VictorJuiz/thesis huggingface dataset:
Reactivation and reinstatement of hippocampal assemblies

New memories are labile, but over time some of them are stabilized. This thesis investigates the network mechanisms in the brain underlying the gradual consolidation of memory representations. Specifically, I performed a causal test of the long-standing hypothesis that the offline reactivation of new, memory-representing cell assemblies supports memory consolidation by stabilizing those assemblies and increasing the likelihood of their later reinstatement—and therefore presumably of memory recall.
I performed multi-unit extracellular recordings in the dorsal CA1 region of behaving mice, from which I detected short-timescale (25 ms) co-activation patterns of principal neurons during exploration of open-field enclosures. These cell assembly patterns appeared to represent space as their expression was spatially tuned and environment specific; and these patterns were preferentially reactivated during sharp wave-ripples (SWRs) in subsequent sleep. Importantly, after exposure to a novel—but not a familiar—enclosure, the strength with which an assembly pattern was reactivated predicted its later reinstatement strength during context re-exposure. Moreover, optogenetic silencing of hippocampal pyramidal neurons during on-the-fly detected SWRs during the sleep following exposure to a novel—but again not a familiar—enclosure impaired subsequent assembly pattern reinstatement. These results are direct evidence for a causal role of SWR-associated reactivation in the stability of new hippocampal cell assemblies.
Surprisingly, offline reactivation was only important for the stability of a subset of the assembly patterns expressed in a novel enclosure. Optogenetic SWR silencing only impaired the reinstatement of "gradually strengthened" patterns that had had a significant increasing trend in their expression strength throughout the initial exposure session. Consistent with this result, a positive correlation between reactivation and subsequent reinstatement was only found for these gradually strengthened patterns and not for the other, "early stabilized" patterns. An interesting interpretation is that the properties of the gradually strengthened patterns are all consistent with the Hebbian postulate of "fire together, wire together".
To enable investigation of the relation between interneurons and principal cell assembly patterns from extracellular recordings, as a final contribution this thesis describes a statistical framework for the unsupervised classification of interneurons based on their firing properties alone.

Keywords: Memory consolidation
Hippocampus
Cell assemblies
Reactivation
Sharp-wave ripples (SWRs)
Advisor: Dupret, D
Renewing Athens: the ideology of the past in Roman Greece

In this thesis we explore the period of renewal that Athens experienced during the second century AD. This century saw Athens at the peak of her cultural prominence in the Roman Empire: the city was the centre of the League of the Panhellenion and hosted a vibrant sophistic scene that attracted orators from across the Greek world, developments which were ideologically fuelled by contemporary conceptions of Classical Athens. While this Athenian ‘golden age’ is a standard feature of scholarship on Greek culture under Rome, my thesis delves further to explore the renewal of the urban and rural landscapes at this time and the relationship between that process and constructions of Athenian identity.
We approach the renewal of second-century Athens through four lenses: past and present in the Ilissos area; the rhetoric of the Panhellenion; elite conflict and competition; and the character of the Attic countryside. My central conclusions are as follows:
1. The renewal of Athens was effected chiefly by Hadrian and the Athenian elite and was modelled on an ideal Athenian past, strategically manipulated to suit present purpose; the attractions of the fifth-century golden age for this programme of renewal meant that politically contentious history of radical democracy and aggressive imperialism had to be safely rewritten.
2. Athens and Attica retained their uniquely integrated character in the second century. Rural Attica was the subject of a powerful sacro-idyllic ideology and played a vital role in concepts of Athenian identity, while simultaneously serving as a functional landscape of production and inhabitation.
3. The true socio-economic importance of the Attic countryside as a settled and productive landscape should be investigated without unduly privileging the limited evidence from survey, and by combining all available sources, both literary and documentary, with attention to their content, cultural context and ideological relevance.

Keywords: Philostratus
Pausanias
Roman Greece
2nd Century AD
Panhellenion
benefactor
countryside
euergetism
culture
Greek culture
elite
Ilissos
city
Marathon
renewal
Athens
Hadrianic
Attica
revival
Second Sophistic
urban landscape
estate
Roman Empire
Cephisia
rural landscape
Emperor
villa
gravestone
Milesian
Hadrian
restoration
sacro-idyllic
Antonine
Marcus Aurelius
Herodes Atticus
Advisor: Moreno, A
Brokering anime: how to create a Japanese animation business bridge between Japan and India

This thesis ethnographically examines the globalising of the Japanese animation (anime) business in the context of the creative industries, of Japan’s politico-economic position in Asia, and of brokerage. Influencing the world’s entertainment, creators, and youth culture, anime is one of the crucial lenses through which one can examine Japan’s presence in the world. Despite the prevalent assumption that anime is globally popular, this thesis highlights the precarious performance of the anime business overseas, and examines it through an entrepreneurial anime business project trying to bridge the Japanese anime business into the Indian market.
The ethnography of the project centres on its founding entrepreneur, focusing on how he tried to ally with insiders in the Japanese anime sector and the Indian market. The thesis’s 12-month fieldwork accompanied his business in Japan (Tokyo) and India (Delhi), revealing a perspective of the entrepreneur as a broker who intermediates between the discrepant positions of his stakeholders to keep his business afloat. It also highlights the two most critical discrepancies: the dichotomies of art versus commerce (one of the central topics in creative industries studies) and the ‘Japanese’ versus ‘Indian’ ways of doing business (one of the prominent topics in Japan’s political economy vis-à-vis the Asian region). The ethnography found the entrepreneur’s liminal dual agency in bridging, blurring and reorienting the dichotomies was a driving force carrying his business forward.
This thesis counterbalances previous anthropological studies on the creative industries (including anime) that tend to advocate the centrality of creators and fans, by focusing on the businessperson in a creative project. It also suggests that the broker is a crucial point of reference when examining how to create workable compromises between art and commerce, and allowing Japanese and Asian businesspeople to get along. The thesis also enhances our understanding of entrepreneurship by revealing most of its function as brokerage.

Keywords: India
business custom
anime
broker
animation
brokerage
Japan
cross-culturtal management
Asia
entrepreneurship
creative industry
Advisor: Goodman, R
Daniels, I
Development and application of bifunctional iminophosphorane organocatalysts

This thesis presents the development and application of bifunctional iminophosphorane (BIMP) organocatalysts, incorporating a triaryl-substituted iminophosphorane organosuperbase for organocatalytic enantioselective reactions.
Chapter 2 describes the design and synthesis of a new class of BIMP catalysts and its application in the first organocatalytic enantioselective sulfa-Michael reaction of alkyl thiols to unactivated β-substituted α,β-unsaturated esters. The conjugate adducts were obtained in up to 94% yield and 94% ee. In addition, the reaction was performed on a 1 gram preparative scale with 1 mol% catalyst.
Chapter 3 describes the application of BIMP catalysts in the enantioselective desymmetrisation reaction via an intramolecular Michael addition of a pendant pronucleophile to prochiral cyclohexadienone. The high Brønsted basicity of BIMP catalysts was demonstrated in the Michael addition of high pKa pronucleophiles, such as α-substituted malonamate and amide.
Chapter 4 describes the application of BIMP catalysts in the challenging Michael addition of malonates to crotonates, cinnamates and methacrylates. For example, the conjugate adduct of malonate and hexafluoroisopropyl cinnamate was achieved in 91% yield and 63% ee in 48 h.
Biochemical characterization of C15ORF41: a novel nuclease

Congenital dyserythropoietic anaemia type I (CDA-I) is a rare autosomal recessive form of anaemia that is characterized by ineffective erythropoiesis and abnormal morphologies of bone marrow erythroblasts. While previous studies have indicated mutations in the CDAN1 gene for a large group of patients with CDA-I, new research has revealed that mutations in the C15ORF41 gene are also linked to patients with the condition.
With the recent purification of the C15ORF41 protein by the Structural Genomics Consortium at the University of Oxford, a series of biochemical assays were conducted in order to characterize the catalytic and mechanistic behaviour of the protein. Nuclease assays indicated that the protein, when co-purified with the CDAN1 protein Codanin1, acts as a single-stranded endonuclease that acts on both DNA and RNA substrates. These assays also revealed that the complex incises in 5-6 nucleotide increments in a 3’-to-5’ directionality and exhibits a preference for 3’ flaps. Electrophoretic Mobility Shift Assays indicated that there is likely a 2:1 protein to substrate stoichiometry. Fluorescence anisotropy data showed that the C15ORF41-Codanin complex appeared to have much higher affinity to DNA substrates than the individual constituent proteins.
The results of this study provided initial evidence into the predicted endonucleolytic behaviour of the protein and established a solid foundation for further investigations of the mechanistic basis of its activity. This is absolutely critical for the molecular understanding of CDA-I for the formulation of future treatments, and is the first step in examining a novel endonuclease that could further our grasp on DNA damage repair proteins.

Advisor: McHugh, P
Brown, T
Engineering ”‘plug and play”’ biosensors in Escherichia coli

The ability of biological components to function reliably in different genetic contexts is one of the underlying fundamental principles in synthetic biology. Application of this principle allows for the development of distinct parts or bio-bricks and for the possibility of genetic abstraction. However, the sensitivity of genetic elements to changes in context can cause issues for this abstracted view of genetic elements as parts. We look at how this context sensitivity effects DNA and RNA based biosensors and we further investigate the ability of feedback to reduce noise in a biological device.
Riboswitches are structural genetic regulatory RNA elements that directly couple the sensing of small molecules to gene expression. They are able to sense a wide range of small molecules and in response regulate gene expression. We investigated how changes in genetic context effected riboswitch function and how these changes affected expression from a riboswitch and adaptation of a riboswitch to a novel downstream application. To overcome these contextual difficulties with riboswitches, we have designed and introduced a novel genetic element called a ribo-attenuator. This genetic element allows for predictable tuning, insulation from contextual changes and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as a truly modular and tunable component, and thus increase their reliability for a wide range of applications.
Many biological processes use a form of feedback to achieve a highly robust and reliable output. Accurate control of a biological process is essential for critical functions in biology, from the cell cycle to proteome regulation. We design a tunable synthetic feedback network using a class of viral proteins called Integrases, which can flip the orientation of DNA segments in a digital manner. Excisionase feedback closes the loop in this system, creating a novel switch that provides a tunable and modular architecture for applications throughout synthetic biology and bio-manufacturing that require a highly robust and orthogonally controlled output. This system is highly orthogonal and evolutionary robust, and demonstrates a strong capability for regulating and reducing the variability in expression genes being transcribed under its control.

Advisor: Armitage, J
Papachristodoulou, A
Rothschild, L
From actions to agents: value representation in frontal cortex

In this thesis, I investigated computational and neural mechanisms underlying foraging-related behavior in humans. A consideration of the ecological constraints under which mammalian behavior first evolved guided my investigation of learning and decision-making in frontal cortex. When engaged in foraging, animals have to figure out how profitable their actions are and whether it is better to continue foraging in their current environment or to switch to an alternative. They have to track the reward income of their actions over time and also take into account that the actions of other foraging animals have a direct influence on their reward income (Chapter 1). Based on these observations, I looked at similar types of behavior in humans using computational modeling and functional magnetic resonance imaging. I studied how people evaluate the profitability of their actions over time (Chapter 2). Dorsal anterior cingulate cortex carried a detailed representation of the value of the current foraging action, which was influenced by reward memories with different time constants (Chapter 3). Tracking the reward income of one's actions is not only important in order to learn about the profitability of the environment, it can also inform estimates of one's own and other people's abilities. Ability estimates can be used in a direct way to predict the reward outcome that the actions of one’s own self and others will have. I found that people learn about their own and others' abilities in a rational manner but also that ability estimates of self and other were partly confused with each other, depending on whether subjects cooperated or competed with each other (Chapter 4). The confusion effect is reflected in Brodmann area 9 activity indicating that area 9 integrates self and other related information. Perigenual anterior cingulate tracked the ability estimates for oneself, suggesting that it might compute the success expectation of an action independent of particular features of the environment (Chapter 5). In sum, different subregions of medial frontal cortex carried different types of action-related value representations that can guide decision-making.

Keywords: Psychology, cognitive Neuroscience, Decision making, Learning, Reward
Advisor: Rushworth, M
Cognitive ability and socio-political beliefs and attitudes

The contribution of this thesis is to demonstrate the importance of cognitive ability (and psychometric traits in general) for understanding the distribution of socio-political beliefs and attitudes within society. For at least the past hundred years, sociologists have sought to explain social phenomena primarily, or indeed exclusively, with reference to social structures that can be considered as external to the individual. While this explanatory paradigm has proved invaluable for understanding many social phenomena, it is not without theoretical deficiency. Certain phenomena can only be fully understood with reference to stable psychological differences between individuals--what psychometricians call individual differences. Toward this end, the present thesis addresses the following research questions. First, are generalized trust and political attitudes associated with cognitive ability? Second, what are the functional forms of any relationships between cognitive ability and socio-political beliefs and attitudes? Third, does cognitive ability explain variance in these traits over and above the effect of traditional sociological covariates, such as age, gender and socioeconomic status? Fourth, can psychometric differences between individuals help to explain one particular well-documented empirical regularity (of very large effect size), namely the fact that individuals with liberal and left-wing views are overrepresented in academia? The thesis comprises nine separate papers: the first two chapters examine generalized trust, while the subsequent seven focus on political attitudes. It concludes by summarising the main findings, discussing important limitations, and outlining avenues for further research.

Advisor: Billari, F
De Graaf, N
Investigation of breathing-disordered sleep quantification using the oxygen saturation signal

This thesis investigates the feasibility of using the non-invasive biomedical signal of oxygen saturation, or SpO2 , to diagnose a sleep disorder known as Obstructive Sleep Apnoea Hypopnoea Syndrome (OSAHS). Epidemiologically, OSAHS is the most common condition investigated by sleep clinics. In a patient suspected of having the disorder, the upper airway is obstructed during sleep and a cessation in respiration results. An apnoea is defined as a temporary cessation of breathing. Similarly, a hypopnoea is defined as any reduction in breathing (i.e., less severe than an apnoea).
The work has three main objectives; the first being to establish automated evaluation procedures for methods of quantifying apnoeic activity from the SpO2 signal, the second being to accurately identify apnoeic and normal activity on a minute-by-minute basis, the third being to create a Respiratory Disturbance Index (RDI) based on the analysis which is comparable to the gold-standard Apnoea Hypopnoea Index (AHI) derived by experts.
The detection of apnoeic activity is determined using three separate analyses: time domain, frequency domain, and autoregressive modelling with an incorporated amplitude criterion. A training dataset is utilised for algorithm development, and an independent dataset is employed for testing . All three methods result in comparable overall classification accuracies of: 81.2% (time domain), 82.1% (frequency domain), and 80.0% (autoregressive modelling with amplitude). In addition, particular attention is given to the resultant sensitivity, specificity, and accuracy values partitioned according to patient category; i.e., patients with OSAHS may be divided into normal, mild, moderate and severe.
Lastly, a simple RDI is computed based on the automated analyses; i.e., the number of apnoeic segments detected divided by the total number of segments used. A comparison between computed RDI and AHI values for the test database show correlation values above 0.8. In conclusion, this thesis shows that through the automated analysis of the SpO2 signal, OSAHS severity in patients suspected of having the disorder can be quantified. The AR-modelling with an incorporated amplitude criterion, in particular, shows the most promise for further work in this area.

Keywords: obstructive sleep apnoea
autoregressive modelling
time and frequency domain analyses
Advisor: Tarassenko, L
The role of the storyteller in old Norse literature

This thesis examines the figure of the oral storyteller as depicted in various Old Norse literary sources written down during the High Middle Ages, the majority in Iceland, between the mid-twelfth and early fourteenth centuries. It comprises a literary-critical discussion of how storytellers and the art of storytelling are imagined, interpreted and represented within these texts. Where possible, connections are drawn between genres, and across considerable temporal and geographical distances, in order to illustrate the strength and endurance of cultural preoccupations with disguise, narrative structure and the role of intermediaries in different historical and creative contexts.
The central contention is that the eddic poets and saga authors shared a common and profound sensitivity to the metatextual dimension of the storytelling endeavour in which they were engaged, and that this sensitivity manifested itself in strikingly similar ways across the whole period. The thesis is structured thematically, rather than chronologically, in order to foreground enduring cultural trends. The first chapter discusses the metatextual tendencies of the eddic poets, noting their recurring interest in disguise and the assertion (or appropriation) of an identity by characters who feature in their stories. It also includes an analysis of Vǫluspá which suggests that the poem lends itself to recitation by multiple performers. Chapter Two analyses depictions of public storytelling in the sagas and the relationship between writer and oral reciter as presented in the prologues and epilogues composed to ‘frame’ a number of these texts. Chapters Three and Four contain close readings of passages from the Sagas of Icelanders and eddic poetry, which demonstrate how certain characters, often of low social status, temporarily take on the mantle of a storyteller and perform their accounts of events so as to illuminate the texts' broader interest in the mechanics of literary narrative.

Keywords: Drama
Medieval
Old Norse
Storytelling
Performance
Middle Ages
Theatre
Advisor: O'Donoghue, H