VictorJuiz/thesis huggingface dataset:
Human Trafficking as a Crime Against Humanity: Puerto Rico’s Innovative Approach to Human Rights Legislation

Julian Bava focused his human rights capstone on analyzing the history and text of Puerto Rico’s Crimes Against Humanity (CAH) legislation in order to determine its potential effectiveness as an accountability tool. Utilizing Article 300 of Title V (“Crimes Against Humanity”) of the Penal Code of Puerto Rico (the “Penal Code”), Julian notes how Puerto Rico is unique in offering a state level framework for prosecuting atrocity crimes and reveals the critical role subnational jurisdictions may play in shaping international law and its application within the United States. With this analysis, Julian shows how Puerto Rico’s atrocity crimes legislation provides a promising landscape that not only pushes international law in a novel direction, but also provides tangible opportunities for victims to seek redress.
Student project deposited by department for archival purposes. Original work unavailable for public download due to permission restriction preferences of the author.

Keywords: Puerto Rico
Crimes against humanity
Transitional justice
Text
Article
Thesis
Hurdles to targeting the CD47-SIRP-alpha interaction for immunotherapy

The CD47-SIRPα signaling pathway has emerged as an important innate immune checkpoint axis, with CD47 acting as a marker of self and health. Numerous cancers have been shown to upregulate CD47 expression, including hematologic cancers such as acute myeloid leukemia (AML) and non-Hodgkin's lymphoma (NHL), and myeloma, and solid tumors such as ovarian cancer, breast cancer, head and neck cancers, colon cancer, pancreatic neuroendocrine tumors, small lung cell cancer, and glioblastoma. The number of pharmaceutical companies and startups developing therapies which target this immune axis has grown exponentially in the past decade. At the forefront are antibodies which bind CD47 and interrupts its binding to SIRPα. The biggest challenges to targeting CD47 are the on-target effects on red blood cells and platelets, both of which depend on cell surface CD47 to avoid phagocytosis. Patients receiving treatments suffer from anemia and thrombocytopenia. Additionally, it remains unclear if other types of healthy cells rely solely on CD47 as a "don't eat me" signal and are subject to depletion like RBCs and platelets. Another hurdle is one that plagues all therapies -- heterogeneity in response within the human population. Further understanding of the CD47-SIRPα pathway is necessary to identify the patients that can benefit the most from treatment. The goal of this thesis is to explore some of these hurdles to inform future decisions that can impact patient health. This thesis will show that marginal zone B cells is another population of cells of the hematopoietic lineage that are depleted during CD47 blockade. It further shows that polymorphisms in SIRPΑ might partially explain some of the heterogeneity seen in response to CD47 immunotherapy and might also regulate platelet numbers and size, with implications for thrombocytopenia, stroke and coronary disease. These findings should initiate new avenues of research which will ultimately give a better understanding of the impact of on-target treatment-related adverse events and genetic variations on therapies targeting the CD47-SIRPα axis

Keywords: Immunology.
Advisor: Weissman Irving L.
Blish Catherine
Shizuru Judith Anne
Sunwoo John B.
"I Didn't Want to Trigger Them": Latinx Student Perceptions of Teacher Political Ideology in the Trump Era

The “Trump Era” has impacted nearly every aspect of American society, including education. With many ethnically and racially minoritized populations, including Latinos, being the targets of harmful and discriminatory rhetoric that has become associated with the Republican Party, this paper examines how the perceptions that students have of their teacher’s political ideology affects their educational experiences. I interviewed seven Latinx-identifying high school students from three different states, two of which are considered “blue states” and the other a “red state” to answer the following question: in what ways does Latinx student awareness of teacher political ideology affect their educational experiences? I asked students multiple questions about how they were able to form an idea of what party their teachers identified with politically, how that made them feel, how it impacted their interactions with the teacher, and how they felt about political disclosure in the classroom. There were three main findings as a result of this study. The first is that political disclosure on behalf of teachers is not the only way in which students develop an understanding of what their teacher’s political ideology is; students use their own lived experiences and outside knowledge to draw conclusions about their teacher’s political leanings, therefore both students and teachers bring politics into the classroom. The second finding is that Latinx student experiences are greatly impacted by their perception of their teacher’s political ideology, but especially so for students who perceive their teachers as conservative. The third finding is that while student experiences are impacted, they are able to rationalize their experiences and acknowledge that their teachers are entitled to their own opinions. This study has implications for the future of teaching, including the call for incorporating culturally responsive training and teaching.

Keywords: Education
Learning
Latin Americans
Students
Teachers
High schools
Politics and government
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Thesis
Advisor: Martinez Ramon
Kelman Ari
Identification of a Myogenic and Highly Transplantable Tert Expressing Non-Satellite Stem Cell Population

Telomerase Reverse Transcriptase (Tert), a component of the telomerase holoenzyme complex, has been previously identified as a marker of stem cell populations across tissues. However, its role in skeletal muscle is poorly understood. In skeletal muscle, volumetric muscle loss injuries pose a unique challenge for cellular-based therapies, which so far have been relatively unsuccessful in preclinical models. Using a Tert-lineage tracing genetic mouse model, we identified a set of rare Tert expressing cells distributed throughout muscle. These Tert-lineage cells expand upon injury and contribute to myofiber regeneration in a delayed fashion. In addition, muscular regeneration upon repeated injuries is impaired by the loss of Tert in Tert expressing cells and their progeny. While a very small population of satellite cells express Tert, we also identified a population of Tert Expressing Multipotent Myogenic Progenitors (TEMMPros). These TEMMPros are multipotent and myogenic in vitro and via transplantation in a Tert-dependent manner. Furthermore, transplantation of these TEMMPros resulted in improved regeneration compared to satellite cells in a mouse model of volumetric muscle loss. Single-cell sequencing reveals that TEMMPros are transcriptionally distinct from other known skeletal muscle cell populations including satellite cells. These observations identify a novel subset of myogenic, non-satellite Tert expressing cells in mice that possess remarkable capacity for regeneration and may serve as a cell-based therapeutic for skeletal muscle damage.

Keywords:  Department of Biology
Biology
Skeletal Muscle
Stem Cells
Telomerase
Regenerative Medicine
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Thesis
Advisor: Artandi Steven
Morrison Ashby
Mudgett Mary Beth
Identifying the long-term effects of maternal immune activation in offspring

There is growing evidence that immune perturbations in the developing CNS can influence neurodevelopment and influence the individual's risk for CNS-related disorders throughout life. In particular, there is strong epidemiological evidence that maternal immune activation (MIA) during early to mid-gestation is associated with increased risk for neurodevelopmental disorders such as autism and schizophrenia in the offspring. However, the molecular mechanism of how MIA impacts neural function and behavior is still unclear. To tackle this challenge, our lab and others have developed mouse models to investigate MIA-induced phenotypes and elucidate the mechanisms by which an early event during pregnancy could induce lasting impacts on the offspring's neural outcomes. Here, we combined high dimensional transcriptional analysis with histological methods and behavioral assays to determine how changes in transcriptional and cellular profiles relate to functional consequences. Better understanding of the underlying mechanisms of how MIA predisposes an offspring to neurodevelopment and neuropsychiatric disorders could allow for targeted therapeutic interventions in the clinic. In this dissertation, I present work characterizing the mechanisms by which MIA influences both early neurodevelopment as well as responses to environmental and genetic insults later in life. In chapter 2, I demonstrate that MIA through TLR-3 versus TLR-4 signaling results in distinct placental and fetal outcomes during development. In chapter 3, I identify long-term transcriptional changes following prenatal immune challenges that subsequently impact neuroinflammatory responses in adulthood. In chapter 4, I elucidate how gene-environment interactions between ASD risk genes and MIA can exacerbate placental and neural phenotypes. Collectively, this dissertation thesis presents fundamental molecular insights into MIA mechanisms with the ultimate goal of understanding how prenatal immune challenges impact brain function and human health

Advisor: Palmer Theo
Idoyaga Juliana
Monje-Deisseroth Michelle
Wyss-Coray Anton
Identifying the mechanism of aged oligodendrocyte progenitor cell rejuvenation by young cerebrospinal fluid

As humans age and develop aging-related diseases, many learning and memory functions can be compromised as the myelin sheath surrounding axons is lost. Previous work has demonstrated that these cognitive functions, which are mainly coordinated in the hippocampus, require the activity-dependent myelination of axons by oligodendrocytes. Given the literature demonstrating myelin degeneration with aging and neurodegenerative disease, we hypothesized that loss of white matter could drive aging-related cognitive decline and that protecting myelin could prevent this decline. This project aims to characterize the effects of exposing aged mice to young mouse cerebrospinal fluid (CSF) and identify the mechanism of oligodendrocyte rejuvenation. The paradigm for this project involved extracting CSF from young mice and transfusing it to aged mice through carefully regulated mini-osmotic pumps. These mice were then used for behavioral studies, immunohistochemistry staining, and sequencing experiments. The results showed increased proliferation and differentiation of aged oligodendrocyte progenitor cells (OPCs) when exposed to young CSF. Further characterization of transcriptomic changes revealed the upregulation of a few transcriptional factors including serum response factor (SRF) which is known to play an important regulatory role in the contraction of muscle cells. Increased expression of these transcription factors and their downstream targets suggest an actin-mediating mechanism for the rejuvenating effects of young CSF. These findings suggest therapeutics targeting SRF and actin pathways in OPCs could rescue myelination and improve cognitive function in aged mice. Developing therapeutics with these abilities could allow for clinical improvements in learning and memory for the growing elderly population, especially those suffering from aging-related memory disorders.

Keywords:  Department of Biology
Biology
Aging
Myelin
Actin
Activity-Dependent
SRF
CSF
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Thesis
Advisor: Wyss-Coray Tony
McConnell Susan
Identifying the sources and drivers of variable nitrous oxide concentrations across the Eastern Tropical North Pacific

Nitrous oxide (N2O) is a powerful greenhouse gas, and oceanic sources account for up to one third of total flux to the atmosphere. In oxygen-deficient zones (ODZs) like the Eastern Tropical North Pacific (ETNP), N2O can be produced and consumed by several biological processes. In this study, the concentration and isotopocule ratios of N2O from a 2016 cruise to the ETNP were analyzed to examine the sources of and controls on N2O cycling across the region. Along the ~1000 km north-south transect, three distinct biogeochemical regimes were identified: background, core-ODZ, and high-N2O stations. Background stations were characterized by smaller variations in N2O concentration and isotopic profiles relative to the other regimes. Core-ODZ stations were characterized by co-occurring N2O production and consumption at anoxic depths, indicated by high δ18O-N2O (> 90‰) and low δ15N2Oβ (< -10‰) values, and confirmed by a time-dependent model, which indicated that N2O production via denitrification was significant and may occur with a non-zero site preference. High-N2O stations, located at the periphery of a mesoscale eddy, were defined by [N2O] reaching 126.07±12.6 nM and low oxygen concentrations expanding into near-surface isopycnals. At these stations, model results indicated significant N2O production from ammonia-oxidizing archaea and denitrification from nitrate at the N2O maximum within the oxycline, while bacterial nitrification and denitrification from nitrite were insignificant. This study also represents the first in the ETNP to link the magnitudes of N2O production mechanisms to a mesoscale eddy through isotopocule measurements, suggesting the importance of eddies to the spatiotemporal variability in N2O cycling and emissions from this region.

Keywords: Nitrogen cycle
Greenhouse gases
Anoxic environments
Stable isotopes
Climate and interannual variability
Chemical oceanography
Oceanography > Research
Biogeochemistry
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Thesis
Advisor: Casciotti Karen
Francis Christopher
IgG Autoantibodies Induced by COVID-19 and Other Respiratory Disease

Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was first identified in December of 2019 and has since spread worldwide, leading to the current pandemic. Symptoms of COVID-19 usually include fever, cough, fatigue, respiratory difficulties, as well as loss of smell and taste. However, the disease is associated with a wide range of clinical manifestations, including hallmarks of autoimmunity and autoantibody production. My lab developed three different protein arrays to measure IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients from three different centers. Autoantibodies in patients with other respiratory diseases, severe Influenza and Acute respiratory distress syndrome (ARDS), from two other centers were also measured. Overall, autoantibodies were identified in approximately 50% of COVID-19 patients, but in <15% of healthy controls. Anti-nuclear antibodies (ANA) were observed in ~25% of patients. In comparison, ANAs were observed in 33% and 22% of severe Influenza and ARDS patients, respectively. For COVID-19 patients, autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. I conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins. However, severe Influenza and ARDS induce fewer autoantibodies than COVID-19.

Keywords:  Department of Biology
Biology
Immunology
COVID-19
Text
Thesis
Advisor: Utz Paul
Morrison Ashby
Imaging the response of mesoscopic devices and materials to magnetic fields

Scanning SQUID Microscopy (SSM) is a powerful tool for measuring nanoscale superconducting heterostructures. In this thesis, I describe results from several projects motivated by the goal of developing foundational models and characterization methods for engineering superconducting heterostructures. First, I discuss an approach to studying the dynamics of vortices in type-II superconductors, which creates unwanted dissipation in superconducting circuits, using a combination of SSM and 2D London modeling (Chapter 2). Next, I cover three projects studying materials systems engineered with the goal of achieving topologically nontrivial quasiparticle states called Majorana modes, which can be used to build qubits for fault-tolerant topological computing. Chapters 3-4 discuss interfacial and thickness effects and domain wall superconductivity in hybrid superconducting-semiconducting-ferromagnetic systems, and Chapter 5 presents SSM imaging results of diamagnetism and vortex motion in superconductor-topological insulator-superconductor junctions. Understanding these effects will be key to controlling the behavior of these devices in future iterations. Finally, Chapter 6 considers a model experimental system that mimics disorder in a natural 2D superconductor using an array of proximity-coupled superconducting islands with engineered disorder. Experimental susceptibility imaging results combined with Josephson Junction modeling show that these arrays can be described as arrays of superconductor-normal metal-superconductor junctions

Keywords: Applied Physics.
Advisor: Moler Kathryn A.
Fisher Ian R. (Ian Randal)
Goldhaber-Gordon David
Immune polyphony : dissecting coordinated multicellular networks of antiviral immunity

Viral diseases remain a major cause of morbidity and mortality worldwide and emerging viral pathogens represent a perennial threat to human health. The rapidity, quality, and duration of the immune response to a viral pathogen is a major determinant of disease outcome in viral disease. This immune response to a viral pathogen involves the activity of multiple cell types with distinct and multifaceted functional roles to mount a response that is appropriate in both time and space. An insufficient response may result in unrestrained viral replication while an overly robust response can result in direct tissue damage. Thus, an effectively regulated antiviral immune response requires complex coordination, communication, and regulation between individual immune cells. We coin the term "immune polyphony" to describe these coordinated multicellular networks -- a reference to musical polyphony where multiple individual voices come together to create harmony. Here we present a framework to study and engineer immune polyphony and apply this framework to dissect the features of well-balanced immune responses in multiple viral diseases. First, we examine immune responses in patients with COVID-19 across the full range of the disease severity spectrum to reveal widespread dysregulation of innate immunity in severe COVID-19. Next, we introduce a novel computational framework for the analysis of cell-cell communication pathways at the resolution of the single-cell. We then apply this methodology to analyze inflammatory networks that distinguish immune responses to pathogenic vs. non-pathogenic lentiviruses. Finally, we describe a technique for bio-orthogonal manipulation of primary immune cells, thus providing a pathway for future efforts to engineer polyphonic immune responses to promote effective antiviral immunity

Advisor: Blish Catherine
Bintu Lacramioara
Greenleaf William James
Kim Peter
Krams Sheri Michele
The impact of identity, situation, and action framing on environmental behavior

Individuals often possess multiple motivations when making decisions related to the environment ranging from the desire to cut down on their utility expenditures to the desire to reduce their environmental footprint. The complexity of optimizing given these multiple motivations may lead individuals to employ rule-based heuristics like March and Olson's logic of appropriateness. March and Olson theorize that, in many situations, behavior is guided by internalized rules of "appropriateness" (March and Olson 1995) where appropriateness is determined by answering the (explicit or implicit) question "what would a person like me do in a situation like this". As a result, choices may depend upon how individuals conceptualize their identity ("what kind of person am I?"), the situation ("what kind of situation is this?"), and the action being considered ("what kind of action is this?"). Each of these conceptualizations is potentially labile and responsive to features of the choice environment. In my dissertation, I explore how approaches that shift the construal of identity, situation, and action can be used to change behaviors in the realm of environmental politics and policy. Chapter 1 tests whether activating an evidence-based identity increases belief-updating among policymakers. Chapter 2 explores how different types of rooftop solar incentives shape the inferences that individuals make about descriptive and injunctive norms. Chapter 3 investigates how a novel non-linear "streak" incentive shapes electricity consumption

Advisor: Miller Dale T.
Wong-Parodi Gabrielle 
DeShazo J. R.
Improved light-field control and light-matter interaction for device applications via optically resonant nanostructures

Starting from the 1970s, great efforts have been made to miniaturize bulky optical devices. This progress accelerated significantly over the last decade due to the emerging field of metasurfaces. These planar nanophotonic devices, made from judiciously engineered, subwavelength-thick optical nanoresonators, are capable of controlling the amplitude, phase, polarization, and spectral properties of light waves with subwavelength resolution, and therefore have the potential to replace a wide range of bulk optical elements with flat optics. Here, we go one step further to explore the emergent properties of optical nanoresonators beyond the concept in conventional optics. The radiative nature of optical resonances results in emerging collective modes in nanoresonator arrays beyond the description of the renowned chemical bonding model, leading to tremendous degrees of freedom for manipulating the light fields. Given the dimension of these flat optical elements becoming compatible with on-chip electronics, we now foresee an unprecedented opportunity to boost the performance and enable novel functionalities in integrated devices by bridging the gap between optics and electronics using metasurfaces. The carefully engineered local photonic environment created by optical nanoresonators can selectively interact with quantum states in a broad range of material systems, probing and extracting the quantum information as needed. In this thesis, I will specifically illustrate how to leverage the above-mentioned emergent properties of optically resonant nanostructures to achieve the improved control over the emission, propagation, and absorption of the light fields at the nanoscale. Eventually, it leads to three representative device applications: a transparent spectro-polarimetric silicon nanowire photodetector, a comprehensive metasurface optofluidic platform for dynamic control of light fields, and an efficient monolayer semiconductor free-space electro-optical modulator operating at room temperature. These works validate the crucial role that optical nanoresonators play in revolutionizing various optical and optoelectronic devices that may find use in real-world applications. The underlying physics behind these applications further reveals the opportunity to employ optical nanoresonators as a tool to probe the fundamental nature of complex physical systems

Keywords: Materials Science and Engineering.
Advisor: Brongersma Mark L.
Dionne Jennifer Anne
Fan Shanhui