VictorJuiz/thesis huggingface dataset:
Euclidean-equivariant functions on three-dimensional point clouds

We present a type of neural network that is locally equivariant to 3D rotations, translations, and permutations of points at every layer. Local 3D rotation equivariance removes the need for data augmentation to identify features in arbitrary orientations. These networks use convolution filters built from spherical harmonics; due to the mathematical consequences of this filter choice, each layer accepts as input (and guarantees as output) scalars, vectors, and higher-order tensors, in the geometric sense of these terms. We exhibit applications of these networks to supervised learning tasks in structural biology.

Keywords: Physics.
Advisor: Hayden Patrick (Patrick M.)
Dror Ron
Ganguli Surya
Eutectic liquids for high-energy density flow batteries

Harnessing variable wind and solar resources for most of our energy use will require advanced energy storage options. Flow batteries have an attractive battery architecture due to their scalability, long cycle-life, and power-to-energy tunability. However, the low energy density of flow batteries (~10-50 Wh/kg practical) limits their application. A significant hurdle to high-energy density flow batteries is finding negolytes and posolytes that remain in the liquid state at extremely high concentrations of redox-active species. One strategy to overcome this hurdle is to employ eutectic mixing properties for the depression of melting points. This dissertation focuses on the prospects of using Na-K liquid metal alloy, which has a eutectic melting point of -13 °C, as the negolyte in a flow battery at room temperature. At room temperature, liquid Na-K has an extremely high capacity of 580 mAh/g and a reduction potential of -2.9 V vs. SHE, assuming K+ is the mobile ion. First, we discuss the stability and compatibility of K-β''-alumina with Na-K. We find K- β''-alumina to be stable in phase and morphology to K-β''-alumina and to be an overwhelming conductor of K+ vs. Na+ when in contact with Na-K. These findings allowed us to demonstrate the cycling of batteries using Na-K, K-β''-alumina, and model aqueous and nonaqueous posolytes. Second, we discuss the different components of area-specific resistance in a Na-K-based flow battery. The interfaces on both sides of the K-β''-alumina can be large sources of impedance. On the Na-K [vertical line] K-β''-alumina interface, although Na-K does not wet K-β''-alumina at room temperature, we find some form of reactive wetting that decreases the interfacial resistance significantly. On the posolyte [vertical line] K-β''-alumina interface, we find that if the posolyte is aqueous, ion exchange of hydrogen/hydronium species and K+ increases the interfacial resistance substantially over time, but this can be greatly decreased through modifying the solution chemistry. These findings allowed us to achieve a high power density for a battery of this kind, 65 mW cm^-2 at 22 °C and > 100 mW cm^-2 at 57 °C. Third, we discuss our efforts to find an ideal posolyte by employing eutectic mixing to decrease the melting points of benzoquinone derivatives, which are redox-active organic molecules. We find that a regular solution model that assumes immiscible solids has predictive power for finding eutectic melting temperatures and compositions for mixtures of multiple components.

Keywords: Materials Science and Engineering.
Advisor: Chueh William
Cui Yi
Salleo Alberto
Evaluating spatially programmable architecture for imaging and vision applications

Fixed function hardware for image processing (ISP) has been used ever since digital cameras were introduced. This solution is efficient but the resulting systems are slow to adapt because creating a new chip takes a long time. While historically this wasnt a problem, the explosion of new applications from computational photography and computer vision fields has made this approach difficult. To address the need for greater flexibility, a number of specialized accelerators were created: PVC, Hexagon, Myriad, etc. These chips rely on programmable SIMD VLIW architectures for increased flexibility. This thesis explores and evaluates an alternative approach that is more similar to traditional ISP engines - a spatially programmable architecture which is in the class of coarse-grain-reconfigurable array (CGRA) machines. We demonstrate that CGRA can be programmed as easily as a conventional CPU or GPU by using a domain specific language (DSL) for image processing like Darkroom or Hailade and leveraging an FPGA development flow based on the VPR toolset. Our evaluation framework shows that programming in space with CGRA archives a modest improvement over programming in time with SIMD: about 1.6x better energy efficiency and 1.4x better area efficiency. However the cost of programmability is still high: compared to an ASIC, CGRA has 6x worse energy and area efficiency, and this ratio would be roughly 10x if memory dominated applications were excluded. To reduce this gap requires each compute unit to do more computation making it more specialized and less flexible. How to accomplish this, while still retaining enough programmability, is the key challenge for future research.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark (Mark Alan) 
Hanrahan P. M. (Patrick Matthew) 
Shacham Ofer
Evaluating the Implementation of a Comprehensive Tobacco Cessation Program

Introduction: Tobacco use remains the leading cause of death in the United States. Smoking cessation at any age provides numerous health benefits and added years of life. The Stanford Tobacco Cessation Program (STCP), started in December 2014, is a comprehensive cessation program that includes group sessions, mindfulness training, NRT and medication management.
Aims: This evaluation examined tobacco cessation outcomes among patients referred to the STCP. Specifically, we examined 1) baseline patient variables predictive of initiating and engaging in tobacco cessation treatment with the program; 2) quit rates at 3- and 9- months for patients who did and did not engage in tobacco cessation treatment with the program; and 3) among those who initiated in tobacco treatment, patient characteristics predictive of being tobacco-free at the 3-month or 9-month follow-up periods. We also summarized reasons for patient non-participation and patient feedback concerning program effectiveness.
Methods: A total of 227 patients have been referred to STCP to date (May 10, 2018); 102 (45%) have completed an intake; and 76 patients (33%) have attended at least one group session. Self-reported 7-day prevalence abstinence from all forms of tobacco at 3-month and 9-month follow-up periods were examined by demographic and baseline characteristics.
Results/Findings: Patients who engaged in treatment with the STCP had significantly higher quit rates than those who were referred and did not proceed in the program (41% vs 11% at 3-months and 54% vs. 31% at 9-months, respectively). Cancer diagnosis and NRT use were predictive of not initiating in the program. Substance use and current NRT use were significant predictors of not engaging in the program. Patients with mental illness were just as likely to engage in treatment and quit smoking as patients without mental illness. A majority (57%) of patients who were referred but did not join the program cited insurance as a barrier.
Conclusions: The STCP is supporting patients with quitting smoking, though remains underutilized. There is opportunity for program growth with a need to address significant barriers to patient participation in the program.

Keywords:  Department of Medicine
cessation
treatment and intervention
tobacco use
smoking cessation
Stanford Prevention Research Center
Stanford University School of Medicine
Stanford Tobacco Cessation Program
Thesis
Advisor: Prochaska Judith J
Kendra Matthew
Hall Sharon M
Excitatory input from the anterior cingulate cortex to the dorsal periaqueductal gray promotes the affective component of pain

Pain is a conscious perceptual experience characterized in large part by its aversive qualities and consequent motivation for relief. The Anterior Cingulate Cortex (ACC) is a critical region for the emotional dimension of pain. In both humans and rodents, acute and chronic pain increase ACC neural activity, while ACC lesions or reduced ACC excitability decrease emotional reactivity during pain. However, the ACC receives diverse inputs from a multitude of brain regions, and is engaged and active during a variety of behavioral experiences beside pain. It thus remains unclear what circuit mechanisms in the ACC contribute to shaping pain experience, and how specific those circuits are to nociception. The Periaqueductal Gray (PAG) is a midbrain structure part of descending pain modulation circuits, but without known function in pain affect. Ventrolateral PAG neurons thus control nociceptive inputs in the spinal cord dorsal horn, through the modulation of spinally projecting medullary neurons. Interestingly, the ACC projects to the PAG, but to its dorsal part (dPAG), which is critical for the expression of defensive behaviors and the acquisition of learned responses to aversive stimuli. Together, these studies suggest that the PAG, under the control of the ACC, might have a previously unrecognized function in pain aversion. Here, we tested the hypothesis that excitatory input from the ACC to the dPAG during pain facilitates the affective-motivational dimension of pain. We first examined ACC-dPAG connectivity using histology as well as optogenetics and electrophysiology in PAG slices. We found that ACC axons terminals terminate in dPAG and monosynaptically excite Vglut2+, but not Vgat+ dPAG neurons. Second, we genetically targeted the ACC neurons projecting to the dPAG with viral vectors to express the hM4Di inhibitory DREADD, and exposed the animals to an assortment of pain tests. We found that inhibition of the ACC-dPAG pathway reduced affective-motivational pain behaviors but not sensory-reflexive responses across acute and chronic pain states. Third, we used fiber photometry to record population neural activity in ACC during a variety of pain tasks and found that neurons projecting to PAG are engaged during a broad array of aversive, rather than exclusively painful, experiences, v and with different structures of activity depending on the task context. Finally we optogenetically inhibited ACC-dPAG neurons during social observation of pain and observed alterations in non-somatically induced pain experience. Collectively, these results uncover the direct contribution of ACC-dPAG neural activity to the aversive experience of pain, and the necessity of this pathway to generate aversive behavioral responses. These results are most supportive of a theory of the ACC contributing a feature of general value appraisal, rather than specifically encoding the unpleasant quality of noxious stimuli.

Keywords: Biology.
Advisor: Scherrer Gregory
Huguenard John 
Luo Liqun
Excitons in monolayer transition metal dichalcogenides : laser annealing and coherent feedback control of radiative coupling

Recently there has been great interest in the monolayer transition metal dichalcogenides (TMDs) and their optical properties. The strong and spectrally narrow excitonic feature exhibited in high quality samples of these materials is of interest for optical devices and optical/excitonic physics. I will present results from several experiments related to excitons in the monolayer TMD MoSe2. First, a laser annealing process for the monolayer TMD MoSe2 which greatly improves the optical properties of suspended chemical-vapor-deposition grown samples is presented. This method removes surface contaminants/dopants and eliminates strain gradients. Surprisingly, the exciton resonance in these annealed samples is radiatively broadened and its quality is comparable to that of state-of- the-art samples prepared by encapsulation in hexagonal boron nitride. The annealing procedure has the potential to enable high quality, large area samples. Results from experiments in which a metal mirror is brought into close proximity with an MoSe2 monolayer will also be presented. The emission of the excitonic dipole is coherently fed back to itself with a variable phase depending on mirror position. This allows for control over the radiative coupling from near zero to 1.8 meV, and also leads to a change in total linewidth of 2.5 X. In contrast to previous experiments in other materials systems such as quantum dots and cold atoms, the transverse coherence of the 2D exciton allows for significant modulation of the radiative coupling at distances relatively far from the mirror. This experiment provides very direct evidence of the radiatively broadened nature of MoSe2 excitons. It also provides information about the relatively large transverse coherence of the excitonic wavefunction.

Keywords: Electrical Engineering.
Advisor: Mabuchi Hideo 
Miller D. A. B. 
Vuckovic Jelena
Expanding the small-molecule toolbox for studying CLC chloride channel physiology and biophysics

The chloride channel (CLC) family is a class of membrane proteins that regulates the flux of chloride ions across cell membranes. These ion channels play critical roles in electrical excitation of muscles and neurons, as well as in maintaining proper water and salt balance in the body. CLCs are traditionally difficult drug targets, as demonstrated by the low potency and general lack of homolog selectivity among existing classes of CLC inhibitors. To address this challenge, we employed a rational-design approach to develop a novel, small-molecule scaffold that displays unprecedented selectivity for one CLC homolog. Specifically, this molecule inhibits one of the two homologs expressed in the kidney, CLC-Ka, with > 20-fold higher potency than the next most closely related CLC homolog, which is 90% identical in sequence. Following a similar approach, we identified and optimized a new class of potent and selective inhibitors for CLC-2, the most abundant voltage-gated chloride channel expressed in the brain. Data from genetic knockout studies in mice suggest a critical role for CLC-2 in ion homeostasis and electrical excitability in the central nervous system (CNS), but the mechanisms for these processes have been difficult to elucidate in the absence of specific and potent chemical modulators of CLC-2. Structure-activity relationship studies have allowed us to develop these inhibitors into a best-in-class molecule that represents the first and only nanomolar potency small-molecule inhibitor to target the CLC family. In addition to extraordinary selectivity among CLCs, we demonstrated that this molecule is highly selective for CLC-2 within the context of the brain, showing no off-target effects among a diverse panel of CNS receptors, channels, and transporters that we screened. Additionally, this inhibitor acutely and specifically blocks CLC-2 current in wild-type hippocampal CA1 neurons with no effect on CLC-2--/-- neurons. This exciting new molecular tool acts as a fast, reversible, and specific inhibitor of CLC-2 function in the brain and should enable study of CLC-2 in the CNS.

Keywords: Chemistry.
Advisor: Du Bois Justin 
Maduke Merritt C.
Cegelski Lynette
Experimental and Computational Identification of Treg Antigens Using a Peptide-MHC Library

More than 23.5 million Americans suffer from an autoimmune disease, which results when the immune system incorrectly identifies and attacks healthy tissue. Regulatory T cells (Tregs) represent a small subpopulation of T cells that play an important role in dampening self-reactive immune responses, and therefore offer an enticing target for a new generation of autoimmune therapies. Although it is generally understood that Tregs downregulate induction and proliferation of effector T cells, there is a lack of understanding about the specific mechanism of action of Treg cells. This has been compounded by the fact that very few peptides have been discovered that are known to elicit a Treg response. We therefore sought to identify and characterize peptides recognized by Tregs. We chose to work with Tregs found in the visceral adipose tissue of mice. These Tregs play a role in diabetes, which is a commonly used model of autoimmune disease. Amplified proliferation of VAT-Tregs is associated with improved prognosis in a diabetes mouse model . To find the endogenous peptides, we have developed a new algorithm that can propose candidate peptides that bind a specific TCR by combining three data sets: the deep sequence data from the affinity-based selection, T cell stimulation data of the most frequently occurring peptides from the affinity selection, and the BLOSUM62 matrix which is used to calculate amino-acid homology. The algorithm combines these three data sets to systematically analyze an inputted organism’s proteome to find probable candidate peptides. Using the algorithm, we identified and confirmed four peptides from the mouse proteome that stimulated the VAT-TCR. With these new tools to aid in identifying peptides recognized by Tregs, we can now design experiments to enhance our understanding of Treg function and regulation, develop proximate translational applications to autoimmune diseases, and ultimately develop a new class of antigen specific therapies.

Keywords: Garcia, K. Christopher
T cell
Regulatory T cells
MHC Class II
Antigen Identification
Department of Biology
Stanford University
Thesis
Advisor: Fernandes Ricardo
Experimental and computational investigations into the mechanics and patterning of adhesive multicellular systems

Cell adhesion is one of the fundamental building blocks of multicellular organisms, and is crucial to their functioning. Creating and harnessing cell adhesion for engineering purposes is the complex challenge that animates my work in this thesis. In the first part of my work, I will describe my study of a complex multicellular organism, the zebrafish embryo, in which I took advantage of the organism's cell adhesion system to attempt to measure forces between adhering cells. For this work, I used a molecular tension sensor created by fusing the epithelial cell adhesion molecule (EpCAM) with a quantitative fluorescence resonance energy transfer (FRET) Tension Sensor Module (TSMod). Using fluorescence lifetime imaging (FLIM) in combination with FRET, I validated the in vivo expression of the sensor and its localization to the membranes of epithelial cells in the embryo, showed using fixed-length controls that the TSMod construct is appropriate for use in the zebrafish embryo, and quantified various sources of error. Overall, we achieved a FLIM resolution of 50ps, which translates to a resolution of 1pN of force. We determined that the EpCAM-TSMod was not holding any statistically significant amount of force, which is consistent with more recent findings that EpCAM may not actually be a cell adhesion molecule at all and therefore would not hold force. However, our imaging methods and analysis should prove useful for future work in the field. In the second part of my work, I built a computational simulation of a synthetic bacterial cell-cell adhesion system that was experimentally created by my colleague David Glass. After evaluating many existing modeling tools, I chose to build my simulation using the Chipmunk/Pymunk physics library. My simulation combines cell adhesion with bacterial run-and-tumble motion as well as cell growth and division, a combination which to our knowledge has not yet been achieved. I was able to reproduce Glass's experimentally-observed patterns of differential adhesion, phase separation, and coaggregation bridging. In sum, my work demonstrates that cell adhesion is a tool we can use, whether it is to build multicellular organisms or to study other scientific phenomena.

Advisor: Riedel-Kruse Hans
Huang Kerwyn Casey
Huang Possu
Exploration of a PEALD platinum thermal accelerometer

The use of microelectromechanical systems (MEMS) inertial sensors for high-bandwidth applications in extreme environments has proved challenging due to inherent limitations imposed by the governing physics and the available sensing mechanisms. Thermal accelerometers rely on an entirely different set of physics and thus are not subject to these same limitations. This thesis presents a thermal accelerometer fabricated with plasma enhanced atomic layer deposition (PEALD). The deposition of thinner Pt films enabled by PEALD allows for decreased parasitic heat pathways, and correspondingly decreased thermal time constants, relative to previous thermal accelerometers. This work first describes the fabrication process for these devices and demonstrates the long-term resistance stability of the individual suspended films. Confirming the film stability represented an important initial step, as such films have had very limited use in sensor applications and thus have not undergone extensive electrical stability validation. Next, the initial performance metrics of our device are investigated. Results show a sensitivity of 0.149 C/g and a noise of 22.5 mg for a heater temperature rise of 290 C. With the addition of a temperature compensation scheme based on the common mode sensor resistances, the device showed no temperature sensitivity. Finally, this work explores several modulated operating modes. Modulating the heater was shown to reduce long term drift by half, whereas modulating the bridge reduced the noise density by about 20%. However, pure AC heating is subject to a extra trade-off between sensitivity and bandwidth: the sensitivity declines for heating frequencies higher than the full system cutoff frequency (which, as it includes the time for the heater to Joule heat, has a longer time constant and thus a lower cutoff frequency than for acceleration), and the chosen heating frequency ultimately defines the ceiling for the potential system bandwidth to acceleration. Pulsed heating offers an alternative modulated heating scheme with the same reduced drift benefits. This pulsed scheme may better optimize for both low noise and low drift without the corresponding bandwidth limitations.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Howe Roger Thomas 
Prinz F. B.
Exploring Augmented Reality with Smart Haptic Tokens in Remote Collaboration

Despite physical interactions being crucial to some learning and collaboration processes, existing tools - such as teleconferencing - tend to ignore the haptic modality. The tools that do embrace physical manipulation tend to use passive tangibles, which are more constrained in possible uses in remote collaboration. Also, many are extremely bulky and offer small workspaces. Others offer only limited ways for users to communicate. We propose a system that integrates augmented reality and active tangibles to alleviate many of these issues and explore new interaction mechanisms. Our joint use of Microsoft HoloLens headsets, multi-robot haptic systems called Zooids, and Leap Motion hand trackers brings many advantages that have not been previously explored. Typically, augmented reality applications lack haptic feedback, while active tangibles usually face strong limits on the amount of information they can display. Our novel system solves both of these problems by combining the two technologies, enabling numerous new collaboration modalities. We present possible applications to leverage the strengths of these conjoined systems with the hope that it pushes the field of remote collaboration forward.

Keywords: Sean Follmer
Symbolic Systems
Human Computer Interaction
Augmented Reality
Haptics
Tangibles
Thesis
Advisor: Le Goc Mathieu
Ye Wang