VictorJuiz/thesis huggingface dataset:
Engineering enhanced enzyme variants to boost photosynthesis in C4 plants
Keywords: plant science
photosynthesis
synthetic biology
phosphoenolpyruvate carboxylase
c4 photosynthesis

Major food and biofuel crops maize, sugarcane and sorghum utilise a specialised type of photosynthesis termed C4 photosynthesis, in which carbon is first fixed into a four-carbon compound by phosphoenolpyruvate carboxylase (PEPC). The enzymatic rate of PEPC limits the rate of photosynthetic carbon assimilation under conditions of low CO2 in the mesophyll cell, for example shortly after photosynthetic induction or under stress conditions when stomatal conductance is limited. Here, a system has been established in which the growth rate of Escherichia coli is dependent on the enzymatic rate of C4 PEPC derived from the model C4 species Setaria viridis. Concurrently, a site-saturation mutagenesis technique has been optimised and libraries of PEPC variants generated, targeting sites that are likely to be influential for C4 PEPC kinetics. E. coli were transformed with PEPC variant libraries, and a screen was undertaken whereby E. coli cells that expressed a PEPC variant that conferred a growth advantage to the cell became enriched in the bacterial culture over time. Three PEPC variants with P531A, F794V and N863K mutations emerged as candidates for in planta testing and provide insight into the molecular basis of C4 PEPC kinetics. In summary, the high-throughput screening pipeline established here has accelerated the identification of promising PEPC variants that could increase the rate of photosynthesis and yield in C4 plants.
Inclusion of nuclear quantum effects in thermal conductivity prediction from path integral techniques
Keywords: path integral molecular dynamics
hydrodynamics
centroid molecular dynamics
molecular dynamics
thermal conductivity

Path integral based methods to approximately include quantum mechanical effects in the motion of nuclei have thus far appeared insufficient to describe the thermal conductivity of a system from the Green-Kubo relation. In this thesis the possible reasons for this are examined, and an approach to improve the estimation of the thermal conductivity using path integral methods is developed.
The thesis begins by considering how the thermal diffusivity, the ratio of the thermal conductivity and the heat capacity, may be related to the equilibrium density fluctuations within a liquid, using the theory of linearised hydrodynamics. Application of this to liquid parahydrogen using centroid molecular dynamics (CMD) showed that the CMD estimate of the thermal diffusivity is accurate, but that the CMD estimate of the heat capacity is not. This is used to propose a means to correct the CMD estimate of the Green-Kubo thermal conductivity, allowing for an efficient and accurate determination of the thermal conductivity in both liquid parahydrogen and normal liquid helium.
Following this, the same methodology is applied to the calculation of the CMD thermal conductivity in liquid water. The agreement with experiment is found to be less convincing, which may partly be due to the use of an inaccurate potential model.
The thesis finishes by showing that the thermal conductivity may be deter- mined from the equilibrium density fluctuations at temperatures above 30 K for crystalline Lennard-Jones argon in the classical limit. At lower temperatures, the fraction of the signal dependent on the thermal conductivity is found to become very small, but it is shown in this case that the equilibrium local temperature fluctuations may be used instead. However, extension of this to an accurate path integral based method for quantum mechanical thermal conductivity prediction in a crystalline solid appears to be a very challenging problem that is beyond the scope of this thesis.
English as a post-colonial lingua franca: 
A multivariate analysis of English-ownership and 
language-In-Eeducation model preference among Ghanaian tertiary students
Keywords: Language Shift
English as a Lingua Franca
Language Policy
Minority Languages
Language-In-Education
Dominant Indigenous Languages
Mother Tongue Medium of Education
Post-colonial Africa
Language Attitudes
English Ownership
Bilingual Education
Endonormatisation
Ghana

Ghana, like many postcolonial African nations, is at a sociolinguistic crossroads in which English is believed to be encroaching on sociocultural domains, while the country’s indigenous languages are being promoted by governments to have a stronger presence in mainstream education. The current study therefore aimed to understand the extent of English ownership and Language-In-Education model preference (LIEMP) among tertiary students in Ghana to investigate whether the attitudes of the country’s most active English users corroborate these governmental initiatives. The study also considered the influence of sociodemographic factors, namely (i) L1, (ii) Age, (iii) Gender, (iv) SES, (v) Region, (vi) Academic Discipline, (vii) Most Spoken Language, and (viii) English Variety Preference, on students’ attitudes towards English in Ghanaian society and indigenous languages in Ghanaian mainstream education. The study employed a mixed-methods approach, with quantitative data collected through an online questionnaire completed by 159 participants and analysed through descriptive, correlative, and regression analyses, and qualitative data obtained through 4 semi-structured interviews that were analysed thematically. While the questionnaire results revealed that most of the sample did not claim ownership of English on a macro-level, their self-directed LIEMP varied strongly based on select sociodemographic factors, namely L1, Home Region, and SES. A relationship was also found between participants’ lack of ownership and LIEMP, with qualitative findings indicating that, regardless of which LIE model the students prefer, they view implementing appropriate curricula for all L1 groups as impractical or simply irrelevant to the Ghanaian market at large. These results demonstrate the importance of attitudinal studies to appropriately strategise language planning through “bottom-up” incentives, as well as the need for prestige planning to accompany acquisition planning in order to facilitate public sensitisation towards L1-incorporated education in postcolonial Africa.
Essays on constraints and solutions to women's human capital development in India
Keywords: human capital development
labour
gender
education

Despite three decades of rapid economic development in India, there continue to be significant gender gaps and challenges for women’s human capital development. This thesis, written in a three-paper format, seeks to identify multiple constraints and test interventions to improve women’s educational and labor market outcomes in India.
Using a combination of experimental and quasi-experimental methods, I present research which sheds light on, as well as addresses, interlinked constraints related to women’s advancement in their education and careers. My first paper examines whether working women in India face a penalty in the marriage market, using an online correspondence study on a marriage website. I find that women who signal wanting to work after marriage face a sizeable penalty in the marriage market, and receive significantly less interest from male suitors relative to women who have never worked or are willing to give up work after marriage. The second paper evaluates a post-primary technology-aided remedial education program to improve learning and educational outcomes, in a context with acute learning deficits. The program leads to large gains in basic reading and math skills for male and female students, but fails to translate into better scores on the national exam which measures grade level competencies. The third paper assesses the implementation and impact of gender quota introduced for boards of all listed companies in India. While the law succeeded in increasing women’s representation on corporate boards, it unexpectedly increased gender pay gaps for board membership. Using an established instrumental variables strategy where I instrument on pre-reform variation, I also find evidence that the law improved firm performance and personnel-related outcomes, but that there was no ripple effect on women’s employment. Taken together, these research papers contribute to a deeper understanding of barriers and potential solutions to enhance women’s human capital development in India.
Homer beyond Homer: a comparative approach to the question of oral composition in performance
Keywords: Homer
oral poetry
Mahābhārata
Beowulf
composition in performance

The present study is an attempt to compare three different poetic traditions whose origins are believed to have been influenced to a significant degree by oral composition in performance: the Ancient Greek, the Sanskrit, and the Old English. These traditions all belong to the Indo-European language family, with interesting parallels not only in the realm of themes and motifs, but also of diction and poetic turns of phrase. The aim of this study is to explore whether similar resemblances may also be found on the deeper level of composition. By taking into account the simplicity and complexity of different poetic units, I investigate (and, wherever possible, reconstruct) certain mechanisms and techniques for the production of poetry during composition-in-performance. The chief texts under scrutiny are four (Iliad, Odyssey, Mahābhārata, and Beowulf), where I explore three distinct poetic contexts: greetings and well-wishes in Chapter 1, traditional similes in Chapter 2, and battle scenes in Chapter 3. My results will hopefully show that, at least in these contexts, we may be able to understand how certain compositional techniques might facilitate the task of the singing poet, as he strived to produce sophisticated lines in his performance under the constant threat of metrical breakdown.
Efficient and elastic LiDAR reconstruction for large-scale exploration tasks
Keywords: active mapping
LiDAR
semantic mapping
reconstruction
robotics

High-quality reconstructions and understanding the environment are essential for robotic tasks such as localisation, navigation and exploration. Applications like planners and controllers can make decisions based on them. International competitions such as the DARPA Subterranean Challenge demonstrate the difficulties that reconstruction methods must address in the real world, e.g. complex surfaces in unstructured environments, accumulation of localisation errors in long-term explorations, and the necessity for methods to be scalable and efficient in large-scale scenarios.
Guided by these motivations, this thesis presents a multi-resolution volumetric reconstruction system, supereight-Atlas (SE-Atlas). SE-Atlas efficiently integrates long-range LiDAR scans with high resolution, incorporates motion undistortion, and employs an Atlas of submaps to produce an elastic 3D reconstruction.
These features address limitations of conventional reconstruction techniques that were revealed in real-world experiments of an initial active perceptual planning prototype. Our experiments with SE-Atlas show that it can integrate LiDAR scans at 60m range with ∼5 cm resolution at ∼3 Hz, outperforming state-of-the-art methods in integration speed and memory efficiency. Reconstruction accuracy evaluation also proves that SE-Atlas can correct the map upon SLAM loop closure corrections, maintaining global consistency.
We further propose four principled strategies for spawning and fusing submaps. Based on spatial analysis, SE-Atlas spawns new submaps when the robot transitions into an isolated space, and fuses submaps of the same space together. We focused on developing a system which scales against environment size instead of exploration length. A new formulation is proposed to compute relative uncertainties between poses in a SLAM pose graph, improving submap fusion reliability. Our experiments show that the average error in a large-scale map is approximately 5 cm.
A further contribution was incorporating semantic information into SE-Atlas. A recursive Bayesian filter is used to maintain consistency in per-voxel semantic labels. Semantics is leveraged to detect indoor-outdoor transitions and adjust reconstruction parameters online.
Advanced control systems for fast orbit feedback of synchrotron electron beams
Keywords: cross-directional systems
higher-order generalized singular value decomposition
fast orbit feedback
spatio-temporal systems
internal model control

Diamond Light Source is the UK’s national synchrotron facility that produces synchrotron radiation for research. At source points of synchrotron radiation, the electron beam stability relative to the beam size is critical for the optimal performance of synchrotrons. The current requirement at Diamond is that variations in the beam position should not exceed 10% of the beam size for frequencies up to 140Hz. This is guaranteed by the fast orbit feedback that actuates hundreds of corrector magnets at a sampling rate of 10kHz to reduce beam vibrations down to sub-micron levels. For the next-generation upgrade, Diamond-II, the beam stability requirements will be raised to 3% up to 1kHz. Consequently, the sampling rate will be increased to 100kHz and an additional array of fast correctors will be introduced, which precludes the use of the existing controller. This thesis develops two different control approaches to accommodate the additional array of fast correctors at Diamond-II: internal model control based on the generalised singular value decomposition (GSVD) and model predictive control (MPC). In contrast to existing controllers, the proposed approaches treat the control problem as a whole and consider both arrays simultaneously. To achieve the sampling rate of 100kHz, this thesis proposes to reduce the computational complexity of the controllers in several ways, such as by exploiting symmetries of the magnetic lattice. To validate the controllers for Diamond-II, a real-time control system is implemented on high-performance hardware and integrated in the existing synchrotron. As a first-of-its-kind application to electron beam stabilisation in synchrotrons, this thesis presents real-world results from both MPC and GSVD-based controllers, demonstrating that the proposed approaches meet theoretical expectations with respect to performance and robustness in practice. The results from this thesis, and in particular the novel GSVD-based method, were successfully adopted for the Diamond-II upgrade. This may enable the use of more advanced control systems in similar large-scale and high-speed applications in the future.
Information, access, and conflict: transnational interest groups and the politics of global tax governance
Keywords: global tax governance

What accounts for variation in technical demand for business supplied information in tax policy processes at the OECD? This study explores the relationship between politicised international corporate tax policy processes and the participation of transnationally active corporate taxpayer interest groups. Existing ‘transnationalist’ tax IPE literature has largely neglected the role of transnationally active taxpayer groups and often deploys explanations centred on logics of ideas and socialisation to explain the nature of transnational tax policymaking (businesses – firms and their advocacy groups). In focusing exclusively on expert networks, much of this literature neglects the role of political interests in the transnational tax policymaking space. This dissertation therefore explicitly focuses on the under-researched study of transnational taxpayer interests by using an approach centred on interest group politics in the international tax policymaking process. The study focuses on why and when interest group input is demanded by policymakers in the OECD (delegates and technocrats), and what the role of intergovernmental conflict in the collective political principal plays in shaping OECD policymaker demand for taxpayer stakeholder participation in transnational tax policymaking. Bringing in insights from the lobbying literature on resource-exchange dynamics, this study evaluates how increasingly tough cooperation problems between countries, ultimately shape technocratic ‘demand’ for informational input from business. Th study explores the varying demand for transnational taxpayer stakeholder input in the OECD's recent work on corporate taxation (2012-2021) in three distinct eras that map onto underlying conflicts of interest with the collective political principal: (I) Transparency (II) Digital Taxation (III) Global Minimum Taxation. The study uses a qualitative methodological approach drawing on interviews and extensive document analysis.
Production networks and planetary boundaries: challenges and opportunities for integrated assessment models
Keywords: network reconstruction
firm-level data
missing information
production networks
planetary boundaries
maximum entropy
integrated assessment models
climate change
input-output analysis
supply chain networks

Integrated Assessment Models (IAMs) are used to understand the complex interactions between the Earth system and socio-economic processes. These models help us understand possible futures associated with different levels of human impact on the climate system. As such, they wield significant influence on policy-making and society as a whole. At the heart of this thesis is a fundamental inquiry into advancing IAMs. This deep inquiry is rooted in the understanding that the economy is a complex system and in the acknowledgement of the intertwined nature of the climate and ecological crises; both are mostly overlooked in IAMs. This thesis provides insights and advances for IAMs with the goal of strengthening their ability to address the climate and ecological crises together.
First, this thesis finds that IAMs are not up to the task of addressing the climate and ecological crises together. Using the Planetary Boundaries (PBs) framework, it assesses the ecological feasibility of Paris-compliant mitigation pathways that were considered in the recent IPCC Sixth Assessment Report. Almost all scenarios transgress PBs. Even “low-demand” or “sustainability” pathways do not meet the ecological feasibility criteria set forth by the PBs framework. These findings highlight the need for a comprehensive and integrated approach.
Second, drawing from complexity economics and recent findings in the literature on supply chain networks, this thesis argues that IAMs overlook key micro-level mechanisms that are essential for understanding the evolution, stability and resilience of the economic system – and thus of society as a whole. It explores how we might have a more fine-grained macroeconomic model that takes into account supply chain interactions at the firm level. It finds that serious data limitations must be overcome before we can achieve this level of granularity in IAMs. Using methods from complexity science, it addresses the data limitations using two different approaches and makes two major contributions: (1) it provides the first comprehensive picture of the most fundamental statistics on production networks, thus providing a basis for generating synthetic data or calibrating macroeconomic models; and (2) it provides the first thorough evaluation of a maximum entropy reconstruction method applied to firm-level production networks. This thesis also contributes to an emerging agenda to develop standards for data collection, cleaning and matching for micro-level production network data around the world.
Optimal transport methods for analyzing highly multiplexed spatial proteomic data
Keywords: optimal transport
spatial biology

Cell microenvironments are complex niches of interacting cells that drive tissue function and disease response. In recent years, in situ multiplexed imaging has en- abled the multi-molecular profiling of single cells while preserving their spatial con- text. Although these new technologies capture cell phenotypes and spatial organization at unprecedented resolution, the technology has many trade-offs, and the analysis of the rich spatial information they provide remains a challenge. In this thesis, we develop novel computational methods tailored for multiplex imaging data leverag- ing principles from Optimal Transport (OT), a branch of statistics for comparing probability distributions.
In the first part, we address the challenge of integrating spatial profiles from different tissues, a task essential to enhancing the information obtained from multiplex experiments. We introduce a novel algorithm for optimizing tissue alignment derived from partial OT, and additionally propose an unbiased statistical estimator for OT distances that scales to massive tissues at a fraction of the cost. We benchmark our method against state-of-the-art algorithms, and demonstrate our method’s improved robustness to rips, tears, and other challenging spatial distortions induced by the multiplexing process.
In the second part, we consider the task of quantitatively characterizing cell microenvironments. We introduce a novel framework that captures both microenvironment cell composition and spatial organization using graph OT, and demonstrate its applications in identifying cell-cell interactions, spatial domains, and disease relevant microenvironments on simulated and real datasets. On pathologist annotated mul- tiplexed lung tissues, we demonstrate that our methods recover microenvironments directly linked to known cell interactions and functions. On multiplexed head neck tumors, we identify microenvironments that are highly predictive of patient outcome. We benchmark our method against two state-of-the-art competitors and various base- lines, and show that our method outperforms all comparisons on each dataset.
Lastly, we present a comprehensive case study that showcases the practical appli- cation of both our methods for spatial integration and microenvironment characterization on a novel dataset of multiplexed mouse colorectal cancer tissues. We align massive tissues with hundreds of thousands of cells, and identify distinct, condition- specific microenvironment subtypes that correspond to unique cell enrichment profiles and spatial domains. Together, our methods provide a powerful approach to mapping the complex landscape of the tumor microenvironment in colorectal cancer.
Where do peacekeepers go? Unpacking the determinants of UNSC-authorized peace operation deployments
Keywords: peacekeeping
civil war
UN Security Council

Where do peacekeepers go? A common assumption in the quantitative study of peace operations is that that peacekeepers are most likely to be sent to difficult-to-resolve conflicts. However, a closer look at the literature reveals that our knowledge on this issue is far from conclusive. Although we know that deployment is not random, we have yet to confidently identify the factors that drive this selection process. The present thesis revisits the question of where peacekeepers go. The starting point of the theoretical and empirical inquiry is the very beginning of the United Nation Security Council’s (UNSC) decision-making process. The first paper develops and statistically tests a novel theory on the role that interests of peacekeeping troop contributing countries can play in formal UNSC agenda-setting. The second paper explores the relation between the quality of the UNSC debates following agenda-setting and the time it takes the Council to authorize a first UN or non-UN peace operation to manage a civil conflict. The third paper presents novel time-varying data on 49 different mandate components of all UN and non-UN peace operations deployed to Sub-Saharan Africa between 1990 and 2019. This approach yields important insights on the role that interests from actors other than the fifteen Council members play in relation to where peacekeepers might eventually get sent. Furthermore, the empirical evidence presented in this thesis indicates that only certain conflict characteristics and attributes of the country experiencing civil strife play a role for the non-random assignment of UNSC-authorized peace operations.