VictorJuiz/thesis huggingface dataset:
RF-penetrable PET insert integrated with a phased-array RF receiver coil for simultaneous PET/MRI

Over the past few years, integrated positron emission tomography/magnetic resolution imaging (PET/MRI) systems emerged with great potential by providing added value that exceeds the sum of each system. However, the system's overall cost has impeded the widespread adoption of PET/MRI and, furthermore, limited research opportunities for finding more clinical applications. To enhance the dissemination of PET/MRI, a brain-dedicated PET insert that can be inserted into any existing MRI for simultaneous PET/MRI was developed in our lab. This cost-effective PET insert with a better imaging performance could improve the adoption of PET/MR and allow more clinical and research opportunities in the Neurology field. This thesis focuses on the development of an RF-penetrable brain-dedicated PET insert; (a) design and performance evaluation of the 1st-generation PET insert prototype are described, (b) its limitations and strategies for design improvements are explained, and (c) design and preliminary performance evaluation of the upgraded 2nd-generation PET insert prototype are presented. The 1st-generation RF-penetrable PET insert prototype that allows the RF field from the MRI body coil to penetrate through small inter-module gaps showed promising results indicating that we can achieve simultaneous PET/MRI without modifying the existing MRI hardware. Nonetheless, some minor issues including the gradient-induced eddy current and low SNR MR image from receive attenuation were observed. These issues could be solved by (a) replacing the solid copper shield with a phosphor bronze mesh shield which has high RF shielding effectiveness and negligible induced eddy current and (b) placing a phased-array RX-only RF coil inside the PET insert for high SNR MR images while preserving the PET performance. With these modifications, the 2nd-generation RF-penetrable PET insert has been designed with a longer scintillation crystal axial FOV (16 cm for a full brain) for better sensitivity that enables it to be practical for clinical brain imaging. Preliminary results of one detector module have been collected and analyzed and overall performance of the MR system and the PET detector module was preserved.

Keywords: Mechanical Engineering.
Advisor: Delp Scott 
Levin Craig 
Glover Gary H.
Ribosomes : stability, instability, and cellular elasticity

The ribosome is usually defined by what it does, what it's made of, or what it looks like. This thesis explores these definitions with the intention of forming a unified appreciation for how the composition of the protein biosynthesis apparatus relates to what it does in a cell. Understanding the compositional nature of ribosomes first requires defining them, and I do this by discussing the stability of the ribosome particle and the instability of associated factors that control the translation mechanism. This framework is critical for appreciating the first major direction of my dissertation research that is described in the first three chapters of this thesis. In these sections, I will describe several approaches to dissect eukaryotic translation at the single-molecule level that established the groundwork of a system to study for many years to come. In recent years, the stability of the mature ribosomal particle has been questioned, raising the possibility that such irregularities might relate to what it does via a ribosome "code". As I hope to demonstrate in the second major direction of my dissertation, there is an enormous gap between the "what it's made of" and "what it does" perspectives on the ribosome. Recognizing the centrality of the ribosome for cellular protein homeostasis is crucial to this end and sometimes necessitates thinking off the ribosome. This thesis will conclude with a discussion of broad implications and future directions that new researchers in the field may pursue.

Keywords: Chemical and Systems Biology.
Advisor: Puglisi Joseph D. 
Brandman Onn
Jarosz Daniel 
Sarnow P. (Peter) 
Wandless Thomas
Risk below the surface: Concussions in artistic swimming

This thesis is a reported piece of journalism. It includes data that I gathered through a survey sent out to artistic swimmers in the United States. My analysis of this data showed that 25 percent of artistic swimmers sustained at least one concussion during their careers and that 15 percent might have sustained one or more, documenting the prevalence of concussions in artistic swimming. The article features four former elite artistic swimmers who sustained concussions and photographs of an award-winning team.
In addition to the article and photographs, there is a 360-degree video experience that showcases the risks below the surface. The video is available at this link: https://youtu.be/EhnrB26rRFg

Keywords:  Department of Communication and Journalism
Communication
Journalism
Stanford University
Master of Arts
artistic swimming
synchronized swimming
concussions
sports
Thesis
Advisor: Phillips Cheryl
Migielicz Geri
Rites of revolution : Chinese revolutionary aesthetics as ritual practice

Rites of Revolution: Chinese Revolutionary Aesthetics as Ritual Practice argues that revolutionary literature and performance should be approached as forms of secular religious ritual. Placing the Cultural Revolution within a longer revolutionary history, and working across media (including the novel, film, opera, and ballet) as well as with diaries and later memoirs, my project demonstrates the centrality of narrative to historical conceptions of Chinese modernity. I show how a socialist philosophy of history emerged from an earlier Chinese discourse of modernity that was explicitly explored in literary texts. This teleological worldview of progressive history came to be gradually encoded into a masterplot that crossed genres and media as it developed in the mid-twentieth century. Informed by work on Soviet aesthetics and in conversation with work on the Cultural Revolution in literature, history, anthropology, and religious studies, I demonstrate that the ritual forms of revolutionary works sought to symbolically reconstruct the world in order to transform it. Engaging a larger question of the role and nature of literature within society, my interpretation of cultural production as a staging of quasi-religious performance addresses the tension between art's aesthetic value and its social utility. By placing literary texts at the intersection of competing philosophies of history and subjectivity, my research provides a particular praxis for the discussion of politics formed through the aesthetics of charismatic rule and aesthetics as a political method for the conditioning of individual consciousness. The role of narrative as both metaphor (for life) and metonym (for a theory of history) joins the interpretive lines of politics and aesthetics and forms the foundation of my argument for the particularly literary roots of Maoist cultural politics.

Keywords: Comparative Literature.
Advisor: Wang Ban
Lee Haiyan 
Palumbo-Liu David
RNA structure regulates HIV-1 reverse transcription initiation

Reverse transcription of the human immunodeficiency virus-1 (HIV-1) RNA genome into double-stranded DNA is an essential, highly regulated step in the viral lifecycle and a common target of antiretroviral drugs. The reaction is catalyzed by viral reverse transcriptase (RT) that is packaged into an infectious virion along with two copies of viral genomic RNA (vRNA) and host transfer RNA lysine 3 (tRNALys3), which serves as the primer for the initiation of reverse transcription. Initiation is distinct from elongation as it is slow and non-processive, with discrete stalling points along the vRNA sequence. Studies over several decades have revealed regions of RNA structure and sequence complementarity between the vRNA template and tRNALys3 primer that appear to regulate reverse transcription initiation. Despite this body of work, the structural basis of RT function during initiation has remained a mystery. Using cryo-electron microscopy, we have determined the structures of several reverse transcriptase initiation complexes representative of key initiation intermediates. In all structures, the primer binding site (PBS) helix formed between tRNALys3 and vRNA lies in the cleft of RT and is extended by additional pairing interactions. We find that during early stages of initiation, the 5′ end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site. Structures of subsequent steps in the initiation process feature a dramatic refolding of the tRNA and vRNA that may govern the transition from initiation into the processive elongation phase. Newly obtained data on the reverse transcriptase initiation complex reconstituted using naturally post-transcriptionally modified tRNALys3 further supports the hypothesis that refolding of vRNA and tRNALys3 does not occur during early stages of initiation. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.

Advisor: Puglisi Elisabetta
Puglisi Joseph D. 
Brünger Axel T.
Robust and accurate shock-capturing in discontinuous Galerkin discretizations

Computational Fluid Dynamics (CFD) has become a critical component in analyzing fluid flows and designing industrial products. Among various numerical methods in CFD, second-order numerical schemes have been widely used in both industry and academia. Second-order methods are robust enough to use on complex geometries and usually provide a sufficient amount of accuracy in flow simulations. However, second-order accurate solutions may not be sufficient for many aerodynamic applications such as vortex flows, Large Eddy Simulations (LES), and aeroacoustics problems. As a consequence, researchers have sought high-order numerical methods to simulate complex flows with low dissipation over the past few decades. Many approaches have been suggested including Finite Difference (FD), Finite Volume (FV), and Finite Element (FE) frameworks for CFD. In the group of high-order methods, discontinuous Galerkin (DG) methods have become popular in academia because of their distinctive benefits. For DG methods, high-order accuracy in flow solutions can be easily achieved by just adding more degrees of freedom in each element. Furthermore, DG methods are well suited to modern computer hardware, even on GPUs, due to high arithmetic intensity and the locality of operations. Despite their numerous benefits, DG methods are not widely adopted because of some remaining challenges, especially in industry. One of these difficulties is shock-capturing. Similarly to other numerical methods in CFD, DG methods also suffer from spurious oscillations if discontinuities arise during flow simulations. The accuracy of solutions will degrade significantly, or solutions may diverge unless these discontinuities are captured appropriately. Therefore, a shock-capturing capability becomes necessary for DG methods to simulate compressible flows with shocks. In this work, robust and accurate shock-capturing approaches for DG methods will be demonstrated. To precisely capture various strengths of shocks, a simple shock-detector is first proposed for DG discretizations, which only relies on local flow information. Additionally, filtering strengths are precalculated to avoid parameter tuning procedures and are optimized to achieve maximum accuracy while capturing shocks. The proposed methods are then applied to two- and three-dimensional canonical problems to demonstrate the shock-capturing capabilities of the proposed methods.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Cantwell Brian 
Lele Sanjiva K. (Sanjiva Keshava)
Robust control, planning, and inference for safe robot autonomy

Integrating autonomous robots into safety-critical settings requires reasoning about uncertainty at all levels of the autonomy stack. This thesis presents novel algorithmic tools for imbuing robustness within two hierarchically complementary areas, namely: motion planning and decision-making. In Part I of the thesis, by harnessing the theories of contraction and semi-infinite convex optimization and the computational tool of sum-of-squares programming, we present a unified framework for robust real-time motion planning for complex underactuated nonlinear systems. Broadly, the approach entails pairing open-loop motion planning algorithms that neglect uncertainty and are optimized for generating trajectories for simple kinodynamic models in real-time, with robust nonlinear trajectory-tracking feedback controllers. We demonstrate how to systematically synthesize these controllers and integrate them within planning to generate and execute certifiably safe trajectories that are robust to the closed-loop effects of disturbances and planning with simplified models. In Part II of the thesis, we demonstrate how to embed the control-theoretic advancements developed in Part I as constraints within a novel semi-supervised algorithm for learning dynamical systems from user demonstrations. The constraints act as a form of context-driven hypothesis pruning to yield learned models that jointly balance regression performance and stabilizability, ultimately resulting in generated trajectories for the robot that are conditioned for feedback control. Experimental results on a quadrotor testbed illustrate the efficacy of the proposed algorithms in Parts I and II of the thesis, and clear connections between theory and hardware. Finally, in Part III of the thesis, we describe a framework for lifting notions of robustness from low-level motion planning to higher-level sequential decision-making using the theory of risk measures. Leveraging a class of risk measures with favorable axiomatic foundations, we demonstrate how to formulate decision-making algorithms with tunable robustness properties. In particular, we focus on a novel application of this framework to inverse reinforcement learning where we learn predictive motion models for humans in safety-critical scenarios, and illustrate their effectiveness within a commercial driving simulator featuring humans in-the-loop. The contributions within this thesis constitute an important step towards endowing modern robotic systems with the ability to systematically and hierarchically reason about safety and efficiency in the face of uncertainty, which is crucial for safety-critical applications.

Keywords: Aeronautics and Astronautics.
Advisor: Pavone Marco
Rock Stephen
Schwager Mac
Robust dimensionality reduction for data visualization and latent structure recovery

High dimensionality is one of the major challenges in the analysis of modern data sets, as it is now common to have hundreds or even millions of simultaneous measurements collected for a single sample. Visualization of the data becomes difficult if not impossible, while standard statistical methods lose power due to the curse of dimensionality. Even if a large volume of data is available, exploring a high dimensional space exhaustively is computationally impractical. Low-dimensional data representations that remove noise but retain the signal of interest can be instrumental in detecting hidden structures and patterns. Our work focuses on improving current methods to perform dimensionality reduction (DR) and interpret its output. Many datasets are governed by a continuous process, which is often unknown. Estimating data points' natural ordering and their corresponding uncertainties often sheds light on these underlying mechanisms. We develop a Bayesian Unidimensional Scaling (BUDS) technique which extracts a dominant source of variation in high dimensional datasets and produces a visual data summary, facilitating the exploration of a hidden continuum. The method maps multivariate data points to latent one-dimensional coordinates along their inherent trajectory, and provides uncertainty bounds estimated using a Bayesian posterior distribution. We then turn our attention to DR techniques for data visualization. In particular, we study the behavior of t-Stochastic Neighbor Embedding (t-SNE), a technique broadly adopted for visualizing high-dimensional datasets. We show why t-SNE is usually unable to recover large-scale structures. We then propose a new embedding method, Diffusion t-SNE, which introduces a time-step parameter that can generate a multi-view representation of the data, recovering its geometry at different scales. We also provide mathematical explanations for why the entropy equalization procedure used in t-SNE results in a loss of information about local variances, leading to data distortions that produce misleading representations with uninformative relative sizes and unidentifiable input data sampling densities and variances. Building upon this analysis, we present a scaling scheme of the pairwise proximities that achieves accurate representations of regional data variances.

Advisor: Holmes Susan
Kitanidis P. K. (Peter K.) 
Kundaje Anshul
Role of CDK4/6 in regulating Rb and the restriction point

Cells escape the need for mitogens at a restriction point several hours before entering S phase. The retinoblastoma protein Rb is a key inhibitor of cell-cycle progression, and irreversible inactivation of Rb via full phosphorylation (hyperphosphorylation) is thought to underpin the restriction point. CDK4/6 has been proposed to initiate Rb phosphorylation before cyclin E/A-CDK completes hyperphosphorylation in a self-sustaining positive feedback loop, providing a plausible molecular model for the transition to mitogen independence at the restriction point. Using single-cell microscopy, we unexpectedly found that cyclin E/A-CDK activity can only maintain Rb hyperphosphorylation from the onset of S phase, while CDK4/6 activity is required to maintain Rb hyperphosphorylation throughout G1. Mitogen removal results in a gradual loss of CDK4/6 activity with a high likelihood of cells sustaining Rb hyperphosphorylation until S phase, at which point cyclin E/A-CDK activity takes over. Thus, it is short-term memory, or transient hysteresis, in CDK4/6 activity following mitogen removal that sustains Rb hyperphosphorylation, demonstrating a probabilistic, rather than irreversible, aspect to cell-cycle commitment.

Keywords: Chemical and Systems Biology.
Advisor: Meyer Tobias 
Ferrell James Ellsworth 
Wang Bo (Researcher in bioengineering)
The role of dorsal premotor cortex in decision-making and action selection

Why do we do the things we do? Understanding cognition is a key step towards understanding our diverse perspectives and behaviors. Over the years, the study of decision-making in neuroscience has shed light on the black box of cognition. Decision-making is the process of arriving at one choice out of multiple alternatives, and correlates of this process have been found in many sensory- and motor-related brain structures. However, we do not have a full account of the way in which brain regions participate in this process, especially given the many potential forms that decision-making can take. Here, we focus in on the dorsal premotor cortex (PMd), a frontal brain region involved in motor preparation and execution, decision-making, and goal-oriented action. We use a perceptual decision-making task in which the subject reports the perceived dominant color of a red-and-green checkerboard by reaching to the corresponding colored target. Studies have previously found that the activity of PMd neurons correlate with the choice report, the evidence supporting that choice, and the time taken to deliberate upon the choice. We now ask: To what extent is PMd involved in the perceptual aspect of decision-making, and how do motor costs affect the decision-making process? First, we separate the perceptual process (whether the checkerboard is mostly red or green) from the motor process (to reach left or right) by presenting a checkerboard decision cue without providing information on how to report. We found that PMd neurons did not encode information about the perceptual color choice, but did exhibit decision-related activity when the subject was able to report the choice. We next randomly assign the positions of the target choices to be near or far relative to the hand's starting position. We found that performance was biased towards the choice that was closer to the animal, and that these target configurations were reflected in neural activity during the report epoch as well. These findings suggest that PMd involvement in the decision process is primarily in an action-decision space, and that relevant motor and perceptual information are combined at the same time. These results provide stepping stones towards understanding how brain regions drive our perception and behavior.

Advisor: Shenoy Krishna V. (Krishna Vaughn) 
Baccus Stephen A. 
Moore Tirin
Newsome William T.
The role of skin deformation feedback in haptic perception of virtual objects

Through exploration and interaction, we rely on haptic information to help perceive the world around us. Haptic devices, which can provide controlled touch feedback, have the potential to improve the realism and utility of virtual environments. Traditional haptic devices impart forces and torques on the user, often through a world-grounded kinesthetic force feedback device. However, it is difficult for these world-grounded devices to match the unrestricted movement of head-mounted virtual reality displays due to the increased cost, friction, and inertia that comes with increased size. Skin deformation feedback offers an alternative, user-grounded form of haptic feedback that, when worn on the fingers, can mimic the cutaneous interaction forces experienced during object manipulation. These devices are not without their own limitations; size and weight constraints often limit the available force output applied to the fingerpad, and thus, the physical properties of a virtual object conveyed to a user. This thesis elucidates the role of skin deformation feedback in human perception of virtual objects to inform haptic device design and rendering algorithms. We started by studying the relative contributions of skin deformation and kinesthetic forces to weight perception. We designed mechanical thimbles to amplify the skin deformation forces felt on the fingerpad when grasping and lifting a real world object, and demonstrated that this changes the weight perceived by human participants. We then augmented an existing three-degree-of-freedom wearable skin deformation device, which provides feedback in the directions shear and normal to the fingerpad, with contact-event based haptics. Then, we showed that adding a high-frequency contact cue to shear-only skin deformation can serve as an alternative to shear-plus-normal skin deformation for a grasp-lift-and-place task of a ``fragile" virtual object. We also found that adding a contact cue to shear-plus-normal skin deformation feedback did not improve the performance of this task. Next, we developed a haptic illusion to alter the perceived weight of virtual objects by scaling inertial forces when using skin deformation haptic feedback. Through human participant experiments, we measured the changes in perceived virtual weight and validated the effect of the illusion. Finally, we combined our scaled inertial forces haptic weight illusion with a visuo-haptic weight illusion, non-unity control-to-display ratio, in complementary and conflicting manners to further alter the perceived virtual weight of virtual objects when using skin deformation haptic devices. These results give insight into how to use the limited available force output of skin deformation feedback devices to help users better perceive virtual worlds.

Keywords: Mechanical Engineering.
Advisor: Okamura Allison 
Cutkosky Mark R. 
Follmer Sean