VictorJuiz/thesis huggingface dataset:
How is information in working memory selected and prioritised for action?

Flexible cognition necessary for everyday behaviour depends on working memory (WM)–the ability to keep information in mind for a later use. Not all items in WM are represented equally. Attention can be allocated to select and prioritise task-relevant content for a forthcoming action.
Chapter 2-3 used behaviour, eye-tracking and electroencephalography (EEG) to investigate the consequences of selecting a single feature in WM for the representation of other features belonging to the same item. Orientation judgements were faster and more precise when another feature of the same object was cued for an orthogonal task during the delay. Colour selection in WM engaged spatial attention, indexed by contralateral alpha suppression and gaze bias, and was associated with a boost in the representation of the cued object’s memorised location (Chapter 2) and orientation (Chapter 3) as decoded from EEG voltages. The results provide evidence for obligatory attentional spread between an item’s features in WM and support a special status of location in selecting and binding features. Finally, EEG decoding revealed that the cued item was automatically compared with the probe at recall, suggesting selected WM content may be in a prioritised state for interacting with new sensory input and guiding decision-making.
WM is more than a passive store of recent experiences and is fundamentally future-oriented. Chapter 4 tested whether WM contents are configured as prospective task-sets for guiding behaviour. In one experiment, a prioritised item drove responses in a task-specific manner even when irrelevant in the context of a nested task. In a second experiment, task-foreknowledge improved WM-guided behaviour and enhanced retro-cued prioritisation on reaction times. Together, the results indicate that prioritised WM items are configured as prospective templates optimised for context-dependent action. Neuroimaging studies are needed to elucidate the precise mechanisms of task-specific coding in WM. Chapter 5 proposes an EEG experiment, in the form of a Registered Report, to test the hypothesis that prioritised content is stored in a functional state that is intrinsically linked to its anticipated use. I predict that patterns of neural activity coding for remembered items will be task-specific. The suitability of the analysis pipeline was demonstrated on simulated neural data.
The results of this thesis highlight a key role of attentional selection in preparing WM representations for future action and motivate further research into the ways information in WM may serve as functional states for decision-making.

Keywords: retro-cue
attention
working memory
EEG
eye-tracking
Advisor: Myers, N
Manohar, S
Stokes, M
Development of a novel outcome measure for forensic mental health services

Forensic mental health services provide care to people in secure psychiatric hospitals and specialised community teams. Such services are typically low-volume and high cost, often highly restrictive and average length of stay is long. Measuring the outcomes of care is important to safeguard patients and the public, monitor progress, inform treatment plans and support service evaluation. Despite this, little is known about which outcomes are most important and existing outcome measures have focused on clinical risk and symptoms, neglecting functioning and quality of life, with limited patient input to their design or reporting. The overall aim of this study was to develop a new empirically-based outcome measure for forensic mental health services. Over four hundred existing instruments were identified and the quality of ten was assessed in detail. The evidence base for their use as outcome measures in forensic mental health services was limited. Clinicians judged these same ten instruments to be unsatisfactory in terms of content validity. Thematic analysis was used to develop an outcomes framework based on patient interviews and multi-stakeholder focus groups. Forty-two outcomes were identified in the six domains of ‘about me, my quality of life, my health, my safety and risk, my life skills and my progress’. In a Delphi process to prioritise these outcomes eight of the top fifteen outcomes were shared between patients/carers and professionals. Based on these results, a new outcome measure, the FORensic oUtcome Measure (FORUM), was developed, including both patient reported and clinician reported questionnaires. In a sample of 62 patients and 35 clinicians encouraging evidence of validity and reliability was established. Feedback from both patients and clinicians indicate that the FORUM is easy to use, comprehensive and relevant. These results indicate that the FORUM is a promising new instrument to measure outcomes in forensic mental health services.

Keywords: Outcome measurement
Forensic mental health services
Advisor: Fazel, S
Fitzpatrick, R
Cook, J
Discernment of phytoplankton groups from optical properties.

The Barents Sea is a highly seasonal and productive shelf ecosystem, representing a gateway between the Atlantic and Arctic Oceans. Anthropogenic climate change is causing rapid changes in temperature, ocean chemistry, water column structure and sea-ice persistence. Sea-ice extents are declining twice as fast in the Barents Sea as other Arctic regions, establishing a mandate to investigate the impact of these environmental changes on productivity in the Seasonal Ice Zone. This is the remit of Arctic PRIZE (PRoductivity in the Seasonal Ice ZonE), and this thesis was conducted under the auspices of work package 3, studying phytoplankton compositional and phenological variability.
Remote-sensing is a key means by which ocean ecosystems are monitored and there have been recent efforts in the literature to employ ocean-colour to recognise different assemblages of phytoplankton. It is routine practice in the remote-sensing literature to distinguish functional assemblages from cell-counts and then seek bio-optical signatures to be targeted in remotely-sensed imagery. The analysis herein suggests that switching between different data types in this way introduces a translation error that undermines remote-detection efforts. We therefore recommend that functional assemblages are defined and identified directly from their bio-optical properties.
Thereafter, a scheme of bio-optical functional types is defined, based on Barents Sea phytoplankton communities, and a bio-optical algorithm is developed with the aim of retrieving this structure in remotely-sensed ocean-colour.
This algorithm is applied to study community compositional change, facilitating the integration of previous in-situ studies towards a more complete understanding of incipient ecosystem change. In addition, the ascendancy of temperate-mode autumnal phytoplankton blooms is investigated and relationships to evolving environmental conditions are explored, producing strong evidence that Atlantic inflow currents regulate the intensity of autumnal blooms in the Barents Sea.
In sum, growing Atlantic influence in the Barents Sea is found both to cause community compositional changes and concomitant phenological shifts that may change Barents Sea ecosystem function.

Keywords: barents
ocean-colour
ecology
ecosystem-monitoring
phytoplankton
remote-sensing
climate-change
arctic
satellite
phenology
Advisor: Bouman, H
McKee, D
Courting beyond the court: performing commensurability in the early European trade with Japan, 1609-1641

Between the years 1609 and 1641, merchants of the English and Dutch East India Companies (EIC and VOC) lived and worked in the port city of Hirado in Tokugawa Japan. The arrival of these companies marks the first time that western Europeans had encountered Japan following the formation of the Tokugawa Shogunate in 1603. Lacking the resources and training of royal embassies, and neither desirous nor capable of military intervention, the English and Dutch merchants were required to pursue strategies of social integration in Japan, in order to develop the network of social relations needed for successful trade.
This dissertation examines the mechanisms by which these merchants were able to integrate with the Japanese they encountered during their time at Hirado. It argues that strangership – the ambivalent and potentially hostile relationship between estranged parties – was a significant threat to trade. By locating points of cross-cultural commensurability between their disparate societies, the European merchants were able to develop trust with the local Japanese and overcome, in large part, the challenge of strangership. It suggests that this process was facilitated by the fact that all three countries were being shaped in broadly similar ways by shared ‘early modern’ forces.
Drawing on written and visual sources from the EIC and VOC factories at Hirado, this study examines the ways in which the European merchants were able to develop cross-cultural commensurability in five central aspects of the Euro-Japanese relationship: the formation of distinct cultural identities, the use of entertainment and socialising as a means of constituting social networks, the impact of space on social relations, the use of formal and informal gift exchanges as a social mediator, and the role of violence in resolving conflicts of honour and status.

Keywords: Richard Cocks
strangership
history
William Adams
Japan
cross-cultural commensurability
global history
Dutch East India Company
East India Company
early modern
Advisor: Strathern, A
Southcombe, G
Affirmative action and the question of general category in India: judicial treatment of constitutional, legislative, and executive interventions in determining backwardness and intra-classification challenges

The proliferation of reservations based on persistent demands of upper-castes or advantaged groups has given rise to a complex set of recurrent legislative interventions in India. 2019-Amendment provision of quota benefits to EWS or socially advantaged sections based on economic disadvantage marks a crucial shift in the constitutional policy of reservations. This thesis critically engages with the constitutional and state legislative reservations policies, and their judicial treatment, for EWS and upper-castes in Maharashtra, Gujarat, and Haryana. The thesis is divided into three chapters. The first chapter undertakes an analysis of the legislative and judicial history of Indian interventions and outlines the political economy behind them. The second chapter critically analyses the judgements challenging the constitutionality of the 2019-Amendment and state measures. Chapter 3 carries out an analysis of major problems and themes inductively identified and evaluates how discrimination law theory best explains the implications of the post-2019 regime on Indian affirmative action and multi-dimensional substantive equality. It is argued that reservations for upper-castes are not affirmative action measures and substantive equality. They amount to collateral discrimination as they burden cognate groups with quotas not meant for reducing relative group disadvantage. They are also discriminatory towards existing status groups. The de facto nature of EWS is of ‘upper-caste Hindu men’ which misses addressing intersectional poverty discrimination. As a key implication, the commitment of the Constitution towards substantive equality stands diluted and symbolised by enabling advantaged groups access to quotas historically devised for protected groups. The distinction between historical discrimination-based reservations and general poverty alleviation measures has collapsed giving rise to accommodating all positions of injustices under reservations. In the long-term, such developments may lead to withering-down and may displace historical discrimination-foundation for reservation policy to a general system of communal quotas for all castes and classes based on income poverty ground.

Keywords: economically weaker sections
affirmative action
reservation
socio-economic disadvantage
Advisor: Havelkova, B
Carers’ experience of assistive technology use in dementia care

Introduction:
Assistive technology such as motion detectors, tablet computers, and wearable sensors has the potential to support persons with dementia and their carers. This study investigated the experiences and impact of assistive technology on carers (family, friends and neighbours) who support persons with dementia living at home in the United Kingdom.
Methods:
Multiple methods were used in this study. Study 1: A systematic review of carers’ experiences of assistive technology use in dementia care. Study 2: Exploratory interviews to identify the support carers need and how carers use assistive technology. Study 3: Cognitive interviews to develop the carers’ assistive technology experience questionnaire and using this in a sequential explanatory mixed-method study, through a cross-sectional survey (quantitative phase), to identify types of assistive technology carers use and prefer and the benefits and disadvantages of using AT. Study 4: Explanatory interviews (qualitative phase) to describe the experiences and impact of assistive technology on carers.
Results:
Fifty-six studies were included in the systematic review and found a variety of assistive technologies. Twenty-three participants in the exploratory interviews and 201 participants in the cross-sectional survey confirmed assistive technology was predominantly used for safety and reassurance, followed by communication and reminders. Assistive technology is seen as an adjunct to providing care and carers perceived it as helping manage their stress and anxiety. Explanatory interviews with twenty-three participants showed that carers had predominantly positive experiences of using assistive technology and it often required adjustments to the role of carers and supported their wellbeing.
Conclusion:
Assistive technology development and its continued use should incorporate carers and match the needs of the person requiring it. This study demonstrated that assistive technology has a beneficial impact on carers and could be one way of supporting carers and ensuring people with dementia continue to live at home.

Keywords: cognitive intervirews
assistive technology
quantitative
dementia
mixed-methods study
qualitative
carers
Advisor: Peters, M
Jenkinson, C
Applying single cell-based technologies to the characterisation of human haematopoietic stem cell heterogeneity

Haematopoiesis is essential for all vertebrate life. It involves the generation of terminally differentiated blood cells from a small pool of self-renewing multipotent haematopoietic stem cells (HSCs) through a series of lineage-restricted progenitors. HSCs form the basis of bone marrow (BM) transplantations and enable the treatment of patients with genetic blood disorders and leukaemia. It has long been assumed that individual HSCs have the capacity to produce all blood lineages in equal proportions. However, recently, single cell and serial transplantation studies in mice demonstrated a profound degree of heterogeneity within murine HSCs with a substantial proportion displaying a restricted pattern of lineage output. Consequently, these studies in mice have challenged the traditional view of a functionally homogeneous HSC population and instead suggested that individual HSCs differ in their properties. In contrast, human HSC heterogeneity has not yet been fully elucidated. The aim of this work was to characterise heterogeneity in human adult BM-derived HSCs, particularly focusing on the identification of human HSCs with distinct lineage outputs and their transcriptional differences. For this purpose, human HSCs were purified from adult BM, barcoded with unique DNA sequences encoded by lentiviruses, and transplanted into non irradiated, immunedeficient NBSGW mice. We performed single-cell RNA sequencing of the engrafted barcoded HSCs and bulk RNA sequencing of their cellular in vivo output. We identified several human HSC subtypes with biased and restricted lineage outputs, as well as associated transcriptional differences, revealing correlated functional and molecular heterogeneity of human adult BM HSCs. This work may lead to the identification of potential molecular and/or surface markers that can help to determine HSC subsets with specific haematopoietic fate restrictions. Ultimately, characterisation of the human HSC heterogeneity in terms of the molecular signatures of specific HSC subtypes with distinct lineage outputs may allow us to predict how transplanted HSCs behave in patients.

Keywords: haematopoiesis
single cell
heterogeneity
lentiviral barcoding
bone marrow
HSC
haematopoietic stem cells
Advisor: Nerlov, C
T-cell interactions with second generation glass-supported lipid bilayers

T cells must efficiently scan and discriminate foreign antigen from self. Failure to do so leads to immunodeficiency or autoimmunity. How this process is achieved remains unclear, but recent developments have indicated the topology of the T-cell membrane, and nature of the contact interfaces formed with antigen presenting cells (APCs) may be key. Due to the difficulty of studying cellular contacts, in vitro systems that isolate and test specific elements of T cell-APC interface have been essential. One key example is glass-supported lipid bilayers (SLBs) functionalised with foreign antigen and the large adhesive protein ICAM-1 (referred to as ‘first generation’ SLBs). First generation SLBs have provided unparalleled insight into the spatiotemporal dynamics of key proteins at the T-cell membrane, however, to study the topology of initial membrane contacts, whereby antigen is first detected and discriminated, additional components must be considered. The work described in this thesis sought to establish a novel SLB that builds upon the strong foundation of first generation SLBs by additionally incorporating two key elements of the APC membrane: small adhesion molecules and the glycocalyx (referred to as ‘second generation’ SLBs). Using second generation SLBs, the results of this thesis addressed the competing effects of adhesion proteins, the glycocalyx, and different antigen density on T-cell contacts, signaling, and antigen discrimination. By visualising the T-cell membrane and exclusion of the glycocalyx on the SLB, small, dynamic membrane protrusions, referred to as microvilli, dominated the contact interface between T cell and SLB. T-cell signaling was rapidly initiated from few microvillar contacts even in the presence of very low densities of antigen, highlighting the sensitive and efficient nature of antigen detection. Finally, antigen discrimination was found critically dependent on the small and constrained geometry of microvillar contacts. In summary, second generation SLBs are a powerful approach to dissect the early events that govern T-cell activation.

Keywords: Microvilli
Antigen sensitivity
TIRF
Glycocalyx
Antigen discrimination
T-cell
glass-supported lipid bilayers
TCR
Adhesion proteins
Advisor: Davis, SJ
Eggeling, C
Scalable and data-driven approaches to convex programming

Mathematical optimisation plays a crucial role in providing efficient solutions to modern engineering applications. Despite enormous advances in the past decades, some of these applications involve solving optimisation problems that may not be computationally tractable or that call for new theoretical advancements. Hence, obtaining robust and scalable methods and developing new analytic tools to optimisation problems is of paramount importance. This thesis addresses some of the main challenges when solving optimisation programs, namely, scalability, the presence of integer decision variables and the presence of uncertainty.
Scalability throughout this thesis is achieved by means of distributed computation. Technological advancements that lead to the increase of computational devices per capita have attracted research on the development of algorithms that can exploit such a distributed and unstructured computational power to solve large-scale optimisation problems. In this context, multi-agent optimisation has emerged, as it enables distributed computation by allowing devices (or agents) to communicate over a network. This thesis proposes an algorithmic scheme based on subgradient averaging to perform multi-agent optimisation.
Some optimisation problems are computationally intractable due to the presence of integer variables. Optimising over integers is, in general, hard due to the lack of polynomial-time algorithms to obtain an optimal solution. In fact, some well-known NP-hard problems can be cast as optimisation programs involving integer decision variables. In this thesis we investigate the so-called actuator placement problem and show that a particular instance of this problem, despite being an integer program can be solved exactly by means of a convex relaxation. We also link such a relaxation to the multi-agent optimisation framework explored previously, showing how distributed schemes can be leveraged to obtain the optimal solution.
Other challenging optimisation problems arise with the presence of uncertain constraints. Indeed, even the well-studied class of linear optimisation problems may require theoretical and algorithmic advancements under this type of constraints. Uncertain constraints represent our lack of knowledge about the underlying phenomena and appear in several applications, including the optimal power flow problem under renewable energy generation, robotics, and transportation applications. Motivated by this fact, the last part of this thesis focuses on a randomised approximation to chance-constrained optimisation problems. We show a new theoretical bound on the probability of constraint violation that can improve the conservatism with respect to the state-of-the-art.

Keywords: distributed optimization
scenario approach theory
optimization
uncertain optimization
actuator placement
Advisor: Papachristodoulou, A
Margellos, K