VictorJuiz/thesis huggingface dataset:
Reservoir modeling with multiple geological scenarios for deformation of reservoir structure and evolution of reservoir properties [electronic resource]
Keywords: Energy Resources Engineering.

Deformational uncertainty about subsurface structures and accommodational uncertainty about rocks are not only closely linked to each other, but also significantly impact reservoir responses. The main objective of this dissertation is to investigate the effects of these two geological uncertainties on reservoir responses. To achieve this goal, we aim to develop and test a reservoir modeling and evaluation workflow that accounts for the mode of deformation of a reservoir and the mode of accommodation of reservoir properties for a given deformation, by utilizing structural attributes and rock physics models. First, we investigate the sources of geological uncertainty in structural deformation and rock accommodation. We employ different combinations of structural geometry and deformation models to represent multiple scenarios for structural deformation. Distributed and localized accommodation styles and their subsets can represent scenarios for rock accommodation. Second, we develop a new geomodeling workflow accounting for the mode of structural deformation and rock accommodation. The new workflow links the forward deformation and restoration of the reservoir structure to the same processes on the rock. An application on a synthetic field demonstrates that realizations and dynamic responses from different scenarios can be distinguished from one another by comparing seismic responses. Next, we propose a new rock physics method, Reconstruction of Equivalent Isotropic Medium (REIM), which allows us to compute the angular variation of seismic responses of arbitrarily oriented fracture inclusions in an anisotropic medium, and to apply our new workflow to unconventional shale resources. Specifically, we apply these tools to an unconventional Marcellus gas field in which structural complexity and sparse data cause substantial difficulties in evaluation. We identify the sources of geological uncertainties and define multiple scenarios based on basin-wide and field-specific observations. By using rock physics models as vehicles to link geological scenarios with reservoir properties, we propagate geological assumptions to reservoir responses. We then select combinations of structural deformation and rock accommodation scenarios by comparing the actual and synthetic seismic responses. The selected scenario and models successfully explain the field-specific anomalies.
Results on the broadcast channels [electronic resource]
Keywords: Electrical Engineering.

The broadcast channel, first studied by Tom Cover, is a model for one-to-many communications, such as the downlink of a cellular system. The capacity region of this channel, defined as the closure of the set of all achievable rate tuples, characterizes the optimal tradeoff among simultaneously achievable data rates. Inner and outer bounds on the capacity region have been obtained, but they coincide only under certain conditions, and the capacity region in general remains unknown. This dissertation establishes new capacity results for broadcast channels with and without feedback. First, we simplify the superposition coding inner bound and establish new optimality results for the superposition coding inner bound for a 2-receiver discrete memoryless broadcast channel. Second, we show that the capacity region of the continuous-time Poisson broadcast channel is achieved via superposition coding for most channel parameter values. Interestingly, the channel in some subset of these parameter values does not belong to any of the existing classes of broadcast channels for which superposition coding is optimal. For the rest of the channel parameter values, we show that there is a gap between the best known inner and outer bounds, namely, Marton's inner bound and the Nair--El Gamal outer bound. Third, we establish the capacity region of several classes of broadcast channels with random state, in which the channel to each user is selected from two possible channel state components and the state is known only at the receivers. Some classes of broadcast channels for which we establish the capacity region do not belong to any class of broadcast channels for which the capacity region was previously known. Last, we show that the Maddah-Ali--Tse scheme, which establishes the symmetric capacity of two example broadcast channels with strictly causal state information at the transmitter, is a simple special case of the Shayevitz--Wigger scheme for the broadcast channel with generalized feedback. We then introduce a new broadcast channel example that shares many features with the Maddah-Ali--Tse examples, for which we show that another special case of Shayevitz-Wigger scheme attains a higher symmetric rate than the MAT scheme. The symmetric capacity of this example is not known, however. The combined results of this work shed light on our understanding of broadcast channels, and the tools and intuition developed during the research could also be applied to other network information theory problems.
Revealing electron-phonon coupling in quantum materials using equilibrium and nonequilibrium photoemission spectroscopy [electronic resource]
Keywords: Applied Physics.

The electronic behavior of solids is largely determined by the interaction between electrons and other emergent particles. The quantized excitation of lattice vibrations, also known as phonons, is a fundamental emergent particle in solids. The success of Bardeen-Cooper-Schrieffer (BCS) theory in conventional superconductors highlights the importance of understanding electron-phonon coupling for advanced materials, in particular superconductors. On the other hand, the role of electron-phonon coupling in unconventional superconductors is under intensive debates. This thesis aims at understanding electron-phonon coupling quantitatively using equilibrium and non-equilibrium photoemission spectroscopies. In particular, it focuses on novel experimental ideas which provide access to fundamental quantities. By case studies on three representative materials, I provide compelling evidence for the predictive power of the BCS theory on graphitic materials, and for the impact of correlation effects on electron-phonon coupling in unconventional superconductors.
Richards on Imagination: Reanimating a Psychological Poetics
Keywords:  Department of English
I.A. Richards
Coleridge
poetics
literary criticism
philosophy
Department of English
Thesis

I.A. Richards was one of the most formative, if inconsistently understood, literary critics of the 20th century. This thesis seeks to clarify a key move in Richards' work: his ability to reapply and thus arguably "reanimate" the thought of major historical intellectual figures. In his (1934) book Coleridge on Imagination, Richards applies the 19th-century idealist philosophy of the Romantic poet Samuel Taylor Coleridge to the analysis of 20th-century poetry and in the same move brings Coleridge into dialogue with 20th-century psychology. Arguing that "reanimation" was one of Richards' modus operandi, the thesis abstracts the method from his book on Coleridge and turns it on him to capture the reinvigorating potential of his criticism.
Ringleaders of redemption [electronic resource] : the religious authorization of western medieval dance
Keywords: Religious Studies.

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.
RNA-dependent regulation of SUV39H1 and constitutive heterochromatin in human cells [electronic resource]
Keywords: Biochemistry.

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.
RNA-mediated genome instability [electronic resource] : elucidating novel contributions to R-loop-dependent DNA damage
Keywords: Biology.

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.
Robot status [electronic resource] : investigating the perception of social status in a robot
Keywords: Communication.

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.
Robust image processing for cryo-electron tomography using sparse priors [electronic resource]
Keywords: Electrical Engineering.

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.
Role objectification [electronic resource] : perceiving targets as (only) their roles
Keywords: Business.

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.
Role of AF10 in chromatin regulation and cancer [electronic resource]
Keywords: Biology.

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.
The role of human-animal relations in the social and material organization of Çatalhöyük, Turkey [electronic resource]
Keywords: Anthropology.

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.