VictorJuiz/thesis huggingface dataset:
Mechanobiology of aortic disease in animal models [electronic resource]

The aorta is the largest blood vessel in the body, responsible for carrying blood from the heart directly to most major organs and ending at the iliac arteries which feed the lower extremities. This elastic vessel provides much of the vascular system's compliance and is composed of a heterogeneous mixture of smooth muscle cells, collagen, and elastin. The general purpose of our work has been to use in vivo imaging to determine abdominal aortic dynamics in a variety of healthy and diseased cases. First, a cross-species analysis in mice, rats, rabbits, pigs and humans showed with M-mode ultrasound that infrarenal abdominal aortic motion was similar in animals and humans, regardless of aortic size. Greater anterior than posterior wall motion was observed and aortic wall displacement increased linearly with diameter. Next, cardiovascular abnormalities in a recently developed mouse model for Williams-Beuren Syndrome (WBS) were investigated. WBS is a rare genetic disorder caused by a heterozygous 1.5-megabase deletion, which typically includes the elastin gene. In this study, we showed that Wbs mice have hypertension, reduced in vivo cyclic strain, and fragmented medial elastin sheets - all characteristics similar to human WBS. These data provide insight into the genotype-phenotype relationship between elastin levels, aortic stiffness, and the cardiovascular abnormalities associated with WBS and other microdeletion syndromes. Finally, the biomechanical influences on murine models of abdominal aortic aneurysms (AAA), a pathological dilation of the abdominal aorta, were investigated using magnetic resonance imaging. From this work, we showed that the location of aneurysm development may be correlated with the location of maximum abdominal aortic curvature in angiotensin II-induced murine AAAs. This model consistently forms abdominal aneurysms with repeatable leftward vessel expansion above the renal arteries. Our work has shown that this leftward saccular shape is likely influenced by leftward suprarenal aortic curvature and motion. Histological analysis provided evidence for degradation of medial elastin at one focal location on the left side of the vessel, with a majority of animals also developing an adventitial hematoma at a similar circumferential location. Conversely, elastase-induced infrarenal murine AAAs do not form in a location of high vessel curvature and do not expand in one general direction. This work will help to further our understanding of the role mechanics may play in AAA formation, progression, and eventual rupture.

Keywords: Bioengineering.
Advisor: Taylor Charles A. (Charles Anthony)
Tsao Philip primary advisor. Thesis advisor
Dalman Ronald L. advisor. Thesis advisor
Mediated transcendence [electronic resource] : realism and revelation in Russian Fiction, 1863-1898

"Mediated Transcendence: Realism and Revelation in Russian Fiction, 1863-1898" investigates the relationship between literary form and transcendence in representative texts of the Russian Realist tradition. The author identifies scenes of literary transcendence, spanning transformative religious and psychological experiences, as epiphanies, which display a unique confluence of content and form -- at once a narrative event, in the life of the character, and a locus of literary devices. The project proceeds from the premise that the ineffable content of epiphany exceeds the verisimilar parameters of literary realism, and even the semiotic capacity of prose language. In response to this representational problem, the authors analyzed elaborate narrative and poetic strategies for the purposes of framing transcendence, augmenting discursive representation with performative presentation. Beginning with Tolstoy's model of the literary epiphany in War and Peace in the introduction, the dissertation subsequently explores the theme and forms of transcendence in Fyodor Dostoevsky's "The Idiot, " Nikolai Leskov's "The Sealed Angel, " and selected stories of Anton Chekhov. Incorporating elements of theology, phenomenology, and critical theory, these individual readings reveal the aesthetic nature of visionary experience, and the way such experience is conveyed by the appropriately aesthetic means and potential of the literary text. In challenging notions of the empirical and positivist biases of Realism, the dissertation reevaluates the historical position of the movement, indicating its formal and theoretical debt to Romanticism, as well as its subsequent influence on Modernism.

Keywords: Slavic Languages and Literatures
Advisor: Greenleaf Monika
Safran Gabriella
Gumbrecht Hans Ulrich advisor. Thesis advisor
Mental time lines across the world [electronic resource] : how do people think about time in Hebrew, Mandarin, and English?

Across cultures people rely on space to represent time. However, the particular spatial layout created to represent time differs across cultures, and is affected by different sources of culturo-linguistic experience. In the studies described in this dissertation I focus on two such sources of information; reading directionality and spatial metaphors. First, I show that Hebrew and English speakers consistently arrange temporal sequences in a way that is congruent with their writing directionality, left to right for English speakers, and right to left for Hebrew speakers. Moreover, making judgments about earlier and later events with a key orientation that is incongruent with one's writing directionality (e.g, 'right' for earlier events in the English speaking group) creates interference, and produces slower responses. I then compare English and Mandarin speakers, to see whether the way speakers of these languages think about time reflects the way they habitually talk about it. In Mandarin, vertical metaphors of time are used more frequently and systematically than they are in English. Accordingly, the findings suggest that Mandarin speakers are faster to make temporal order judgments when the 'earlier' key is positioned on top of the 'later' key. English speakers do not show that congruency effect. Overall, the findings presented in this work suggest that culturally specific spatial representations are accessed automatically when people think about time, even in non-linguistic tasks, for temporal sequences that are not usually laid out in space in a particular directionality, and even when space is implicit to the task.

Keywords: Psychology
Advisor: Boroditsky Lera primary advisor. Thesis advisor
Clark Eve V. advisor. Thesis advisor
Clark Herbert H. advisor. Thesis advisor
Method for removing hydrogen sulfide from sour-gas and converting it to hydrogen and sulfuric acid [electronic resource]

A method for removing hydrogen sulfide from a sour-gas stream is investigated and found to be promising. The method oxidizes hydrogen sulfide to sulfuric acid by reducing aqueous bromine to hydrobromic acid in solution. Sulfuric acid is concentrated to eliminate its bromine content prior to being removed from the system, while the remaining hydrobromic acid solution is electrolyzed to regenerate aqueous bromine and produce hydrogen. The aqueous bromine solution does not react with hydrocarbon components common to natural gas including methane and ethane. This allows the process to both sweeten sour-gas and convert its hydrogen sulfide content to sulfuric acid in a single step. Specific reactor conditions were found to produce sulfur instead of sulfuric acid. Hydrobromic acid electrolysis requires less than half the energy required by water electrolysis and is an inherently flexible load that can shed or absorb power to balance supply and demand. Thus the electrolysis of hydrobromic acid may provide a route to produce inexpensive hydrogen and improve the electric grid.

Keywords: Aeronautics and Astronautics
Advisor: Kroo Ilan primary advisor. Thesis advisor
Mitchell Reginald primary advisor. Thesis advisor
Da Rosa Aldo Vieira advisor. Thesis advisor
Hoflund Gar B. advisor. Thesis advisor
Springer George S. advisor. Thesis advisor
Methods and applications of topological data analysis [electronic resource]

The focus of this dissertation is the development of methods for topological analysis as well as the application of topological tools to real world problems. The first half of the dissertation focuses on an algorithm for de-noising high-dimensional data for topological data analysis. This method significantly extends the applicability of many topological data analysis methods. In particular, this method extends the use of persistent homology, a generalized notion of homology for discrete data points, to data sets that were previously inaccessible because of noise. The second half of this dissertation focuses on a method for using topology to simplify complex chemical structures and to define a metric to quantify similarity for use in screening large databases of chemical compounds. This method has shown very promising initial results in locating new materials for efficiently separating carbon dioxide from the exhaust of coal-burning power plants.

Keywords: Mathematics
Advisor: Carlsson G. (Gunnar)
Kerckhoff Steve advisor. Thesis advisor
Mazzeo Rafe advisor. Thesis advisor
Methods for the wafer-scale encapsulation of MEMS [electronic resource]

The packaging of microelectromechanical systems (MEMS) is one of the most important design considerations in taking a product from a research environment to a commercial application. It must not only provide a suitably clean and stable environment for the device, but it should also withstand any harsh post-processing steps (such as wafer dicing and wire bonding) needed to integrate the device into its final system. As a result, the cost of packaging is typically a large portion of the overall cost of any commercial MEMS product. Addressing these needs for electrostatic silicon MEMS, this work describes the development of multiple wafer-scale encapsulation techniques that allow for a wide range of devices to be fabricated in a single fabrication process. Expanding on the thin film, 'epi-seal' encapsulation technique developed jointly by Stanford University and Bosch, a packaging method was developed that makes use of a thick sacrificial oxide deposition and subsequent planarization to allow for large lateral deflection structures side-by-side with proven narrow gap devices, such as tuning fork resonators. In an effort to further increase the capabilities of wafer-scale encapsulation, a process combining fusion wafer bonding and epitaxial reactor sealing was also developed. Unlike many packaging techniques using wafer bonding, the overall package size is only slightly bigger than the device itself and results in a stable, clean environment for the device. The final encapsulated part consists of a single crystal silicon structure free of native oxide inside a single crystal silicon cap layer. In addition, this encapsulation can support numerous process variations, such as oxide-coated composite device structures and the first MEMS devices packaged at the wafer scale using the surface migration of silicon atoms.

Keywords: Mechanical Engineering
Advisor: Howe Roger Thomas primary advisor. Thesis advisor
Kenny Thomas William primary advisor. Thesis advisor
Peumans Peter
Microfluidic, gradient-generator devices as in vitro mimics of cellular microenvironments [electronic resource]

The larger goal of this work is to engineer an appropriate in vitro platform to understand the complex interplay of various effectors in vivo. The specific approach taken was to develop and utilize microfluidic devices to study the impact of stable soluble biochemical gradients on cellular behaviors. Microfluidic devices are tools capable of recreating many critical aspects of the natural microenvironments of cells and tissues in a controllable and reductionist manner. Several microfluidic device geometries were evaluated through computational finite element modeling and experimental characterization studies to produce predictable and stable concentration gradients over multiple days of cell culture. We implemented these helpful devices in order to study the mechanism of cellular responses to various biochemical and biomechanical factors in both two and three dimensions for several cellular applications. First, this device was used to perform an in depth study of the complex interplay between soluble biochemical and biomaterial effectors of endothelial cell sprouting. The sprouting of endothelial cells into capillary-like structures is an early critical step in angiogenesis, the formation of new blood vessels from existing conduits. Time-lapse microscopic images of endothelial sprouts within the devices were quantified to determine the role of matrix density in regulating sprout initiation, elongation, and navigation. Matrix density was found to have profound effects on sprout kinetics, morphology, and alignment within gradients of vascular endothelial growth factor. Use of these novel microfluidic devices was expanded to include proof-of-concept experiments demonstrating the high-throughput screening of multiple engineered biomaterials to identify scaffold properties conducive to endothelial network formation. Finally, the microfluidic devices were utilized in preliminary studies of neuronal cell behavior within gradients of various neurotrophins and bone marrow derived mast cell chemotaxis within gradients of Kit ligand. Taken together, the results of this thesis demonstrate the usefulness of microfluidic devices as well-controlled in vitro culture platforms capable of creating stable, soluble biochemical gradients. Furthermore, these devices may lead to future techniques to provide directional cues during cell and tissue growth for regenerative medicine applications. For example, our results may be useful for developing potential pro- and anti-angiogenic therapeutic strategies for clinical treatment of ischemia and cancer, respectively.

Keywords: Mechanical Engineering
Advisor: Heilshorn Sarah primary advisor. Thesis advisor
Barron Annelise E. advisor. Thesis advisor
Shaqfeh Eric S. G. (Eric Stefan Garrido) advisor. Thesis advisor
Migration-velocity analysis using image-space generalized wavefields [electronic resource]

An accurate depth-velocity model is the key for obtaining good quality and reliable depth images in areas of complex geology. In such areas, velocity-model definition should use methods that describe the complexity of wavefield propagation, such as focusing and defocusing, multiple arrivals, and frequency-dependent velocity sensitivity. Wave-equation tomography in the image space has the ability to handle these issues because it uses wavefields as carriers of information. However, its high cost and low flexibility for parametrizing the model space has prevented its routine industrial use. This thesis aims at overcoming those limitations by using new wavefields as carriers of information: the image-space generalized wavefields. These wavefields are synthesized by using a pre-stack generalization of the exploding-reflector model. Cost of wave-equation tomography in the image space is decreased because only a small number of image-space generalized wavefields are necessary to accurately describe the kinematics of velocity errors and because these wavefields can be easily used in a target-oriented way. Flexibility is naturally incorporated into wave-equation tomography in the image space by using these wavefields because their modeling have as the initial conditions some key selected reflectors, allowing a layer-based parametrization of the model space. To use the image-space generalized wavefields in wave-equation tomography in the image space, the method is extended from the shot-profile domain to the image-space generalized-sources domain. In this new domain, the velocity updates are very fast. Migration with the optimized velocity model provides good quality and reliable depth images, as can be seen in a 3D-field data example.

Keywords: Geophysics
Advisor: Biondi Biondo
Claerbout Jon F. advisor. Thesis advisor
Harris Jerry M. advisor. Thesis advisor
Miniature and mass-producible fluorescence microscopes for biomedical imaging [electronic resource]

Fluorescence microscopy has emerged as a workhorse of modern biology and medicine. Fluorescence microscopes are indispensable as tools for basic research in the biological sciences, enable platforms for drug discovery in the biotechnology and pharmaceutical industries, and are increasingly aiding in several clinical diagnostic applications. However, state-of-the-art fluorescence microscopes remain bulky and expensive benchtop instruments with an architecture that impedes usage in certain applications and a cost that precludes adoption in large numbers. For example existing benchtop fluorescence microscopes are not amenable for in vivo imaging in animals, with the mouse being a common animal subject, especially during awake, active behavior. For the field of neuroscience in particular, such an experimental capability permits correlating causal cellular processes with animal behavior -- a longstanding goal. Inspired by this need, we have designed a miniature fluorescence microscope that can be borne by a mouse during active behavior. We have fabricated several such microscopes, each less than 2 g in mass, perhaps heralding a transformation in fluorescence microscopy from today's bulky and expensive benchtop paradigm towards miniature and mass-producible devices. Our fabricated microscopes achieve 2.5 [mu]m spatial resolution imaging fields-of-view up to 800 [mu]m x 600 [mu]m at 36 Hz, suitable for cellular-level imaging at high temporal resolution. To facilitate design of our microscopes, we have adopted a modeling-based microscope design methodology, akin to that used in the design of integrated circuits, and have developed a set of tools to model the microscope as an integrated device from the specimen to final digital image. We have experimentally validated fabricated microscopes for in vivo brain imaging in freely behaving mice, specifically using them for: 1) Imaging cerebellar vasculature and hemodynamics during activity; and 2) Imaging cerebellar Purkinje cell Calcium dynamics, analyzing spiking activity of populations of neurons with single neuron specificity during different motor behaviors. We also show how several of these microscopes imaging in parallel can enable new high-throughput imaging solutions with the potential to achieve broad impact, specifically demonstrating high-throughput image-based assays for: 1) Mutant phenotype screening in genetic model species such as the zebrafish; and 2) Multiple well plate cell analyses. Finally, we use a Bayesian iterative image restoration algorithm to enhance acquired microscope images, and show how spatial resolution can be further scaled into the sub-micron regime by leveraging advances in digital image sensing technology in conjunction with our post-acquisition image restoration algorithm.

Keywords: Electrical Engineering
Advisor: El Gamal Abbas A. primary advisor. Thesis advisor
Schnitzer Mark Jacob
Gambhir Sanjiv Sam advisor. Thesis advisor
Missing in metastasis mediates directional sensing during guided cell migration [electronic resource]

While directed cellular migration facilitates the coordinated movement of cells throughout development, in wound repair, and during an immune response, the precise mechanisms regulating such migration in vivo remain inadequately understood. Missing in Metastasis (MIM) is a defining member of the I-BAR subfamily of lipid binding, actin cytoskeletal regulators whose levels are altered in a number of cancers. Here I provide the first genetic evidence that I-BAR proteins regulate directed cell migration in vivo. MIM regulates the directional migration of several cell types responding to a number of different guidance cues. While regulating the directionality of migrating cells has been demonstrated in vitro, this role of an I-BAR protein in vivo was not previously observed. I demonstrate in these studies that Drosophila MIM (DMIM) is required for border cell migration, with loss of dmim function resulting in a lack of directional movement by the border cell cluster. In vivo endocytosis assays combined with genetic analyses demonstrate that the dmim product regulates directed cell movement by inhibiting endocytosis and antagonizing the activities of the endophilin/CD2AP/cortactin complex in these cells. These studies demonstrate that competition between BAR family members for pro-endocytic components underlies a directional sensing mechanism during guided cell migration.

Advisor: Oro Anthony
Chen James Kenneth advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Fuller Margaret
Mobile collection routing protocol [electronic resource]

The dissertation presents an in-depth study of mobile routing protocols, particularly mobile collection protocols through a literature study, a theoretical model, and thorough experimental studies both in simulation and testbeds. A mobile collection service provides data delivery from stationary source nodes to a mobile user (or a sink) over multihop networks. One of the main contributions of this dissertation research is the Whirlpool Adhoc Routing Protocol (WARP), which efficiently routes data to a mobile destination within a static network. The key insight in WARP's design is that, when a destination moves, data traffic can use the existing topology to efficiently probe, repair, and communicate changes with the few control packets. Using simulation, controlled testbeds, and real mobility experiments, we find that using the data plane, rather than control plane, is highly effective due to the incremental nature of mobility updates. WARP leverages the fact that converging flows at the destination makes it the region of highest traffic. The dissertation also provides a theoretical basis for WARPs behavior, defining an update area where the topology must adjust when a destination moves. As long as packets arrive at a destination before it moves outside of the update area, WARP can repair the topology with the data plane.

Keywords: Electrical Engineering
Advisor: Levis Philip primary advisor. Thesis advisor
Guibas Leonidas J. advisor. Thesis advisor
Katti Sachin advisor. Thesis advisor
Mobile Medic: Extending the Effective Reach of Mobile Data Infrastructure for Data Collection Applications in Emerging Regions

The recent explosion of mobile phone penetration in developing regions enables a variety of empowering new applications for mobile devices. A significant example of such an application is communication between hospitals in developing regions and their rural healthcare workforces.
The challenges of designing a data collection tool for healthcare workers in these environments are substantial: financial constraints prevent reliance on SMS as a go-to data transport mechanism, but infrastructural limitations prevent reliance on GPRS or other more sophisticated mobile web protocols. The complexity of these data transport requirements can necessitate limitations on data input, which must not interfere with the functionality needs of the target user group, which has little technical knowledge. This paper examines a number of methods that can be employed to design a better data collection tool targeted at community healthcare workers in developing regions, and presents a prototype tool that incorporates these advances.

Keywords: Computer Science.
Cell phones
Community health services
Data collection
ICTD
Community healthcare workers
Thesis
Advisor: Winograd Terry