VictorJuiz/thesis huggingface dataset:
Ringleaders of redemption [electronic resource] : the religious authorization of western medieval dance

In traditional thought and theology, Christianity tends to oppose dance. Conventional scholarship traces this controversy back to the Middle Ages. Throughout the medieval era, the Latin Church denounced and prohibited dancing in religious and secular realms, often aligning it with demonic intervention, lust, pride, and sacrilege. Historical sources, however, suggest that medieval dance was a complex and ambivalent phenomenon. During the High and Late Middle Ages, western theologians, liturgists, and mystics not only tolerated dance; they transformed it into a dynamic component of religious thought and practice. This dissertation investigates how dance became a legitimate form of devotion in Christian culture (c. 1200-1450). Sacred dance functioned to gloss scripture, frame spiritual experience, and imagine the afterlife. Invoking numerous manuscript, primary, and visual sources (biblical commentaries, sermons, saints' lives, ecclesiastical statutes, mystical treatises, vernacular literature, and iconography), this project highlights how medieval dance helped shape religious identity, social stratification, and human intention. Moreover, this study shows the political dimension of dance, which worked in the service of Christendom, conversion, and social cohesion. In sum, this dissertation reveals a long tradition of sacred dance in Christianity, one that the professionalization and secularization of Renaissance dance obscured, and one that the Reformation silenced and suppressed.

Keywords: Religious Studies.
Advisor: Gelber Hester Goodenough
Bashir Shahzad
Griffiths Fiona J. advisor. Thesis advisor
RNA-dependent regulation of SUV39H1 and constitutive heterochromatin in human cells [electronic resource]

Genome regulation in eukaryotes is largely achieved through the specialization and modification of nucleosomes, the fundamental subunits of chromatin. Gene-poor, repetitive regions of the genome concentrated near centromeres must be transcriptionally silenced by constitutive heterochromatin to maintain genome stability. Constitutive heterochromatin is characterized by H3K9 methylation catalyzed by the SUV39 family of methyltransferase enzymes, and is bound by HP1 proteins to mediate chromatin compaction and transcriptional repression. Although SUV39 proteins have been studied for many years as a model for epigenetic chromatin regulation, the biochemical interactions that govern their association with chromatin and regulate their specificity and stability are not well understood. In this work, we uncover a role for chromatin-associated RNA in localizing SUV39H1 to constitutive heterochromatin in human cells. We find that although transcription is mostly silenced during mitosis, RNA molecules associate with pericentric heterochromatin on mitotic chromosomes, and are transcribed directly from pericentric DNA sequences. The SUV39H1 protein shows the capacity to bind nonspecifically to RNA directly in vitro, associates with pericentric repeat sequencing in cells, and relies on direct binding to RNA for its localization in mitosis as well as interphase. We propose a model in which nonspecific RNA interactions stabilize the interaction between SUV39H1 and chromatin, and together with other interactions such as H3K9me3 binding, regulate and define SUV39H1's sites of action throughout the genome. We strive to further understand the role that SUV39H1-RNA interactions have in heterochromatin function, and to use this system as a model for how noncoding RNAs mediate diverse chromatin-protein connections.

Keywords: Biochemistry.
Advisor: Straight Aaron
Artandi Steven E. advisor. Thesis advisor
Das Rhiju
Theriot Julie advisor. Thesis advisor
RNA-mediated genome instability [electronic resource] : elucidating novel contributions to R-loop-dependent DNA damage

R-loops are co-transcriptional structures that form when the nascent RNA hybridizes to the complementary DNA. While R-loops serve a variety of physiological functions in regulating key cellular processes, R-loop formation has also been shown to cause DNA damage and genome instability. Specifically, loss of RNA processing and R-loop modulating factors has been shown to cause an increase in DNA damage and hyper-recombination that are R-loop dependent. The processes that contribute to R-loop formation and the mechanisms that contribute to R-loop induced DNA damage are not fully understood. In this thesis, we first examine a novel mechanism by which R-loops are processed into DNA damage. We then interrogate how changes in transcription alter R-loop levels and explore the consequences of changes in R-loop levels on DNA damage formation. In Chapter 2, we demonstrate in human cells that R-loops induced by loss of RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are processed into DSBs by the nucleotide excision repair (NER) endonucleases XPF and XPG. We find that the processing of R-loops into DSBs requires the transcription-coupled NER (TC-NER) factor CSB but occurs independently of global genome repair. These findings suggest that TC-NER factors play a role in generating R-loop-induced DNA damage and genome instability. The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability and elevated E2 levels are tied to breast cancer. In Chapter 3, we show that E2 stimulation causes a rapid and global increase in the formation of R-loops. We show that E2-dependent R-loop formation is highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many of the DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility. Taken together, these findings offer insight into the role of elevated transcription and RNA processing factors in R-loop formation and demonstrate a novel mechanism by which R-loops are processed into DNA damage.

Keywords: Biology.
Advisor: Cimprich Karlene primary advisor. Thesis advisor
Gozani Or Pinchas advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Wysocka Joanna
Robot status [electronic resource] : investigating the perception of social status in a robot

Media technology enables people to have social interactions with the technology itself. Robots are a new form of media that people can communicate with as independent entities. Although robots are becoming more naturalized in social roles involving companionship, customer service and education, little is known about how people will perceive the status of these robots. This dissertation investigates how locomotion and occupational title influence the perception of status in a robot. In a series of experiments, I find that locomotion of a non-humanoid robotic footstool can communicate high and low status (Study 1) and that the occupational title of a humanoid robot lecturer does not communicate status (Study 2). This provides evidence that the motion of a robot is a powerful cue of its status, a finding relevant for the design of robots with limited expressive capabilities.

Keywords: Communication.
Advisor: Ju Wendy
Bailenson Jeremy advisor. Thesis advisor
Reeves Byron
Turner Fred advisor. Thesis advisor
Robust image processing for cryo-electron tomography using sparse priors [electronic resource]

Cryo-electron tomography(CET) is the only imaging modality that can image 3D density maps of cells and viruses at their native state. It covers the resolution range of 4 - 8nm, and can reach resolutions as low as 2nm and under by using subtomogram averaging. As such, it bridges the gap between high resolution techniques such as the X-ray crystallography, and low resolution ones such as the light microscopy. Thanks to this unique property, CET has been extensively used to reveal the molecular organization of cellular structures in bacterial cells and viruses. Although CET can provide a higher resolution reconstruction of macromolecules than other imaging modalities can, there are several challenges to overcome to achieve high-quality 3D reconstructions of these structures. First, raw CET projections and tomograms have very low SNR typically less than 1. Second, due to the limitations of the arrangement of the sample holder and the transmission electron microscope, it is not possible to obtain informative tomographic projections from all angles, which distorts the 3D reconstructions. Due to these difficulties, conventional image processing techniques often fail to achieve their goals. To make the image processing pipeline for CET more robust, utilizing the prior information known about tomographic projections and reconstructions of interest is crucial. In this thesis, two such examples are presented. One is an image in-painting algorithm using l1 norm minimization to remove interferences in CET. This particular example exploits the fact that CET projections are sparse in the discrete cosine domain (DCT). The other example is subtomogram averaging via nuclear norm minimization where we exploited the observation that aligned structures span a very low dimensional space. Both examples deliver promising results even when original density maps are heavily distorted and covered with significant noise.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark
Candès Emmanuel J. (Emmanuel Jean) advisor. Thesis advisor
Moussavi Farshid
Role objectification [electronic resource] : perceiving targets as (only) their roles

How do social roles influence attention to and expectations of role occupants? Across nine studies, I demonstrate that occupying professional social roles (e.g., police officer, doctor) reduces attention to individuating information and restricts the traits that are expected and allowed of the role occupants. In a visual recognition paradigm, I show that attending to the social roles that individuals occupy leads to reduced attention to individuating qualities of the occupants within the roles (Chapter 1, Study 1-4). Deindividuation can be instantiated by subtle orientations toward an individual's functional utility in a given context (Study 3). Even a manipulation intended to focus participants on interpersonal qualities appeared to result in role objectification (Study 3). I find that may be due to an attentional prioritization of role information over individuating information about the target (Study 4). Roles also narrow the breadth of traits and qualities that are expected and allowed of occupants. They are expected to possess only role-prescribed traits; perceivers are surprised when they possess even role-peripheral traits (Chapter 2, Study 5). When occupants do possess peripheral traits, they are expected to perform their roles less well (Study 6). However, I do not find that individuals are expected to perform a central role worse when they also occupy additional roles in their free time (Study 7). Despite trait restrictions due to roles, I do not find that people expect individuals to possess fewer total personality traits (i.e., the combination of central and peripheral traits) when an individual occupies a role versus does not (Study 8-9). In total, these findings help to explain how social roles can lead to objectifying perceptions of occupants.

Keywords: Business.
Advisor: Lowery Brian
Miller Dale T. advisor. Thesis advisor
Monin Benoît
Role of AF10 in chromatin regulation and cancer [electronic resource]

Histone lysine methylation plays a critical role in gene transcription regulation, cell cycle control, and DNA damage repair. One of the major diseases that histone lysine methylation plays an important role is chromosomal rearrangement mixed lineage leukemia (MLL). In MLL, the H3K4 methyltransferase MLL1 is frequently fused with other protein partners, including AF4, AF9, AF10 and ENL. Studies have found that most of these fusion partners are in complexes with H3K79 methyltransferase Dot1L. Among these proteins, AF10 was identified as a DOT1L cofactor. AF10 is required for H3K79 methylation and cooperates with DOT1L in leukemogenesis. However, the molecular mechanism by which AF10 regulates DOT1L-mediated H3K79 methylation in MLL is not clear. In the first part of this dissertation, I investigate the biochemical, molecular, and cellular roles of AF10 in Dot1L-addicted leukemia. I identified the PHD finger-Zn knuckle-PHD finger (PZP) domain of AF10 as a novel 'reader' that couples unmodified H3K27 recognition to regulate H3K79 methylation. In Chapter 1, I briefly introduce the essence background of histone lysine methylation and its role in biology and human diseases. In Chapter 2, I report the discovery of PZP as a novel histone methylation reader domain. In Chapter 3, I present the solution of AF10PZP crystal structure in H3 binding. In Chapter 4, with reconstitute systems, I establish the role of PZP recognition of H3 in Dot1L function and leukemogenesis in cells. Summarizing in Chapter 5, this work uncover a pivotal role for H3K27 - via readout by the AF10 PZP domain - in regulating the cancer-associated enzyme DOT1L. At the end, I explored the role of non-histone lysine methylation in Chapter 6. I investigate the BAH domains of DNA methyltransferase DNMT1 as a potential lysine methylation reader. I found that KAP1 is heavily methylated in cells, and the first BAH domain of DNMT1 (BAH1) can specifically recognizes both histone H4K20me2 and non-histone protein KAP1 methylation.

Keywords: Biology.
Advisor: Gozani Or Pinchas primary advisor. Thesis advisor
Chua Katrin Faye advisor. Thesis advisor
Morrison Ashby J.
The role of human-animal relations in the social and material organization of Çatalhöyük, Turkey [electronic resource]

How do interfaces between humans and non-humans mediate and transform social phenomena? This dissertation explores how interactions between humans and animals were entwined with and embedded within the very threads of the origins of agriculture. Enframing animal art and faunal remains associated with houses, at the Neolithic settlement of Çatalhöyük (7100-6000 BC) in Anatolia, this dissertation examines the entanglement of social practice and the materialization of hunted wild mammals. These wild animals permeate the subject matter of various media including figurines, plastered faunal installations, moulded reliefs, and wall paintings. Combining data mining, geographic information systems (GIS), and statistical tests, this dissertation synthesizes both quantitative and qualitative datasets from specialist labs, museum collections, archives, and over twenty years of excavation in order to understand the ontological geographies within which animals were placed.

Keywords: Anthropology.
Advisor: Hodder Ian primary advisor. Thesis advisor
Marciniack Arek advisor. Thesis advisor
Meskell Lynn advisor. Thesis advisor
Role of natural killer cells and the natural killer cell receptor NKG2D in the recognition and killing of stem cell derived hepatocyte-like cells [electronic resource]

Recent advances in methods to efficiently and reproducible differentiate stem cells into hepatocyte like cells (HLC) has opened up potential opportunities in the field of transplantation. In order for this technology to be successfully used clinically, an understanding of their immunogenicity must be carefully defined. Conflicting results suggest that the stem cell source, the stem cell type, and the differentiated cell type may alter their immunogenicity. Thus, the goal of this study is to determine the expression of immune recognition proteins on HLC derived from ESC (ES-HLC), HLC derived from iPSC, (iP-HLC) compared to Ad-Hep and second, to determine if there is a difference in the immunogenicity of ES-HLC, iP-HLC, and Ad-Hep. Here, we report that HLC lack MHC class I expression, and that ES-HLC have higher expression of the activating ligands Rae1, H60, and Mult1 than iP-HLC and Ad-Hep. Moreover, we report that the lack of MHC class I make ES-HLC and iP-HLC susceptible to killing by syngeneic and allogeneic NK cells, and that syngeneic NK cells efficiently ES-HLC and iP-HLC at higher levels than Ad-Heps. We also demonstrate that NKG2D receptor mediates NK cell killing of HLC, suggesting that the presence of both the NKG2D ligands on HLC, as well as the NKG2D receptor on the NK cells, play an important role in the killing of ES-HLC, but not iP-HLC.

Advisor: Martinez Olivia
Glenn Jeffrey S.
Krams Sheri Michele advisor. Thesis advisor
Maltzman Jonathan advisor. Thesis advisor
The role of neuronal activity in glioma growth and progression [electronic resource]

High-grade glioma (HGG) is the leading cause of brain tumor death in both children and adults. Active neurons exert a mitogenic effect on normal neural precursor and oligodendroglial precursor cells, the putative cellular origins of HGG. Using optogenetic control of cortical neuronal activity in a patient-derived pediatric glioblastoma xenograft model, we demonstrate that active neurons similarly promote HGG proliferation and growth in vivo. Conditioned medium from optogenetically stimulated cortical slices promoted proliferation of pediatric and adult patient-derived HGG cultures, indicating secretion of activity-regulated mitogen(s). The synaptic protein neuroligin-3 (NLGN3) was identified as the leading candidate mitogen, and soluble NLGN3 was sufficient and necessary to promote robust HGG cell proliferation. NLGN3 induced PI3K-mTOR pathway activity and feed-forward expression of NLGN3 in glioma cells. NLGN3 expression levels in human HGG negatively correlated with patient overall survival. These findings indicate the important role of active neurons in the brain tumor microenvironment and identify secreted NLGN3 as an unexpected mechanism promoting neuronal activity-regulated cancer growth. We next sought to determine if neuronal activity similarly promotes invasion and migration of pediatric HGG (pHGG), and to elucidate the mechanisms that mediate this effect. Diffuse infiltration is a characteristic hallmark of pHGG, but the molecular and cellular determinants of this behavior are incompletely understood. Using in vitro invasion assays, we demonstrate that exposure to activity-regulated secreted factors in conditioned medium from optogenetically stimulated and spontaneously active cortical slices increases the degree of pHGG cell infiltration through Matrigel, but that silencing neuronal activity with tetrodotoxin abrogates the pro-infiltrative effect. This effect was observed only when pHGG cells were seeded together with conditioned medium; pHGG cells do not preferentially migrate towards conditioned medium versus plain medium, suggesting that factors secreted into conditioned medium in an activity-dependent manner influence migration/invasion by inducing a pro-infiltrative phenotype rather than acting as chemoattractants. Taken together, these data indicate that active neurons play an important role in pHGG progression as well as growth. Candidate pro-infiltrative factors identified by proteomic analyses of conditioned media, including lead candidates 78-kDa glucose-regulated protein (GRP78) and cartilage acidic protein 1 (CRTAC1, or LOTUS), are presently undergoing necessity testing, and if confirmed in vivo, may represent new approaches to targeting the diffuse spread of these devastating tumors.

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Monje-Deisseroth Michelle
Oro Anthony
Palmer Theo advisor. Thesis advisor
The role of physical activity in facilitating affect regulation [electronic resource]

Despite the known benefits of physical activity, many Americans remain physically inactive, leading to an increased risk for all-cause mortality, heart disease, and a number of other physical health consequences. While research has primarily focused on the physical health consequences associated with participating in physical activity, there are important psychological consequences as well. Research has demonstrated that physical activity can lead to beneficial changes in affect, successfully reduce symptoms of various clinical disorders, and buffer against stress. Evidence also suggests that physical activity may reduce the use of rumination, implying that physical activity may influence the ability to effectively regulate affective states in daily life. To further explore this relationship, I examined associations between physical activity and affect regulation in a series of three studies. In Study 1, I used structural equation modeling to clarify the relationships among activity levels, experienced affect, and affect regulation. Findings suggested that physical activity is both directly and indirectly related to affect regulation. Subsequent mediation analyses indicated that physical activity may directly influence affect regulation and lead to subsequent changes in experienced affect. In Study 2, I employed an intervention that increased physical activity and decreased sedentary behavior. Subsequently, I examined changes in affect and affect regulation over time. Physical activity was associated with positive affect, but not negative affect. Measures related to affect regulation increased immediately after the intervention and remained higher up to 6 months following the intervention. Sedentary behavior predicted positive affect immediately after the intervention but did not predict negative affect or affect regulation. In Study 3, I examined whether physical fitness, which serves as a marker for repeated engagement in physical activity, facilitated affect regulation in younger and older adults. Specifically, I assessed whether physical fitness was associated with better working memory performance following a negative mood induction. Results indicated that physical fitness facilitates working memory performance during a negative mood induction in both younger and older adults. Together, these findings provide initial evidence that physical activity may be associated with effectively regulating affective states.

Keywords: Psychology.
Advisor: Gross James
Carstensen Laura L. advisor. Thesis advisor
Zaki Jamil
Sampling-based motion planning for safe and efficient spacecraft proximity operations [electronic resource]

Autonomy has demonstrated success in many vehicle control problems, but has yet to show significant breakthroughs for spacecraft guidance during proximity operations. In part due to a costly verification and validation process as well as from limited access to formally-safe guidance algorithms, mission planners have instead had to rely on maneuver plans with straightforward, easily-verified trajectories and extensive human oversight. Unfortunately, this strategy often introduces propellant inefficiencies, adds significant labor overhead, and limits missions to Earth proximity where two-way communication times are short. This dissertation seeks to remedy these issues by developing a provably-safe and propellant-efficient sampling-based motion planning framework for fully-autonomous spacecraft proximity operations. The framework is designed for a wide range of hazardous guidance scenarios, including autonomous orbital rendezvous and inspection, pinpoint small-body descent, and on-orbit satellite servicing. Due to the dangers associated with operating near other objects, special care is taken to enable real-time guidance as well as ensure the availability of safe abort trajectories so that spacecraft can respond quickly and safely to control failures and sudden environmental changes. Through its generality, efficiency, and speed, the proposed approach offers the potential to enable entirely new capabilities for next-generation space missions, while also increasing the frequency, flexibility, and reliability of present-day operations in space.

Keywords: Aeronautics and Astronautics.
Advisor: Pavone Marco
Close Sigrid
Rock Stephen