VictorJuiz/thesis huggingface dataset:
The adaptation and critique of the Abhidharmic theory of perception in the Yogācāra works of Vasubandhu and their commentaries by Sthiramati

The purpose of the dissertation is to analyse the Yogācāra adaptation of the Abhidharmic theory of perception in the late works of Vasubandhu and their commentaries by Sthiramati. The framework of my investigation is provided by the Triṃśikāvijñaptibhāṣya where, following the Abhidharmic model, Sthiramati claims that all forms of consciousness necessarily possess a cognitive object (ālambana), a support (āśraya), an object-form or mode of grasping (ākāra) and are associated with certain mental concomitants (caitta). The core chapters of the thesis explore how these four constituents of the perceptual process are (re)interpreted by Vasubandhu in his Yogācāra works.
Focusing primarily on the difference between the ontological stances of the Abhidharma and the (idealist) Yogācāra works, scholarly narratives tend to emphasise the two traditions’ critical relationship. However, putting the ontological perspective aside, we find remarkable continuities between their doctrines that call for more attention. In this thesis, I aim to show that, despite the various criticisms raised by Vasubandhu, the theory of perception he puts forward in his Yogācāra treatises remains continuous with its Abhidharmic past. Vasubandhu does not only preserve many of the Abhidharmic notions, definitions and even classifications concerning ordinary, unenlightened sense perception. But he also adheres to traditional frameworks such as the abovementioned fourfold model of the perceptual process, even if he spells out some of its constituents differently in terms of the entities they refer to.
The dissertation provides a close reading and historically sensitive comparison of primary sources preserved either in their Sanskrit originals or in Tibetan translations, first of all, the Karmasiddhiprakaraṇa, the Pañcaskandhaka, the Triṃśikā, the Viṃśikā (together with its vṛtti) as well as their commentaries by Sthiramati, the Pañcaskandhakavibhāṣā and the Triṃśikāvijñaptibhāṣya. As for the Abhidharmic background, I rely on Vasubandhu’s magnum opus, the Abhidharmakośa(bhāṣya) and its commentary by Yaśomitra, the Sphuṭārthā Abhidharmakośavyākhyā.

Keywords: Yogācāra
Vasubandhu
Abhidharma
perception
Sthiramati
Buddhist philosophy
Advisor: Westerhoff, J
Polyphonic vespers c.1550 – c.1700: Sources, repertory, genres and performance practices in six Iberian religious institutions

This dissertation focuses on the sacred polyphonic repertory for the liturgical Hour of Vespers performed in religious institutions in the Iberian Peninsula, within the chronological period c.1550-c.1700. Six institutions were chosen as case-studies for this research.
The project examines the musical and liturgical practices (and the interface between them) at polyphonic Vespers in terms of its sources, the settings chosen by the chapel masters for performance (among the ones in each institution’s collections) and also performance practices. The genres most commonly set in polyphony at Vespers are analysed and exemplified from both printed and manuscript musical sources.
The choice of the above-mentioned time frame is based on questions of production and of musical style, liturgical reform, and of broader historical forces, already under way before the mid-sixteenth century, such as the crucial importance of text and textual perception.
All these had a direct influence on both the composition and the performance of Vespers music. The changes taking place, both from a textual and musical point of view, are patent not only in newly-composed items but also in those settings which became part of these institutions’ repertory for lengths of time which surpass, in some cases, the chronological limits of this dissertation.
The study of sources and repertory in different Iberian religious institutions reveals some settings common to all (the most obvious example of which is the collection of Morales’s Magnificat settings) but also locally produced unique works, something particularly noticeable in the genre of hymns.
Ceremonials and other sources show a wide variety of performance practices at Vespers, especially with regard to their alternatim practices, which reveal a much richer and diverse pattern than the standard odd-and-even-verse scheme usually found in printed sources from this period.

Keywords: Iberian Renaissance polyphony: Vespers Music: Sacred Music
Advisor: Rees, O
Musico-dramatic spatial analyses of aerial action in contemporary opera performance

Operatic performances invoking circus action have gained prominence since the late twentieth century. This thesis argues for the musico-dramatic contribution of aerial circus action in contemporary opera performance. There are two central claims of the thesis. One, that the spatial relationships created by the actual aerial circus actions in an opera performance contribute to musico-dramatic interpretations of an opera. Two, that the interdisciplinary study of opera and circus can offer insights into our understanding of how an opera in performance creates and communicates meaning.
By adopting a performative approach to the analysis of opera in performance, I isolate the musico-dramatic functions of spatial relationships produced by and complicated through the execution of circus action by an aerialist with a circus apparatus. Through an examination of a high-wire act in Alvis Hermanis’s 2012 Salzburg Festival production of Bernd Alois Zimmermann’s Die Soldaten (1960-64), aerial rope and aerial harness ensemble actions in Louise Moaty and Raphaëlle Boitel 2017 staging of Marin Marais’s Alcione (1706), and Japanese bondage in suspension and aerial contortion in Romeo Castellucci’s 2011 production of Richard Wagner’s Parsifal (1882), the thesis demonstrates the musico-dramatic contributions of spatial relationships created through aerial circus action in opera performance.

Advisor: Burden, B
Jones, S
Using extraterrestrial 3He concentration to examine changing sedimentation rates over climate cycles and climatic disturbances: evidence from the Cenomanian-Turonian of the Umbria-Marche Basin, Italy

The concentration of extraterrestrial 3He (3HeET) measured in pelagic sediments may be used as a proxy for sedimentation rate, allowing the construction of high-resolution timescales over “short” geological intervals (100s kyr), with temporal resolution in theory limited only by sampling resolution. The construction of a 3HeET timescale through the Bonarelli Level, a ~1 m thick interval of interbedded black and grey shales and radiolarian sands which is the sedimentary expression of Oceanic Anoxic Event 2 (~94 Ma) in Umbria–Marche, Italy, provides not only a novel method for estimating the duration of this record (478±160 kyr), but also allows rates and durations to be attached to the environmental shifts recorded in changing styles of sedimentation and/or changing geochemical records. Slow-downs in sedimentation rates are associated with the intervals of biotic turnover represented by the lithological shift from limestone to black shale at the base of the Bonarelli Level, and from black shale to limestone at its top. A transient increase in the accumulation rate of carbonates above the Bonarelli Level likely reflects enhanced biogenic calcite preservation due to build-up of excess alkalinity during OAE 2.
Precession cycles within the rhythmically bedded Scaglia Bianca Formation, a sequence of pelagic limestones well characterised by cyclostratigraphy that underlie the Bonarelli Level, were also investigated using 3HeET timescales. Exploration of the timings and possible drivers of lithological change within these Scaglia Bianca precession cycles provides insight into how local palaeoclimatic and Earth System processes reacted to ‘base level’ orbital forcing in the Cenomanian prior to the perturbation associated with OAE 2. Precession cycles deposited under eccentricity maxima (expressed as limestone-black shale-black chert sequences) and minima (expressed as limestone laminated limestone-grey chert) were selected for comparison. Calculation of the proportion of time per cycle represented by silica- and organic-rich facies indicates that, when the amplitude of precessional insolation forcing was greatest (at eccentricity maxima), the palaeoenvironmental system spent longer in the more nutrient-rich environment under which silica- and organic-rich sediments were deposited, reflecting increased time spent above a ‘threshold’ insolation level.
This work expands the use of extraterrestrial timescales to stratigraphic sections with heterogeneous lithologies, including organic-rich black shales and cherts. 3HeET is shown not to be liberated during the diagenetic process of chert formation. Various methods of calculating 3HeET background flux in sections with heterogeneous lithology were also evaluated, and a best-practice method proposed.

Keywords: Cenomanian
age model
OAE2
precession
helium
IDP
Advisor: Robinson, S
Jenkyns, H
Chris, B
High-precision molecular measurements in an electrostatic fluidic trap

Measurement of molecular properties at the single-molecule level can reveal valuable information, often hidden in ensemble measurements. In this Thesis, we present a range of novel high-precision molecular measurements in solution enabled by the electrostatic fluidic trapping approach.
The working principle of an electrostatic fluidic trap relies on the equilibrium thermodynamic repulsion experienced by a charged object confined in a fluidfilled gap between two like-charged surfaces. Geometric tailoring of one of the surfaces by nanostructured surface indentations reduces interaction energy, creating an electrostatic potential well capable of stable trapping of a charged object in solution. The ability of a recently developed escape-time electrometry (ETe) technique to precisely measure the depth of potential well underlies the high-precision measurement of effective electrical charge, qeff, of a trapped molecule.
In the original work, upon which this Thesis is based, we first focus on expanding the capabilities of the electrostatic fluidic trapping approach. We demonstrate the ability of stable trapping in a range of solvents of different polarities and present a novel approach for measuring the net surface charge at the solid-liquid interface. We further explore the applicability of charged lipid bilayer systems for single-molecule electrostatic trapping and describe how chemical composition of nanostructured supported lipid bilayers can be measured by means of ETe.
We finally demonstrate the ability to use the qeff of a biomolecule in solution to infer key details of its atomic level structure. Performing ETe measurements on A- and B-form (RNA and DNA) double helixes, we achieve a ∼ 1Å and ∼ 0.1Å precision on the helical radius and rise per basepair, respectively. Moreover, in conjunction with a recently developed theoretical approach to model electrostatics of biomolecules in solution, our examination of structural parameters provides an unprecedented new view of the molecule-solvent interface.

Keywords: single-molecule trapping
molecular modeling
molecular structures
escape-time electrometry
electrostatics
Advisor: Krishnan, M
Evolutionary drivers of mobile colistin resistance

Antibiotics are our strongest defence against disease causing bacteria. This makes the threat of widespread antibiotic resistance all the more concerning. Last-resort antibiotics such as colistin are especially important as they are effective against multiple-drug resistant pathogens. The recent emergence and spread of the mobile colistin resistance gene mcr-1 threatens the efficacy of colistin. Although the gene incurs a large fitness cost, mechanisms such as compensatory adaptation could reduce costs associated with MCR-1 carriage and enable its maintenance and spread in the absence of colistin selection. To test if compensatory adaptation was playing a role in mcr-1 evolution, I first studied the impact of non-synonymous coding sequence variants and found that although some provided fitness benefits, most variants were deleterious (Chapter 2). Next, I focused on variants found in mcr-1 regulatory sequences and found that regulatory variants generally caused increased fitness in the presence and absence of colistin selection (Chapter 3). Additionally, I discovered that E. coli carrying regulatory variants had reduced transcript levels and MCR-1 protein activity. From these results, I concluded that regulatory variants reduce the costs of MCR-1 by reducing protein levels via reduced transcription and/or translation. Interestingly, regulatory variants also increased colistin resistance suggesting that they are not traditional examples of compensation but rather regulatory fine-tuning to obtain optimal balances between MCR-1 activity and fitness costs. Lastly, I studied the impact of MCR-1 on cell morphology and behaviour, particularly in regards to bacterial conjugation (Chapter 4). I found that MCR-1 activity lead to increased conjugation rates and plasmid stability of transferable mcr-1-positive plasmids.
Overall, these results have important implications on the control of MCR-1 mediated colistin resistance. Although intragenic compensation is not prevalent, mcr-1 regulatory variations are observed in multiple plasmid backgrounds and are increasing in prevalence among mcr-1-positive sequence isolates. Additionally, MCR-1 can facilitate its own transfer in the absence of selection though its effects on conjugation and plasmid stability. These factors could make mcr-1 genes difficult to eliminate even in the absence of colistin selection.

Advisor: Maclean, C
Topics in applied topology: actions, knots and proteins

This thesis consists of three parts in which we explore different topics in pure and applied topology; in Part I, we develop an equivariant version of discrete Morse theory compatible with complexes of groups. In Part II, we link discrete Morse theory to knot projections, and in Part III we apply tools from knotoid theory to the study of knotted proteins. The two overall themes running through the thesis are discrete Morse theory and knot theory.
In Part I we construct a version of discrete Morse theory for simplicial complexes endowed with group actions. We characterise the compatibility of an acyclic partial matching on the quotient space with an overlaid complex of groups. We use the discrete flow category of any such compatible matching to build the corresponding Morse complex of groups, and prove that the development of the Morse complex of groups recovers the original simplicial complex up to equivariant homotopy equivalence.
In Part II we obtain a simple and complete characterisation of which matchings on the Tait graph of a knot diagram induce a discrete Morse function (dMf) on the sphere. We show these dMfs are in bijection with certain rooted spanning forests in the Tait graph. We use this to count the number of such dMfs with a closed formula involving the graph Laplacian. We then simultaneously generalise Kauffman’s Clock Theorem and Kenyon-Propp-Wilson’s correspondence in two different directions; we first prove that the image of the correspondence induces a bijection on perfect dMfs, then we show that all perfect matchings, subject to an admissibility condition, are related by a finite sequence of click and clock moves. Finally, we study and compare the matching and discrete Morse complexes associated to the Tait graph, in terms of partial Kauffman states, and provide some computations.
Understanding how knotted proteins fold is a challenging problem in biology. Researchers have proposed several models for their folding pathways, based on theory, simulations and experiments. The geometry of proteins with the same knot type can vary substantially and recent simulations reveal different folding behaviour for deeply and shallow knotted proteins. In Part III, we analyse proteins forming open-ended trefoil knots by introducing a topologically inspired statistical metric that measures their entanglement. By looking directly at the geometry and topology of their native states, we are able to probe different folding pathways for such proteins. In particular, the folding pathway of shallow knotted carbonic anhydrases involves the creation of a double-looped structure, contrary to what has been observed for other knotted trefoil proteins. We validate this with Molecular Dynamics simulations. By leveraging the geometry and local symmetries of knotted proteins’ native states, we provide the first numerical evidence of a double-loop folding mechanism in trefoil proteins.

Advisor: Nanda, V
Tillmann, U
Bridging probabilistic forecasts and power system optimization considering uncertainty: a joint chance-constrained perspective

Power systems globally are significantly integrating renewable energy to achieve net zero emission targets. Nonetheless, these renewable energy sources are weather-dependent and uncertain, bringing challenges to ensure operational reliability. Additionally, extreme weather and natural disasters damage power infrastructure, leading to contingencies or large-scale blackouts occasionally. These pressing issues necessitate uncertainty-aware power system management and give rise to the main research question, how to apply the joint chance-constrained (JCC) formulation in uncertainty-aware power system operations using probabilistic forecasting information?
A literature review discusses different machine learning (ML) probabilistic forecasting models and uncertainty-aware formulations in power system operations. Selected ML models are then compared for weather-informed net-load probabilistic forecasting. Leveraging probabilistic forecast, this thesis investigates and applies two uncertainty-aware formulations in power system operations, the JCC and distributionally robust optimization (DRO). Case studies are demonstrated on solar-powered networked microgrids.
The first case study investigates solar-powered networked microgrids during utility contingencies. A distributionally robust joint chance-constrained (DRJCC) framework is developed to control this networked microgrid considering the worst-case solar forecast error distribution. The DRJCC problem is reformulated into a tractable individual chance-constrained formulation with unspecified individual violation rates. A novel evolutionary algorithm is designed to approximate the optimal individual violation rates, known as the NP-hard Bonferroni Approximation problem. The solution is proven to be reliable and less conservative in out-of-sample tests compared to other methods.
The second one focuses on networked microgrids in the power markets. It envisages that, due to stochastic solar power generations, the imperfect real-time reserve provisions from multiple microgrids simultaneously could result in unexpected load shedding. Lever- aging historical forecast error samples, the reserve bidding strategy of each microgrid is formulated into a two-stage Wasserstein-metrics DRO model. A JCC regulates the under-delivered reserve capacities of all microgrids in a non-cooperative game. To approximate the optimal individual violation rates of microgrids with the changing correlation, the Bayesian optimization method is introduced. This DRJCC game framework is simulated with up to 14 players in a 30-bus network. The proposed Bayesian optimization method can identify the optimal reserve violation rates, which effectively regulate the joint violation rate of the under-delivered reserve whereas securing the profit of microgrids.

Keywords: distributionally robust optimization
uncertainty quantification
probabilistic forecasting
power system operations
joint chance-constraints
Advisor: McCulloch, M
On the margins but not of the state: young Jerusalemites' navigating citizenship and welfare in a settler-colonial context

This thesis explores notions of ‘citizenship’ among young Palestinian Jerusalemites displaced by the Separation wall, in occupied East Jerusalem. Jerusalemite Palestinians’ only ‘legal’ bond to the state and access to their city is through the ‘permanent residency status’, which may be revoked at the discretion of the Israeli Interior Minister, rendering it particularly precarious. The historical trajectory of Israeli policies since the 1967 annexation of East Jerusalem has created a situation in which Palestinian Jerusalemites have been gradually encouraged to move to areas beyond the Separation Wall, ultimately displacing thousands and effectively containing them in a series of enclaves.
The thesis comprises four stand-alone papers; ‘Citizenship, surveillance and control: Young Palestinians navigating transitions on Jerusalem's margins’; ‘Health on the margins of Jerusalem: Privilege or Control?’; ‘Compromised belonging and (ID)entity crisis: The case of Palestinian youth on Jerusalem’s enclaves’; and, ‘Thresholds of dughutaat: Future oriented hopes and decisions in slow violence’; all linked in relation to the localised enclave context, with a focus on young people’s experiences. Each paper addresses the themes arising from young people’s narratives on their experiences navigating a tenuous legal status and living in precarity, and within a broader context of military occupation and settler-colonialism. As a whole, they discuss the interlinked, and at many times ‘messy’ contours of what is referred to as a form of ‘coercive non-citizenship.’ The thesis concludes with a discussion of how the overall context, and the narratives of young people in particular, problematize notions of citizenship in a context of prolonged military occupation and settler colonialism and render existing theories inadequate in illuminating this seemingly paradoxical reality.

Keywords: citizenship
settler-colonialism
welfare
Advisor: Chase, E
Surender, R
Inferring eco-evolutionary feedbacks from time series data using neural ordinary differential equations

Ecological and evolutionary dynamics were thought to operate on different time scales. Recent evidence showed that evolution could be rapid enough to interplay with ecological dynamics and form eco-evolutionary feedbacks. These feedbacks are hard to identify in nature, due to the complexity of the mechanisms and the difficulty of obtaining phenotypic, demographic, and environmental variables. We lack quantitative evidence on feedback effects in real systems, which prevents us from painting a complete view of feedback architectures. We develop a mathematical framework, neural ordinary differential equations (NODEs), to quantify feedbacks from time series data of the evolutionary, ecological, and environmental variables in the system. The framework combines ordinary differential equations and artificial neural networks, to identify, non-parametrically, drivers of evolutionary and ecological dynamics, and relies on the Geber method to recover the contribution of ecological change to evolution, and vice versa. We apply the technique to recover the coupling between the dynamics of three species in a prey-predator system. We find that main interactions, between the prey and top predator are conserved across replicates, while weaker interactions, between the intermediate predator and the other species, are not. We also apply the technique to recover eco-evolutionary feedbacks in two of Darwin’s finches species. We find that feedbacks involve a direct coupling between population dynamics and phenotypic change in only one of the species, while the other involves a coupling with resource levels. Our work demonstrates the potential of NODEs in uncovering drivers of dynamics in systems where prior mechanistic knowledge is lacking, and shows the importance of indirect effects in driving eco-evolutionary feedbacks in nature.

Keywords: eco-evo feedbacks
ecological interactions
neural networks
neural ordinary differential equations
time series
eco-evolutionary dynamics
Darwin's finches
rotifer
Advisor: Sheldon, B
Coulson, T