VictorJuiz/thesis huggingface dataset:
Driver behavior and state changes in autonomous vehicles

While human drivers are currently responsible for almost all of the transport of goods and people, autonomous vehicles are near-at-hand and are expected to replace human drivers in the next few decades. Several vehicle manufacturing and tech companies have begun testing their autonomous vehicles on public roads. During this period of testing, human drivers are employed to ensure the safety of the passengers and those in the immediate vicinity in the event of a failure of automation. Moreover, lower levels of automation, that are currently available to the general public, also require constant human supervision to ensure safety. This makes the study of the cognitive, behavioral and psycho-physiological state of drivers of automation crucial. In this thesis, I review existing literature on the study of driver state and behavior and on the methodologies employed by researchers to study them. I present a series of studies that investigate the changes in driver state while using automated vehicles. To this end, I employed various physio- logical sensors such as near-infrared spectroscopy, galvanic skin response, and electrocardiography. I argue the case for driver state monitoring in automated vehicles to ensure vigilance and driver availability for a take over of control. The first study I present investigates the reasons for the presence of sleepy and drowsy behavior in drivers of automated vehicles. I found that the reason for drowsy behavior was prolonged intervals of low cortical activity. The second and third study investigate the changes in cortical activity across different levels of automation and over time. These studies showed that drivers who used partially automated vehicles had the highest levels of cognitive activity and drivers of partial and fully automated vehicles showing significant decreases in cortical activity over time. In the last study, I employ a panel design to investigate the impact of prior and knowledge and training on driver preparedness and behavior. I found that drivers are prepared when they are trained on the possible failure modes of automation. However, this preparedness decreases over time in both drivers with and without any training. These studies add to the existing knowledge of driver state investigations while providing much needed insight into the longitudinal changes in driver state. It is my hope that this thesis provides the foundation for future investigations into training programs for safety drivers in autonomous vehicles and serve as guidance for developers of automated driving technology

Keywords: Mechanical Engineering.
Advisor: Leifer Larry J. 
Cutkosky Mark R. 
Follmer Sean 
Ju Wendy
Drug altered brain-state in the medial entorhinal cortex

The non-medical use of methamphetamine (MA) is a growing public health problem in the United States. MA use causes devastating behavioral and physiological changes in humans and experimental animal models. Previous studies have shown that hippocampus-associated reward circuitry, such as the dopaminergic pathways and serotonergic pathways, plays an important role in drug addiction. It has further been suggested that the hippocampal formation is responsible for the strong associative memory linked between the drug-induced rewarding effect and the spatial context during both a drug-taking behavior and relapse. Little is known, however, about how the neural substrates of context and spatial information are directly altered during drug-taking behavior. In the current study, we investigated the direct effects of MA on neuronal activities and spatial representations in the medial entorhinal cortex (mEC), a brain structure that is fundamental to an animal’s spatial cognition and learning. To map the anatomical location of MA-activated neurons in the mEC, we employed a Fos-iCreER (TRAP2) transgenic mouse line to genetically tag neurons that were activated after acute MA exposure, under the control of the c-Fos immediate early gene. We found c-Fos-expressing neurons significantly increased in a laminar specific manner in the mEC of MA-treated mice when compared to saline treated controls. More specifically, while layers 2 and 3 of the mEC showed a prominent increase in MA-induced neuronal activation, layer 5 did not. To further investigate MA-induced physiological and cognitive changes in mEC neurons, we trained mice to run on a virtual reality linear track while using a Neuropixel probe to perform high-density electrophysiological recordings. We found that MA significantly suppressed the firing rate of all neurons as well as spatially tuned cells recorded from the mEC. These spatial cells also demonstrated a strong remapping in their spatial representations and a disruption in their speed tuning after MA injection. Together, MA heavily alters the anatomical activation pattern of mEC neurons and further changes the physiological function and spatial cognition that are important for animals’ spatial navigation and self-motion.

Keywords:  Department of Biology
biology
methamphetamine
medial entorhinal cortex
grid cells
addiction
c-fos
neuron activation
reward
remapping
Thesis
Advisor: Giocomo Lisa
Chen Xiaoke
Sun Yanjun
Dynamic glass based on reversible metal electrodeposition

Dynamic windows enable electronic control of light and heat flow and demonstrate potential for increased energy efficiency in buildings and improved well-being for the people inside them. Despite four decades of research and development, the traditional approaches to dynamic windows have failed to meet the criteria for widespread adoption. Today, dynamic windows are only employed in niche environments that can tolerate the high cost, poor aesthetics, and limited contrast that are inherent to the incumbent technologies. In this dissertation, I present a novel approach to dynamic windows through the use of reversible metal electrodeposition (RME) that enables color-neutral tinting over thousands of cycles and a wider range of solar energy modulation than any existing technology

Keywords: Materials Science and Engineering.
Advisor: McGehee Michael
Salleo Alberto
McIntyre Paul Cameron
The dynamic linkage of actin to focal adhesions

Cells exert cytoskeletally-generated force to the surrounding extracellular matrix using specialized integrin-based focal adhesion complexes. Part 1 characterizes force transduction of fibroblasts in a soft fibrin extracellular matrix. Part 2 characterizes the force-dependent kinetics of the bond between focal adhesion protein talin and F-actin using single-molecule force spectroscopy

Advisor: Dunn Alexander Robert
Weis William I.
Zuchero J.
Dynamic multi-clock management for embedded systems

This dissertation proposes a kernel-based dynamic clock management system, Power Clocks, which saves energy in embedded microcontrollers by changing the clock based on computation and I/O requests. In Power Clocks, kernel hardware drivers asynchronously request clocks, providing a set of constraints (e.g., maximum speed), which the kernel uses to dynamically choose the most efficient clock. To select a clock, Power Clocks makes use of the observation that though slower clocks tend to use less power and are suited for fixed time I/O operations, faster clocks generally use less less energy per clock tick, making them suitable for computation. Using Power Clocks, a networked sensing application consumes 31% less energy than the best static clock, and within 4% of an optimal hand-tuned dynamic clock strategy, achieving significant energy savings at no implementation cost to the application developer. Unlike application-level clock control, which is limited to a single application, Power Clocks provides energy savings even when there are multiple independent applications

Keywords: Electrical Engineering.
Advisor: Levis Philip
Engler Dawson R.
Horowitz Mark (Mark Alan)
The dynamics of conduit flow in dome-forming volcanic eruptions : steady-state and time-dependent models applied to the 2004-2008 Mount St. Helens eruption

When multiple time series datasets are available at an erupting volcano, they enable studies of the volcanic system from different perspectives but should ultimately derive from common physical processes. Physics-based models of volcanic eruptions provide a natural, physical basis for integrating diverse volcanological datasets, at the same time improving our understanding of volcanic processes. By relating subsurface physical and chemical processes to observations, these models reveal controls on eruption characteristics such as magma ascent rate and explosivity. Many studies that develop physics-based models focus on qualitative comparisons between observed and predicted magma flux, a direct model output. To further realize the potential of physics-based models, we need to quantitatively incorporate multiple datasets to identify critical processes in the volcanic system. In this way, we can advance towards leveraging physics-based models to make deterministic forecasts of volcanic eruptions. In this thesis, I employ physics-based models of the shallow magma system at Mount St. Helens to understand the magma plumbing system and the dominant controls on eruptive behavior for the 2004-2008 eruption. In particular, I evaluate the roles of crystallization and gas escape in determining magma flux in dome-forming eruptions. Chapter 2 develops a steady-state model for flow in the conduit that connects the magma chamber to the surface. I apply this model to the Mount St. Helens eruption and estimate critical system parameters given data from the quasi-steady phase in the later half of the eruption. Chapter 3 extends this model to the time domain. I compare time-dependent and steady-state solutions for representative conditions at Mount St. Helens to quantify the influence of transient processes. I also determine the most influential parameters in controlling eruption behavior. Chapter 4 applies this time-dependent model in joint inversions with extruded volume, ground deformation and gas emissions data to further resolve essential properties including magma reservoir geometry, volatile contents and material properties

Keywords: Geophysics.
Advisor: Segall Paul
Dunham Eric
Suckale Jenny
Dynamics of translation termination and ribosome recycling

Translation is the final checkpoint of gene expression during which the genetic information in messenger RNA (mRNA) is converted into protein by the ribosome. One crucial piece of information encoded in the mRNA, the stop codon, instructs the ribosome to end protein translation once the full-length protein has been synthesized. The stop codon triggers arrival of release factors (RF) to promote release of the nascent protein from the ribosome (termination). Additional translation factors then bind to disassemble the ribosome off the mRNA (recycling). These protein factors facilitate the fast termination and recycling important for regular production of functional proteins and dysfunction of these stages of translation is linked to genetic diseases and cancer. Despite their importance, our current knowledge on the mechanism of even simple prokaryotic termination and recycling is incomplete. Here, I present my thesis work studying this mechanism in bacteria using single-molecule fluorescence. The simultaneous tracking of translation factor binding events and ribosome conformational changes during termination and recycling revealed the short-lived intermediates of termination and recycling that were previously elusive. Particularly, the restructuring of the ribosome that occurs during termination after class I RF catalyzes peptide release helped us understand how the ribosome is primed for the subsequent recycling of the complete translational machinery by three other factors (RRF, EF-G, IF3). These changes in the global conformation of the ribosome became the framework for the subsequent study of the mechanism of class II RF

Advisor: Puglisi Joseph D. 
Bryant Zev David 
Sarnow P. (Peter)
Dysregulation of the Circadian Clock Gene Bmal1 in Oligodendrocyte Precursor Cells and the Glial Microenvironment

Myelination is one of the brain’s most essential processes, occurring across the lifespan and suffering impairment in an array of neurological and neuropsychiatric diseases. Oligodendrocyte precursor cells (OPCs) are the proliferative progenitors that maintain a stable cell reservoir and give rise to myelinating oligodendrocytes (OLs), therefore enabling this lifelong process. Through its molecular coupling with the cell cycle, the circadian system has emerged as a distinct regulator of OPC density, proliferation, and differentiation. Here we show that the effects of circadian dysregulation in OPCs extends beyond the immediate OPC population. Microglial reactivity across mice lacking circadian clock gene Bmal1 and variation in the extent of polarization suggest intricate networks of communication between distinct glial cell populations. Future research will characterize whether those results extend to astrocytes, if circadian dysregulation affects cellular-level functions like remyelination, and whether the observed effects of knocking out Bmal1 in OPCs extend to BMAL1’s central role in the circadian system. By investigating the regulation of glial cell populations and how changes in those regulatory systems may be transduced to neighboring cell types, we hope to develop a more nuanced understanding of how these systems may be therapeutically targeted.

Keywords:  Department of Biology
Biology
Glia
Circadian
Oligodendrocyte Precursor Cells
Microglia
Thesis
Advisor: Monje Michelle
Heller Craig
Gibson Erin
Early Childhood Education Enrollment Expansion and Primary Education Achievement: Evidence from Brazilian Municipalities

Early Childhood Education (ECE) is the foundational beginning of the educational process and pivotal for future educational attainment and improving of academic potential across countries and contexts. In 2009, Brazil changed its legislation by establishing as mandatory the enrollment of 4-year-olds in the formal ECE. Since then, the country has never nationally evaluated the association between attending ECE and improvement in primary education academic achievement. Using a fixed effects panel model regression, this paper analyzes the association between 4-year old ECE enrollment rates on 5th grade test scores of Brazilian Municipalities measured in Prova Brasil between 2005 and 2017 from ECE cohorts between 1999 and 2011. The findings show that ECE was positively and statistically associated with 5th grade students’ mathematics and language scores, controlling for state fixed effects, observable municipal variables, and time fixed effects. Specifically, math and language scores increased by .05 standard deviations for every standard deviation increase in 4-year old ECE enrollment rates.

Keywords: Early Childhood Education
Standardized Testing
Academic Achievement
National Policy
Brazil
Stanford Graduate School of Education International Comparative Education
Thesis
Eco-cultural Management Implications of California Hazelnut Treatment with Wild and Prescribed Fire: A Case Study in Northern California

The tribal nations of northwest California are restoring their practice of cultural prescribed burning to facilitate the regeneration of basket-making materials, medicines, and food. Among the cultural foods are California hazelnut nuts (corylus cornuta var. californica). California hazelnut nut production was hypothesized to improve through the application of fire at certain points in the development of hazelnut stands and the biological communities surrounding them. In order to investigate the effect of fire on California hazelnut nut productivity, multiple 100 m2 sampling plots were created within areas where wildfires or prescribed burns had occurred, and areas where they have not occurred in >13 years. In those plots, precipitation, nuts per shrub, solar access of individual shrubs, stem diameter, number of stems, among other relevant factors in nut production were measured. Time since last fire (TSLF) was later calculated based upon CalFire fire perimeter maps. Monitoring areas were identified through the local knowledge of Tribal and United States Forest Service staff. Generalized linear mixed models (GLMMs) indicate that the number of nuts produced by individual hazelnuts varied based on interactions between solar access and TSLF. Based on the results of this study, there are multiple ways to manage hazelnut shrubs in order to optimize nut production for cultural food usage. Future studies need to focus on the correlation between fire regime factors and the prevalence of other cultural resources in order to determine the most economically efficient way of applying fire to tribal and public lands.

Keywords:  Earth Systems Department
Fire
Wildfire
Tribal Governance
Cultural Resources
Text
Thesis
Advisor: Vitousek Peter
Effect of cervical spine and helmet properties on traumatic brain injury

The human brain is the most vital organ in the body, acting as the command center of the nervous system and embodying the essence of the human ingenuity that separates our species from the rest of the animal kingdom. Injuries to the brain, known as traumatic brain injuries (TBI), can be devastating and cause a wide-range of physical and psychological effects, even from mild forms of these injuries. Mild traumatic brain injury (mTBI), more colloquially known as "concussion, " is extremely common in sports and recreation, yet is notoriously difficult to diagnose or prevent. With mounting evidence that mTBI can cause long-term neurodegeneration and cognitive disorders, an increased scrutiny has been placed on contact sports, with many suggesting that sports like football face an existential crisis as parents consider them unsafe for their children. This thesis furthers our knowledge of brain injury prevention. First, a methodology for evaluating mTBI risk from sensor data is presented. Second, the role of the cervical spine musculature and skeletal configuration in mTBI risk is investigated. Building off of this work, the most vulnerable locations on the head to injury are identified, and implications for helmet design are discussed. Lastly, we propose a novel helmet technology based on a hydraulic shock absorption system and evaluate this system using simulation and experimentation. Using American football as a model system for brain injury, this thesis contributes a comprehensive view of how neck musculature, impact location, and helmet properties can be modified to reduce the risk of brain trauma in contact sports

Keywords: Mechanical Engineering.
Advisor: Camarillo David 
Cutkosky Mark R. 
Delp Scott
The effect of chief accounting officers on financial reporting quality

This study examines the effect of Chief Accounting Officers (CAOs) on financial reporting quality. I hypothesize that firms that employ a CAO will have better financial reporting quality. I posit that the CAO is different from other executives in incentives, priorities, and background and that they therefore provide valuable oversight over the firm financial reporting process. Indeed, I find that firms with CAOs have lower rates of severe restatements, instances of just meeting or beating earnings targets, and internal control weaknesses. I further structure tests that control for the firm's endogenous choice to appoint a CAO, with results that are generally consistent. I also test financial reporting quality by examining earnings management around seasoned equity offerings. I find that accruals earnings management is mitigated in CAO firms. Next, I examine CAO, CEO, and CFO compensation and career concerns to determine if differences in incentives drive these findings. CAO turnover occurs in the years around restatements and ICWs. I also find that CAO tenure is negatively associated with severe restatements, abnormal accruals, instances of just meeting or beating earnings targets, and internal control weaknesses Overall, these results suggest that having a designated CAO is associated with various improvements in financial reporting quality and that these improvements are related to the CAO's tenure within the firm

Keywords: Gipper, Brandon degree committee member.
Business.
Advisor: McNichols Maureen
Kasznik Ron
Effect of imagine-self and imagine-other virtual reality perspective taking tasks on affective empathy and prosocial behaviors

The present investigation examined whether there are differential effects on empathic concern, personal distress, and prosocial behaviors based on the type of virtual reality perspective taking (VRPT) task employed, and explored the underlying mechanism mediating the effect of VRPT tasks on prosocial behaviors. Participants performed either an imagine-self VRPT task (i.e., imagined how they would think and feel if they were in the target's situation as they virtually experienced the target's situation), an imagine-other VRPT task (i.e., imagined what the target thought and felt as they virtually experience the target's situation), remained objective during a VRPT experience, or did not complete a VRPT task at all. Results from three planned contrasts revealed any type of VRPT is more effective at eliciting empathic concern, personal distress, and prosocial behaviors than not completing a VRPT task at all. Results also showed that participants who remained objective during a VRPT experience reported lower levels of personal distress but similar levels of empathic concern compared to the VRPT conditions. Additionally, participants who remained objective performed a similar proportion of prosocial behaviors, but only when the effort required to perform the prosocial behavior was low. Moreover, the final contrast revealed that participants who performed an imagine-self VRPT reported higher levels of personal distress, believed the world to be less just, and performed more prosocial behaviors requiring more effort than participants in the imagine-other condition. Mediation and moderation analyses revealed that personal distress mediated the relationship between type of VRPT task and prosocial behaviors while empathy moderated the relationship between personal distress and prosocial behaviors. However, this was only true when the prosocial behavior required high empathic effort. These results suggest that a combination of both subcomponents of affective empathy are necessary to motivate participants to perform effortful prosocial behaviors

Keywords: Communication.
Advisor: Bailenson Jeremy
Hancock Jeff 
Reeves Byron
Zaki Jamil
Effect of maternal obesity on preimplantation embryo development and non-invasive densitometry aproach to select healthy embryos in mice

Poor fertility outcomes in obese women have been well recognized, but the underpinning causes are still poorly understood. While overall the fertility is impaired, wide heterogeneity in successful pregnancy has been observed, suggesting that some embryos have the intrinsic ability to develop to term but efforts in developing a non-invasive selection of healthy embryos have been limited. In order to study the effects of obesity on preimplantation embryos we studied two mouse models of obesity, leptin mutant ob/ob and diet induced obesity (DIO) models. Here we demonstrate that obese female mice show poor quality in oocyte and preimplantation embryos, and retardation of development, elevated lipid contents. Transcriptomic analysis revealed disruption of metabolic genes and downregulation of AMPK pathway. For the first time, we measured preimplantation embryo density with non-invasive method and showed that density is correlated with lipid content and can be used as a predictive parameter for successful postimplantation development. This is a proof of concept of using density measurements as noninvasive method to select healthy embryos in obese mothers as early as 4 cell stage

Keywords: Biology.
Advisor: Sebastiano Vittorio
Demirci Utkan
Red-Horse Kristy
Winn Virginia