VictorJuiz/thesis huggingface dataset:
Quantifying biases in a long-term field study: finding Wytham’s missing tits
Keywords: Parus major
Wytham Woods
Great Tit

Inferences drawn from long-term field studies of animals are vulnerable to biases in observability of different classes of individuals, which may lead to biases affecting ecological and evolutionary conclusions. Advancing statistical techniques are providing increasing evidence that individuals missing from population samples show consistent individual differences, although any resulting biases remain poorly understood. In this thesis, I investigate how biases can occur in estimating individual variation in reproductive success and residence behaviour within a natural great tit (Parus major) population. The primary objective of this thesis is to investigate whether individuals that are detected using standard sampling techniques are representative of the entire population. To do so, I use RFID technology to sample more completely across seasons, investigating individual detectability throughout the year.
I show that females that fail early in their breeding attempt, before they are identified under standard sampling protocols, are more likely to be young and immigrants from outside the study population and breeding in poorer quality habitats. As a consequence, estimates of the fitness of immigrants versus residents, age effects on fitness, and the age and immigration specific effects of habitat quality derived from standard survey methods are likely to be underestimates. I show that the high failure rate amongst immigrant females may be a result of late arrival time to the breeding grounds. These findings imply that costs of dispersal might impact on reproductive success. Moreover, I show that the exclusion of early nest failures from analyses can lead to underestimates in the effects of dispersal on reproductive success; as a consequence, current work concluding that immigrants have lower fitness than residents is likely to underestimate the size of this effect.
This thesis also provides some of the first baseline data tracking the presence or absence of passerines within a population across seasons. Our findings suggest that certain individuals are less likely to be detected as a function of their phenotype. We identify sex as a predictor of failure to be detected breeding, with males less likely to be detected. We also find that the likelihood of detection during successive breeding and winter surveys is repeatable across years. This adds to a gathering body of knowledge suggesting that sampling at certain times of the year selects for specific phenotypes. This thesis represents the first large-scale investigation of individuals that remain undetected in a long-term great tit population study, demonstrating that more attention should be given to the question of whether methods for surveying natural populations introduce systematic biases that influence conclusions about ecological and evolutionary processes.
'Local, loyal and constant'? On the dynamism of terroir in sustainable agriculture
Keywords: Drink
Terrior
France

Terroir is a concept that is used in France, and increasingly elsewhere, to evoke character and quality in food and drink in relation to the place it comes from. In this thesis, I investigate how terroir has attained its present-day economic value and cultural resonance; how it is subject to multiple forms of articulation across France; and how it is put to use as part of the philosophies and practices of environmentally sustainable modes of production. I use cultural and historical modes of enquiry and I draw upon interviews, participant observation, discourse and archive analysis carried out on fieldwork in three production chains in eastern France; being wine production in Burgundy, walnut production in the Isère valley, and Reblochon cheese production in the Alps. In the course of this thesis, I elucidate the cultural significance and epistemology of the concept, and make arguments that propositions for terroir consist of both specific geographical extent and historical density of explanation; that the rhetorical assembly of stories about terroir permits claims for continuity in production and tradition; and that the adoption of organic and biodynamic methods of farming troubles inherited understandings of what terroir is, through the intervention of the lively propensities of biotic actors. This is a story about food, farming and culture in France that I tell to critically examine the local, loyal and constant predicates of terroir, and to make an original contribution to our understanding of the cultural and historical background to the French and European systems of geographical protection in food and drink.
Materiality in numerical cognition
Keywords: Cognitive Archaeology
Numeracy
Numerosity

Using the Material Engagement Theory of Cognitive Archaeologist Lambros Malafouris as its framework, the thesis offers a unique synthesis of data from neuroscience, ethnography, linguistics, and archaeology to outline how number concepts are realized, manipulated, and elaborated. The process is described as an interactivity of psychological processes like numerosity, behaviors that manipulate objects into concept-generating stimuli, and material objects with semiotic qualities distinct from those of language and agency distinct from that of brains and bodies.
The counting technologies of the Ancient Near East (ANE) are then analyzed through archaeological and textual evidence spanning the late Upper Paleolithic to the Bronze Age, from the first realization of number concepts in a pristine original condition to their elaboration into one of the ancient world’s greatest mathematical traditions, a foundation for mathematical thinking today. Insights from the way numbers are realized through psychological–behavioral–material interactivity are used to challenge three dominant conceptualizations of ANE numbers: first, the idea that the ANE numerical lexicon would have counted only to very low numbers; second, that Neolithic tokens were the first counting technology; and third, that numbers were ‘concrete’ before they became ‘abstract’. Considering archaeological evidence from the Epipaleolithic Levant and drawing on linguistic and ethnographic evidence to characterize the regional prehistory, the thesis suggests that the numerical lexicon would have included relatively high numbers prior to the Neolithic; that finger-counting (linguistically attested) and tallies (archaeologically attested) would have preceded tokens; and that numbers are ‘abstract’ concepts whose content changes in conjunction with the incorporation and use of different material forms. The evidence provided to support these alternatives implies that numbers may have originated in the late Upper Paleolithic and arithmetic early in the Neolithic, pushing the onset of these capabilities further back than is commonly held.
In addition to tallies and tokens, the thesis explores fingers and numerical notations as material artifacts, enabling an analysis of how materiality might structure numerical concepts, influence a number system’s capabilities, limitations, and elaboration potential, and affect brains and behavior over cultural spans of time. Insights generated by the case study are then applied to the role of materiality in cognition more generally, including how concepts become distributed across multiple material forms; the reasons why materiality might be transparent (or invisible) in cognition; and the differences between thinking through and thinking about materiality.
Imitation: evaluating neurophysiological signatures and clinical significance
Keywords: autism
imitation
mirror neurons
language impairment

Imitation and its neural basis has been the subject of great interest, particularly for researchers interested in autism spectrum disorders (ASD). Research has reported imitation deficits in ASD, which have been theoretically linked to the condition’s sociocommunicative difficulties. Abnormalities in the mirror neuron system (MNS), as measured using EEG techniques, have also been reported in autism, and linked to imitation skills. In this thesis, I examine questions both around behavioural imitation deficits, and the validity of EEG techniques used to investigate the MNS. I consider whether children with other communication disorders show similar imitation deficits to children with autism, examining verbal and motor imitation. I report data from non-autistic children with and without language problems, and children with autism and normal language (ANL) and children with autism and language-impairment (ALI). In contrast to previous studies, I find similar verbal imitation performance in children with ALI and non-autistic language impaired children, but limited motor imitation impairments in the disorder groups. I also examine the evidence from mu suppression studies for the role of the MNS in language, social processes and the development of ASD. I present findings from a preregistered study that show that methodological factors such as baseline condition have important effects on mu suppression studies’ results, and question its validity as an MNS measure. I also examine how imitation skills, self-reported communication abilities and autistic traits relate to individual differences in mu suppression. I find limited support for the theory that mu suppression correlated with behaviours and traits proposed to be underpinned by the MNS. I discuss the implications of these two projects for future research and clinical interventions for children with communication disorders.
Investigating primary and secondary B cell responses in cattle after immunisation with existing and novel vaccines
Keywords: foot-and-mouth disease virus
bovine
B cell

Antibodies play a pivotal role in protecting against viral infection, maintenance of this protective response is provided by plasma and memory B cells. Foot and mouth disease virus (FMDV) is a highly contagious pathogen and studies in cattle have shown that protection from the virus is antibody-mediated. However, FMDV vaccines are unable to achieve long durations of immunity. Therefore, understanding the FMDV-specific B cell responses in cattle is essential to inform future vaccine design.
Antigen-specific ELIspot assays were used to determine the kinetics of the bovine B cell response to T-dependent and -independent antigens. An ELIspot assay was developed to allow enumeration of FMDV-specific plasma and memory B cells following vaccination and live-virus challenge. In addition, a novel surgical technique was also developed to allow enumeration of antigen-specific B cells when exiting a regional lymph node, following vaccination. The bovine immunoglobulin repertoire was investigated at the peak of the B cell responses using deep sequencing.
T-dependent B cell responses in cattle were characterised by a small burst of antigen- specific plasma cells occurring after the primary vaccination, which was coupled with an increase in antigen-specific IgG titres. In keeping with the central dogma of immunolog- ical priming, the plasma cell burst post booster vaccination was larger and more rapid. Antigen-specific memory B cells were detectable for over 6 months. In contrast, immu- nisation with a T-independent antigen resulted in no detectable plasma or memory B cells. Vaccination with inactivated FMDV, novel FMDV antigens and live-virus chal- lenge induced in a burst of FMDV-specific plasma cells but low numbers of memory B cells. Deep sequencing of immunoglobulin transcripts at the peak of the antigen-specific plasma cell response post vaccination, detected increases in bovine IgG transcripts in both blood and efferent lymph following booster vaccination, indicating that they are likely to be FMDV-specific. Deep sequencing has also revealed that cattle exhibit a broad range of heavy chain CDR3 lengths and highly similar light-chain transcripts that are shared between animals. Overall, this data suggests that the kinetics of the bovine plasma and memory B cell response to antigen is similar to that demonstrated in humans and mice. However, the bovine antibody V region structure is different and is likely to interact with its cognate antigen differently.
Religious landscapes, places of meaning: the religious topography of Arcadia from the end of the bronze age to the early Imperial period
Keywords: ancient religion
ancient history
sanctuaries
Arcadia
ancient Greece
Greek religion
Pausanias

The thesis examines the religious topography of Arcadia through two particular aspects: the built and the natural landscape, and how each relates to human communities, their places of living, and their understanding of the world around. It relies on the assumption commonly made in the field that, since ritual practice was of prevalent importance for the Greeks, cult sites are the most important places for the communities, and therefore they can tell us a lot about the people who built, visited and looked after them.
The first part rests on the acknowledgement that sanctuaries are places of interaction for a certain community of cult (which can but need not overlap with a given polis) and explores how they can be indicators of social change, defined here as responses to changes with large impact on the human milieu. These changes and their response articulated in sacred space are identified in four chapters. The first sets the stage and surveys the known sacred sites of Arcadia at the end of the Bronze Age and during the Early Iron Age. The second looks at how the building of temples after the eighth century indicates a significant change in the way communities were structured in Arcadia. The third looks at how Arcadian sanctuaries responded to the increased religious mobility of the Classical and Hellenistic period. Finally, chapter four evaluates the impact of the Roman conquest on Arcadian religious sites.
The second part explores how myths and rationalising discourses allowed the Greeks to make sense of the salient characteristics and numen of their surrounding natural landscape. Each of the three chapters departs from a situation observed in Arcadia by ancient sources and examines the responses articulated to explain it. Among the variety of topics to pursue, three have been selected because they exemplify a typical characteristic of Arcadia: its wetness. They also allow spatial areas that were less prominent in part one to be explored. The first chapter investigates the attribution of Mycenaean waterworks in Arcadia to Herakles in myth. The second chapter examines the connection made in ancient sources between Poseidon’s lordship over the Peloponnese, earthquakes, floods and cults of Poseidon Hippios in Arcadia. Finally, the last chapter explores the apparent contradiction of having infernal rivers observable in the world of the living, such as the Styx flowing in the Aroania Mountains.
Complexity of mixed equilibria in boolean games
Keywords: Game theory
Boolean games
Propositional logic
Computational complexity

Boolean games are a succinct representation of strategic games wherein a player seeks to satisfy a formula of propositional logic by selecting a truth assignment to a set of propositional variables under his control. The difficulty arises because a player does not necessarily control every variable on which his formula depends, hence the satisfaction of his formula will depend on the assignments chosen by other players, and his own choice of assignment will affect the satisfaction of other players' formulae.
The framework has proven popular within the multiagent community and the literature is replete with papers either studying the properties of such games, or using them to model the interaction of self-interested agents. However, almost invariably, the work to date has been restricted to the case of pure strategies. Such a focus is highly restrictive as the notion of randomised play is fundamental to the theory of strategic games – even very simple games can fail to have pure-strategy equilibria, but every finite game has at least one equilibrium in mixed strategies.
To address this, the present work focuses on the complexity of algorithmic problems dealing with mixed strategies in Boolean games. The main result is that the problem of determining whether a two-player game has an equilibrium satisfying a given payoff constraint is NEXP-complete. Based on this result, we then demonstrate that a number of other decision problems, such as the uniqueness of an equilibrium or the satisfaction of a given formula in equilibrium, are either NEXP or coNEXP-complete. The proof techniques developed in the course of this are then used to show that the problem of deciding whether a given profile is in equilibrium is coNP#P-hard, and the problem of deciding whether a Boolean game has a rational-valued equilibrium is NEXP-hard, and whether a two-player Boolean game has an irrationalvalued equilibrium is NEXP-complete. Finally, we show that determining whether the value of a two-player zero-sum game exceeds a given threshold is EXP-complete.
Representations of the princesse de Lamballe (1749-1792): the portraiture, patronage and politics of a royal favourite at the court of Marie-Antoinette
Keywords: Hôtel de Lamballe
Anglomania
Versailles
Hôtel d’Eu
Duc de Penthièvre
Hôtel de Toulouse
Rambouillet
Courtiers
Female patronage
Print collecting

This thesis examines the portraiture and patronage of Marie Thérèse Louise de Savoie-Carignan, the princesse de Lamballe (1749-1792). It is the first comprehensive and detailed study to be undertaken of the princess's activities as patron. Lamballe was Marie-Antoinette's longest-serving confidante and Superintendent of the Queen's Household. Through close formal analysis of the portraits combined with careful consideration of the sitter's personal circumstances and the wider cultural and historical context, the thesis challenges scholarly assumptions that the princess had only negligible influence as a sitter and patron. As a case study of an independent, professionally ambitious and childless widow, it identifies a wider range of motives and cultural meanings than has previously been ascribed to female court patronage of this period.
The first chapter demonstrates that the early depictions of Lamballe as a docile and grieving princess were largely dictated by her father-in-law, an identity the princess subsequently discarded when she assumed a professional role at court. Chapter two examines portraits executed during the princess's rise to political and social prominence and shows that her attachment to the queen and the length of time she spent in her company and service, together with her publicly visible roles as freemason and salonnière, made her a figure of considerable renown and influence and thereby a highly significant patron at the French court. This was enhanced by the princess's international reputation as a talented amateur artist in her own right and by her financial and social support of aspiring artists and art institutions. The princess's engagement with the cult of sentiment and advocacy of women artists is allied to the sorority encouraged by Marie-Antoinette within the women of her select circle. Complementary chapters on the princess's previously unknown anglophile inclinations (discussed in Chapter three) and her private collections, library, and musical and literary patronage (considered in Chapter four) further reveal that Lamballe was an informed and cultivated female patron who operated at the very centre of Marie-Antoinette's circle.
The coinage of the Gallic Empire
Keywords: Gallic Empire
coins
coinage
Roman Empire numismatics

This thesis presents a new systematic arrangement of the coinage of the Gallic Empire as the basis for a revised edition of Roman Imperial Coinage. The coinage of all denominations, gold, silver and bronze, are unified into a single structure of issues.
In 260, Postumus revolted against the Roman emperor Gallienus and took control of the Gauls. The chronology of his reign and of his successors is reviewed. The short reign of Domitianus II is interpreted as a revolt against the elevation of Tetricus. A rearrangement of Tetricus’s coinage supported by the epigraphic evidence proves that the elevation of Tetricus II to the Caesarship must be redated from 273 to 272. The location of the mints is discussed. Conclusive hoard evidence proves that the main mint was located at Trier, and not at Cologne. The study of iconography implies that choices were not necessarily made by the imperial authorities, but that more freedom was given to engravers than is usually assumed. The use of earlier coins as an iconographic repertoire strongly suggests that earlier coins were brought to the mint to be melted down. Metrological analyses of gold coins of the Gallic emperors show for the first time that silver was deliberately added to the alloy, following a practice introduced by Valerian and continued by Gallienus. The debasement of the ‘silver’ coinage is studied in parallel with its contemporary evolution within the Central Empire. Coin circulation is used in order to determine the frontiers of the Gallic Empire. It is demonstrated that the Gallic Empire reached its apogee between 262 and 265, ruling over Britain, the Gauls, Hispania and Raetia. The nature of the Gallic Empire is discussed. It is argued that this ‘Empire’ should not be viewed as a form of separatism, as often claimed, but as the unintended result of a status quo following Postumus’s acclamation and the long postponement of a final confrontation against the emperor of Rome.
The acquisition of coarse gaze estimates in visual surveillance
Keywords: randomized fern
surveillance
randomised fern
machine vision
thesis
head pose
video surveillance
randomised tree
gaze
tracking
visual surveillance
predicate fern
MCMCDA
video analysis
randomized tree
computer vision
attention
head tracking

This thesis describes the development of methods for automatically obtaining coarse gaze direction estimates for pedestrians in surveillance video. Gaze direction estimates are beneficial in the context of surveillance as an indicator of an individual's intentions and their interest in their surroundings and other people. The overall task is broken down into two problems. The first is that of tracking large numbers of pedestrians in low resolution video, which is required to identify the head regions within video frames. The second problem is to process the extracted head regions and estimate the direction in which the person is facing as a coarse estimate of their gaze direction.
The first approach for head tracking combines image measurements from HOG head detections and KLT corner tracking using a Kalman filter, and can track the heads of many pedestrians simultaneously to output head regions with pixel-level accuracy. The second approach uses Markov-Chain Monte-Carlo Data Association (MCMCDA) within a temporal sliding window to provide similarly accurate head regions, but with improved speed and robustness. The improved system accurately tracks the heads of twenty pedestrians in 1920x1080 video in real-time and can track through total occlusions for short time periods.
The approaches for gaze direction estimation all make use of randomised decision tree classifiers. The first develops classifiers for low resolution head images that are invariant to hair and skin colours using branch decisions based on abstract labels rather than direct image measurements. The second approach addresses higher resolution images using HOG descriptors and novel Colour Triplet Comparison (CTC) based branches. The final approach infers custom appearance models for individual scenes using weakly supervised learning over large datasets of approximately 500,000 images. A Conditional Random Field (CRF) models interactions between appearance information and walking directions to estimate gaze directions for head image sequences.