VictorJuiz/thesis huggingface dataset:
A developmental approach to the patent-competition interface

This thesis proposes an approach to the patent-competition interface for developing countries. It puts forward a theoretical framework for the patent-competition interface for developing countries after canvassing relevant policy considerations. It examines the many reasons why patent protection is often not essential for generating innovation incentives in developing countries. These include the tendency of the patent system to overcompensate innovators, the availability of other appropriation mechanisms for innovators to monetize their innovations, and the lack of appropriate technological capacity in many developing countries to take advantage of the incentives generated by the patent system. It also argues that developing countries with a small population need not pay heed to the impact of their patent system on the incentives of foreign innovators. It then proposes a classification of developing countries into production countries, technology adaptation countries, and proto-innovation countries and argues that dynamic efficiency considerations take on different meanings for developing countries depending on their technological capacities. For the vast majority of developing countries bereft of meaningful innovation capacity, foreign technology transfer is the main vehicle for technological progress. The chief dynamic policy consideration for these countries is hence incentives for technology transfer instead of innovation incentives. There are three main means of voluntary technology transfer, importation of technological goods, foreign direct investment, and licensing. Competition law regulation of patent exploitation practices interacts with these three means of technology transfer in different ways and an appropriate approach to the patent-competition interface for these countries needs to take these into account. Distilling all these considerations, the thesis proposes an industry-specific approach to the patent-competition interface that is adjusted based on the country’s technological capacity. This approach is then applied to two patent exploitation practices, unilateral refusal to license and patent tying for illustration.

Keywords: developing countries
patent law
competition law
patent-competition interface
Advisor: Ezrachi, A
Double past participle forms in the Sicilian dialects

This work sets out to explore the phenomenon of double past participle forms exhibited by certain verbs across the Sicilian dialects. It starts with the definition of the past participial class, its role in Latin and its formal categorization among other parts of speech in Chapter 1. It then provides a summary of the research done so far on the topic of the past participial doublets in Chapter 2. It then moves to the overview of the same phenomenon in various Romance varieties, including Portuguese, Spanish, standard Italian, Venetan and Old Tuscan in Chapter 3. Chapter 4 provides a brief summary of the main relevant characteristics of the Sicilian dialects. Chapter 5 is dedicated to the analysis of the phenomenon of the past participial doublets in selected modern literary sources. Chapter 6 provides discussion of the second part of my data collection, in which I asked some native speakers of various Sicilian dialects to translate 52 sentences containing past participle (used in different functions) in standard Italian into their linguistic varieties.
When giving examples in Sicilian (and other dialects) and Italian, I have made the decision to gloss only ambiguous ones. Furthermore, since there is considerable variation within the Sicilian dialects too, I decided to write the names of the analysed verbs in standard Italian and provide examples in the respective dialects.

Keywords: syntax
dialect
Sicilian
past participle
morphology
Romance languages
The development of neuronal responses in the primate lateral intraparietal area

This thesis develops biologically plausible neural network models of how the response properties of certain classes of visual neurons in the primate parietal cortex may emerge through visually-guided learning. We start with an investigation of how different functional forms of gain modulation of neuronal responses, in particular gain modulation by the position of the eye, may develop in the brain. Gain modutalion refers to the modulatory effect that a particular bodily state or posture has on the firing rate of some visual neurons responding in a given reference frame. The remainder of the thesis focuses on the development of neurons with head-centred receptive fields. Such neurons respond maximally to a visual stimulus in the same head-centred location across all eye positions. In this thesis we show that different functional forms of gain modulation deeply affects the self-organisation of head-centred responses using simulated training data. We then recorded simultanous eye and head movements from human participants during a visual search task and used these to train our self-organising model of coordinate transformation. A further contribution of this thesis is the development of an open source scientific tool for Android devices to record rotation movements. Our neural network models were trained using a biologically plausible visually-guided learning process and then tested in simulated conditions similar to the experimental tasks used when the investigated responses were observed in the primate brain. The trained responses of our models showed a broad agreement with neurophysiological observations and our simulations help advance understanding of how the neuronal response properties investigated in this thesis may develop in the visual brain.

Keywords: visual cortex
self-organising
theoretical neuroscience
computational neuroscience
biological plausibility
gain modulation
area LIP
artificial intelligence
lateral intraparietal area
Advisor: Stringer, S
Smithson, H
Delineation of meiotic gene expression in male mice

Meiosis is a specialised cell division producing the haploid gametes required for sexual reproduction. A key function of this process is to generate genetic diversity through recombination and independent assortment of homologous chromosomes. Delineation of gene expression during this process has been challenging due to the heterogeneity of testis tissue and the lack of faithful in vitro models.
Here we jointly analyse a single-cell resolution transcriptomic dataset of over 20,000 cells from both wild type and mutant mice. We use dimensionality reduction methods to infer latent components of variation that represent transcriptional programmes, mutant specific pathological processes, and technical effects. This approach simultaneously soft clusters cells, infers corresponding groups of co-expressed marker genes, and imputes sparse, noisy gene expression. We were also able to infer, de novo, transcription factor binding motifs for each component, revealing a general switch at the meiotic divisions. We facilitate access to this resource by providing an interactive website testisatlas.ml.
The high-resolution delineation of gene expression during the spermatogenic programme provides high-resolution clues to the function of understudied genes. One such gene, Zcwpw1, is highly co-expressed with Prdm9, and has domains capable of recognising the unique combination of histone marks that PRDM9 deposits (H3K4me3 and H3K36me3). By using a human in vitro system of Zcwpw1 co-transfection with either human or chimp Prdm9, we show that PRDM9 causes the recruitment of ZCWPW1 to its binding sites. This recruitment is stronger than for sites with H3K4me3 alone and is CpG dependent.
Male Zcwpw1-/- mice have completely normal double strand break positioning, but severe repair and synapsis defects leading to complete testicular azoospermia. Although PRDM9’s effect of DSB positioning remains intact, PRDM9’s effect of aiding synapsis appears to be abolished, with persistent DMC1 signal - most dramatically at the most strongly PRDM9 bound hotspots.

Keywords: epigenetics
single cell RNAseq
testis
meiosis
ZCWPW1
spermatogenesis
Advisor: Myers, S
Marchini, J
Steroid receptor-dependent regulation of prostate-like secondary cells in Drosophila

The paired lobes of the male Drosophila accessory gland (AG) contain two epithelial cell types, main cells (MCs) and secondary cells (SCs). SCs are a useful in vivo genetic model system to study fundamental mechanisms regulating cell growth and secretion, and they share several properties with the human prostatic gland. The SCs in adult virgin males grow with age in a BMP-dependent manner, and this growth can be further enhanced upon mating. During my DPhil, I have developed the SC as a model to study steroid receptor-dependent growth regulation. The fly nuclear steroid receptor, the ecdysone receptor (EcR), and the human androgen receptor (AR) share similar structural and functional domains. I show that a complex interplay between the BMP and EcR signalling pathways is involved in the regulation of SC growth in both virgin and mated males, an interaction which may allow mated males to rapidly replenish the expelled contents of their AG. The growth that occurs after mating is partly accounted for by genome endoreplication which is BMP/EcR-dependent, as is the secretory activity of SCs. I show that SCs can synthesise the hormone ecdysone, much like the prostate gland which produces the most active form of androgen. Interestingly, SC growth that occurs in virgin males requires ecdysone, but in mated males, endoreplication-dependent growth occurs independently of this hormone. The switch from hormone-dependent steroid receptor signalling to hormone-independent signalling mirrors the transition from androgen-dependent prostate cancer to the more aggressive and incurable form of prostate cancer, androgen-independent ‘castration-resistant prostate cancer’ (CRPC). I demonstrate that the cell cycle regulators, Cyclin D (CycD), Cyclin E (CycE), Retinoblastoma (Rbf) and E2F1, which are all implicated in prostate cancer, are key regulators of SC growth and endoreplication both in virgin and mated males. Furthermore, CycD/Rbf/E2F1/CycE interacts with the BMP/EcR signalling axis to regulate the transition from hormone-dependent to hormone-independent steroid receptor signalling in SCs, mirroring some of the mechanisms associated with the transition to CRPC. Overall, my work suggests that there are parallels between the physiological roles of the EcR’s switch to hormone-independence in SCs and the pathological changes seen in CRPC, and indicates that further genetic analyses in SCs may unravel the complex signalling mechanisms that mediate the transition to this lethal form of cancer.

Keywords: castration-resistant prostate cancer
secondary cells
drosophila
post-mating responses in adult drosophila males
cell cycle
steroid receptor signalling
prostate cancer
ecdysone
accessory gland
BMP signalling
ECR signalling
hormone
Advisor: Wilson, C
The role of ABCC5 in the transport of inhibitory neuropeptides into vesicles

ABCC5 is an ATPase dependent membrane transporter capable of transporting many structurally unrelated substrates such as glutamate conjugates and cyclic nucleotides. Previous work has found that high ABCC5 expression in human adipose tissue has been associated with an increased incidence of Type 2 diabetes mellitus. Global Abcc5 knock-out mice had significant accumulation of the inhibitory neuropeptide N-acetylaspartylglutamate in their brains and had reduced adipose tissue depots, were more insulin sensitive and had raised post-prandial plasma levels of the incretin hormone GLP-1. We propose that ABCC5 may be involved with the loading of NAAG into synaptic-like microvesicles in gut endocrine cells and neurons. The work outlined here aimed to identify where ABCC5 is expressed in gut endocrine cells and to confirm the NAAG transporter activity of ABCC5. Through fixed cell immunolabelling and live cell dye staining, we show that ABCC5 is not expressed on the cell membrane of model enteroendocrine cells and has a punctate, intracellular expression pattern. We also adapted a method to isolate ex vivo synaptic vesicles from mouse brains and developed a vesicular transport assay with NAAG13C5 substrate detection based on NMR spectroscopy. The preliminary data we have generated supports our hypothesis that ABCC5 is expressed intracellularly and participates in the loading of substrates in intracellular vesicle pools.

Keywords: ABCC5
Advisor: de Wet, H
Claridge, T
Vehicle detection using radar and vision with noisy data

Autonomous vehicles operating in on-road environments need to be aware of the presence and motion of other actors in the environment. The detection of other vehicles is therefore a key component of an autonomous driving system. This thesis investigates how the highly complementary characteristics of radar and vision can be combined to tackle the problem. It first discusses the issues surrounding the implementation of a multi-modal sensing system, including calibration and synchronisation. It then shows how the range and direct velocity measurements of radar can be used to improve the performance of current image-based detectors when detecting small, distant vehicles. Given the importance of labelled data to the training of modern object detectors, it introduces a method for automatically labelling a dataset utilising cameras of different focal lengths. The impact of errors in the training labels on the performance of the trained detector is then demonstrated. To mitigate that impact, a technique for training object detectors using noisy labels is introduced. Finally, the use of the radar as a labelling source is considered along with a novel process for training a detector using the radar labels.

Advisor: Newman, P
Validating an implicit cognition battery in Parkinson’s disease and assessing its sensitivity to pharmacological manipulation

Introduction: Cognitive decline is one the most common and debilitating non-motor symptoms associated with Parkinson’s disease. Currently, no treatment options exist for cognitive impairment in PD, partly due to the lack of measurement tools sensitive to the subtle early cognitive changes and pro-cognitive pharmacological manipulation in the disease. Implicit cognition shows promise in detecting these otherwise overlooked changes.
Methods: Two studies were performed. One between-subject study comparing the performance of healthy controls (n=30), REM sleep behaviour disorder (n=30), a prodromal population for Parkinson’s disease, and Parkinson’s disease (n=30) on a previously validated battery of implicit cognitive tasks. The second was a blinded and randomized within-subject study looking at performance on the same implicit task battery in patients with Parkinson’s disease (n=30) on two occasions, both ‘on’ and ‘off’ their dopaminergic medication.
Results: The first study successfully detected implicit cognitive difference in RBD individuals compared to healthy controls and Parkinson’s disease, specifically on the positive location priming effect. The second study failed to detect any changes between Parkinson’s patients ‘on’ and ‘off’ their medication, although there was an effect on an explicit measure of visuospatial memory.
Conclusion: These results indicate that visuospatial positive priming could be a promising avenue of future research in detecting the early cognitive changes associated with PD. These results also indicate that implicit cognition may not be sensitive to pharmacological manipulation in PD.

Keywords: PD
implicit cognition
RBD
REM sleep behaviour disorder
Parkinson's disease
Advisor: Harmer, C
Murphy, S
Measuring structure and interactions in colloidal fluids using test-particle insertion

We use the Potential Distribution Theorem to evaluate distribution functions from equilibrium configurations using test-particle insertion. We use this methodology to determine the contact value of the pair distribution function in hard-disk systems: in contrast with the conventional distance-histogram method, the insertion measurement is exact and does not require an approximate extrapolation. The resulting equations of state in both simulations and a hard-disk colloidal model system agree well with the predictions of Scaled Particle Theory. We also provide the first experimental measurement of the cavity distribution function y(2)(r) inside the hard core.
We next develop a model-free technique for measuring the pair potential u(2)(r) in pairwise-additive fluids, by matching the insertion and distance-histogram measurements of g(2)(r) using an iterative predictor-corrector scheme. We test the method extensively in simulation, before applying it successfully in a fluid of superparamagnetic colloidal particles, obtaining the anticipated form of u(2)(r) and the correct dependence on the applied magnetic field. We then extend the scheme to measure the full set of pair potentials in multicomponent fluids, demonstrating its efficacy in a three-component simulation.
We show that a given n-body distribution function g(n) (n>2) can be measured using n different insertion routes, which correspond to simultaneous insertion of between 1 and n test particles. We use these methods to measure g(3) in simulation: while the noise depends strongly on the number of simultaneous insertions, the resolution is superior to that of the distance-histogram method. Finally, we consider systems with three-body interactions. We show that matching g(2)(r) alone gives an effective pair potential which is unable to reproduce g(3) in pairwise-additive simulations. We therefore extend the predictor-corrector scheme to measure the three-body interaction u(3) by matching g(3), and test it in simulation. The scheme broadly recovers the correct u(3), but requires further development to reduce the noise.

Keywords: Hard disks
Colloids
Three-body interactions
Liquid state
Structure
Interactions
Statistical mechanics
Pair potentials
Superparamagnetic particles
Advisor: Dullens, R
Aarts, D
The social media challenge for democracy: propaganda and disinformation in a platform society 

What is the nature of private platform authority and its causal and consequential role in shaping contemporary political communication and the spread of disinformation and propaganda online? This thesis integrates three distinct studies that examine how platform authority – including the technical, social, economic, and institutional practices of private companies – shape contemporary political communication and the creation and dissemination of propaganda and disinformation. By illuminating some of the hidden affordances of digital platforms and their algorithms, I explore how people find, watch, and discuss news and politics in a mediated environment that is increasingly characterized by attention economics, surveillance capitalism, and black-box decision-making. My first study examines the politics of Google Search and explores when keyword metadata generated top placements for “junk news” and other conspiratorial, hyper-partisan, or disinformation websites. My second study looks at the politics of Twitter and examines how hashtags and automation were used by foreign state actors to demobilize, target, and harass civil society activists working on issues pertaining to women’s rights and empowerment. My third study looks at the politics of YouTube, and how the introduction of state-backed media labels affected how users consume, comment on, and criticize information from these sources. Each of these chapters show that social media platforms all have affordances that are open for political manipulation by actors with very few resources and technical skills. But more importantly, these studies also demonstrate the importance of private actors for contributing to strong institutions of political communication in private spaces: we depend on Google Search, Twitter, and YouTube to faithfully implement technologies and policies that support the civic functions they often deny they perform. I show how the privatization of democracy – through the institutional and technical decisions of platform companies – shape public life, not always for the better.

Keywords: Democracy
Computational Propaganda
Disinformation
Social Media
Platform Governance
Advisor: Howard, PN
Wright, J
The normativity of constitutional conventions, with special references to the UK, USA and Greece

This thesis answers a twofold question regarding the nature and normativity of constitutional conventions, making special references to three jurisdictions, the UK, US and Greece. Conventions are political rules that regulate the constitutional edifice. The normativity of conventions is based on the coordination of political actors toward the principal goal of enhancing democratic accountability. They are a species of the genus of constitutional norms, with their distinguishing characteristic being non-enforceability in court, a quality that safeguards an area of autonomy for political actors. Thus, issues arising out of conventional rules are resolved in political fora, like the electorate and the Parliament.
The analysis begins with the theoretical positions regarding conventions in the three jurisdictions in order to examine the influence of academic tradition: Greek and UK scholarship represent opposite approaches on the issue of conventions, while in the US conventions have received relatively little attention from theorists. Next, conventions are shown to be normative. They guide the conduct of political actors, either limiting or enabling their action, and involving negative consequences—‘political difficulties’—for those who breach the rules. The genus, constitutional norms, and differentia, non-enforceability of conventions, are explained, associating the latter with the choice of a political forum for the resolution of the relevant issues. Conventions and the UK ‘political constitution’ are closely connected; conventions are the central case of political constitutional regulation through a normative, Aristotelean view of politics. The reason behind the normativity of conventions is not content-free coordination but rather coordination towards a purpose, that of enhancing democratic accountability. This is why conventions retain their importance today. The reason for their existence is of particular importance for dealing with new challenges, allowing flexible regulation of new areas of constitutional activity and providing essential support for the democratic coexistence of political and constitutional actors.

Keywords: constitutional conventions
Advisor: Yowell, P