VictorJuiz/thesis huggingface dataset:
Towards equity in algorithmic decision making
Keywords: Management Science and Engineering.

In recent years, many high-stakes societal decision-making systems have begun incorporating data and algorithms. This trend raises the question of how decision makers can do so in a way which creates equitable systems which ameliorate inequities. This dissertation considers two broad paths forward towards this goal. First, we review a series of interventions at various stages of the model-building and deployment process. Specifically, we consider how a model-builder might selectively acquire additional information, adaptively sample training data, and add personalization. We show that these interventions allow for model-builders to efficiently allocate resources to create decision-making systems which are inclusive of individuals from vulnerable groups. Second, we review two pieces of work where modern, online data sources give insights which can inform improvements for existing systems. In particular, we first consider how telematics data, containing records on the true prevalence of speeding, sheds light on inequities in traffic enforcement. Then, we see how online game records provide valuable insight into how users make decisions within social networks. Findings from both studies can be incorporated in future design of or interventions in decision-making systems within both spaces. Overall, this dissertation demonstrates two concrete paths for moving towards equitable decision making: intervening to efficiently improve outcomes for underserved groups, and leveraging insights from modern data sources to improve societal decision making systems
Towards irregular computation on regular dataflow
Keywords: Electrical Engineering.

This thesis presents my work on expanding the bounds of programmability for vectorized reconfigurable dataflow accelerators (vRDAs). vRDAs, including Plasticine and the SambaNova RDU, promise users more eﬀicient computation by eliminating the overheads of modern von Neumann machines—instruction fetch, dynamic scheduling, speculation, and caching. Instead of fetching instructions from a cache and data from a register file and then executing code in a single physical location, vRDAs lay out computation across an entire chip. Each instruction is mapped to a pipeline stage, and data flows through those stages. Similarly, instead of coordinating memory transfers through a cache hierarchy (with the overhead of prefetching and reordering), vRDAs use explicitly coordinated scratchpads to provide low-overhead, high-throughput on-chip accesses. However, to practically use a vRDA, applications must be compiled from a high-level language, and previously only dense linear algebra could be compiled to Plasticine using the MapReduce programming model as implemented in Spatial. This programming model limited applications to counter-based iteration with aﬀine memory accesses and prevented control flow within the innermost parallel region. I overcome these limitations via Capstan and Revet. First, Capstan uses new hardware to introduce support for direct iteration on a variety of sparse tensor formats, including sparse-dense and sparse-sparse iteration. Then, Revet builds on Capstan and Aurochs to support inner-loop control flow by compiling an imperative language to dataflow using a streaming, embedded-control tensor format. For vRDAs, Capstan and Revet both provide zero-to-one improvements: they enable applications that could not previously be mapped. They are 4.3x smaller than an Nvidia V100 GPU, 17x faster for sparse applications, and 3.8x faster for applications with inner-loop control flow
Tracking charge migration with attosecond X-ray pulses from a free-electron laser
Keywords: Physics.

The motion of electrons in molecular superposition states happens on the attosecond timescale, roughly three orders of magnitude faster than nuclear motion. To study the first steps in a photochemical reaction, then, we must study the electron dynamics in early times before the nuclei have a chance to move. These purely electronic dynamics, uncoupled from nuclear motion, are dubbed charge migration (CM). CM can be described as a coherent superposition of delocalized electronic states evolving in time, which appears as a time-dependent oscillation in charge density across the molecule. On longer timescales, thought to be tens of femtoseconds, nuclear motion couples to the pure electronic CM. This tends to average out the CM, and there is evidence that this process can influence the nuclear reaction pathways. One can further envision using sequences of laser pulses to prepare CM states as a method of coherent control directing photochemical reaction pathways. However, understanding the loss of electronic coherence as nuclear motion occurs is difficult. Theoretical modeling of CM is computationally challenging, and there are open questions about the effects of nuclear motion. Experimental measurements can guide us towards better, more efficient approximations to help answer these outstanding questions. To this end, I present two experiments towards developing two separate methods for measuring CM. Both methods rely on the recently developed attosecond X-ray free-electron laser source at the LCLS free-electron laser facility. These two methods for measuring CM serve as early implementations of this new attosecond X-ray source. The first method to study CM, impulsive ionization, prepares a CM state by ionizing with an attosecond X-ray pulse which has coherent bandwidth large enough to populate multiple cationic states. The final state is then measured with X-ray absorption spectroscopy. I present preliminary results showing signatures of CM and nuclear motion damping the time-dependent charge density. The second method, nonlinear X-ray spectroscopy, is a sophisticated toolset using sequences of X-ray pulses to prepare and measure CM states. I present a measurement of a basic building block of nonlinear X-ray spectroscopy, impulsive stimulated X-ray Raman scattering, and use this result to show the feasibility in the near future of measuring valence CM states in a neutral molecule
Transcriptomic analysis of Ustilago maydis infection and improving cassava brown streak disease surveillance in sub-Saharan Africa
Keywords: Bioengineering.

Ustilago maydis is a smut fungus that is distinctive for its ability to infect and form tumors in all aerial organs of corn. Previous research has shown that different sets of fungal effector genes are expressed depending on the tissue and cell type being infected although there is limited information on how the gene expression changes over the course of the infection, particularly in anthers. In this thesis I study early infection of maize tassels using both whole tissue and single cell RNAseq. Problems with being able to select infected tissue and the sc-RNAseq sequencing depth, severely limited the conclusions I was able to draw, and I propose potential improvements for subsequent studies on cell type specific plant infection. Cassava brown streak disease (CBSD) is a looming threat to food security for small holder farmers as it rapidly spread across sub-Saharan Africa. Currently, many countries across sub-Saharan Africa conduct annual surveys on the prevalence of CBSD, and a range of management interventions have been proposed to minimize yield loss in regions where CBSD has become endemic. In this thesis, I developed two stochastic epidemiological models for the spread of CBSD with a field and for conducting country wide surveys that I used to compare the efficacy of different interventions and survey protocols. At the scale of a individual farmer's field, I find that introduction of virus-free 'clean seed' effectively increases yield across a wide range of disease pressures. I evaluated the effectiveness of the current survey protocol at detecting the presence of CBSD within a field, and found that it is relatively effective at low levels of CBSD prevalence and that the probability of detection can be meaningfully increased by surveying later within the growing season, particularly in areas with high vector density. I then extended the field level model to simulate the effectiveness of different protocols for conducting annual country level surveys for CBSD by combining it with a second model of landscape level CBSD spread. I find that with the current protocol, detection of newly infected districts is limited by the small number of infected fields surveyed. Changing the current protocol of uniformly allocating surveys across Nigeria to surveying locations proportional to the density of cassava greatly improves the effectiveness of CBSD detection, and to a lesser extent so does increasing the annual number of surveys conducted. This effect is consistent across multiple districts in Nigeria and multiple ways of quantifying survey efficacy. Finally, with these simulation results I also propose guidelines for practical, actionable recommendations for the deployment of management strategies and survey protocol modifications in sub-Saharan Africa
Transformers, Humans in Disguise: Applying NLP Based Computational Techniques to Deliberative Democracy
Keywords: Deliberative democracy
Natural language processing (Computer science)
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Thesis

This project seeks to apply a scalable, NLP based computational mechanism to automate portions of the work done by the Center for Deliberative Democracy (CDD) in their Deliberative Polling project. The machine based classifier that this project is attempting to profile is intended to emulate the currently manual task of tagging transcripts of worldwide deliberations about controversial topics with the intention of 1. Extracting argument dialogue segments and 2. Assessing argument deliberative quality as per the conventions set forth by the CDD. Top level, these techniques involve humans tagging transcripts using a 0, 1, 2, 2+ scale, reflecting the respective number of provided reasons to support an argument. The computational techniques that will be profiled for their capacity to replicate human tagging that this project will explore will be transformer based language models such as XLNet, a custom bag of words (BOW) + random-forest based classifier, and random chance. Empirical results have displayed an increase in model generalizability when transferring to the XLNet model, indicating a better capacity to emulate human transcript tagging across all categorizations, conversational subjects, and discussion locales.
TRAPing Context- and Region-Specific Ensemble Activity Induced by (±) 3,4- Methylenedioxymethamphetamine
Keywords:  Department of Biology
MDMA, fenfluramine, methamphetamine, TRAP, neurobiology, biology, psychiatry
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Thesis

(±)3,4-Methylenedioxymethamphetamine (MDMA) has gained considerable traction as a novel therapeutic avenue for treatment-resistant psychiatric illness. Prior research suggests MDMA exerts its prosocial therapeutic effects via discrete nuclei in the striatum. Yet, the anatomical and functional features of these neuronal populations remain unclear. Using transgenic mice enabling activity-dependent neuronal labeling, we examine the region- and context-specific characteristics of neuronal ensembles generated following systemic MDMA delivery. This approach reveals MDMA-induced ensembles in unique segments of the nucleus accumbens (NAc) alongside the extended dorsal endopiriform cortex and claustrum (DEn/Cl). Ensembles in the NAc lateral shell are comparable following drug administration in social or nonsocial environments. By contrast, ensemble densities in the NAc medial shell and DEn/Cl are more robust when MDMA is delivered in social versus nonsocial conditions. This effect is replicated by d-fenfluramine (FEN), a selective serotonin-releasing compound. In describing the anatomical and context-dependent features of distinct MDMA ensembles, we set the foundation for broader functional studies.
Trauma-Informed Practices for Teachers of Refugee Students
Keywords: Psychic trauma in children
Immigrants
Refugee children
Mental health services
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Thesis

April Ball centered her capstone project on creating a compilation of the available literature on trauma informed care for immigrant and refugee populations. This included an analysis of the impact of trauma on children and a practical list of tangible skills and practices teachers can employ when working with traumatized children. Informed by her time as a student in HUMRTS 108- Advanced Spanish Service-Learning: Migration, Asylum, and Human Rights at the Border, April recognizes how trauma can detrimentally affect people’s lives if not managed correctly and staunchly believes mental healthcare is not only a human right, but necessary and essential in the recovery and integration process for refugee communities. With this research, April hopes to contribute to the expanding field of trauma informed care and hopes to contribute to a cohesive understanding of the intersection between immigrant rights and mental health.
Treatment-induced antigen presentation in cancer
Keywords: Chemical and Systems Biology.

Determination of self versus non-self is vital to the health of all organisms, and is in part determined by Major Histocompatibility Complex (MHC) proteins in mammals. While evolved to protect against pathogens, MHC molecules may also present tumor-associated antigens to cell surfaces for T-cell surveillance. Presentation of tumor-associated antigens on MHC is vital for efficacy of most currently available immunotherapy regimens. Therefore, cancer immunotherapy treatments such as Immune Checkpoint Blockade are ineffective in malignancies that have mid- to low- Tumor Mutation Burden (TMB). This work outlines the effect of three treatments on various human cancer cell lines. The first study determines the effect of mTOR inhibitor rapamycin on Burkitt Lymphoma (Raji) cells and concludes that rapamycin upregulates the expression of several MHC molecules, leading to the presentation of more unique peptides. The second study analyzes the effect of interferon-gamma, a cytokine that upregulates the expression of MHC molecules as well as other components of the antigen processing and presentation (APP) pathway. Our results indicate that interferon-gamma increases the proteome coverage of MHC-associated peptides due to these effects on APP proteins. The final study in this work elucidates the effect of gamma-irradiation on the head and neck squamous cell carcinoma (HNSCC) cell line, PCI-13, in a 3D cell-derived xenograft model. The results of gamma-irradiation were surprising: irradiated tumors had markedly fewer MHC-associated peptides than matched controls. In conclusion, exogenous perturbations can have dramatic effects on antigen presentation and should be studied further in order to better understand how cancer therapeutics affect antigen presentation, and therefore immunotherapy efficacy
Trends in COVID-19 transmission across United States Immigrations and Customs Enforcement facilities and the effectiveness of prevention strategies, 2020-2022
Keywords: Lo, Nathan
Ulrich, Angela
COVID-19/epidemiology, COVID-19/statistics and numerical data, United States Government Agencies, Jails, Policy/trends, Interrupted Time Series Analysis
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Thesis

Background: The Covid-19 pandemic has significantly increased the health risks posed to incarcerated populations, including individuals detained by the United States Immigration and Customs Enforcement agency (ICE). Despite the enactment of preventative strategies (Pandemic Response Requirement; PRR), it is unclear whether these policies have reduced Covid-19 transmission in ICE facilities. In this study, we describe trends in Covid-19 cases across ICE facilities and model the effects of two significant PRR policies (V5.0 and V6.0) on viral transmission to inform future infection prevention strategies.
Methodology: We estimated trends for a series of descriptive measures of Covid-19 transmission, including point prevalence, across the ICE detention system from March 2020 through January 2022. After identifying facilities with complete datasets, we estimated the effective reproductive number of Covid-19 (Rt) per facility. Finally, we used an interventional time series model to estimate the effects of two significant PRR policies on facility effective reproductive numbers and performed sensitivity analyses.
Findings: Across the ICE system, 37,720 cumulative cases of Covid-19 were reported through January 2022 with a median point prevalence of 3.295% (IQR:2.472 - 4.309%). Across the facilities included in the model (N=93 of 146), the median population-weighted effective reproductive number was Rt=1.279 (IQR: 1.091 – 1.532). PRR policies V5.0 and V6.0 were not associated with immediate effects (V5.0: -0.196, 95%CI of -0.591 – 0.199; V6.0: -0.076, 95%CI of -0.304 – 0.152) or sustained effects (V5.0: <0.001, 95%CI of -0.001 – 0.002; V6.0: 0.001, 95%CI of <0.001 – 0.002) on facility effective reproductive numbers. The effects of PRR policies were sensitive to the variations in the delay from policy enactment to implementation.
Interpretation: Revisions to ICE PRR policies to improve testing, screening, and vaccination strategies did not reduce the transmission of Covid-19 within detention facilities with peak transmission found months after the changes were enacted. We recommend a comprehensive evaluation of the effectiveness of current public health policies utilized in detention facilities and the development of novel strategies to reduce infection risk.
Tuning optical properties of 2D semiconductors by strain and electrostatic gating
Keywords: Applied Physics.

Due to their two-dimensional (2D) nature, atomically thin transition metal dichalcogenides (TMDCs) exhibit properties that are greatly distinct from their bulk counterparts. At the single layer limit, the strong light-matter interaction and transition from indirect-gap to direct-gap enable new fundamental physics and optoelectronic applications. It is of great significance that the optical properties of atomically thin TMDCs could be controlled by external tuning knobs. In the dissertation, two external knobs are presented: strain and electrostatic gating. For strain tuning, we use bendable flexible substrates to apply uniaxial tensile strain to monolayer WSe2 samples and probe them with absorption and PL measurements. We show that tensile strain around 2.1% not only reduces the optical band gap by around 100 meV, but also greatly narrows the exciton linewidth. By modeling different components to excitonic linewidth, we attribute this reduction to the suppressed intervalley exciton-phonon scattering under tensile strain. This explanation is further consolidated by measurements on monolayer WS2 and bilayer WSe2. Another external tuning knob investigated is the presence of free charge carriers in the system, which could be injected into 2D materials by electrostatic gating. A high carrier concentration (~ 1013 cm-2) is realized through the electric-double-layer gating technique with ionic solid LaF3. Doping-dependent absorption measurements on monolayer WSe2 show that excitons are dissociated due to increased Coulomb screening at high free carrier concentrations. As a result, excitonic peaks are gradually replaced by a step-function like band-to-band transition feature in absorption spectra. Distinctive effects of screening and state filling due to free carriers are also observed through the different behaviors of A/B excitonic features. The works presented in this dissertation demonstrate that strain and electrostatic gating are two powerful knobs for both probing the fundamental physics in 2D semiconductors and realizing novel optoelectronic applications
Two languages, Many Stages: Bartolomé de Alva’s Nahuatl Theatrics in Seventeenth Century Nueva España
Keywords: Nahuatl language
Nahuatl drama
Nahuatl language > Study and teaching > Spanish speakers
Conversion > Christianity
New Spain
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Thesis

In the seventeenth century in Nueva España, Bartolomé de Alva, a multilingual Jesuit priest of Spanish and noble Texcoco descent, produced three works: a Spanish-Nahuatl guide to Confession, three translations of Spanish Golden Age plays into Nahuatl, and an introduction to Horacio Carochi’s Nahuatl grammar and dictionary. Throughout all three of these works, despite their differing genres, I identify theatricality. In the Confessionario I see this in the script and stage directions Alva gives to the characters he constructs. Theatricality is intentionally avoided in Alva’s Nahuatl translation of meta-theater in Pedro Calderón de la Barca’s original “El gran teatro del mundo.” Lastly, the liberties that Alva takes with the introduction to the dictionary defy the bureaucratic genre and replace it with his own personal monologue. In each of these objects, Alva uses or avoids theatricality alongside Nahuatl to mediate and soften differences between the Nahua life and the colonial vision of Christian conversion and assimilation. Yet, use of these languages is based in the faulty notion that Spanish and Nahuatl provide two sets of words that can be exchanged and still inform the same worlds. Ultimately, these three translation projects reveal the Nahuatl language’s incongruity with the goals of Alva’s religious and epistemic colonization, which only exist in his theater.
Uncovering host responses to malaria infection in the hematopoietic niche
Keywords: Microbiology and Immunology.

Intensive malaria threatens maternal and child health among the world's most impoverished populations in the tropical and subtropical zone. Malaria is a mosquito-borne disease caused by apicomplexan parasites of the genus Plasmodium. Profound anemia is a frequent complication of severe malaria in young children living in areas of high transmission. Severe malarial anemia results from infection and destruction of RBCs in circulation and inadequate replenishment with fresh RBCs differentiated from erythroid stem cells in the bone marrow (erythropoiesis). Parasites are known to localize to the bone marrow which recent work has highlighted as a site of gametocytogenesis. How interactions between host and parasite in the bone marrow contribute to altered red cell production (dyserythropoiesis) in malaria infection remains a crucial missing piece in the current understanding of malarial pathogenesis. The research described in this dissertation addresses a substantial gap in knowledge about host-parasite interactions in the hematopoietic niche that may contribute to dyserythropoiesis. Here, an ex vivo system of erythroid differentiation from primary human bone marrow stem cells is used to investigate the stage-specific responses of developing erythroblasts to P. falciparum. Transcriptomic and proteomic approaches to analyzing infected erythroblasts at various stages of development reveal substantial disruption to programs of erythroid gene expression and induction of proteotoxic stress in response to P. falciparum. This work opens new avenues for investigating an understudied site of malaria pathogenesis and a major niche for cellular development of both host and parasite