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The Price of a Neighbor's Hate: Assessing the Educational Impacts of the 2019 Xenophobic Uprising in South Africa
No full textXenophobic uprisings in South Africa have killed, injured, and displaced hundreds of Black, African migrants. Using school location as a proxy for exposure to xenophobic violence, I estimate a difference-in-differences model on immigrant performance in the South African National Senior Certificate Examinations (NSC). From this estimation, I find that the 2019 xenophobic uprising led to a 12 percentage point decline in immigrants’ NSC Overall Pass Rate. This effect is unique to immigrant students, whose 2019 pass rates declined by 8% relative to non-immigrants and immigrants far from attacks. Adverse impacts are, however, short-term, and do not persist past the year of exposure. For all other NSC outcomes, including Mathematics pass rates and Distinction attainment, noisy nulls obscure the full scope of the uprising’s educational impacts.Applied Mathematic
Economic and Environmental Sustainability of Smallholder Agriculture: The Case of Maize Monocropping in North Thailand
No full textThe northern region of Thailand is known for upland maize monoculture due to the crop’s demand-price stability and resilience to the arid hot season. Due to the scarcity of economically viable alternatives, smallholder farmers manage crop residue by burning, causing hazardous air quality in the surroundings. My thesis aimed to determine if and how upland smallholder farmers could farm more sustainably without reducing their income. To do so, I estimated the net present value (NPV) and benefit to cost ratio (BCR) of farm income over 15 years for maize monoculture (Bm), maize-mungbean intercrop (Bbi), avocado mono (Am), greenhouse tomato (Tg), macadamia mono (Mm), and macadamia-coffee intercrop (Mci). The study was conducted in Pang Hin Fon, Kong Bot, and Huay Fa villages of Chiang Mai’s Mae Chaem district.
I hypothesized that incorporating legumes with maize (Bbi), replacing maize with vegetables (Tg), and replacing with perennials (Am and Mm) would increase NPV by 20%, 30%, and 70% respectively, and that multi-crop agroforestry (Mci) would add another 30% on top of the perennial monoculture (Mm). I found the NPVs of Bm, Bbi, Am, Tg, Mm, and Mci to be 21,136 (BCR 1.9), 483,025 (BCR 4.9), 75,557 (BCR 6.2) respectively. This was much higher than expected: a minimum increase of 53% (Bbi vs Bm) and more than 3,000-fold increase in NPV under Tg (vs expected 30% for vegetables). Mci had a 35% higher NPV than Mm, slightly more than the expected 30%. Meanwhile, the payback periods for Am, Tg, Mm, and Mci were four, one, seven, and three years respectively.
My second goal was to determine variables affecting farm income the most. The results met expectations—market prices affected income the most for Bm, Bbi, Tg, and Am, followed by yield for Mm and food loss for Mci. I also evaluated the NPVs under optimistic and pessimistic scenarios by jointly varying the yield and price. Tg was the most volatile, with a net loss of $85,247 (-118%) in the worst scenario (78% less yield; 74% less selling price). The risk of disease (wilt) outbreak caused a higher variance in the NPV of Am; however, it remained healthy even in the worst scenario. Finally, I compared the climate change and human health impacts of Bm and Bbi production using a life cycle assessment (LCA) approach. The LCA included the footprints of equipment, agricultural inputs, and open burning of residue. Bm had a climate change impact of 2.62 tonne (T) CO2eq and human health impact of 36.99*10-3 DALY. Eliminating open burning reduced the climate change impact of Bbi by 29% (1.87 T CO2eq) and the human health impact by 71% (10.65*10-3 DALY) compared to Bm. Human health was most impacted by open burning and climate change by fertilizers. Since legumes improve soil health, agricultural inputs could be optimized to further reduce the environmental impact.
I found that multi-cropping systems integrating perennial trees, understory crops, vegetables, and legumes improved farm income, resilience, and external impact. The farmers I met were aware of and open to alternatives, but held back due to insufficient water and road infrastructure, weak supply chains, demand uncertainty, and lack of institutional support. To overcome these barriers, I recommend improving the upland water and road infrastructure, incentivizing novel supply chains and farm-to-fork solutions, institutional support for credit and training, and research into nature-based solutions for water conservation, crop protection, and yield increase of alternate crops.Extension Studie
Sustainability Assessment of Large-Scale Green Hydrogen Production Systems for the Energy Transition
No full textThis research provides a framework for a broader assessment of the sustainability
of investment in large-scale hydrogen generation facilities, encompassing ultrapure water
units, electrolyzers of type PEM, AEL, or SOEC, and gas purifiers. The results should
improve the business case by understanding the level of risk and proposing mitigation
options for the most critical impacts on the sustainable development goals. The study
included mapping and quantifying the environmental and social impact of these green
hydrogen value chain components and a techno-economic review of 29 global technology
suppliers. It evaluated the sustainability of a typical corporate financial business model
with and without the effects of carbon pricing due to CO2 emissions reductions, the
impact of hydrogen leakages, depletion of fresh water, the liabilities for mining metals
for catalyzers, and fabrication of water splitting systems, among others. The individual
performance of equipment was assessed using the leverage cost of energy and LCA
methods.
The key questions of this research focused on the environmental externalities of
the ultrapure water unit and PEM electrolyzer and their role in the sustainability of large
infrastructure until 2050. Other key questions were related to the potential social and
environmental impacts on the facility's economy and their impact on the business case.
Finally, I tested a hypothesis about the main variables of the levelized cost of hydrogen to
understand the effect of direct subsidies on capex versus the cost of renewable electricity
and other value chain elements.
I performed a financial analysis of the cost of equity that is sensitive for later
analysis of levelized costs and a business model built on a spreadsheet. The factors used
for liabilities were extracted from the LCA literature review and engineering proxies for
estimating H2 leakages into the atmosphere. The forecast for 2030 and 2050 used time
series analysis and official projections from the IEA.
The research confirmed a levelized cost of hydrogen of 5.11 USD/Kg and a cost
of ultrapure water of 0.045 USD/Kg of H2, with a pivotal price of 2.3 USD/Kg to be
competitive versus fossil fuel options. The cost of electricity was the most sensitive value
in the business case, and the sensitivity analysis confirmed a potential perverse incentive
if subsidies continue in an electricity market below 20 USD/MWH. The water cost was
irrelevant for H2 production, making reverse osmosis for seawater the option with fewer
social and environmental risks. The cost of equity used in the research was 12%, which is
adequate for the level of risk from a corporate perspective. The forecast of the potential
transformation of fossil fuel consumption in OECD and non-OECD countries, the
upgrade of current blue and gray hydrogen, and the coming PtX energy products
confirmed an important role of green H2 in the following decades, replacing fossil fuel
based global energy systems.
Finally, to allow a more transparent comparison of projects and components under
an ESG approach, a spreadsheet tool was constructed to incorporate the previous findings
to understand the effect of profitability versus the impacts on sustainability. The main
output was a comprehensive framework for this category of energy system (>1MW),
which is critical for the energy transition until 2050.Extension Studie
How antibiotic resistance evolves in patients with acute bloodstream infections
No full textAntibiotic resistance can cause treatment failure when a patient with a previously antibiotic-suscpetible infection develops a resistant infection. This can occur through three distinct processes: (1) de novo evolution, where mutations in the bacterial genome confer resistance; (2) horizontal gene transfer, where bacteria acquire resistance genes through gain of mobile genetic elements; or (3) change of strain, where the patient is reinfected with a distinct antibiotic resistant strain. Understanding these frequencies can inform treatment and improve patient outcomes; however, the relative contribution of each mechanism to resistance evolution is unclear for most types of infections. Here we quantify the frequencies of resistance gain mechanisms using a dataset of paired blood samples from patients in the Mass General Brigham hospital system. We developed a bioinformatics pipeline to classify the resistance gain mechanism between two samples from whole genome sequencing data, detecting 10 instances of de novo evolution, 4 instances of horizontal gene transfer, and 5 instances of change of strain. Our findings show that, in contrast to other infections, all three resistance mechanisms contribute to within-patient antibiotic resistance evolution in bloodstream infections. We further identify reinfection from a bacterial reservoir to be a potentially prominent but overlooked mechanism of resistance gain. We anticipate our analyses to lay the groundwork for future studies investigating resistance evolution at the within-patient scale and ultimately inform treatment through the framework of evolution.Applied Mathematic
Shades of Sunshine: Adaptation of Contract Completeness in Florida Public Procurement
No full textPublic procurement contracts often fail, leading to cost overruns and amendments negotiated ex post. We examine how government agencies modify successive contract completeness—the degree to which all contingencies are specified in a contract—in response to contract failures. Utilizing a novel preprocessing methodology that extends previously developed measures of completeness to produce more granular insights, we measure the completeness of 7,725 construction and maintenance contracts from the Florida Department of Transportation between 2008 and 2024. The findings show a rise in contract completeness and a corresponding decline in contract failures in the long term. No adaptation of contract completeness to failures is found in the short term. Furthermore, we observe evidence of a discounting mechanism for transaction costs associated with writing complete contracts, which allows completeness levels to remain high even during months with a high volume of contract drafting.Applied Mathematic
Peri-implant soft tissue health in relation to depth of implants
No full textPositioning the implant-abutment interface deeper than 3mm apical to the buccal gingival zenith is frequently observed in the clinical setting. While histological evidence from animal studies has shown that deeper implants exhibited greater biologic widths with greater ratios of junctional epithelium to connective tissue attachment that may impede the effectiveness of oral hygiene practices, there is a lack of evidence from human trials. The objective of this clinical study is to evaluate peri-implant soft tissue health in relation to the depth of implants by evaluating peri-implant inflammation levels. Sixteen subjects with Straumann Bone Level Tapered SLActive Roxolid implants were divided into deep (>3mm) and shallow (≤3mm) groups by digitally measuring the distance from the implant platform to the buccal gingival margin. Peri-implant soft tissue health was evaluated clinically by measuring probing depths, modified plaque indices, and gingival indices. Pro-inflammatory cytokine levels (IL-1β and TNF-α) were measured by collecting peri-implant crevicular fluid via paper strips and performing laboratory analysis. Multiplex protein analysis was performed by the Multiplex Core Facility at ADA Forsyth (Cambridge, MA). Differences between deep and shallow groups were assessed with the Mann–Whitney U test. Probing depths, modified plaque indices, and gingival indices exhibited no statistically significant difference between the two test groups (P > 0.05). Both pro-inflammatory cytokines (IL-1β and TNF-α) showed no statistically significant difference between the two groups (P > 0.05). However, a trend was observed in the data where the deep group demonstrated higher values across IL-1β levels, modified plaque indices, and modified gingival indices. The depth of implants relative to the peri-implant soft tissue margin is expected to be a critical factor in the ability to resolve peri-implant mucositis and effectively prevent peri-implantitis. The results did not mirror those of similar studies on natural teeth, namely that the effectiveness of oral hygiene practices around teeth decreases as pocket depth increases. However, the trend observed in the data may be a starting point for future controlled clinical trials for more evidence that may help both patients and clinicians with better long-term maintenance of dental implants.Prosthodontic
Deep Learning as a Scientific Method and a Model Organism of Intelligence
No full textThe nature and origin of intelligence is a fundamental question in science that has been studied throughout history in psychology, neuroscience, and artificial intelligence. Recent advances in machine learning point to a promising direction: deep learning. Training neural networks by optimizing their parameters via gradient descent has shown success in both practical AI applications and in the pursuit of artificial general intelligence. This thesis investigates both the practical applications of deep learning and its scientific foundations.
The first part focuses on using deep learning to accelerate experimental neuroscience. I present two applications developed during my PhD: one that uses deep learning and synthetic data generation to track neurons in multi-channel 3D videos with improved efficiency by generating training data for rare postures not covered in the original dataset; and another that employs an uncertainty-aware system to actively guide electron microscope image acquisition in real time, achieving higher throughput by focusing the time budget on critical pixels.
The second part addresses the robustification of scientific data analysis using deep learning. I discuss how neural networks can either correct systematic errors in data or generate synthetic samples for better calibrated error estimates. The first approach is applied to hyperspectral data to remove cloud shadow’s effects on acquired spectra, while the second is used to generate probabilistic dark matter maps that quantify uncertainties in density fields without known ground truth.
The third part examines how intelligent abilities emerge in modern AI models during training. I first explore how AI models learn underlying concepts and compose them, discovering that compositional abilities may emerge without obvious behavioral signs. I then investigate how models develop in-context learning abilities based on their training data distribution, revealing a phase diagram composed of different algorithms the model implements.
The final part analyzes how large language models perform complex intelligent tasks. One study reveals that models generate task-specific representations in their internal activations when presented with new data generation processes at inference time. Another evaluates how language models integrate new information into their internal world models. I conclude by discussing the fundamental cognitive abilities that current models need to improve on to arrive at a general form of intelligence.
In summary, this thesis presents investigations of deep learning both as a tool to enhance scientific discoveries and as a model organism for studying intelligence.Physic
Hormone Replacement Therapy, Breast Cancer & Renovascular Disease
No full textThis thesis investigates the risks and benefits of hormone replacement therapy (HRT) in high-risk populations, particularly in women who have undergone prophylactic risk-reducing surgeries (PRRS) to prevent familial ovarian cancer and women with chronic kidney disease. It comprises two manuscripts that address the effects of HRT on breast cancer and chronic kidney disease (CKD) progression.
Manuscript 1 focuses on the association between breast cancer risk and HRT use after PRRS in women at increased risk of familial ovarian cancer. A systematic review and meta-analysis were conducted, synthesizing data from 8 studies involving 2,689 participants. The analysis revealed no significant increase in breast cancer risk for women using HRT post-PRRS, suggesting that HRT may be a safe option for managing menopause symptoms in this high-risk population. Despite previous concerns over estrogen’s potential to elevate breast cancer risk, the results indicated that estrogen-only HRT did not increase the risk compared to non-users.
Manuscript 2 explores the association of exogenous estrogen use with CKD progression and adverse cardiovascular outcomes in women with CKD, using data from the Chronic Renal Insufficiency Cohort (CRIC). The study demonstrated that estrogen use was associated with a 47% lower risk of CKD progression, although it did not show a reduction in adverse cardiovascular events or all-cause mortality. This finding provides some reassurance for the use of estrogen in women with CKD, particularly for those at risk of kidney decline.
In both manuscripts, the results emphasize the need for personalized treatment strategies and further prospective studies to validate these findings. This research contributes to understanding the role of HRT in managing risks related to ovarian cancer, breast cancer, and CKD in high-risk women.Graduate Educatio
Work, Vocation, and Talent in the Poetry of the Long 18th Century
No full textMomentous changes in the types and availability of work, its remuneration,
required training, as well as its social, cultural, and religious significance occurred in
England between the years 1650-1800. These changes would have a lasting cultural
impact still felt in the present. This thesis proposes that literature, and particularly poetry,
is a fruitful and underutilized source for understanding what these changes mean.
Examining the work of six major poets from this period (Milton, Dryden, Swift, Pope,
Johnson, and Cowper) for depictions and evaluations of work, it suggests that these are
inseparable from two related conceptions of vocation and talent. These, it hopes to show,
are also a valuable framework from which to approach poetry, allowing novel
interpretations of the works under investigation while also producing a valuable
reconstruction of the social, economic, and cultural history of the period.Extension Studie
Grasping the Sacred: Disability, Media, and the Embodied Theology of Appalachian Serpent-Handlers
No full textThis thesis examines the intersection of embodiment, disability, and religious practice within the serpent-handling churches of Appalachia, focusing on how these communities interpret bodily risk and impairment through their theological framework. Drawing on disability theory, media studies, and ethnographic research, the study argues that serpent-handlers' internal understanding of disability, rooted in biblical literalism and divine obedience, differs sharply from external portrayals that sensationalize their practices.
Central to the analysis is the "victim-hero paradigm," which distinguishes between disabilities acquired involuntarily (viewed as afflictions requiring healing) and those resulting from intentional religious ritual (seen as marks of faithful obedience). The thesis further analyzes how popular media, particularly photography, employs visual rhetorics (wondrous, sentimental, exotic, and realistic) to frame serpent-handlers as cultural "others," mirroring historical representations of disabled bodies. By contrasting the communities' self-perception with their mediated depictions, the study reveals how dominant narratives obscure the theological and historical complexities of serpent-handling, reinforcing stereotypes of Appalachian religiosity as deviant or irrational.
Through this interdisciplinary approach, the research challenges reductive portrayals of serpent-handling, advocating for representations that acknowledge the agency, theology, and lived experiences of these practitioners. The study underscores the ethical stakes of documenting embodied faith and the cultural frameworks that shape perceptions of risk, devotion, and difference.Author's Origina