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Modeling Exoplanet Demographics Across Detection Methods
No full textExoplanet demographics leverages large-scale survey data to give us population-level in- sight to questions of planet formation, evolution, and habitability. Few exoplanet surveys to date have enabled more demographic studies than the Kepler mission, which leveraged the transit method of exoplanet detection to deliver thousands of confirmed and candidate planets. But despite this revolutionary insight, a paucity of reliable detections of Earth-like planets makes measuring their frequency – a key parameter in the search for life – extremely difficult. In this work, we present several studies leveraging the Kepler sample and recent innovations therein to provide some of the most up-to-date, comprehensive estimates for the frequency of Earth-like planets and its dependence on stellar mass. Additionally, we move beyond single-survey studies and supplement the limitations of Kepler by developing a new technique to constrain occurrence rates using data from multiple surveys. We then use this technique to constrain the occurrence distribution of giant planets as the first work to combine transit, radial velocity, and direct imaging surveys. Across all these studies, we comment on the potential for demographics to support current and future surveys as the community continues searching for life beyond our solar system
Drift-Kinetic Particle Dynamics in Black Hole Accretion Flows
No full textLow density plasmas in curved spacetimes, such as those found in accretion flows around black holes, are challenging to model from first principles, owing to the large scale separation between the characteristic scales of the microscopic processes and large mean-free-paths comparable to the system sizes. Kinetic approaches become necessary to capture the relevant physics but lack the dynamic range to model the global characteristics of the systems. The guiding center formalism has been proposed as a powerful tool to bridge the gap between these scales. Despite its usefulness, the guiding center approach has been formulated successfully only in flat spacetimes, limiting its applicability in astrophysical settings. In this thesis, I develop new covariant guiding center equations of motion for charges in general relativistic spacetimes that are computationally tractable. I derive covariant conservation laws for the motions of the guiding centers and show, through several limiting cases, that the equations contain all known drift mechanisms. Through a variety of experiments, I demonstrate that my equations capture all known gyrocenter drifts while overcoming one severe limitation imposed on numerical algorithms by the fast timescales of the particle gyromotion. I generate a new hybrid numerical algorithm based on this formalism, which evolves the trajectories of charged particles over macroscopic timescales in general relativistic magnetohydrodynamic (GRMHD) backgrounds. I apply my method to GRMHD simulations of black hole accretion flows, demonstrating its accuracy and efficiency across a range of physical conditions. Lastly, I present the general relativistic drift velocities and accompanying parallel and temporal acceleration equations in a 3+1 decomposition applicable in non-spinning black hole spacetimes.
The culmination of the work presented in this thesis will enable explorations of a variety of global plasma kinetic phenomena in the curved spacetimes around black holes and neutron stars
Trogocytosis and Horizontal Gene Transfer Between Immune Cells and Renal Cancer Cells Alters Tumor Cell Gene Transcription and Is Promoted by Mer Signaling
No full textTrogocytosis is an underappreciated phenomenon that has been shown to play an important role in many aspects of both normal physiology and oncogenesis. The transfer of surface membrane fragments from infiltrating immune cells to tumor cells can have profound effects on tumor progression, immune evasion, and treatment efficacy. These studies demonstrate how trogocytosis and horizontal gene transfer between immune cells and renal cancer cells results in phenotypic changes in cancer cells. These changes result in expression of immune-specific proteins (such as CD45) on the surface of cancer cells. In addition to changes at the protein level, we also observed that internal cellular components such as genomic DNA can be transferred to cancer cells through physical contact. This transfer can induce changes to gene transcription that create a new cancer cell phenotype with access to previously inaccessible immune cell protein expression. Finally, we provide evidence that the Mer tyrosine kinase receptor is a key regulator of trogocytosis in renal cancer cells. This is significant because previously, no specific mechanism of trogocytosis had been identified. This work illustrates the complexity of the tumor-immune microenvironment and may provide the foundation for future therapeutic strategies that target trogocytosis to improve treatment efficacy
Radicalization Pathways in the Online Context: Accounting for User Trajectories Across Extremist Spaces
No full textThe issue of radicalization has drawn significant attention over the last decade, as high-profile mobilizations and far-right violence grow increasingly prevalent in the United States. This has been accompanied by a particular interest in radicalization in the online context, as far-right recruitment and organizing increasingly leverages the affordances of digital platforms. In this dissertation, I advance theoretical understandings of online radicalization processes by analyzing differential participation within one growing and under-examined segment of the far-right: secular male supremacist movements. Based on prior literature identifying increasing extremism in these spaces, and increasing instances of users moving between distinct but related communities, I address two specific research questions: 1) what individual and community-level factors drive differences in engagement in male supremacist communities; and 2) what individual and community-level factors predict user migration to more extreme male supremacist communities? To answer these questions, I draw on data from five male supremacist groups active across 52 forums on Reddit, drawing on longitudinal data from the Pushshift Reddit dataset to analyze three radicalization-related outcomes: rates of engagement, migration to new and more toxic communities, and disengagement. I draw on literatures on secular male supremacist ideology, differential participation and radicalization in the online context, and online engagement more generally to develop and test hypotheses regarding factors expected to predict these outcomes; I then utilize quantitative analysis, including fixed-effects negative binomial regression and discrete-time event history analysis, to identify significant predictors of differential participation and radicalization. Overall, results show that radicalization within secular male supremacist communities on Reddit is shaped primarily by group identity, certain individual features of engagement or extremity, and the qualitative components of users’ interactions within these spaces, all of which work in concern to ‘push’ or ‘pull’ users through—or anchor them within—secular male supremacist spaces. These factors then operate alongside platform-level repression efforts to influence differential participation and user trajectories into extremism. Taken together, the analysis advances scholarship by highlighting the bolstering effect of having a diverse set of extremist spaces in which users can engage, identifying important effects of toxicity on extremism, determining which features of interaction are important for driving differential participation, and implicating platform-level repression efforts in driving radicalization
Persist or Give Up? Social Insect Decision-Making When Faced With Problems
No full textA social insect colony is a self-organized system with a few reproductive queens and multiple sterile workers performing various tasks cooperatively. As a result, the colony as a whole is a unit of selection. Most social insects are clustered within the order Hymenoptera. Haplodiploidy within this order (and beyond) leads to unusual relatedness among sisters, and this has been hypothesized to promote the evolution of cooperation. Workers can use different communication systems to coordinate recruitment to food sources and to perform various other tasks. Social insect colonies can face various problems, such as environmental perturbations, internal errors, and competition from other colonies. My thesis aims to understand how social insects respond to these problems and to understand whether haplodiploidy drives the evolution of eusociality. Specifically, my thesis accomplishes the following:
(1) I applied a robustness mechanism categorization framework from systems biology to understand how individual Solenopsis xyloni workers respond to a perturbation of an already established pheromone trail using a classic T-maze setup. I found that S. xyloni workers abandoned the sucrose feeder when the already established pheromone trail was perturbed. Ants that managed to make a choice with the disrupted trail made random choices and did not reinforce the pheromone trail. However, when the sucrose concentration in the feeder was doubled, ants were less likely to abandon the trail, but continued to make random choices, and did not reinforce the pheromone trail. This study suggests a way forward to systematically study individual and collective responses to different perturbations. (2) I designed an agent-based model in Netlogo to examine how different types of errors affect collective foraging outcomes, and how different communication systems modify these outcomes. Overall, I found that errors led to decreased exploration and exploitation. Errors that had a high probability of occurring (false positive and forgetting errors) were the most detrimental to collective foraging performance. Communication overall improved resource collection rate and efficiency, but surprisingly led to an increased exploration for resources. In addition, communication presence mitigated the effects of errors rather than exacerbating them (i.e., there were no misinformation cascades). The results from my model suggest that the evolution of communication systems may also have been shaped by selection on exploration and robustness against different error types, as well as selection on efficient foraging. (3) I examined whether individual Temnothorax rugatulus ants can assess each other’s fighting abilities during a dyadic contest. I used contest duration as the response variable, and dry weight (proxy for body size) and head width (proxy for weaponry) as proxies of fighting abilities. I found that neither proxy of fighting abilities predicted the contest duration, indicating an absence of assessment. However, since I did not provide any resource for the ants to fight over, the ants may not have perceived this interaction as a contest. My study shows that individual contests are not identical to colony-level contests, and needs further investigation. (4) I investigated whether the evolution of eusociality is correlated with the evolution of haplodiploidy using a family-level hexapod phylogeny. I used three phylogenetic comparative methods (Pagel’s test, phylogenetic logistic regression, and D-test) to tackle this question. Two of three tests (Pagel’s test and D-test) show a clear support for haplodiploidy driving the evolution of eusociality. Experimental manipulations of data reveal that the non-significance of the logistic regression was due to the absence of haplodiploidy in aphids and termites. Overall, my study provides mixed support for the haplodiploidy hypothesis
Rewriting the Parrot’s Tales: Narrative Structure and Literary Craft in Nakhshabi’s Ṭuṭināma
No full textThis dissertation examines a fourteenth century Persian adaptation of the Sanskrit Shukāsaptati (“Seventy Tales of a Parrot”), titled the Ṭuṭināma (“Tales of a Parrot”) by Żiāʾ al-Din Nakhshabi. The Tales of a Parrot story cycle, which originated in India and circulated across Persian, Arabic, and European literatures, yet has remained understudied compared to similar works like Kalila va Demna. Nakhshabi’s Ṭuṭināma is a creative rewriting of an earlier Persian translation, Javāher al-asmār (“Gems of Stories”) by ʿEmād bin Moḥammad S̱aghari and became the most influential version of the tradition. This study explores Nakhshabi’s stylistic and narrative innovations and exhibits how his reworking of S̱aghari’s text was transformed into a distinct literary masterpiece. It investigates how Nakhshabi uses of rhetorical embellishment, narrative framing, and temporal structuring to enhance the text’s didactic and aesthetic dimensions. Additionally, the dissertation examines the Ṭuṭināma’s engagement with themes of gender, power, and morality, situating it within the broader “wiles of women” tradition while highlighting its conflicted portrayal of female autonomy
Illuminating Cosmic Reionization with Galaxies in the First Billion Years
No full textIn the last two decades, observations with state of the art optical and near-infrared telescopes have greatly advanced our understanding of the Epoch of Reionization. Measurements based on quasar spectra, the cosmic microwave background, and observations of Lyman-alpha (Lyα) emission in early galaxies have constrained the timeline of reionization, placing the conclusion at z~5.3, while reionization is still ongoing at z~7-8. However, though we have made significant progress understanding the volume-averaged timeline of reionization, many questions remain open about the details of the reionization process and the nature of the galaxies that produced the ionizing photons that reionized the Universe. In this dissertation, I explore both of these topics, with the goal of developing a holistic picture of how galaxies drove the reionization process. Using the most comprehensive extragalactic imaging survey available to date from the James Webb Space Telescope (JWST), I quantify the abundance of galaxies at z~9-16 by measuring the rest-UV continuum luminosity function, and examine implications for early star formation processes and the ionizing photon budget available to reionize the Universe. Next, I examine the properties of galaxies at z~7 and z~9 in more detail, focusing on characterizing the star formation histories of the population and the evolution thereof over cosmic time, in order to better understand how early galaxies formed stars and produced ionizing photons. Then, I turn towards directly linking the reionization process to specific populations of galaxies that created early, large ionized regions, first leveraging photometric signatures of overdensities of galaxies to identify candidate ionized bubbles, then following these candidates up with spectroscopy to measure Lyα emission and constrain ionized bubbles on local scales. Finally, I discuss future prospects for furthering our understanding of the star-forming and ionizing properties of early galaxies using deep near-infrared observations, alongside direct constraints on the topology of the reionization process from Lyα emission
The Impacts of Environmental Change on Plant and Microbial Communities: A Turf Transplant Experiment in the Colorado Rocky Mountains
No full textClimate change is rapidly altering temperature and moisture regimes, reshaping species distributions, interactions, and ecosystem processes worldwide. High elevation mountain ecosystems are especially vulnerable due to accelerated climate change and limited opportunities for upslope range expansion, particularly as low elevation competitors move in. Responses to climate change are driven by a complex interplay of direct climatic effects and indirect species interactions. As a result, predicting how communities and ecosystems will change remains challenging, especially across biological scales.To address this, I established a reciprocal whole-community turf transplant experiment in the Colorado Rocky Mountains, relocating intact plant and soil communities across an elevational gradient characterized predominantly by shifts in temperature and moisture. This design allowed me to assess how community composition, flowering phenology, functional traits, and ecosystem functioning respond to environmental change. By transplanting both up and down elevation I tested for asymmetries in ecological sensitivity to climate shifts. Turfs transplanted downhill and exposed to a warmer environment had rapid, directional shifts in community composition, which were stronger in soil bacteria/archaea and weaker in plants and soil fungi. In contrast, turfs transplanted uphill and exposed to a cooler environment had slower, weaker, and more variable changes in community composition, with limited turnover. These asymmetrical responses suggest that upslope colonization by low-elevation species is more likely than downslope persistence, increasing the vulnerability of high-elevation communities to novel competitors and altered interactions. Flowering phenology shifted rapidly with both uphill and downhill transplantation, suggestive of strong plastic responses to both warming and cooling that mirrored natural elevational patterns. Community-level flowering and production converged with the destination sites within five years, despite differences in species composition. However, phenological shifts were only weakly associated with reproductive output and unrelated to species dominance, suggesting that timing differences are consistent responses to climate, but are poor predictors of broader ecological outcomes. Plant functional traits also shifted rapidly under warmer conditions, changing from traits associated with fast growth and resource use to traits linked to resource conservation and survival, similar to those found in the lower elevation, warm-adapted communities. In contrast, cooling led to slower and more inconsistent changes. These shifts were driven primarily by plasticity and, to a lesser extent, changes in species dominance. Notably, carbon and water fluxes increased under warming despite more conservative trait profiles, which suggests context-dependent links between local conditions, traits, and function. In summary, transplantation to warmer sites drove rapid reassembly of high elevation communities and altered ecosystem functioning, while transplantation to cooler sites overall led to slower, less consistent responses. These asymmetries indicate a heightened vulnerability of high elevation ecosystems to climate change, and the potential for upslope establishment of lower elevation species. While some community responses shifted predictably, others were context-dependent, indicating the complexity of ecosystem responses to environmental change. This dissertation reveals that complexity by empirically demonstrating the range of ecological responses to environmental change and exploring the mechanisms driving divergence. Although many ecological models and management plans depend on generalizable, predictable patterns, this work shows that in subalpine ecosystems, responses are often nonlinear, variable, and shaped by local context. In a time of urgent environmental decision-making, understanding this ecological complexity is essential for building informed strategies for a changing climate
Conversion of the Chemistry by Design Database into a Machine-Readable Format for Training and Testing Machine Learning and Artificial Intelligence Models
No full textThis dissertation is organized into six chapters, encompassing both the expansion of our group's native methodologies around indole synthesis and our anionic amino-Cope platform, as well as the exploration and enhancement of our educational outreach initiatives such as the Top 200 Drug Posters and Chemistry by Design. Chapter 1 introduces my graduate research with a new methodology employing a dearomatization-rearomatization approach via Wessely oxidation and LTA. Chapter 2 shifts focus to a brief biological collaboration that entailed the total synthesis of (-)-iridomyrmecin. The objective was efficient production rather than developing a novel synthetic route, thus existing synthesis strategies were followed, leading to some inventive methods for diastereomer separation due to limitations in available techniques. Chapter 3 presents a novel entry into the anionic amino-Cope platform, driven entirely by computational results; a first for the Njardarson lab. Chapter 4 provides an in-depth discussion on Chemistry by Design, including its conversion into a machine-readable format for training and testing computer models, detailing the dataset extraction processes, encountered challenges, and solutions. Chapter 5 continues from Chapter 4 and focuses on analyzing the content of the dataset, highlighting significant insights gleaned from accessible data. Chapter 6 concludes with an overview of the current state of the Njardarson Lab’s Top 200 Drug Posters, showcasing the transformation of the creation process into an automated procedure, significantly reducing the production time from days or hours to minutes.Release after 08/21/202
Impact of Teacher and Classroom Characteristics on Affective Empathy Development in Upper Elementary Students
No full textAffective empathy has been shown to positively impact prosocial behavior, buffer against antisocial behavior, and improve school functioning. The present study examined affective empathy and teacher and classroom characteristics in a sample of 822 students in Grades 4 and 5 across two timepoints. Primary aims were to investigate how student empathy changes over the course of a school year, and how it may be affected by student perceptions of teacher-student closeness, teachers ignoring bullying incidents, and anti-bullying classroom norms. Additionally, the study explored potential moderating effects of student gender on the hypothesized relationships. Results showed that empathy decreased from Time 1 to Time 2 similarly in boys and girls, and that student-teacher closeness positively predicted empathy over time in both gender groups. Ignoring bullying incidents negatively predicted empathy in girls only, and the positive relationship between anti-bullying classroom norms and empathy trended toward significance in boys only. These findings indicate that classroom-level microsystem factors, particularly student-teacher relationships, have a marked influence on students’ empathic development. Furthermore, findings have potentially important implications for school-based social-emotional interventions and curricula