VictorJuiz/thesis huggingface dataset:
Taste shaping natures: a multiplied ethnography of translated fermentation in the New/er Nordic Cuisine

Culinary innovators in Copenhagen are combining far-flung fermentation techniques with Nordic ingredients to yield products and flavours that have not existed before. This flavour-oriented ‘translated’ fermentation is also having broader cultural and material consequences, for these culinary practitioners as well as for their microbial partners’ biogeography, ecology, and likely their evolution. To account for these novelties, I bring together critical scholarship on nature, more-than-human geographies and multispecies studies, theories of taste, and STS, to develop the concept of a ‘taste shaping nature’: a nature shaping and shaped by taste. Employing a novel combination of multispecies multisensory ethnography, collaborative microbiological experiments, and DNA sequencing—an approach I shorthand as ‘multiplied ethnography’—I conducted fieldwork around two sites in Copenhagen, Restaurant Noma and Empirical Spirits, leaders in the culinary movement sometimes known as the ‘New Nordic Cuisine’ (NNC). Linking my fieldwork and the literature, I develop each part of ‘taste shaping natures’ across four analytic chapters: on ‘Nature’, ‘Consipience’, ‘Experiment’, and ‘Interest’. ‘Nature’ investigates how the NNC has mixed ‘wild’ and ‘postpastoral’ natures, how these ‘multinatures’ have shifted over time, and how they have shaped and been shaped by different approaches to fermentation. ‘Consipience’ articulates how humans and microbes—or any creatures—come to know each other through taste and smell, within and across species, as a contribution to STS, multispecies studies, and sensory ethnography. ‘Experiment’ examines the role of technoscience in how humans and microbes know and shape each other in translated fermentation, and proposes a model of experiment as a contribution to STS. ‘Interest’ brings together the aesthetics, ethics, politics, and biological consequences of translated fermentation’s taste shaping natures, and suggests the supporting concept of ‘micro-governmentality’ as a complement to ‘microbiopolitics’. In conclusion I reflect on fermentation politics, and consider how fermentation contributes to ongoing debates around domestication.

Keywords: innovation
New Nordic Cuisine
microbes
fermentation
multispecies
domestication
taste
Advisor: Lorimer, J
Greenhough, B
The Attic elite beyond the polis in the sixth and fifth centuries BC

This thesis concerns the extra-polis activity and relationships of elite Athenians in the sixth and fifth centuries BC. It studies the range and character of the economic opportunities outside Attica in which elite Athenians participated, arguing that in the late archaic period as well as afterwards the most successful individuals and families prospered at home not (or not only) because they happened to be the largest landowners in Attica, but because they best exploited the extra-polis opportunities afforded by their particular freedom of movement and by their privileged access to productive relationships of xenia.
Such activities and relationships have often been construed, indeed were often presented by those involved, as driven by philotimia (the desire to be valued in and by a community). My thesis emphasises the importance of philochrēmatia (the desire for property) and alignments and tensions between these twin motivations. It seeks to characterize the Attic elite across both centuries, rather as Thucydides’ Corinthian characterized the Athenians collectively, as ἀποδημηταὶ πρὸς ἐνδημοτάτους: οἴονται γὰρ οἱ μὲν τῇ ἀπουσίᾳ ἄν τι κτᾶσθαι (1.70.4). Elite Athenians were part of a thriving economy above and beyond the polis, and this needs to be a central part of our picture of late archaic and early classical Athens, not least because successful participation in that economy was a major component of what constituted them as an elite.

Keywords: Cleruchy
Athenian Empire
Athenian Economy
Athenian Elite
Advisor: Thomas, R
"Especially the poor": The London City Mission, 1835-1914

This dissertation considers the work of the London City Mission (LCM) between 1835 and 1914. It presents an analysis of the evangelical faith, agency, and achievements of LCM’s working-class missionaries as they lived and worked among people whom many have believed to have been religiously ignorant and indifferent. This was not the case. This dissertation is not a study of LCM’s success measured by the details of new evidence of working-class churchgoing and churchgoers, but an analysis of the way in which LCM’s missionaries’ undenominational religious teaching became available to substantial numbers of those whom they sought to reach in anything they might be doing, and everywhere they might be met. It is a dissertation whose perspective is different. It is a discussion of working-class Christian faith that was experienced at a significant distance from the sacraments and structures of institutional and denominational religion. Its evidence is drawn from the hitherto unknown eye-witness accounts of LCM’s missionaries that are contained within LCM’s extraordinary archive. This study details the fundamental principles of LCM, identifies its unique character, and reveals the unrecognised scale and scope of their evangelical mission. It discusses LCM’s working-class missionaries, their backgrounds, their motivation in their work, and illustrates the way in which their spiritual imperative in mission was inseparable from their deep social concern. It explores the diversity and creativity of the missionaries’ agency. It demonstrates how over generations, in their districts and fields of special mission, because of their mutual understanding, and support, LCM’s evangelical mission thrived and was accepted as an integral part of everyday life by hundreds of thousands of working-class people.

Keywords: a study of nineteenth century working-class religion and evangelical mission in London
Advisor: Smith, M
Chemically modified guide RNAs to expand CRISPR functionality

CRISPR-Cas, a bacterial adaptive immune system against viruses, has been repurposed into a biological research tool that is invaluable due to its simplicity and programmability. Composed of a Cas endonuclease that is directed to its nucleic acid target by a guide RNA (gRNA), CRISPR has been used for genome editing, live-cell imaging and even diagnostics. In this work, the goal is to chemically modify gRNAs to expand CRISPR functionality. A ‘split-and-click’ strategy for generation of Cas9 gRNAs via CuAAC ‘click’ ligation of shorter oligonucleotides is developed. The approach provides a simple and cost-effective route to individual or pools of single guide RNAs (sgRNAs), while providing scope for further chemical modification to improve sgRNA activity. The click sgRNAs are functional both in vitro and in cells, demonstrating artificial linkages can be tolerated in functionally critical regions of sgRNA. To illustrate the capabilities of the system, work towards an on-field forensic analysis of Short Tandem Repeats (STR) is described using CRISPR, Ramified Rolling Circle Amplification (RAM) and Oxford Nanopore sequencing. sgRNAs were also tagged with small molecule fluorophores to provide greater flexibility in colour choice and expand the colour range for live-cell imaging. Imaging of repetitive elements of telomeres is feasible with these constructs if GFP-tagged dCas9 is used for cross validation; due to high cytoplasmic background fluorescence, methods to turn on fluorescence in the nucleus are also explored. Finally, two CRISPR-AsCas12a gRNAs are chemically ligated to yield a 3'-3' dual gRNA with the aim of altering the DNA cleavage pattern of the Cas12a protein. Chemical ligation in this context impaired gRNA activity in vitro, however unexpected single-stranded DNase activity is described for AsCas12a.

Keywords: Imaging
sgRNA
CuAAC
Click chemistry
Advisor: Brown, T
Micro-mechanical testing of the hex-BN interphase in SiCf/SiC composites for aero-propulsion

This thesis provides an overview of micro-level mechanical testing of the BN interphase in SiCf/BN/SiC composites, in the context of lifing models for aero-engine components. A wide number of variables were tackled in the development of both traditional and novel techniques to assess micro-level properties of the composites. The latter included the interfacial shear strength (varied), modulus (25.9 ± 5.4 GPa), hardness (1.3 ± 0.1 GPa), fracture toughness (6.7 ± 2.4 MPa.m1/2), debonding toughness (13.3 J.m-2), and frictional sliding resistance (4 ± 1 MPa) of the interphase, alongside other composite constituents where applicable.
The use of a nanoindentation apparatus was central to this work – both Berkovitch and flat-punch tip geometries were made use of. Established techniques were assessed in their viability for probing the properties of the BN interphase on its own: these included the fibre push-out, push-in and push-back. Due to the sheer volume of data, the significance of results was assessed statistically.
Upon completion of method development, material-dependent variables and their effects on the change in micro-mechanical behaviour were subsequently investigated. The parameters tackled included the variability in measurements from tow location at weave-architecture level (inter-tow), tow level (intra-tow), BN interphase thickness, nature of fibre type, cyclic testing, interphase doping levels and neighbouring fibre geometry; where it was found that a need for intra-tow variability was to be stressed over the importance of inter-tow variability in measurements of mechanical properties, although both were found to be statistically relevant.
The ceramic-matrix composites were subsequently exposed to high relative humidity and elevated temperatures; and tests repeated. The degradation from intermediate-to-high temperatures showed little to no change in mircromechanical performance (strength retention ratio of 79.1%) when compared to low-temperature high humidity exposure (strength retention ratio of less than 50% after 500 hours exposure). Despite results from these chapters, a further understanding of the dominating failure mechanism needed to be understood. This led to the development of miscellaneous micro-mechanical techniques performed in-situ (both in SEM, micro and nano-XCT), including the novel trench push-out which imaged mixed-mode failure (simultaneous inside and outside debonding) and defective interphases leading to linking of smaller cracks before push-out.
In the context of work by Rolls-Royce plc, the body of results yields both quantitative and qualitative information, for incorporation in coupon-level lifing models. The academic merit of this work lies in the investigation of variability in measurements of composite interphase properties, as well as micromechanical-technique development for a clearer understanding of the damage mechanisms at hand.

Keywords: ceramic matrix composites
materials science
fibre push-out
aerospace
composites
silicon carbide
micromechanics
Advisor: Armstrong, D
Marrow, T
Learning new words via reading: the influence of context and diversity


From mid-childhood onwards, the majority of new words are incidentally acquired via independent reading. Numerous studies have shown that the linguistic contexts in which a new word appears influences the ease with which the word is processed and acquired. Some contextual characteristics (e.g., high topic familiarity) are more beneficial to learning than others. The focus of this thesis is a relatively new contextual characteristic, known as semantic diversity, defined as the degree to which a word’s surrounding contexts overlap in terms of semantic content. The overarching aim of this thesis is to investigate how semantic diversity influences the learning of novel words in young adults. This thesis comprises a total of four word-learning experiments and three computational simulations. They all contrasted two learning conditions: high semantic diversity (multi-themed) and low semantic diversity (single-themed). Both Experiment 1 and Simulation 1 demonstrated that novel words experienced multiple times in one familiar topic (i.e., low semantic diversity) were advantaged in initial learning, a finding attributed to what I refer to as “anchoring”, a process of securing novel words onto long-term memory. On the other hand, Simulation 2 and Experiment 2 showed that novel words that had an anchoring opportunity were better placed to take advantage to high semantic diversity, suggesting that anchoring may benefit initial but not later learning. Simulation 3 used word vectors to mathematically simulate how semantic diversity influences the learning of meanings across Experiments 1 and 2. The simulation results showed that high-diversity words tend to have sparser semantic spaces, potentially indicative of weaker integration into pre-existing knowledge. In order to consolidate the results from Experiment 2, Experiment 3 monitored participants’ eye movement during reading. The results suggest that novel words appearing in high-diversity contexts are encoded more strongly during reading and tend to have more context-independent representations. Finally, while Experiments 2 and 3 showed that experiencing a novel word multiple times in a repeated topic could serve to anchor, Experiment 4 demonstrated that an explicit definition could also achieve the same effect, enabling the novel words to be better placed to take advantage of high semantic diversity. Together, this research demonstrated that initially restricting a novel word’s semantic diversity (i.e., starting small) and capitalizing on learners’ prior knowledge can support anchoring, which can facilitate subsequent learning in more diverse contexts.

Keywords: Semantic Diversity
Anchoring
Reading
Contextual variation
Word learning
Advisor: Nation, K
Social and environmental factors in the evolution of signalling

Offspring across the animal kingdom have evolved a variety of vocalizations, postures and structural ornaments to help them solicit more food from their parents. These signals are typically assumed to convey information about offspring state that helps parents decide which offspring to feed, and the dominant framework holds that begging is a signal of need. However, species differ both in how they beg and how they respond to begging, and signalling theory has been unable to account for this variation. In this thesis, I use a combination of comparative, observational and theoretical data to explore how the degree of within-family conflict leads to differences in parent-offspring signalling systems both across and within bird species. I also explore the possibility that some signalling systems function differently because the information they transmit is not cryptic. Specifically: 1) I show that offspring signals of need are more likely to evolve in species living in predictable and/or unusually good environments, while signals or cues of quality are more likely to evolve in unpredictable and/or unusually poor environments, when conflict over food is greater because brood reduction is probable; 2) I show that the same patterns hold within-species, indicating that parents can facultatively adjust their responsiveness based on the risk of brood reduction; 3) I show that offspring signals of need are less honest when sibling competition is greater, due to offspring number and/or relatedness; 4) I argue, using a simple game, that signals of non-cryptic condition can be stable if signalling provides an efficiency benefit compared to parents’ using cues; and 5) I provide a potential example of such a signal in nature, gape size, and show that its honesty fluctuates based on local conditions.

Keywords: parental care
social evolution
communication
Advisor: Griffin, A
West, S
Declarative nested data transformations at scale and biomedical applications

While large-scale distributed data processing platforms have become an attractive tar- get for query processing, these systems are problematic for applications that deal with nested collections. Programmers are forced either to perform non-trivial translations of collection programs or to employ automated flattening procedures, both of which lead to performance problems. These challenges only worsen for nested collections with skewed cardinalities, where both handcrafted rewriting and automated flattening are unable to enforce load balancing across partitions.
In this work, the TraNCE compilation framework is proposed that translates a program manipulating nested collections into a set of semantically equivalent shredded queries that can be efficiently evaluated. The framework employs a combination of query compilation techniques, an efficient data representation for nested collections, and automated skew-handling. Biomedical case studies are presented that outline research and clinical applications for the platform, including data integration support for building feature sets for classification. An extensive experimental evaluation is provided using both synthetic and real-world dataset from the biomedical domain. The evaluation shows that the system is capable of outperforming the common alternative, based on “flattening” complex data structures, and runs efficiently when alternative approaches are unable to perform at all.

Keywords: nested data
unnesting
shredding
genomic analysis
distributed processing platforms
nested relational calculus
Advisor: Benedikt, M
Protein folding and structure prediction: biological and physical perspectives

Protein folding is poorly understood and distinct from protein structure prediction, encompassing the translation and folding process of proteins in vivo and in vitro. In this thesis, we examine the protein folding process from several perspectives. First, we implement models of the spatial constraints that the ribosome introduces in the protein folding process. We are unable to show that these constraints have a particular effect on the formation of protein structure. However, we identify and describe a method which improves protein structure prediction in SAINT2 by avoiding the disruptive effects of certain extension protocols. Then, we study the relationship between protein structure and the coevolutionary constraints under which the structure has evolved. We identify several relationships between the structure of the protein and the coevolutionary constraints that are found in the protein. We further compare contact prediction methods and show that different contact prediction methods identify different types of amino-acid contacts. Finally, we investigate obligate cotranslational protein folding in the E. coli proteome. We find a relationship between the behaviour of several folding analysis methods and the necessity of cotranslational folding for our proteins.

Keywords: Protein folding
Mutual information
Cotranslation
Coevolution
Advisor: Deane, C
Mechanistic insights into the HPF1/PARP1 complex

ADP-ribosylation is a vital post-translational modification associated with a large range of processes including DNA damage repair, transcription, replication, mitosis, inflammation and cell death. ADP-ribosylation arises through the covalent attachment of ADP-ribose from NAD+ onto target proteins. The modification strongly varies in size, ranging from a single ADP-ribose unit (MARylation) to large, branched chains (PARylation). In humans, one major family of ADP-ribosyltransferases constituting 17 members are poly-ADP-ribose polymerases (PARPs). Their most prominent member, the nuclear protein PARP1, alone is responsible for the overwhelming majority of ADP-ribosylation in cells. While PARP1 was originally described to modify target substrates on glutamate and aspartate sites, it has become apparent in recent years that the presence of another protein, histone PARylation factor 1 (HPF1), switches its preference to serine target sites. Following this discovery, serine ADP-ribosylation was shown to be the main type of ADP-ribosylation in response to DNA damage. However, how HPF1 engages with PARP1 and is able to change the nature of its catalytic activity has remained unclear. This thesis explores the interaction between HPF1 and PARP1 in human cells, the molecular basis of HPF1/PARP1-catalyzed serine ADP-ribosylation and the consequences of aberrations in both proteins. Crucially, colleagues and I describe the interaction sites on both proteins and show that HPF1 in cells is required for the catalytic completion of PARP1 through a glutamate "finger". Furthermore, we identify the main sites of PARP1 serine auto-modification and illustrate their significance for PARP inhibitor-resistant PARP1 auto-modification and the release of PARP1 from sites of DNA damage. Finally, we explore in human cells the phenotypic consequences of losing the main PARP1 serine auto-modification sites, the HPF1 catalytic glutamate finger or HPF1-PARP1 interaction. Altogether, these results draw a comprehensive picture of HPF1-PARP1 mechanistic functions and the wider implications of its disruption.

Keywords: PARP inhibition
HPF1
PARP1
serine ADP-ribosylation
Advisor: Ahel, I
Charge mobility in π-conjugated polymer systems

Conjugated polymers represent a class of materials which exhibit excellent potential as versatile and cheap semiconductors in microelectronic devices. Their use in OLED displays is already wide-spread, and increasingly efficient solar cells are reported continuously. A key theoretical challenge in π-conjugated polymer systems is the incomplete understanding of charge transport mechanisms, and how competing microscopic and macroscopic effects influence it. In this thesis, charge transport and charge mobility are modelled at various length scales and varying levels of computational accuracy to better understand these processes. The models are based on phenyl-containing polymeric systems, but are generic in their implementation and would be adaptable to a range of comparable systems.
A novel atomistic model of charge mobility in bulk poly(p-phenylene-vinylene) (PPV) is presented. The incorporated structural and energetic disorder results in Anderson localised and quasi-extended donor and acceptor states. Charge migration through the system is facilitated by a kinetic Monte Carlo algorithm, aided by transition rates of separate inter- and intra-chain events defined within the framework of Marcus theory. The effects of disorder, temperature, field strength bias are studied. The log µ ∝ √F field dependence of mobility, which has already been widely reported in literature, naturally emerges at high electric field values. Crucially, the relative importance of inter-chain and intra-chain is highlighted by this model – at low fields, charge transport occurs almost entirely intermolecularly, between highly localised states, while at high fields, intramolecular transitions with the aid of quasi-extended states become most important.
The nature of intramolecular charge dynamics is further examined using a mixed quantum-classical model of charge-polaron transport. The dynamics of the charge follows the time-dependent Schrödinger equation, while the rotational motion of monomers is modelled via the Langevin equation, encapsulating the effect of Brownian fluctuations in rotational displacements. The two are coupled using the Ehrenfest equations of motion. The emergence of two distinct temperature regimes are observed. At the lowest temperatures, the polaron `crawls' along the polymer chain stochastically, while remaining fully localised and in the lowest quasidiabatic state. As the temperature increases, an activated, Landau-Zener type of dynamics is observed, leading to hopping transport between diabatic states. This additional pathway provides a link to the bulk charge transport mechanism.

Keywords: π-Conjugated Polymers
Charge Transfer
Quantum Mechanics
Advisor: Barford, W