two-ion quantum logic gates, which suppresses errors from both fluctuations in the qubit frequency and imperfection in the decoupling drive itself. Using a microwave-integrated surface-trap which is operated cryogenically at 25 K and a magnetically insensitive 43-Ca+ qubit at 288 G, we demonstrate a 331 us two-ion quantum logic gates, with 4.9(11)e-3 logic error probability. This is below the 1% error threshold required for quantum error correction and represents a ~10x gate time reduction when compared to previously demonstrated near field gradient driven microwave gates below the 1% error probability threshold. Additionally, two faster gates were demonstrated without the use of dynamical decoupling. Respectively, these two gates had gate operation durations of 216.8 us & 153.8 us and measured gate error probabilities of 8.5(20)e-3 & 9.8(21)e-3. Further, we develop a method for rapid calculation of ion transport operations. We successfully demonstrate ion transport as well as crystal splitting and merging operations within two different ion traps using the waveforms calculated by this ion transport toolbox.
Exploiting ion-charged dielectrics for high efficiency solar cell architectures
Keywords: ion migration
inversion layer cells
dielectrics
charge-induced emitter
silicon solar cells

This thesis studies the production and performance of p-type inversion layer (IL) Si solar cells. IL cells use an electric field to induce an inversion layer and create a pn junction. Compared with the mainstream diffused pn junctions, the advantages of field-induced junctions include lower fabrication costs and less carrier recombination. IL cells have been studied since the 1970s. In previous work, intrinsic charge in dielectric materials has been used to induce the inversion layer. However, the charge density was not high enough to induce a sufficiently conductive junction emitter (n-type surface layer). In this thesis, a field and temperature-assisted ion migration method was used to incorporate a controllable amount of positive ionic charge into dielectric thin films and fully exploit IL cells.
The ion migration method was first used to induce an electron accumulation layer on n-type substrates. The lowest accumulation layer sheet resistance (Rsh) obtained is 950 W/sq, which is the lowest reported in the literature. A model was developed in Sentaurus TCAD to study the formation and properties of field-induced layers. The simulation results suggested that the Rsh is determined by charge density, band-tail interface state density, and illumination. With optimised charge density and interface parameters, the lowest IL Rsh that can be achieved in the dark is 1.1 kW/sq. Although such Rsh is ~7 times higher than that of typical n-type phosphorous-diffused emitters (150 W/sq), the cell performance evaluated by device simulations is not limited by the high Rsh. The simulation model comprises a field-induced emitter and a PERC-like structure at the rear. The best simulated IL cell shows an efficiency of 24.8%, comparable to the best predicted for PERC. This indicates that field-induced emitters can perform as well as P-diffused emitters.
Proof-of-concept IL cells were fabricated via laser doping, annealing, ion migration, and light-assisted electroplating. The formation and uniformity of the field-induced emitter were confirmed by taking a photocurrent map of the IL cell. The champion cell presents an efficiency of 10.8%, demonstrating that IL cells can be fabricated using the ion migration method. Although the efficiency is low, simulation results suggest that an efficiency of as high as 24.8% can be achieved with optimised processing. With low fabrication costs and high potential cell efficiencies, field-induced emitters can become competitive alternatives to P-diffused emitters in commercial applications.
Panoptic dual-use management: preventing deliberate pandemics in an age of synthetic biology and artificial intelligence
Keywords: technology governance
biosecurity
pandemic virus
dual-use risks
artificial intelligence
pandemic prevention
dual-use dilemma

Powerful new technologies can have profound global security implications. In this thesis, I investigate how advances in synthetic biology and artificial intelligence could have dual-use potential and enable the deliberate release of pandemic pathogens. I review risks from synthetic biology based on case studies on wildlife virus discovery, viral engineering for vaccine design, and viral engineering for gene therapy. For assessing impacts of artificial intelligence, I consider large language models and biodesign tools. I find that related advances can create new methods to engineer pathogens and make such capabilities increasingly accessible to non-specialists.
These risks are not well captured by existing risk mitigation measures. I argue that the management of dual-use virological research is currently defined by oversight of individual research projects. This is effective for addressing high-risk research but fails to address risks from a more diffuse set of research and technologies with dual-use potential.
To help mitigate these risks, I introduce the idea of panoptic dual-use management. Inspired by methodologies to reduce carbon emissions, panoptic dual-use management involves treating associated dual-use risks as negative externalities and creating appropriate incentives so they are accounted for in decisions between projects. I explore ways in which such incentives could be created for various stakeholders. For instance, funding bodies could use dual-use risks as a tiebreaker between projects on the brink of getting funded, a practice which would incentivise researchers to preferentially propose projects with lower dual-use risks. To realise this proposal, I sketch out a framework for assigning tiered dual-use scores to virological research.
I conclude by highlighting the importance of combining different dual-use management approaches across stakeholders and geographies to establish an effective complex of overlapping mitigation regimes.
Business and contested authority in Colombia, 1996-2016
Keywords: Conflict
Business
Contested authority
Civil war
Colombia

Businesses are prominent actors in areas of contested authority, yet they respond in varied ways to its challenges, from seizing expansion opportunities, negotiating with armed groups, working with state armed forces, or leaving altogether. What are the conditions that affect businesses in areas of contested authority, how do they respond, and what security outcomes do they experience? I argue protection quality – whether protection is reliable and affordable – and business power – a business’s capacity to deploy financial or political resources – are the key conditions that affect business security outcomes in areas of contested authority. Businesses respond through three pathways: they pursue accommodation by passively absorbing the costs of insecurity, they use voice to influence coercive actors to gain better protection, or they choose to exit by closing their business, seeking alternative protectors, or leaving altogether. The underlying conditions create four distinct security outcomes: coexistence, entanglement, survival, and victimisation. I present a series of cases across Antioquia and Valle del Cauca in Colombia from 1996-2016, comparing the conditions, responses and outcomes for agricultural firms, capital-intensive enterprises, neighbourhood shopkeepers, and mining companies. When protection quality and business power are high, businesses maintained a state of coexistence with coercive actors. When business power is high, yet protection quality is low, businesses experience entanglement with coercive actors. When protection quality is good, but businesses have less power, they experience survival, and when businesses have low power and poor protection, they experience victimisation. I draw from interviews with businesspeople, business association officials, journalists and observers gathered over the course of fieldwork in 2019, supplemented by newspaper articles, court documents, government data, and secondary sources.
Fisher-Hartwig asymptotics and log-correlated fields in random matrix theory

Keywords: Gaussian Multiplicative Chaos
Riemann-Hilbert Problems
Log-Correlated Fields
Toeplitz and Toeplitz+Hankel Determinants
Mathematical Physics
Fisher-Hartwig Singularities
Random Matrix Theory
Complex Analysis

This thesis is concerned with establishing and studying connections between random matrices and log-correlated fields. This is done with the help of formulae, including some newly established ones, for the asymptotics of Toeplitz, and Toeplitz+Hankel determinants with Fisher-Hartwig singularities.
In Chapter 1, we give an introduction to the mathematical objects that we are interested in. In particular we explain the relations between the characteristic polynomial of random matrices, log-correlated fields, Gaussian multiplicative chaos, the moments of moments, and Toeplitz and Toeplitz+Hankel deter- minants with Fisher-Hartwig singularities. Chapter 1 is based on joint work with Jon Keating [FK21], Tom Claeys and Jon Keating [CFK23], and Isao Sauzedde [FS22].
In Chapter 2, based on joint work with Jon Keating [FK21], we establish formulae for the asymptotics of Toeplitz, and Toeplitz+Hankel determinants with two complex conjugate pairs of merging Fisher-Hartwig singularities. We prove those formulae using Riemann-Hilbert techniques, which are heavily inspired by the ones used by Deift, Its, and Krasovsky [DIK11], and Claeys and Krasovsky [CK15].
In Chapter 3, based on joint work with Jon Keating [FK21], we complete the connection between the classical compact groups and Gaussian multiplicative chaos, by showing that analogously to the case of the unitary group first estab- lished by Webb [Web15], the characteristic polynomial of random orthogonal and symplectic matrices, when properly normalized, converges to a Gaussian multiplicative chaos measure on the unit circle.
In Chapter 4, based on joint work with Tom Claeys and Jon Keating [CFK23], we compute the asymptotics of the moments of moments of random orthogonal and symplectic matrices, which can be expressed in terms of integrals over Toeplitz+Hankel determinants. The phase transitions we observe are in stark contrast to the ones proven for the unitary group by Fahs [Fah21].
In Chapter 5, based on joint work with Isao Sauzedde [FS22], we establish convergence in Sobolev spaces, of the logarithm of the characteristic polynomial of unitary Brownian motion to the Gaussian free field on the cylinder, thus proving the dynamical analogue of the classical stationary result by Hughes, Keating and O’Connell [HKO01].
Ring-theoretic properties of augmented Iwasawa algebras
Keywords: Canonical dimension
Smooth representations
Noncommutative rings
Langlands programme
Completed group algebras
Coherent rings
p-adic Lie groups

Let p be a prime, G be a p-adic Lie group and k be a field of characteristic p. The augmented Iwasawa algebra kG is a noncommutative algebra extending the construction of the Iwasawa algebra of a compact p-adic Lie group. In this thesis we investigate the ring-theoretic properties of augmented Iwasawa algebras.
We prove that a split-semisimple group over a p-adic field F has a coherent augmented Iwasawa algebra if and only if its root system is of rank one, and deduce that kGLn(F) is coherent precisely when n is at most two. We also characterise when certain solvable p-adic Lie groups have a coherent augmented Iwasawa algebra. When kG is a coherent ring, the category of finitely-presented smooth representations of G over k is abelian. We give a module-theoretic characterisation of the latter property, and hence give examples of p-adic Lie groups for which it fails. These results are achieved by developing the theory of augmented Iwasawa algebras in detail, including their relation to smooth and admissible representations of G.
The Iwasawa algebra of a compact p-adic Lie group is always an Auslander-Gorenstein ring. Thus finitely-generated modules over Iwasawa algebras have a canonical dimension. Let G be a compact p-adic Lie group whose Lie algebra is isomorphic to a split simple F-Lie algebra. We prove that whenever F is a non-trivial finite extension of the p-adic numbers, kG has no modules of canonical dimension one. Consequently kG has a module of canonical dimension one only if the Lie algebra of G is isomorphic to sl2(Qp). As a corollary we obtain a new upper bound on the Krull dimension of kG.
When G is an arbitrary p-adic Lie group, any smooth admissible representation V is the dual of a kG-module M, finitely-generated over the Iwasawa algebra of a compact open subgroup of G. The canonical dimension of M measures the rate of growth of invariant subspaces of V. We prove a canonical dimension-theoretic criterion for V to be a finite length representation. We deduce that the finite length smooth admissible representations of GL2(Qp) with central character are precisely those whose duals have canonical dimension at most one. Finally, let F be a non-trivial finite extension of the p-adic numbers, G = GLn(F), and V be a smooth admissible representation of G with central character. A combination of our results shows that V has finite length if its dual has canonical dimension two.
Passionate correction: the theory and practice of modernist revision
Keywords: W. H. Auden
typewriter
modernism
T. S. Eliot
Virginia Woolf
Henry James
drafting
editing
revision

The early twentieth century in literature was a period of second chances. James Joyce and Virginia Woolf each spent a decade on their first novels, discarding complete drafts along the way; Henry James took three years to revise his already published work for the New York Edition. The poets fared no better. The Waste Land, Ezra Pound's first Canto, W. H. Auden's Collected Poems, and Marianne Moore's Complete Poems were all multiply rewritten.
This dissertation examines the importance of textual revision to Anglo-American modernism. I ask why modernist writers revised so laboriously, what modes of selfediting they preferred, and how they figured the process of textual genesis. Revision is not normally understood as an activity exceeding the idiosyncrasies of individuals. My work shows that it can and should be historicized as a form of cultural practice. In the first chapter, I discuss and criticize available models for theorizing revision. In subsequent chapters, I make use of methods from genetic criticism and social text editing to analyze the process of textual development from early manuscript drafts to final published editions.
The modernist practice of revision was enabled by changes in technology and the literary marketplace in the 1890s. At the same time, revision is an exemplary figure for modernism itself. By rereading a text, the revising writer pays homage to what is already there, but rewriting devalues and may even destroy the original version. This oscillating movement answers to a fundamental tension or puzzle in modernist thought between innovation and tradition, "making it new" and nostalgia for the past.
Where pre-twentieth century writers were uncertain and uneasy about the benefits of revision, modernist writers tend to portray textual change in positive terms as an inevitable process of "gradual betterment." Literary critics and editors have gladly adopted this teleology. At the same time, the most famous acts of modernist revision display a surprising pleasure in textual destruction. In chapters on Henry James, Virginia Woolf, T. S. Eliot, and W. H. Auden I explore the relationship between textual practice and early twentieth-century ideas about progress, selfhood, efficiency, and organic form.
A computational corpus study of harmony in the music of Anton Webern
Keywords: harmony
music analysis
pitch-class distribution
discrete fourier transform
corpus study
music21
atonal
pitch-class set
music information retrieval
serialism
Webern
computational musicology
dodecaphony

This thesis sets out to apply digital analysis to the music of Anton Webern, with the aim of quantifying elements of his harmonic style, and tracing their change across his practice. It is a corpus study, taking Webern’s 31 works with Opus numbers as its subject, and uses music21 for the data collection. Analytical subjects include distributions of pitch classes, intervals, and pitch-class sets; techniques for assessing these include clustering, regression analysis, and the Discrete Fourier Transform. Along the way, the thesis interrogates commonly-held assumptions about Webern’s music for which there is often little empirical evidence, and provides a multi-level perspective on the corpus, from the wide angle of whole-movement macroharmonies to the close-up detail of individual pitch-class sets. Chronologically, the results suggest that the advent of dodecaphony in Webern’s music had a limited effect on the surface features of the music he presented; rather that the major shift in his practice happened in his mid-period Lieder. Contra Allen Forte, I downplay the importance of octatonicism in his harmonic language in favour of a quartal quality, but in the process I explore the differing features between the various harmonic levels of Webern’s music.