VictorJuiz/thesis huggingface dataset:
Evaluating spatially programmable architecture for imaging and vision applications
Keywords: Electrical Engineering.

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.
Evaluating the Implementation of a Comprehensive Tobacco Cessation 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

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.
Excitatory input from the anterior cingulate cortex to the dorsal periaqueductal gray promotes the affective component of pain
Keywords: Biology.

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.
Excitons in monolayer transition metal dichalcogenides : laser annealing and coherent feedback control of radiative coupling
Keywords: Electrical Engineering.

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.
Expanding the small-molecule toolbox for studying CLC chloride channel physiology and biophysics
Keywords: Chemistry.

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.
Experimental and Computational Identification of Treg Antigens Using a Peptide-MHC Library
Keywords: Garcia, K. Christopher
T cell
Regulatory T cells
MHC Class II
Antigen Identification
Department of Biology
Stanford University
Thesis

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.
Exploration of a PEALD platinum thermal accelerometer
Keywords: Mechanical Engineering.

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.
Exploring Augmented Reality with Smart Haptic Tokens in Remote Collaboration
Keywords: Sean Follmer
Symbolic Systems
Human Computer Interaction
Augmented Reality
Haptics
Tangibles
Thesis

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.
Exploring Motivational Strategies in the WHISH Trial: An Embedded Substudy
Keywords:  Department of Medicine
Stanford University Department of Medicine
Community Health and Prevention Research
CHPR
Women's Health Initiative Strong and Healthy
WHISH
motivation
physical activity
cardiovascular disease
pragmatic trial
older women
Thesis

The Women's Health Initiative Strong and Healthy (WHISH) trial is testing the hypothesis that a centralized, public health intervention designed to increase and/or maintain physical activity levels and reduce sedentary behavior will reduce incidence of major CVD clinical events (myocardial infarction, stroke, cardiovascular disease related death) in older women. The efficacy of the trial depends on the ability of the intervention materials to increase physical activity and decrease sedentary behavior in the intervention group compared to the control group. Effectively motivating participants is of great importance.
This sub-study examines motivation in WHISH intervention women through an analysis of participant responses to the question "Think about the last time you didn't feel like being active. How did you get yourself to move or get up?" Analyses of the 4,092 participant responses provides a basis upon which relevant motivational messages will be generated to encourage physical activity in the intervention participants. In addition, findings will contribute to the understanding of how older women motivate themselves to be physically active.
Exploring Perceptions of International Philanthropy
Keywords:  Department of Science
Voluntourism
Philanthropy
Service-learning
Science Technology and Society
Thesis

This thesis explores the sense of philanthropy by examining the different ways in which students from highly selective universities make sense of international public service and volunteer tourism. This paper explores the implications and effects of volunteer tourism on the student and receiving community. While volunteer tourism is treated skeptically at Stanford University, it remains a popular phenomenon throughout the western world and is a common activity listed on Stanford students’ admission applications. While many schools, especially medical schools, require some sort of volunteer work -- especially devoted, seemingly-well-rounded projects such as international volunteer work -- could schools and students be permitting and contributing to a system promoting more harm than good? Often, these international volunteer endeavors have a program fee restricting their access to those who can pay to “help.” I am not the first to recognize that this notion of volunteer travel is a problem, but there is a great divide between those who view it as a benefit and those who view it as a harm. I find that articles either dismiss or praise this notion of active philanthropy. I seek to entertain both perspectives and negotiate a way in which the altruistic urge to help is not disposed of, but rather the harmful ways in which philanthropy can be conducted are eliminated. This paper collates my personal experience, scholarly research, and original interviews of individuals who have participated in international service work. My research questions are: What are the different ways in which students from highly selective universities make sense of international public service and volunteer tourism? How can we better guide the young person’s desire to help the world? My aims are to promote an awareness of the potential harms in a seemingly benevolent effort to do good and avoid the failure that ensues from misaligned intentions. I seek to provide actionable conclusions in order to fill gaps I found present in the literature. Could international service be promoting more harm than good?
Exploring Solutions for Ocean Sustainability
Keywords:  Technology and Society
Ocean Plastic Pollution
Ocean Sustainability
Solutions for Pollution
Experiential Awareness
Attitudes of Accountability
Bermuda
Science Technology and Society
Thesis

This study seeks to evaluate the effectiveness of solutions for ocean plastic pollution by addressing the following research questions: 1) How does the perception of plastic ocean pollution vary by geographic region? And further, 2) how can more cognizant attitudes from coastal regions be applied to less cognizant attitudes in landlocked regions? The study has three key objectives. First, it examines existing literature on the issue of ocean plastic pollution. Second, it provides context for the history of plastic. In doing so, this study problematizes the cultural phenomenon of “material consumption,” examining plastic’s journey from being perceived as a design innovation to a destructive influence on the environment. Third and finally, in the data analysis section, this study assesses how a person’s “notion of the ocean” informs their attitudes of accountability towards plastic consumption and pollution. This data, taken from survey and interview responses, uses Bermuda as a case study to compare sentiments and behaviors among citizens of landlocked regions to those in coastal regions. This third component also has far-reaching implications in seeking effective solutions to mitigate the harmful impact of ocean plastic pollution worldwide.