VictorJuiz/thesis huggingface dataset:
Investigating genetic and cellular determinants of small cell lung cancer initiation and progression
Keywords: Medicine.

Small cell lung cancer (SCLC) is a highly aggressive form of lung cancer with poor response to therapy. While the recent approval of immunotherapy as a first-line treatment for extensive-stage SCLC patients has improved patient survival, there still exists a dearth of targeted therapy options for SCLC patients. To better address SCLC progression and resistance to therapy, a greater molecular understanding of the disease is needed. To this end, we developed a higher-throughput method to screen for drivers of SCLC initiation and progression in in vivo settings. Using this method, we identified TSC1 as a strong tumor suppressor of SCLC and demonstrated potential therapeutic benefit of mTOR inhibition in patients with TSC1 alteration and/or patients that present with mixed SCLC/giant cell carcinoma histology. Among other drivers, we also identified ARID1A and ARID1B as oncogenes in SCLC, suggesting an important role for the SWI/SNF complex in modulating SCLC disease state. While cGRP+ pulmonary neuroendocrine cells have traditionally been thought to be the cell-of-origin for SCLC, recent experiments using mice with various genetic backgrounds and findings that non-neuroendocrine subtypes of SCLC exist have challenged that assumption. Because cell-of-origin has been shown influence the genetic mechanisms SCLC co-opts for progression and metastasis, we tested several cell-of-origin candidates such as PCSK1+ neuroendocrine cells, K5+ basal cells, TERT+ progenitor cells, and endothelial cells. We demonstrate that PCSK1+ neuroendocrine cells can serve as cell-of-origin for SCLC, while the other cell types provide potential models for several other histopathology, such as pancreatic islet hyperplasia, adrenal medullary hyperplasia, and angiosarcoma
Investigating impacts of heat stress on symbiosis in cnidarian larvae using high-throughput fluorescence-based quantification
Keywords: Pringle, John
Coral bleaching, cnidarian-algal symbiosis, heat stress, cnidarian larvae
Text
Thesis

Reef-building corals (phylum Cnidaria) exist in symbiotic relationships with photosynthetic dinoflagellate algae in the family Symbiodiniaceae. Under heat stress, corals lose these algal symbionts, resulting in a phenomenon known as coral bleaching. Due to rising seawater temperatures, more frequent bleaching events have led to significant degradation of coral-reef ecosystems worldwide. Much recent research has focused on whether the preferential association of adult coral polyps with thermotolerant species of algae improves resilience to bleaching. However, similar work on coral larvae has been limited. This study investigated the impacts of heat stress on the uptake and ejection of algae by cnidarians at the earliest stage of their life cycle, free-swimming larvae. Using the sea anemone Aiptasia as a model system, we addressed two questions ­– (1) the impact of heat stress on algal ejection by larvae populated with three different strains of algae of known thermal tolerances: SSA01, SSB01, and Mf2.2b (bleaching experiments) and (2) the impact of heat stress on symbiosis establishment in Aiptasia larvae with these three strains of algae (acquisition experiments). Uptake and ejection of algae by larvae were quantified using a novel high-throughput fluorescence-based sorting protocol employing the Union Biometrica BioSorter. Under control conditions in the bleaching experiments, Aiptasia larvae infected with SSA01 had the highest algal density, and in the acquisition experiments, larvae infected with SSB01 reached the highest algal density. The latter preference mimicked that of adults. Under heat stress, larval acquisition of algae was reduced across all three strains of algae; however, larvae that acquired SSA01 had higher algal densities than larvae exposed to the other two strains. Similarly, larvae already infected with SSA01 retained higher algal densities and even displayed proliferation of algae upon exposure to heat stress, compared to larvae infected with SSB01 or Mf2.2b. These results are surprising as Mf2.2b has been characterized before to be the most thermally tolerant algal strain in culture and in corals, followed by SSA01 and SSB01. One possible explanation might be that, unlike Mf2.2b, SSA01 and SSB01 are the native symbionts found in the male and female parent strains, respectively, with SSA01 being the more thermally tolerant of these two strains. This study is the first to investigate algal preferences in cnidarian larvae under heat stress at a high-throughput scale, and it provides new insights into the relatively understudied early life stage of cnidarians.
Investigating information framing with natural language processing
Keywords: Humanities and Sciences.
Linguistics.

Words can influence both who and what we believe. Consider these headlines, which report on the same vaccine: "Moderna Vaccine Proves 96\% Effective in Teens," "Moderna Vaccine Highly Effective in Adolescents, Company Says." The first presents the efficacy as an established fact, while the second presents the efficacy as an assertion made by its manufacturer. Word choice regarding how assertions are made also matters: a company's "findings" (with semi-factive "find") strengthens the validity of its assertions, while a politician's "admission" carries negative connotations about their trustworthiness. Prior work studying information framing, or discourse acts in which a writer or speaker signals their stance with respect to a proposition from some source entity, has been restricted to a relatively narrow set of framing strategies over small-scale datasets. As a result, we know little about systematic patterns in information framing within real world contexts, and even less about its downstream effects on people's beliefs. In my dissertation I combine methods from linguistics, social psychology, and natural language processing (NLP) to study information framing in a data-driven way. In my first series of studies, I use my tools to discover linguistic strategies for conveying trust and doubt and I expose partisan patterns in how journalists exploit information framing to cover scientific issues. Next, I quantitatively measure the persuasiveness of framing strategies in social media arguments and reveal an interaction between epistemic commitment and politeness: high commitment is viewed as face-threatening and less persuasive when framing personal opinions, but has no effect on persuasion when framing scientific evidence. Finally, I conduct behavioral experiments to study the effect of information framing on attitude formation. I show that presenting information as opinions using non-factive verbs (e.g., "Scientists believe climate change is a serious concern") can affect what readers think is true, and to a greater extent, whether they think a ground truth exists in the first place. Together, this work contributes to our understanding of the role of language in how people form, update, and spread their beliefs, and contributes tools and datasets that may be applied to public interest messaging, conflict resolution and negotiation, and bias and misinformation detection systems.
Investigating regulatory mechanisms of T cell effector function
Keywords: Medicine.

T cells play an important role in recognizing and eliminating malignant cells, as well as providing protection from infectious pathogens. Multiple therapeutic modalities including vaccination, immune checkpoint blockade, and adoptive T cell therapy depend on robust T cell responses. Tumor microenvironments are often characterized by local immunosuppression and decreased T cell effector function. Consequently, increasing T cell effector activity in tumors is a common objective for the development of cancer therapeutics. Conversely, autoimmune disease progression is mediated by an imbalanced effector and regulatory immune response, prompting development of therapeutics to diminish T cell effector activity. Therefore, regulatory mechanisms that control differentiation and function of T cells are relevant for applications in medicine. In this dissertation, I will describe our work to identify regulators of T cell effector function. This question is first addressed in the context of cancer using a model system that mimics chronic antigen exposure to induce T cell dysfunction. Using genome-wide CRISPR screening, we identify the Meditator kinase module as a novel regulator of T cell function. We demonstrate this finding can be leveraged through genetic engineering and pharmacological approaches to augment T cell anti-tumor activity. This study further implicates interactions between the kinase module and core Mediator as a major axis of regulation of T cell differentiation. Technologies to inactivate genes are increasingly available for emerging applications in human medicine highlighting the potential for clinical translation of these findings. In the final chapter of this dissertation, I investigate the expression of immunomodulatory receptors in T cells isolated from patients with autoimmune disease. We identify receptors that are differentially expressed between effector and regulatory T cell subsets, providing a basis for selectively targeting effector T cells while preserving the function of regulatory T cells. Collectively, these studies explore multiple mechanisms to enhance or diminish T cell effector responses, providing new avenues for development of T cell directed therapeutics
Investigating the functional effects of enhanced glucose metabolism in T cells with chimeric antigen receptors
Keywords: Medicine.

The combination of intensive nutrient requirements needed to sustain T cell activation and proliferation, alongside competition for nutrients within the tumor microenvironment suggest that glucose availability could limit CAR T cell function. Here we sought to test the hypothesis that stable overexpression (OE) of the glucose transporter GLUT1 in primary human CAR-T cells would improve function and antitumor potency. We observed that GLUT1OE CAR T cells manifest increased glucose uptake at rest and following activation, and this is associated with increased glycolysis and oxidative phosphorylation. In addition, GLUT1OE also enhanced MTOR signaling and broadly modulated metabolic programming, with substantial increases in glutathione mediated resistance to reactive oxygen species, and enhanced urea cycle and arginine metabolism. We observed no evidence for increased T cell exhaustion with GLUT1OE, but rather observed increased TCF1+ and CD62L, consistent with stemness programming. GLUT1OE CAR T cells showed increased cytokine production in response to tumor challenge and manifested superior tumor control in vivo. Our collective findings support a model wherein glucose availability is rate limiting for optimal effector CAR-T cell function and demonstrate that enhancing glucose availability via GLUT1 OE provides a new approach to augment antitumor immune function.
Investigating the Immunogenicity of CBFA2T3-GLIS2 Positive Pediatric Acute Megakaryoblastic Leukemia for an Engineered T Cell Immunotherapy
Keywords: Acute megakaryoblastic leukemia (AMKL)
Leukemia in children
Immunotherapy
T cells > Receptors
T cells > Therapeutic use
Proteomics
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Thesis

The CBFA2T3-GLIS2 fusion oncogene is found in 18.4% of non-Down syndrome (DS) acute megakaryoblastic leukemia (AMKL) patients and is the oncogenic driver. These patients have the worst prognosis of acute myeloid leukemia patients (AML), having only a 14% overall survival, even with current treatments of chemotherapy and hematopoietic stem cell transplantation. These poor treatment outcomes highlight the need for novel therapies for AMKL. Recent novel therapies in other cancers engineer the immune system to target cancerous cells. These therapies include monoclonal antibodies, chimeric antigen receptor T-cell (CAR-T), and engineered T-cell receptor T-cell (TCR-T) therapies that function by binding to tumor-specific or tumor-associated antigens and stimulating a cytotoxic immune response. However, in the context of AMKL, there are currently no immunotherapy options. To explore potential AMKL targetable antigens, we screened the surfaceome of CBFA2T3-GLIS2+ patient cells that were expanded in a patient-derived xenograft (PDX) murine model. We eluted peptides from surface HLA:peptide complexes and utilized mass spectrometry for immunopeptidomics analysis. We identified 242 total peptides, 141 of which were not found in the human ligand atlas, indicating these peptides are leukemia-specific and not presented on normal cells. Of particular interest, we found a peptide from the BMP2 protein, which we have shown contributes to CBFA2T3-GLIS2 driven enhanced self-renewal, and a peptide from the DDX3X protein, which has been reported immunogenic in melanoma.
In an additional PDX murine model, mice engrafted with patient AMKL cells received healthy donor peripheral blood mononuclear cells (PBMCs) from a 6/6 HLA class I match individual. We observed variable reduction in leukemic burden and found those with the most significant reduction also showed a decrease in TCR clonotype diversity, suggesting the healthy T cells underwent clonal expansion directed against leukemia antigens. The clonally expanded TCRs were cloned into expression vectors and will be overexpressed in human CD8+ T cells to test functional response against artificial antigen-presenting cells (aAPCs) presenting the aforementioned peptides of interest through tandem minigene (TMG) assays and peptide stimulation assays. The identification of AMKL- directed effector CD8+ T cells and their corresponding immunogenic antigens will contribute towards the development of an immunotherapy for AMKL to improve patient outcomes.
Investigating the use of small molecule inhibitors for area-selective atomic layer deposition
Keywords: Engineering.
Chemical Engineering.

Area-selective atomic layer deposition (AS-ALD) is a materials synthesis technique with the potential to support the production of featured materials with single-nanometer accuracy. Conventional AS-ALD has used pretreatment with organic self-assembled monolayers (SAMs) as a step to enable the controlled placement of a given ALD material by blocking film growth on certain areas of the substrate. However, SAM molecules are often on the length scale of many of the features being created and also can be challenging to volatilize. Research into low molecular-weight molecules that can inhibit growth while being compatible with high-volume manufacturing is therefore of interest. In line with this research is the need to understand the surface chemistry and interfacial phenomena that support the inhibitory performance of small molecule inhibitors (SMIs), with the final goal being to understand the best ways to control and prevent nucleation of ALD depending on the growth surface of interest. This thesis explores the potential of several small molecule inhibitors to support AS-ALD, and seeks to elucidate the functionalities that contribute to high-performance blocking
Investigating translational machinery heterogeneity across cell types, development, and diseases
Keywords: Medicine.
Genetics.

Recent studies have shown that ribosomes with distinct compositions can differentially regulate gene expression. This compositional heterogeneity can arise from a few sources: ribosomal RNA (rRNA) sequence variation, differential incorporation of ribosomal proteins (RP), binding of ribosome-associated proteins (RAPs) that link translation to cellular processes, and rRNA and RP modifications. Although there have been a few examples of heterogeneity described in prior literature, we lack a full understanding of the extent of ribosome heterogeneity and how ribosome composition changes due to our inability to systematically characterize ribosomes among different biological samples. This dissertation focuses on the diversity in rRNA sequences and RAP compositions that contribute to translational machinery heterogeneity across cell types, tissues, and diseases. We developed novel methodologies to systematically analyze complete rRNA sequences and RAPs for the first time. With respect to rRNA, we built the first comprehensive functional human rRNA sequence variant atlas. This atlas revealed different ribosome subtypes that are genomically clustered in different chromosomes. With this resource, we then showed these variants can be expressed in a tissue-specific or cancer-specific manner. With respect to RAPs, we developed a novel, label-free methodology called RAPIDASH to enrich ribosomes and their associated proteins from any biological sample. We applied this technique to mouse embryonic forebrain, limbs, and liver tissues, which allowed us to identify RAPs with tissue-specific functions. Among these is LLPH, which forms forebrain-specific ribosomes that are important for neurodevelopment. RAPIDASH thus allows us to identify RAPs and understand their roles in modulating gene expressions in development. Together, these techniques enable an in-depth characterization of translational machinery heterogeneity and its role in gene regulation
Japanese diaspora in a WWII incarceration camp : archaeology of Gila River
Keywords: Humanities and Sciences.
Anthropology.

"Japanese Diaspora in a WWII Incarceration Camp: Archaeology of Gila River" challenges narratives of closure and removal through an examination of the material lives of 16,000 Japanese Americans imprisoned on a Native American Reservation during WWII. Drawing from archaeological surveys conducted in collaboration with the Gila River Indian Community, as well as archival, oral historical, and ethnographic sources, it traces the connections maintained, formed, and transformed through material practices during the incarceration camp period. By weaving together these threads, I argue that the incarceration camp system reordered the social connections of the Japanese American community. I utilize community-based research methodologies to work towards building decolonized praxis in recognizing diverse community connections and Indigenous sovereignty. Through an attention to the landscape and the material, I show how the expectations of War Relocation Authority administrators were unfulfilled and incarcerees worked to safeguard individual and community health. By using the concept of diaspora to interrupt the notion of the camp, I challenge notions of isolation and control and theorize the camp as a site of connectivity
Japan’s Security Strategies Towards China in the Scope of Defense White Papers, 1972-2014
Keywords: Japan-China relations
Security policies
White papers
Text
Thesis

This project explored Japan’s changing security attitudes from 1972 to 2014 under the scope of its official defense white papers, using a method of sentiment analysis. Consistent with previous studies, Japan was highly cooperative with China during the period from 1972 to 1992, a period rightfully characterized as the “Golden Age.” Starting from 1993, faced with a rising China, Japan maintained an overall neutral posture on the official and legal level towards China, but subtle attitudinal changes could be seen. While Japan had praised China for its cooperative efforts to denuclearize the Korean peninsula and active involvement in UN peacekeeping, it also pointed to China’s covert purposes for engaging in such activities and repeatedly raised concerns about a perceived violation of state sovereignty by China on the “Senkaku Islands,” as well as over Beijing’s human rights issues and lack of transparency in military spending. The current project shows that Japan has continued to adopt non-confrontation, non-provocative language even when describing its disputes with China.
Kant and the dynamics of pure thinking : essays on Kant's theoretical philosophy
Keywords: Humanities and Sciences.
Philosophy.

In this dissertation, I defend new readings of arguments and claims found in Kant's Critique of Pure Reason. Chapter One defends a new reading of Kant's two-step proof structure in his B-edition of the Transcendental Deduction. Chapter Two defends a new reading of Kant's distinction between general and transcendental logic; Chapter Three defends a new reading of his 'Refutation of Idealism' by examining the legal, logical, and critical uses of 'refutation' in Kant's work
Knowledge work reimagined : lyric life writing and the university
Keywords: Humanities and Sciences.

Postwar academic culture has seen the rise of a literary consciousness and an autobiographical mode. One instantiation of this mode is a contemporary style of writing called "autotheory." While some scholars interpret autotheory as a para-academic literary phenomenon, wishing to trace its lineage outside the university, I show that it is, in fact, rooted in the postwar university, and should be seen as a challenge to prevailing mechanistic epistemologies within the university. As a third way between strictly creative and strictly scholarly writing, autotheory works against prohibitions of self and self-assembly found in a host of humanistic discourses, including philosophy, theory, literary studies, and creative writing. However, I also show that autotheory is a direct outcome of philosophy, specifically the ordinary language philosophy of Ludwig Wittgenstein and Stanley Cavell, and that it plays out key elements of that philosophy. The self-assembly that is accomplished by autotheory is neither narcissistic nor "neoliberal." It is an antidote to the radical self-displacements found in knowledge work. These cultures of radical self-displacement, engaged in what I call the search-for-method paradigm, undermine actual insight in favor of scientism and the administration of concepts. In contrast to this, autotheoretical works, and the tradition of lyric philosophy from which they stem, can be seen as recuperating personality, the experience of meaning, and a coherent political consciousness.