VictorJuiz/thesis huggingface dataset:
Computer age sociology
Keywords: machine Learning
data science
computational social sciences
reproducibility
prediction

Quantitative sociology is dominated by 'beta hat'-questions, which refer to the process of defining a model of the world and interpreting its estimated coefficients when fit to data. Unfortunately, the situations where we actually know how this model should look are few and far between, yet a monolithic focus on 'beta hat' remains. This leads to a number of issues, ranging from i) a lack of appreciation of our social theories' ability to reflect the actual world, ii) misrepresentation of the actual patterns of interest resulting in biased findings, and iii) free range for researcher degrees of freedom to muddy findings. Instead, we can learn much from 'y hat'-questions that embrace the fact that we do not know the true model of the world, and should approach sociological questions accordingly. In this state of the world, there is great benefit in exploiting ever more powerful computers to assist us in making sense of social life. In this thesis, I explore how two simple ideas from fields that embrace computational power can be used to assist sociologists in their empirical workflow. First, that prediction can be used as a broad model analysis tool that can help sociologists estimate and interpret their models in a better way. Second, that methods from the machine learning domain that excel in finding patterns in data can be used to improve sociological model-building. I illustrate both ideas throughout this thesis with a range of empirical examples and case studies. The goal throughout is to complement --- rather than replace --- the standard empirical workflow of sociologists with computational ideas and methods. Accordingly, the aim remains to distill interpretable findings about the social world from data. However, I propose we do so without shying away from the computational riches and associated exciting methodological developments that characterize this day and age.
Preterm birth screening, prevention and management: a cross-sectional online survey of practice in the Oxford Academic Health Science Network (The AHSN Network)
Keywords: management
prevention
preterm
United Kingdom
practice
screening
variation

Background: A survey in the six hospitals of the Oxford Academic Health Science Network (The AHSN Network) with the aim of establishing current practice for screening, prevention and management of preterm labour and assessing variation in practice.
Methods: A cross-sectional web-based survey was piloted then administered via an online survey software to sixty (60) participants drawn from practitioners involved in the screening, prevention and management of preterm birth in the Oxford Academic Health Science Network.
Results: The survey received responses from all the 6 hospitals in the network. It had a 38.3% response rate and a 73.9% completion rate. The key interesting findings from the survey are summarised as: practice; 94.12% of obstetricians are in favour of selective screening in favour of high-risk women; 18.75% are not offering progesterone, the best evidence-based treatment at the moment; rescue and abdominal cerclages are being performed at district general hospitals instead of tertiary referral centres; a 100% use of diagnostic aids; majority use nifedipine for tocolysis; magnesium sulphate is commonly prescribed but not supported by a recent place of birth audit, and there is use of routine antenatal corticosteroids against NICE guidance. About half of obstetricians are in favour of universal screening and the establishment of a preterm labour service across the network supported by individual units in their hospitals. Patient decision support aids, support groups and patient-reported outcomes were noted as weak areas across the network.
Conclusions: Development of Strategies for improving adherence to the network guidelines are necessary so as to ensure uniformity in practice especially for interventions that are conclusively backed by evidence. It is necessary to further establish the effectiveness of establishment of a preterm birth service and dedicated preterm birth units in each of the hospitals. There is a need to develop decision support aids, establish support groups and patient reported goals and outcomes.
Evolution of the volatile inventory of rocky exoplanets in a runaway greenhouse state with the General Circulation Model ExoFMS-SOCRATES
Keywords: extrasolar rocky planets
exoplanet atmospheres
habitable planets
greenhouse gases

The runaway greenhouse represents the ultimate climate catastrophe for rocky, Earth-like worlds: when the incoming stellar flux cannot be balanced by radiation to space, the oceans evaporate and exacerbate heating, turning the planet into a hot wasteland with a steam atmosphere overlying a possibly molten magma surface. The equilibrium state beyond the runaway greenhouse instellation limit depends on the radiative properties of the atmosphere and its temperature structure. Here, we use 1-D and 3-D radiative-convective models of steam atmospheres to explore the transition from the tropospheric radiation limit to the post-runaway climate state. To facilitate simulations with 3-D global circulation models, a computationally efficient band-grey model is developed, which is capable of reproducing the key features of the more comprehensive calculations. We analyse two factors that determine the equilibrated surface temperature of post-runaway planets. The infrared cooling of the planet is strongly enhanced by the penetration of the dry adiabat into the optically thin upper regions of the atmosphere. In addition, thermal emission of both shortwave and near-IR fluxes from the hot lower atmospheric layers, which can radiate through window regions of the spectrum, is quantified. 3-D GCM simulations were performed, indicating that the runaway greenhouse effect necessarily ends with a thin condensing region located at the uppermost layers of the atmosphere, mostly on the nightside, while dayside condensation is prevented by heating coming from the absorption of incoming stellar radiation caused by the opacity of water vapour. Surface pressures higher than 10 bar feature non-convective regions in the deep layers, whereas the surface temperature of post-runaway atmospheres seem only weakly sensitive to instellation. Combining five secondary eclipse observations of TRAPPIST-1b with JWST/MIRI could yield a 4.5 sigma detection if it has an atmosphere made out of 1 bar of water vapour. The maximum confidence level in the cases explored for TRAPPIST-1d is 2 sigma, making it unsuitable for thermal emission observations with JWST. Astronomical surveys of rocky exoplanets in the runaway greenhouse state may discriminate some of these features using multi-wavelength observations. Further understanding of runaway greenhouse climates will come from more holistic models, more spectroscopic measurements outside Earth-like conditions, and future observatories.
An aptamer-based sensor for the detection of antimalarial drugs
Keywords: malaria
drug detection
drug resistance
aptamer

Artemisinin-based combination therapies (ACTs) have begun to fail as first-line therapies for the treatment of Plasmodium falciparum malaria in Southeast Asia. Preventing the further spread of drug-resistant parasites is a top priority for global malaria elimination campaigns. A low-cost, field-based assay to detect slow clearing ACT compounds from patient samples could allow for improved tracking of antimalarial drug use, monitoring of treatment adherence, and evaluation of therapeutic efficacy and resistance. It could also provide sensitive detection of active components in assessments of tablet quality. This research reports the development of a low-cost, rapid, fluorescent sensor for the specific detection of piperaquine and mefloquine. In order to do this, DNA aptamers were identified that bind and differentiate between small molecule partner drugs. These aptamers were selected from a library of single-stranded DNA molecules for their selectivity and binding affinity. Following their isolation by a capture-SELEX method, a structure-switching aptamer fluorescent sensor was developed. The sensor performance was optimized for the detection of drug from crushed tablets and from human serum, resulting in two fluorescent sensing platforms. The sensors were evaluated for their sensitivity and specificity in relevant sample matrices and the serum sensor was validated against an LC-MS gold standard drug detection method. Feedback from potential assay end-users was collected to inform the assay development and it is believed that these aptamer sensors will be useful tools for monitoring antimalarial drug quality and studying antimalarial drug use.
The dehybridization of social enterprises
Keywords: board heterogeneity
hybrid organizations
dehybridization
hybrids
financial crisis
Brexit
social entrepreneurship
community interest companies
COVID-19
exogenous shocks
social enterprise
hybridity
governance

In the world of hybrid organizations, an important and under-examined phenomenon is the process of transforming from a hybrid structure to an organizational form with fewer logics. This research introduces the concept of dehybridization, which I define as a process through which an organization transforms in a way that integrates fewer institutional logics than previously. To examine the phenomenon of dehybridization in the context of social enterprises, I draw on the hybridity and hybrid organizations literatures. These literatures are integral in gaining a conceptual understanding of the challenges of hybrids and their transformations. Building upon this theory, I propose a conceptual framework that describes how dehybridization occurs in hybrid organizations and empirically study this phenomenon in a three-paper dissertation. The first paper introduces and defines the concept of dehybridization and illustrates the potential process for hybrid organizations. The second paper draws on a dataset of 33,350 Community Interest Companies in the United Kingdom from 2006-2020 to examine the relationship between organizational governance and dehybridization. The third paper draws on the same dataset and examines how three exogenous shocks (2007-2008 Financial Crisis, Brexit Vote, and Covid-19 Lockdown) affected the management of hybrid tensions in social enterprises.
Workplace mindfulness-based programmes for stress and wellbeing: a realist review and evaluation
Keywords: wellbeing
stress
realist evaluation
workplace
realist review
programme
mindfulness

Mindfulness-based programs (MBPs) are increasingly offered in the workplace to reduce stress and enhance wellbeing. A growing body of evidence suggests that these programmes can be beneficial; however, dropout rates are often high, and there is great heterogeneity in both programme content and strength of effects between studies. This thesis contributes to a better understanding of what makes these programmes successful, under what circumstances, for whom, and why. A realist approach was employed that is theory-driven and well-suited to make sense of complex interventions, such as MBPs.
First, I conducted a realist review where I analysed and synthesised data from 75 existing studies of workplace MBPs to identify the mechanisms through which these programmes work or do not work and discover how particular contexts impact these mechanisms and, consequently, outcomes. The findings were consolidated into a programme theory augmented by theories from organisational literature, such as conservation of resources (COR) theory and psychological safety. I then tested and refined parts of that programme theory with realist evaluation methodology. The evaluation consisted of five workplace MBPs and included quantitative and qualitative data collection methods.
The research results show that for managers and employees to invest in an MBP and benefit from it, it is crucial that they feel safe to engage with selfcare at work and show vulnerability to each other. The more participants feel that they are not at work, the safer they feel. To be beneficial, it is also important that managers and employees link the programme and its activities to existing goals and practices. If these conditions are not met, the costs of investing in an MBP may be too high and lead to the strategic use of brief mindfulness exercises, non-adherence, or dropout. These findings should be of value to decision makers and practitioners wishing to offer and implement effective and sustainable workplace MBPs.
Molecular machinery and cell biology of sleep control
Keywords: glutamate
dFB neurons
neuroscience
mitochondria
sleep control
sleep
drosophila
fruit fly
single-cell RNA-sequencing
transcriptomics
plasticity
mitochondrial dynamics
octopamine

Sleep is vital and universal, yet its essential biological functions remain elusive.
The sleep homeostat tracks an internal process that generates sleep pressure during waking, which is then periodically discharged by initiating sleep. Understanding the molecular nature of sleep pressure and its regulation by the homeostat will help to elucidate the physiological variables linked to the essential function of sleep.
In Drosophila, rising sleep pressure increases the activity of sleep-control neurons projecting to the dorsal fan-shaped body (dFB). Sleep need is encoded in the intrinsic excitability of these neurons, which fluctuates because two potassium conductances, voltage-gated Shaker and the leak channel Sandman, are modulated antagonistically. Signalling cascades transducing sleep pressure into sleep must thus converge on the regulation of currents flowing through these two ion channels.
To obtain a comprehensive view of the molecular machinery operating within dFB neurons, I have characterised transcriptomes of single cells isolated from dissociated brains of rested and sleep-deprived flies. These studies revealed a mechanism of bidirectional control of mitochondrial dynamics and sleep in dFB neurons. Sleep loss selectively upregulates genes encoding mitochondrial proteins and alters mitochondrial dynamics in these neurons. Conversely, manipulating mitochondrial fission and fusion in dFB neurons affects sleep in opposing ways. Since mitochondrial dynamics reflect and influence ATP synthesis and ROS production, they suggest a causal link to cellular oxidative stress, which is recorded by Shaker's redox-sensitive β-subunit and converted to heightened neuronal excitability driving sleep.
At the synaptic level, sleep deprivation decreases the strength of dFB neuron output synapses, which release the (in the Drosophila CNS inhibitory) transmitter glutamate. The neurons are heterogeneous in the expression of an octopamine receptor, whose cognate monoamine calibrates sleep.
These studies, based on the first single-cell transcriptome of an animal’s sleep-control neurons in different conditions of sleep pressure, advance our understanding of how sleep-control is implemented in the brain.
Development and characterisation of a novel vaccine for Bordetella pertussis (whooping cough)
Keywords: vaccine development
novel vaccine for pertussis
whooping cough
respiratory infection
vaccine
pertussis
viral vectored vaccines

Bordetella pertussis is the causative agent of pertussis (whooping cough) which is a respiratory infection, particularly dangerous for babies and young infants. Protection against pertussis relies on the induction of potent T-cell and antibody responses. Current acellular pertussis (aP) vaccines induce strong antibody responses and T-cell helper type 2 (Th2) response but are less effective at producing Th1-type immunity necessary for complete and fast bacterial clearance. Although, aP vaccines protect against severe disease, the vaccine-induced protection wanes over time, and despite high aP vaccination coverage in many developed countries, pertussis is a re-emerging disease.
In this thesis, I explored the use of replication-deficient adenovirus (Ad) and modified vaccinia virus Ankara (MVA) vectors as platforms for development of novel pertussis vaccines. Pertussis toxin (PT), fimbriae adhesins (Fim2, Fim3 and FimD), iron-binding proteins (IRP1-3 and AfuA) and adenylate cyclase toxin (ACT) were selected as vaccine candidate antigens. Our aim was to enhance Th1-type responses against B. pertussis and induce strong antigen-specific and neutralising antibodies that prevent lung (and nasal) colonisation of B. pertussis. I therefore evaluated the vaccines’ different immunisation regimens and their potential to mediate such immune responses in mice.
A single intramuscular immunisation with a number of the Ad vaccines induced partial protection in mice. These constructs encoded the full length of the catalytic S1-235 subunit of PT, Fim3, AC and RTX domains of ACT. In particular, the Ad RTX vaccine may have the potential to prevent pertussis infection as 60% of mice immunised with one dose of the vaccine were fully protected against lung infection. In addition, the Ad S1-235 vaccine generated a PT-specific Th1-type response. The results indicate the potential of viral vectored vaccines to prevent pertussis infection either on their own or as future studies may reveal, using them in combination with different types of pertussis vaccines.
Counter-Contagion: The emergence, dissemination and continuing effects of a new apparatus of disease response, 1791- 1958
Keywords: Historical geography
Contagion
NHS
Public health
Counter-insurgency
Infectious diseases

The question of how medical experts and the state respond to rapidly spreading infectious diseases has obvious relevance amidst the current Covid-19 pandemic. The question of when and where these responses actually emerged, however, is far less apparent and far more opaque. This project studies the actions, writings and careers of British experts as they respond to three historic diseases – cholera, plague and tuberculosis – that all posed profound threats to Britain and its colonial empire. Beginning at the end of the 18th century, this postcolonial historical geography of medicine attends to what Chris Philo calls the ‘stuff’ of medicine, with particular focus on the relation between theories of contagion and practices of disease control. I trace the emergence of these acts and ideas through intra-imperial networks, which I argue held colony and metropole together in a state of mutual interpolation and co-constitution. Through this tracing, I uncover a particular arrangement or dispositif of theories, practices, individuals and institutions that were brought together by a single, striking argument: that the spread of disease is a consequence of the disorder innate to racialised populations and their inherent propensity to breach social and spatial boundaries. This argument justifies an expert, interventionist response that seeks to control the spread of disease through the coercive implementation of lines, borders and boundaries to contain disorder. I name this expansive dispositif ‘counter-contagion’.
This project begins by analysing four key components that constituted counter-contagion: Benthamite interventionism, counter-insurgency, racial science and germ theory. While these individual components all arose in the 19th century, it took until the 1890s for all four components to finally come together. During the Third Plague Pandemic in Hong Kong and Bombay (Mumbai), these components were combined into an expert-led, interventionist response that fused the medical with the martial. This new response, and the experts who enacted it, became part of a broader dispositif of counter-contagion that gained institutional weight through the progressive wing of tropical medicine. This institutionalisation effectively embedded the logics of counter-contagion in progressive medicine in twentieth century Britain, with decisive and understudied effects on the medical profession, the political sphere and broader civil society.
An evolving synthetic biological platform for alkane production
Keywords: directed evolution
genetic engineering
molecular biology
biotechnology
energy
alkanes
synthetic biology
bioengineering
renewables
chemical engineering
biofuel

Fossil fuels are finite and polluting, but underpin almost every system and product we use in the modern world. Anthropogenic greenhouse gas emissions from fossil fuel combustion are the major driver of climate change, yet demand for these fuels continues to grow. Alleviating global reliance on fossil carbon, especially in the transport sector, demands a drop-in compatible substitute with comparable energy density and fuel chemistry to diesel, jet fuel, or gasoline. If derived from atmospheric carbon, such a fuel could be central to future low-carbon circular economies. Liquid biofuels, produced via industrial microbial fermentation, have similar characteristics to their petroleum counterparts with a much smaller carbon footprint.
Microbial biosynthesis of advanced biofuels is currently uneconomical, but has been improved by rational engineering efforts. The physiological complexity inherent in living systems often limits such approaches, but can be sidestepped by harnessing natural evolutionary processes to optimise cellular metabolism for production of valuable molecules.
This work presents a novel biosensor-based directed evolution system for improving biosynthesis of alkanes – straight chain hydrocarbons useful as biofuel – in the bacterium Acinetobacter baylyi ADP1: the “artificial evolution”, or Artevo, system.
By placing a growth-essential gene under control of genetic regulators sensitive to alkanes, the Artevo system links alkane productivity of the host cell to fitness. High producing cells grow faster and outcompete their neighbours, resulting in generational enrichment of high-performing alkane biosynthesis genes within a growing population.
The Artevo system can interrogate a small pool of diverse alkane biosynthesis genes and distinguish between them based on relative productivity, conferring a growth advantage to host cells with the highest alkane yields. This system consolidates screening, selection, and amplification of useful biosynthetic genes from potentially large libraries into a single platform, and could form the basis for future continuous directed evolution strategies as it is built in a naturally transformable and recombinant microbe.
Information gathering and motivated decision making in health and disease
Keywords: brain networks
hippocampus
effort-based decision making
depression
Alzheimer's disease
decision making
apathy
anxiety
uncertainty
information gathering
subjective cognitive impairment
limbic encephalitis

Almost every aspect of our lives involves making decisions. From deciding to get out of bed in the morning to saying "I do" at a long-awaited wedding. Humans, like animals, often try to optimise their decisions to maximise reward and avoid losses. Understanding the mechanisms and neural correlates of such behaviours can provide crucial insights into human cognitive and psychological functioning in health and disease. In this thesis, two common forms of motivated decision making are examined: i) decision making under uncertainty and information gathering, and ii) effort-based decision making (EBDM). Through behavioural experimentation, computational modelling, and neuroimaging analysis, I reveal novel mechanisms and brain networks involved in these forms of behaviour and investigate their clinical implication on affect and motivation. In addition to healthy humans, different groups of patients were investigated, including autoimmune limbic encephalitis (ALE), subjective cognitive impairment (SCI), and Alzheimer’s disease (AD). The results across these study groups converged to characterise two potentially dissociable psycho-cognitive-brain axes. The first draws a link between uncertainty processing, affect, and the hippocampus. The second highlights the relationship between apathy (reduced motivation), deficits in EBDM, and key functional brain networks such as default mode and fronto-parietal networks. The findings in this thesis thus highlight an experimental and mechanistic framework for investigating information gathering and EBDM, and provide insights into their clinical implications and associated brain networks.