VictorJuiz/thesis huggingface dataset:
Using machine learning and optical coherence tomography to generate a non contact biopsy images

In vivo Biomedical imaging is an important part of diagnostic, therapeutic medical treatment and research. The field is constantly searching for viable clinical tools at the micro-scale (single cell resolution). Optical Coherence Tomography (OCT) enables real-time imaging of living tissues in 3D up to 1mm. In this work we develop tools and models to better quantify the OCT signal, we then apply those tools on two exciting applications in living mice brain imaging and early detection of skin cancer. We have developed a model to accurately quantify the signals produced by endogenous scattering in OCT imaging. This model predicts distinct concentration-dependent signal trends that arise from the underlying physics of OCT detection. The relation between OCT signal and particle concentration is approximately linear at low concentrations. However, at higher concentrations, interference effects cause signal to increase with a square root dependence on the number of particles within a voxel. Predictions were validated by measuring OCT signals from phantom models as well as living animals. More generally, the model described herein may inform the interpretation of detected signals in modalities that rely on coherence-based detection or are susceptible to interference effects. We then build a theoretical model for speckle noise, one of OCT's most prominent issues preventing us from experiencing the full potential of this technology. Our theoretical analysis using Monte Carlo simulations indicates that pure angular compounding (a common technology for reducing speckle) can improve the signal-to-noise ratio by no more than a factor of 1.3. We conclude that speckle reduction using angular compounding is equivalent to spatial averaging. We then shift gears and present how the above tools could be used to detect microscopic movement in living brain. We introduce a novel OCT-based neuroimaging setting and accompanied feature segmentation algorithm enabling rapid, accurate, and high-resolution imaging of 700 mu depth across the mouse cortex, in-vivo. We demonstrate 3D reconstruction of microarchitectural elements in a whole cortical column. Features as Central Nervous System cell bodies density, volume, and average distance to the nearest cell can be quantified to better study the brain by this highly transformative and versatile platform. We developed a laser-based barcoding technology that allows us to achieve precise registration of OCT images with H&E pathology images. This approach enabled us to assemble a library of > 1000 OCT - H&E images pairs from human skin samples. We then train a generative adversarial neural network on the image library and demonstrate the ability to virtually generate realistic H&E images directly from OCT images. The combination of the above technologies opens the door to a virtual biopsy allowing clinicians to examine H&E sections of a suspected area but bypassing the intensive and expensive biopsy

Advisor: De la Zerda Adam
Chu Steven
Levitt Michael
Validation and development of iron as an imaging-based biomarker of neuroinflammation in Alzheimer's disease

Despite decades of research, Alzheimer's disease (AD) remains poorly understood and without effective treatment or prevention. The presence of amyloid beta and tau pathology together is thought to result in neurodegeneration, or the loss of synapses and neurons, but the mechanism by which the two interact to produce this neurodegeneration is unknown. Recent data suggest an interplay between inflammation and iron dysregulation in the pathogenesis of AD that may be a key component of AD pathology. Most of this work, however, has lacked the simultaneous analysis of iron, inflammation, and hallmark AD pathology, necessary to elucidate the mechanistic link between iron and neurodegeneration in AD. To address this gap and deliver iron as a biomarker for AD, we have developed a novel, multimodal ex vivo imaging pipeline, integrating novel correlative MR-histology tools with advanced microscopy, including electron microscopy and x-ray microscopy techniques, to interrogate iron deposition and oxidation state in human brain tissue in situ. We have additionally implemented a novel prospective motion correction system for high-field MRI to enable ultra-high-resolution human brain imaging and facilitate the translation of our ex vivo findings to the patient setting. While the initial application of these tools has been to validate iron as a biomarker of neuroinflammation in AD, we have developed a broadly applicable set of imaging tools with the potential to molecularly validate and translate MRI-based biomarkers across tissue types and diseases

Keywords: Bioengineering.
Advisor: Pelc Norbert J.
Zeineh Michael 
Hargreaves Brian Andrew
Rusu Mirabela
Validity of at-home rapid antigen lateral flow assay and artificial intelligence read to detect SARS-CoV-2

Background: RT-PCR—the current reference standard to detect SARS-CoV-2—is costly and
slow, requiring a sophisticated laboratory with an average test turnaround time of one to two days. Rapid at-home and point of care (POC) testing is urgently needed to prevent COVID-19 transmission throughout the world, particularly in low and middle-income countries.
Objective: We assessed the diagnostic accuracy of an at-home rapid lateral flow antigen assay (Cellex) with artificial intelligence interpretation by smartphone (Gauss) to detect SARS-CoV-2 antigen (Lateral flow with AI read; LFAIR). We also serially assessed the diagnostic accuracy of the LFAIR in SARS-CoV-2 positive individuals over several days and compared the LFAIR results with polymerase chain-reaction cycle threshold (CT) value.
Methods: We recruited 33 individuals from two clinical treatment trials of COVID-19 and 88 participants from a population-based surveillance study. Individuals recruited from the clinical trials were asked to complete the LFAIR daily for five days. Participants from the population-based study completed one LFAIR. All participants were provided kits with no instructions from study personnel and were asked to complete the tests at home. The LFAIR results were compared to RT-PCR, the current reference standard, as either dichotomous outcome or as continuous CT value. We also assessed LFAIR results by days since symptom onset.
Results: Using the first test completed by each subject, the LFAIR was 86.2% sensitive (95% CI 73.6% - 98.8) and 94.3% specific (95% CI 88.8% - 99.7%). With a GEE model that adjusted for days since symptom onset and repeat testing, the sensitivity was predicted to be 97.78% (95% CI 89.9% - 99.5%) on the first day with a 0.89% (95% CI 0.30 - 1.61%) decrease in sensitivity with each additional day after symptom onset. The LFAIR test line intensity decreased inversely with CT value, a proxy for viral load (McFadden pseudo R2 = 0.49; Nagelkerke pseudo R2 = 0.99)
Conclusions: An at-home LFAIR shows high levels of diagnostic accuracy. Intensity of the at-home antigen test line is inversely related with an individuals’ SARS-CoV-2 viral load. The test has potential for broad-scale implementation to minimize the spread of SARS-CoV-2.

Keywords:  Department of Epidemiology & Population Health
Department of Epidemiology &amp; Population Health
Stanford University
School of Medicine
SARS-CoV-2
COVID-19
Antigen test
Diagnostic accuracy
Thesis
Advisor: Parsonnet Julie
Kohn Michael
Visual anemometry : wind speed measurement through visual observation of fluid-structure interactions

Information about the flow incident on an object is encoded in the observable characteristics of the structural response. Fluid-structure interactions such as the flapping of flags and swaying of trees are ubiquitous in the built environment and in nature. This thesis explores methods by which visual observations of such fluid-structure interactions can be used to make quantitative, instantaneous flow speed measurements. Videos capturing the responses of flags, flexible cantilevered cylinders, and trees were collected in laboratory and field experiments. Visual anemometry techniques were developed to infer the incident wind speeds from the observed structural responses, using both data-driven and physical modeling approaches. Results suggest that observations of common structures such as trees can be leveraged for quantitative flow speed measurement

Keywords: Mechanical Engineering.
Advisor: Dabiri John O. (John Oluseun)
Lele Sanjiva K. (Sanjiva Keshava)
Eaton John K.
Gorle Catherine
Visual intelligence through human learning

At the core of human development is the ability to adapt to new, previously unseen stimuli. We comprehend new situations as a composition of previously seen information and ask one another for clarification when we encounter new concepts. Yet, this ability to go beyond the confounds of their training data remains an open challenge for artificial intelligence. My research designs visual intelligence to reason over new compositions and acquire new concepts by interacting with people. I draw on ideas from human learning---from human cognition and human interaction---to deliver representations, training frameworks, models, evaluation protocols, and interactions for computer vision. My dissertation will explore some the challenges associated with existing vision methods and present the two following lines of work: Drawing on human cognition, I will introduce scene graphs, a cognitively-grounded, compositional visual representation. With the scene graph representation, I will show that it possible for models to learn from a finite set of situations outlined in their training data and allows models to recognize new composition of previous seen concepts. I will build scene graph models that can recognize new visual relationships with as few as

Advisor: Bernstein Michael S.
Li Fei Fei
Agrawala Maneesh
Manning Christopher D.
Wars on drugs and uprisings : the maintenance of everyday intervention in Peru

This dissertation critically investigates how state-led, US-supported war and intervention are governed, maintained and experienced. This research is based on twenty months of ethnographic fieldwork in Peru's Huallaga Valley, where for decades the governments of the Peru and the United States have conducted militarized and development-based interventions in the name of the war on drugs and war on terror. These interventions are premised on the Huallaga as a site of conflict between Shining Path insurgents, civilians, and the state in Peru's internal war in the 1980s and '90s, and as a former global leader in the production of illicit coca, the leaf crop used to make cocaine. These efforts are carried out through state-based, internationally-supported "alternative development" programs that simultaneously aim to disable internal conflict, eradicate drug crops, and promote new licit economies in place of illicit drug crop production. In this way, state and international agencies make the war on drugs an essential aspect of efforts to establish peace in drug-crop producing countries during and after internal conflict. While men and weaponized violence are often centered in public imaginaries of war and the illicit drug trade, this research focuses on the people, politics, and intimate everyday experiences that exist beyond these frames. Drawing on research with development officials, former and current drug crop farmers, domestic workers, coca eradicators, sex workers, military personnel, and Peruvian and US government employees, this work analyzes how the embodied and affective labor of a wide range of actors contributes to the maintenance of protracted war. It also discusses less-considered forms of violence, including domestic violence, that persisted before, during, and after internal conflict. While political and interpersonal violence are often analyzed separately, this work details the ways they were intricately linked. It shows how these linkages were integral to the governance of protracted war, and to the ways that cycles of violence against rural mestizo and Indigenous women, men, and gender-nonconforming people were perpetuated in landscapes of sustained intervention. In investigating extended forms of US and state interventionism deployed through the war on drugs and the complexities of everyday life as they existed in within and around these circumstances, this research demonstrates how hegemonies of power were constructed and challenged in daily life

Keywords: Anthropology.
Advisor: Ebron Paulla A.
Ferguson James
Mathews Andrew S.
Thiranagama Sharika
We Built This City: An Analysis On The Environmental Impacts Of Gentrification

Issues of sustainability and environmentalism are becoming increasingly problematic in urban planning and city structures. These issues are being amplified through the process of gentrification. This paper aims to investigate and determine the environmental impacts of gentrification on urban districts. Gentrification is the action by which the character or a poor urban area is changed by an influx of wealthier residents, improved building structures, and new businesses. Gentrification is increasingly problematic because this rapid transformation displaces the current inhabitants who can no longer afford to live in their own neighborhood. While the societal implications are clear, there is little existing work on the environmental implications of this process. Therefore, the main research question of this paper is: what are the environmental impacts of gentrification?
The goal of this honors thesis is to understand, analyze, and discuss gentrification, in terms of both environmental and social justice. To understand the potential environmental impacts associated with gentrification, this study leverages an energy optimization model that predicts patterns and changes in gentrified districts. The thesis specifically looks at energy supply, energy demand, carbon emissions, and changes in building mix in gentrified districts and compares this analysis to districts that have not been gentrified. This paper also analyzes the greater repercussions and history of gentrification to make these findings more inclusive and holistic. Hopefully these conclusions will allow us to better understand the impacts of gentrification and offer solutions to make this process more sustainable and less harmful to the lower-income communities being driven out of their homes.

Keywords:  Department of Science
Gentrification
Sustainability
Energy
Urban District
China Town
Thesis
Advisor: Lepech Michael
Kalehbasti Pouya Rezazadeh
"We can do better": how land trusts engage with environmental justice

The mainstream environmental movement in the U.S. has long promoted land conservation and natural resource management. More recently, some within the movement have begun to emphasize environmental justice, examining the ways in which conservation intersects with social and political issues. Using the 1991 Principles of Environmental Justice as an orienting framework, this study uses surveys and interviews to examine the ways in which land trusts engage with issues of equity, justice, and access in their work. Land trusts are private nonprofit conservation organizations which have traditionally worked to conserve ecologically and scenically important land through a variety of acquisition mechanisms, including land purchase and conservation easements. A subset of these organizations are increasingly interested in environmental justice. Using the Land Trust Alliance’s 2015 Census data, I find that significant justice, equity, and access work is most likely to occur within organizations that protect land in urban areas, draw on a broad base of volunteers and visitors, and prioritize local community work over broader landscape-scale conservation efforts. Through six case study interviews, I find that land trusts engage in a wide variety of programming that centers marginalized communities, including education, community gardens, local partnerships, and active community governance. Yet many roadblocks, both practical and systemic, prevent broader implementation of environmental justice principles. In addition, because land trusts are constantly beholden to competing and varied interests and stakeholders, I find that programs run by individual land trusts may simultaneously promote and undermine the principles of environmental justice. Ultimately, I propose a series of recommendations at both the individual and systemic levels for land trusts to align their purpose and programming with environmental justice principles.

Keywords:  Earth Systems Program
Earth Systems
School of Earth Energy &amp; Environmental Sciences
land trusts
environmental justice
Thesis
Advisor: Ardoin Nicole
Thompson Barton H.
Casciotti Karen
We Never/Land: Shifting Perspectives on Social Death Through Music, Affect, and Adventure

Afro-pessimist theorists Saidiya Hartman, Jared Sexton, Frank Wilderson, and Orlando Patterson argue that Black people exist in a state of social death, defined as the condition of enslavement or lack of personhood. This project investigates the application of social death, specifically how the abstraction of the theory creates a disjunction with the everyday. I argue that regardless of the critical analysis Afro-pessimism invites, it does not fully reckon with the affective experience of Black people today. I wrote and produced Never/Land, an interactive album, in order to explore the affect of social death and its impact on my Black consciousness. By bringing awareness to the suffering that I experience as a result of the legacy of enslavement, I found that social death is an opportunity for new possibilities of Black life. Ultimately, Black people must mourn the death of the social in order to find a world capacious enough to hold the simultaneity of life and death. From social death emerged the archive of Never/Land, a documentation of beautiful things found by those in bondage.

Keywords:  African and African American Studies Program
social death
affect
race theory
black consciousness
music
afropessimism
African and African American Studies
Institute for Diversity in the Arts
Thesis
Advisor: Robinson Aileen Kaye
Wearable haptic devices for social and virtual interaction

Augmented and virtual reality allow users to visually experience fantastic artificial environments. Haptic technology increases immersion and realism in these environments by allowing users to touch and interact with virtual objects. For example, using haptic technology, surgeons can practice surgical tasks in simulation and people can virtually feel a comforting touch from loved ones at distant locations. Specifically, haptic technology is the design of devices to communicate information through touch. The information could be a message from a person, robot, or virtual avatar, or the mechanical properties of a virtual object. Wearable haptic technology allows users to receive haptic information without constraining their movement in space, giving them the ability to perform other tasks simultaneously. In this talk, I will present three strategies that can be used to increase the amount of information communicated by a wearable haptic device. First, we describe, demonstrate, and validate a device framework for a body-mounted vibrotactile display. The display allows users to receive haptic signals at the forearm, where the device is mounted, and at the fingertips when the user chooses. We show that stimulating the forearm and fingertips simultaneously does not affect user performance compared to stimulating the fingertips alone when large amplitude signals are used. The display is wearable yet allows for communicating signals to the fingertips, which have the densest packing of mechanoreceptors, without impeding manipulation tasks by mounting the display directly to the finger. Next, we record subject's expressing a set of emotions to a body-mounted pressure sensor array. We describe a data-driven method to produce haptic signals based on the data recordings and we validate that the haptic signals successfully communicate emotions in a user study with a physical haptic device. The results show that a discrete representation of touch signals can be recorded and used to relay emotions to humans without training. Finally, we fabricate two 4-degree-of-freedom origami haptic devices for the fingertip that can deliver normal force, shear force, and torsion. We evaluate the performance of each device via analysis of their workspace, bandwidth, and force output. The two devices are created using novel manufacturing processes that enable affordable and scalable haptic technology for the fingertip or other locations on the body. Classically, haptic signals are designed by hand by haptics researchers or study participants; here I present strategies that enable the future of content creation for haptic devices. The combination of a body-mounted framework, a data driven approach for effective haptic signal generation, and novel 4-degree-of-freedom fingertip devices comprise a suite of hardware and software that creates compelling and lightweight wearable technology

Keywords: Electrical Engineering.
Advisor: Okamura Allison
Cutkosky Mark R.
Fan Jonathan Albert
Wetzstein Gordon
Wearable systems for monitoring physical activity and optimizing an ankle exoskeleton

Globally, hundreds of millions of people face mobility challenges in their daily life due to obesity, injury, muscle weakness and deterioration, and age. Mobility is closely related to people's independence and quality of life. Having limited mobility impacts many factors such as physical activity, quality of sleep, and symptoms of depression and anxiety. Historically, people address these mobility challenges by visiting experts in a clinic. The patient discusses the problem, performs some physical or medical tests using laboratory equipment, and then receives a diagnosis or rehabilitation instruction from the clinician. Periodic visits may be needed for rehabilitation or monitoring their progression. People must be able to reach a clinic, afford the payments, and make the time for the visits and tests in order to try to solve their mobility challenge. Thus, only a small fraction of the global population can benefit from the knowledge and solutions provided by a clinic. Translating these clinical solutions for use at home could address mobility challenges on a larger scale. Creating at home solutions to these mobility challenges is difficult because the technology must be both portable and accurate. Ideally, these at home solutions would be wearable, low-cost, and easily used for days or weeks. In addition, these at home solutions must be accurate enough to provide meaningful outcomes to mobility. Clinical solutions may rely on expert knowledge, careful calibration of sensors, and specialized equipment which are challenging to imbue into a device that can be operated by any person. This thesis presents the design and evaluation of wearable systems to monitor movement, estimate energy expenditure, and optimize exoskeleton assistance. These projects explore how clinical mobility tools can be translated into wearable solutions. Wearable technology may be able to provide the same functionality as clinical tools to a much broader population facing mobility challenges. Thus, these wearable tools may allow many more people to improve their mobility

Keywords: Mechanical Engineering.
Advisor: Delp Scott
Kochenderfer Mykel J.
Collins Steve (Steven Hartley)