VictorJuiz/thesis huggingface dataset:
The validation and optimization of CT perfusion for stroke assessment

Each year, approximately 800,000 people in the United States have a stroke. Early diagnosis and tailored treatment are critical for optimal patient outcomes. Physicians utilize cerebral perfusion maps (e.g., cerebral blood flow, cerebral blood volume, transit time) derived from dynamic magnetic resonance (MR) or computed tomography (CT) scans of the brain to prescribe the optimal plan of care for stroke patients. However, noise and variability in scanning techniques and post-processing software can impact perfusion maps. To determine which techniques are acceptable for clinical care, it is important to validate the accuracy and reproducibility of the perfusion maps. Validation using clinical data is challenging due to the lack of substantial clinical data sets in which the pathology is well known. Furthermore, it is impractical to scan patients multiple times with different scanning techniques to optimize protocols. In contrast, simulated data from a realistic digital phantom of the cerebral perfusion in acute stroke patients would enable studies to validate and optimize the scanning and post-processing techniques. This work presents a complete framework to simulate and evaluate CT perfusion studies for stroke assessment. To generate realistic CT perfusion test data, the framework includes (1) a digital brain phantom composed of NURBS surfaces whose material properties can be dynamically set to model spatially varying dynamics; (2) a model of contrast agent enhancement in the brain starting from first principles by using the phantom geometry and tissue perfusion parameters; (3) an efficient dynamic CT simulator that reduces simulation times by 95% compared to traditional simulation methods; and (4) an accurate method to insert noise in the image domain with computation time on the order of seconds, rather than minutes, to generate unique noise realizations. We use this simulated data to generate perfusion maps with four perfusion post-processing software packages. We first perform a visual comparison against the known underlying ground truth and propose a method to quantitatively assess the accuracy of computer-generated perfusion maps. We segment the brain tissue and plot the computer-generated perfusion map pixel values versus the ground truth pixel values, perform a linear fit, and calculate the r-squared value. Through this analysis, we observe differences in r-squared values achieved for each package and each perfusion map, with dependence on dose and smoothing. This comprehensive framework and quantitative assessment, therefore, enables a robust assessment of CT perfusion techniques and post-processing methods for stroke imaging. Ultimately, this has the potential to improve diagnostic tools for stroke patients and increase physicians' ability to prescribe a plan of care driven by quantitative data

Keywords: Electrical Engineering.
Advisor: Pelc Norbert J.
Lansberg Maarten
Nishimura Dwight George
Validation of novel markers of cell subtypes in the neonatal mouse utricle

The utricle is a component of the vestibular system that stimulates hair cells that function to detect motion and orientation and transduce sound. The murine utricle undergoes dynamic cellular maturation after birth. Previous histological studies have demonstrated an increase in the number of hair cells from postnatal day 0 to 8 and show that hair cell subtypes mature at least during the first month. Thymidine analog studies have demonstrated a decrease in proliferative cells in the utricular sensory epithelium and the presence of proliferative cells located in the organ's peripheral regions. However, the mechanism of cell addition and maturation of different hair cell subtypes is poorly characterized. We asked whether the postnatal utricle contains transcriptionally unique cell subtypes and how they may relate to one another. To probe the postnatal mouse utricular sensory epithelium in an unbiased manner, we performed single cell RNA sequencing at post-natal days 2, 4, and 6 (P2, P4, P6) using the Smartseq2 protocol, which allows for comprehensive “deep” sequence assessment of expressed transcripts. We profiled approximately 1000 cells with a median read count of 515,842 per cell and median gene count of 3,485 detected genes per cell. Clustering analysis revealed four hair cell states, two supporting cell states (striolar and extrastriolar), and two transitional cell states. We validated marker genes for the various identified cell states with immunofluorescence and in situ hybridization. Multiplex fluorescent in situ hybridization identified over a dozen novel markers. In summary, we have generated a deep sequenced single cell RNAseq profile of the developing murine utricular sensory epithelium with validation of novel markers and delineation of the previously poorly characterized transitional epithelium.

Keywords:  Department of Biology
Biology
Hair Cells
Utricle
scRNAseq
Regeneration
Validation
Thesis
Advisor: Cheng Alan
Red-Horse Kristy
Variability of saxiphilin across poison frog toxicity phenotypes

Chemical defense is a complex trait by which organisms carry toxic or repellant compounds to discourage predation. South American poison frogs (Family Dendrobatidae) are particularly famous chemically defended organisms. Previous research has shown that these frogs take up potent organic alkaloid toxins from their diet and sequester them to be released when threatened – all without intoxicating themselves. The mechanism by which poison frogs resist self-intoxication is not fully understood. One way of dealing with ingested toxins is compound sequestration via circulating toxin-binding proteins that soak up excess alkaloids and protect vulnerable tissues. One such protein, saxiphilin, is thought to play a similar role in bullfrogs. This project examines saxiphilin: a blood-bound toxin-binding protein found in multiple species of poison frogs. My thesis aims to elucidate the role of saxiphilin as a proposed mechanism of toxin resistance in poison frogs. I first assessed how saxiphilin varies genetically and structurally between poison frog species with different toxin-carrying abilities or “toxin profiles,” analyzing expression patterns across tissues, and computationally predicting the binding activity of saxiphilin between species. Saxiphilin sequence is variable within and across poison frog species, but is largely conserved at regions corresponding to toxin-binding sites on the protein. Moreover, computational models of saxiphilin predict differential binding activity between saxiphilin derived from the bullfrog Rana catesbeiana and saxiphilin derived from poison frogs. Lastly, qPCR results demonstrate that expression of saxiphilin varies between tissues, with highest expression in the liver, brain, and eyes. These results support previous hypotheses that saxiphilin could act as a protective protein, conferring toxin resistance by binding to and neutralizing toxins in the frogs’ bodies. Overall, this research expands our understanding of poison frog toxicity, and addresses a long-standing question about poison frog physiology and biochemistry.

Keywords:  Department of Biology
Biology
poison frog
chemical defense
toxin
toxin resistance
saxiphilin
alkaloid
Thesis
Advisor: O’Connell Lauren
Heller Craig
Variation in Health Care Prices Across Public and Private Payers

I study a unique all-payer data set spanning 38 U.S. states to examine the differences in inpatient reimbursement rates paid by traditional Medicare (TM), Medicare Advantage (MA), Medicaid, and private (under 65) insurers, and the differences in negotiated rates across the 60 largest private insurers. After controlling for enrollee and hospital mix, I find that private insurers pay 37 percent more than TM, and MA pays 10 percent more than TM for the five most common inpatient diagnoses. National MA insurers reimburse hospitals at rates similar to TM, but smaller, regional MA insurers pay more than TM. The correlation in mean risk-adjusted payments by private insurers and by TM at the same hospital for the same diagnosis is only 0.10. There is also significant variation in negotiated prices within and across private payers. For the five largest U.S. insurers, the least expensive insurer negotiates prices that are 6-27 percent lower on average than the mean price and the most expensive insurer negotiates prices that are 5-26 percent higher than the mean price for the 20 most common inpatient diagnoses. Additionally, I find that a 10 percent increase in insurer market share corresponds to a 7 percent decrease in inpatient negotiated prices. Furthermore, a 10 percent increase in insurer market share is associated with a 10 percent decrease in the standard deviation of inpatient prices paid by the insurer at a given hospital for a specific diagnosis. This finding suggests that increased insurer market power allows payers to negotiate prospective payment contracts--rather than the more common fee-for-service payments--thereby offloading financial risk to providers.

Keywords:  Department of Economics
Health Insurance
Hospital Payment
Competition
Medicare
Medicare Advantage
Private Health Insurance
Department of Economics
Thesis
Advisor: Bhattacharya Jay
Variation in Insect Herbivory, Palatability, and Plant Defensive Traits across sympatric California Oak species

Plants and their insect herbivores comprise over half of all described nonmicrobial species and interact in ways that influence key community- and ecosystem-level processes. A prevalent pattern in nature is that herbivory –the consumption plant tissue or fluids by herbivores, particularly insects– varies across species. Researchers have developed hypotheses to explain and predict what determines such variation. The Apparency Hypothesis suggests that plant species that are more “apparent” (long-lived, large, evergreen) to herbivores have evolved stronger anti-herbivore defenses than not-so-apparent plants (short-lived, small, deciduous), but empirical tests of this hypothesis have yielded inconsistent results. Furthermore, research on this topic has focused largely on species belonging to different lineages, so information is limited regarding the variation across species within the same lineage. Sympatric oaks provide an opportunity to examine this knowledge lacuna. Oaks influence forest structure, biodiversity, and community composition in California ecosystems. A suite of anthropogenic stressors including habitat loss, invasive species, and climate change threaten California oaks. Understanding the patterns of herbivory in four sympatric California oak species can help inform the differences in susceptibility to insect attack and plant characteristics potentially related to their apparency: local relative abundance and phenology (evergreen/deciduous) underlying such differences. My work reveals that the most apparent (the most abundant and evergreen) Q. agrifolia had a lower proportion of herbivory damage by type (i.e., the type of herbivore responsible for such damage) than the less abundant and deciduous oaks (Q. douglasii, Q. lobata and Q. kelloggii). Herbivory rates and palatability assays using a generalist herbivore exhibited little interspecific variation. The more apparent Q. agrifolia had a higher carbon nitrogen ratio, lower water content, and tougher leaves than the three less apparent deciduous oak species, suggesting that Q. agrifolia has stronger anti-herbivore defenses than the other species. Pubescence, a trait potentially associated with ant-herbivore defense, did not consistently vary in relation to species apparency, suggesting pubescence may relate to environmental factors such as drought tolerance. These results partially support the apparency hypothesis and suggest that the most abundant oak, Q. agrifolia, is better defended against herbivory challenges, while Q. kelloggii, the rarest species, is most vulnerable to herbivores and thus a conservation priority.

Keywords:  Department of Biology
Biology
Ecology and Evolution
Herbivory
Oaks
California ecosystems
Apparency Hypothesis
Thesis
Advisor: Dirzo Rodolfo
Gordon Deborah M.
The varieties of minimalist experience : the roles of psychological states in the reception of American minimalism during the long Sixties

This dissertation examines the reception of compositions by Pauline Oliveros, Philip Glass, Steve Reich, Terry Riley, and La Monte Young in the long Sixties, uncovering how concepts of American whiteness and American Cold War Orientalism intersected with low-level psychological states to shape listeners' aesthetic experiences and judgements. By incorporating methods and literature from music studies and experimental psychology, this dissertation analyses interconnected cultural, musical, and psychological forces that contributed to the reception of the music and simultaneously offers a mutually-beneficial research paradigm between these disciplines

Keywords: Music.
Advisor: Fujioka Takako
Hadlock Heather
Kronengold Charles (Charles Stewart) 
Schultz Anna C.
Virtual exchange : collaboration and problem-solving across continents and cultures

Opinion polls in multiple countries recount a grim story, that people from Western and Muslim-majority countries regard one another as arrogant, intolerant, and violent, and that attitudes are not improving. Student exchange programs, which were widely expanded after World War II and during the Cold War, have become a vital component of public diplomacy in countries across the globe. Designed around the principles of Contact Theory, exchange programs have demonstrated reduction in stereotypes, improvement in attitudes, building of relationships, and development of professional capacity among students from distant backgrounds. However, traditional in-person exchange is an expensive and demanding form of educational experience, one more often available to students from high-income countries, and one that requires even these students to have sufficient means and flexibility to live far from home for extended periods of time. For this reason, in-person exchange programs have proven difficult to scale. Moreover, students with fewer resources and non-dominant forms of social capital, including many from underserved racial and ethnic communities, are much less likely to participate. Along with lost opportunity for these individuals, in-person exchange exposes peers in host countries to a skewed sample of travelers. This Design-Based Research (DBR) comprises an investigation into Virtual Exchange, informed by principles of Contact Theory and related pedagogical approaches, including Problem-Based Learning, Collaborative Learning, and Interdependent Learning. The investigation focuses on whether this new form of learning has potential to reduce pernicious stereotypes, broaden personal perspectives, foster productive relationships, and build professional capacity among students from geographically, economically, and culturally distant backgrounds. Results of extended trials, conducted with faculty partners around the world, suggest that it does, for a small fraction of the cost of in-person exchange, with real potential to increase access

Keywords: Education.
Advisor: Goldman Shelley V. 
McDermott Ray (Raymond Patrick)
Thille Candace
Vision modeling tools for evaluating next-generation displays

Nearly all metrics for evaluating display image quality operate on the RGB representations used to control conventional flat displays. One computes image quality by comparing an idealized version of the RGB image (reference) and a version rendered by the display under design (test). This framework has been important historically, and it remains suitable for developing metrics that evaluate several aspects of conventional flat display image quality, such as spatial resolution, intensity quantization, and color gamut. There are several limitations of the RGB methods, however. First, standard RGB image quality metrics do not include display characterization, which limits their ability to generalize across ambient viewing conditions, display size, viewing distance, or biological differences between viewers. Second, the RGB representation does not extend to advanced displays where the image is delivered using more complex technology, such as light field, augmented reality, or multi-planar displays. To evaluate the quality of these 3D display technologies, it is necessary to develop a new framework that accommodates the diversity of emerging display technologies. In this dissertation, I adopt a universal representation at the initial stages of the visual pathways by representing display images as retinal photoreceptor (cone) excitations. This is a display-independent representation: all display technologies initiate vision with the retinal images incident on the two eyes. The ISETBio and ISET3d software provides a platform for developing next generation image quality metrics for displays based on cone excitations. The software includes tools for computing not only the retinal image, but also the cone excitations to display images and 3D scenes. In this dissertation, I describe the development of these two toolboxes to model and evaluate next-generation displays that cannot be fully represented by RGB data. First, the existing vision modeling tools were first expanded from 2D image-formation (planar, 2D stimuli) to 3D image-formation (3D virtual models) through the creation and development of ISET3d. Next, the modeled cone excitations from ISETBio/3d were used as input to existing image quality metrics, improving generalization and extending the calculations to novel displays. Lastly, the expanded vision modeling tools were used to model a next-generation, multi-focal display

Keywords: Electrical Engineering.
Advisor: Wandell Brian A. 
Girod Bernd
Wetzstein Gordon
Visions of democracy in the information society : the theories of Daniel Bell, Manuel Castells, and Yochai Benkler

In this dissertation, I unearth the common threads and subtle evolution of democratic ideals in mainstream theories of the information society that span over thirty years. I apply the lens of democratic theory, with a primary focus on liberal and republican traditions, to perform a close reading of seminal works such as Daniel Bell's (1973) Post-Industrial Society, Manuel Castells' (1996; 1997; 1998) Information Age trilogy, and Yochai Benkler's (2006) Wealth of Networks. Through a comparative analysis, I expose the democratic canvas upon which these scholars paint their images of a rising social organization that is structured around flows of information and knowledge. Two democratic axioms stand at the center of an emergent model of information democracy. The first axiom prescribes the ideal democratic subject with the affective trait of social awareness; this model of democracy, I argue, presumes that its citizens are always ready and willing to understand, to share, and to empathize with others in their community. The second axiom refers to the idea that technologically facilitated communication can help deliver, grow, and sustain the individual citizens' capacity for social awareness. Flows of information operate as the democratic citizens' eyes and ears into the lives of others, facilitating mutual understanding. Thus, democracy in the information society realizes the common good through the affective orientation of each and every individual towards the social other, and through flows of information and knowledge that support such an orientation. The presence of these two axioms allows these scholars, in turn, to weld two ideals usually considered antithetical to each other -- the liberal ideal of individual freedom and the republican ideal of the common good

Keywords: Communication.
Advisor: Turner Fred 
Christin Angèle 
Denson Shane 
Hamilton James
Visual agency in Euclid's elements : a study of the transmission of visual knowledge

Through investigation of diagrams in Euclid's Elements, this dissertation aims to study how visual knowledge has been transmitted. In the study of the history of the Elements, there has been an assumption that the text and diagrams in the work were both conveyed together. Upon this conventional assumption, the diagrams were regarded as static or subordinate to the text. This dissertation questions the supposed diagrams' dependence on the text, and argues that we should study the transmission of diagrams as their own process. Visual agency will be explored as an autonomous function of diagram makers to draw according to their discretion. According to the history of the Elements, I classify diagram makers who held visual agency into four groups: scribes, translators, readers, and printing presses. These four types of visual agents interpreted and reinterpreted diagrams over time: 1) scribes corrected diagrams mathematically and systematized them visually; 2) translators filtered the variants of diagrams and invented derivatives of diagrams; 3) readers expanded and proofread mathematical ideas through diagrams; 4) printing presses standardized diagrams and enhanced pedagogical value of them. This analysis of visual agencies leads us to a more comprehensive understanding of the transmission of diagrams. While past scholarship only understood the transmission of diagrams as a perceptual process (conducted through textual instruction and archetype diagrams), this dissertation examines both the perceptual process and the conceptual process (through visual agency). This work reveals the characteristics of the transmission of diagrams as an autonomous and knowledge-conducive process. Indeed, Euclid's diagrams have been the space where the continuous birth of mathematical ideas was invited. The discussion of the visual agency in Euclid's Elements reaches beyond the transmission of mathematical diagrams. The patterns of changes found in the transmission of mathematical diagrams may be compared with those of all sorts of other diagrams such as schematic maps, astronomical diagrams, and theological diagrams. This comparison tells us whether and how mathematical diagrams were different from other diagrams in terms of transmission. In this way the project serves to explore the complex transmission of visual knowledge latent beneath the surface of textual transmission

Keywords: Classics.
Advisor: Netz Reviel 
Findlen Paula
Saitō Ken
Stephens Susan A.