VictorJuiz/thesis huggingface dataset:
Dynamic procedure aids support crisis attention [electronic resource]

Medical checklists can improve performance in the volatile, uncertain, complex, and ambiguous domain of emergency medicine. Such procedure aids are only now being adopted, in paper form, in hospitals and clinics across the world. Software-based aids offer an opportunity to improve upon the effectiveness of static, paper aids, since digital aids afford interactivity, high-speed distribution, and dynamic content. However, software-based medical checklists must work seamlessly in uncertain, time-pressured scenarios. In these team-based, multitasking environments, a users attention is limited. These attentional aspects of crisis computing--supporting highly trained teams as they respond to real-life emergencies--have been underexplored in the user interface community. This dissertation describes research that begins to address these challenges with design prototyping, constraint analysis, engineering, simulation, and evaluation. This dissertation describes an interactive software system, dpAid, that supports medical teams in action by displaying relevant checklist aids. dpAid helps doctors follow Advanced Cardiac Life Support (ACLS) protocol, as they respond to emergency codes such as heart attacks in operating rooms or hospital wings. The design of this system was based on 18 months spent observing Stanford medical residents responding to simulated crises in high-fidelity medical simulators with realistic patient mannequins. I develop and analyze users' time- and attention- constraints, leading to four design concepts: shared displays for ready access, step-at-a-glance for rapid assimilation, resources-at-a-glance for professional acceptance, and attention aids for limited attention. I present a simulation/evaluation approach, narrative simulation that comparatively assesses expert performance through a score-and-correct approach. I present data on the effectiveness of dynamic and interactive aids for supporting doctors as they respond to simulated ACLS scenarios, suggesting that the software-based dpAid system effectively supports crisis attention and performance. More broadly these experimental results suggest that the Dynamic Procedure Aid (dpAid) approach can improve user performance in complex, high-risk domains.

Advisor: Card Stuart K.
Hanrahan P. M. (Patrick Matthew)
Klemmer Scott
Early-arrival waveform inversion for near-surface velocity estimation [electronic resource]

Early-arrival Waveform Inversion is a powerful tool for high-resolution near-surface velocity estimation. By matching observed diving waves and refractions with forward modeled diving waves and refractions, high-resolution near-surface models can be obtained. However, conventional waveform inversion requires accurate starting models and exact matching of data amplitude. Both of these requirements are difficult to meet in field data, especially land data applications. In addition, current industry implementations of waveform inversion encounter serious I/O bottlenecks in large 3D applications.This dissertation addresses these three problems associated with practical applications of waveform inversion. The constraint of accurate starting models is relaxed by applying wave-equation traveltime inversion before applying the waveform inversion. The requirement of exact data amplitude matching is relaxed by applying a new objective function that relies heavily on phase and waveform matching, while ignoring absolute amplitude. The I/O bottleneck associated with the current industry implementations is eliminated by using a low-frequency random boundary scheme. I demonstrate the effectiveness of the methodologies using synthetic and field data examples.

Keywords: Geophysics.
Advisor: Biondi Biondo
Claerbout Jon F. advisor. Thesis advisor
Clapp Robert G. (Robert Graham) advisor. Thesis advisor
Lawrence Jesse advisor. Thesis advisor
Economic and distributional impacts from carbon fee and dividend policies [electronic resource]

The U.S. energy and climate policies currently in discussion have the potential to deliver a sizable reduction in carbon emissions. While many studies have modeled how similar polices might affect the economy, relatively few have assessed household implications. Furthermore, none of those have been under the current post-recession, post-shale gas boom economy. This dissertation examines the effects of a range of carbon fee and dividend policies in the current economic climate. The research evaluates individual economic sectors, as well as households at different income levels, and in different regions and states. The carbon fees range from
5/tCO2, each escalating at 2-8% annually. The U.S. Government's energy-economic model (the National Energy Modeling System—NEMS) was used to identify impacts to each part of the economy. To determine the outcome for households, two external consumer expenditure surveys were incorporated. The results show that this range of policies could reduce carbon emissions between 5-24% over ten years, while reducing GDP by 0.4-1.6%. Most of the avoided emissions (85%) would result from decarbonizing the electricity sector. The carbon fees would raise

Keywords: Management Science and Engineering.
Advisor: Weyant John P. (John Peter) primary advisor. Thesis advisor
Koomey Jon
Wara Michael
Education and the open mind [electronic resource] : an inquiry into the intellectual virtue of open-mindedness and its role in educational justice

Open-mindedness has been touted by philosophers as a vital characteristic of the educated mind and by educational scholars as an important component of critical thinking. This dissertation investigates open-mindedness and its educational significance. It aims to establish that open-mindedness is fundamental to the pursuit of knowledge and understanding, that it contributes to the preparation of individuals for citizenship and for pursuit of the good life, and that teachers and systems of education that undermine open-mindedness in their students are guilty of indoctrination. My consideration of open-mindedness and its educational significance comprises three papers. The first paper answers the question: what is open-mindedness? With this definition of open-mindedness in hand, the second paper considers the value of open-mindedness in greater depth through an analysis of its relationship to the liberal democratic value of autonomy. The third paper considers the demands on educators to support the development of open-mindedness through an investigation of indoctrination -- a type of bad teaching that produces or reinforces closed-mindedness. Together these three papers develop a conception of open-mindedness, explore the role of open-mindedness in autonomy and citizenship education, and consider the responsibility of educators to promote this virtue.

Keywords: Education.
Advisor: Callan Eamonn primary advisor. Thesis advisor
Labaree David F.
Reich Rob advisor. Thesis advisor
Effect of ActA expression On Intracellular Replication of Listeria monocytogenes

Expression of the bacterial protein ActA is essential for Listeria monocytogenes actin-based polymerization, motility, and subsequent cell-to-cell spread. Despite in depth characterization of the role of ActA in L. monocytogenes motility, little is currently known regarding the effect of ActA expression on bacterial growth rate. Characterization of bacterial growth rates of L. monocytogenes strains expressing or lacking ActA sheds light on the impact of the proteins expression on bacterial growth. Induced ActA expression in extracellular growth curves suggests a minimal difference in replication rates. However, cell lysis of infected endothelial cells suggests that intracellular production of ActA is correlated with a decrease in the intracellular growth rate of L. monocytogenes. This impact was found to be independent of bacterial motility associated with ActA expression. Because ActA expression is a pivotal part in L. monocytogenes pathogenisis, understanding the effect of ActA on bacterial replication during intracellular invasion sheds light on the infectious life cycle of the bacterium.

Keywords:  Department of Biology
ActA
Listeria monocytogenes
Biology
Biochemistry
Thesis
Advisor: Theriot Julie
Nelson W. James
The effect of context on teaching approaches and preschool students' learning and motivation [electronic resource]

This study examined the effects of pressure to maximize student performance on teacher intrinsic motivation for teaching and behavior (autonomy support versus control) and on child intrinsic motivation for the learning tasks and performance on the tasks. It also assessed the association between child distractibility and teacher behavior and tested whether child distractibility moderated the effect of pressure on teacher behavior. Forty-six undergraduates who volunteered or worked in preschool classrooms served as teachers for a one-on-one teaching session with a preschooler, with teachers randomly assigned to either a pressure condition (in which they were told that the child would be tested on the tasks at the end of the teaching session) or control condition (with no mention of testing). In contrast to the study's hypotheses, teachers in the pressure condition were rated as more autonomy supportive than teachers in the control condition for the tangram task. Results for distractibility were also opposite of what was hypothesized; teachers of children who were high on distractibility were rated as more autonomy supportive than teachers instructing children with relatively low levels of distractibility for both tasks. Possible explanations for the findings are discussed.

Keywords: Education.
Advisor: Stipek Deborah J.
Lit Ira W. advisor. Thesis advisor
Obradović Jelena (Education professor) advisor. Thesis advisor
Effect of Schistosomiasis Infection on the Predator-Prey Dynamics of Host Snails and Freshwater Prawns

Schistosomiasis is a parasitic disease that affects over 200 million humans across the globe, largely in sub-Saharan Africa. It is transmitted between humans and various species of freshwater host snails. One possible technique for reducing disease transmission is biological control: introducing competitors or predators of host snails to suppress their population and reduce transmission. However, little is known about the effect of parasitic infection on predator-prey interaction, especially in the case of schistosomiasis. This study details laboratory tests performed on B. truncatus and B. glabrata snails to investigate both behavioral differences between uninfected snails and those infected with schistosomiasis, and differences in consumption based on infection status by the snail predator M. vollenhovenii. Predation trials with these prawns showed a statistically significant preference for consuming snails infected with schistosomiasis. Behavioral trials aimed at explaining this preference showed infected snails to be more sluggish and less likely to avoid predation by exiting the water and hiding under vinyl substrate, providing a rationale for why infected snails were more readily available for consumption. These results both suggest increased efficacy of predation as a means of control for schistosomiasis infection in humans and provide greater insight into the effects of parasitic infection on predator-prey dynamics.

Keywords:  Department of Biology
Biology
Stanford University
Hopkins Marine Station
schistosomiasis
predator-prey interaction
Biulinus truncatus
Biomphalaria glabrata
prawn
Thesis
Advisor: DeLeo Giulio
Dirzo Rodolfo
Effects of Distracter Location on Visual Target Discrimination in Chickens

Selective visual attention has previously been studied only in humans and non-human primates. I have measured its effects in chickens. The effect of attention on perception can be measured by shape discrimination of various stimuli. When multiple stimuli are present, animals differentially process selected stimuli known as targets and suppress stimuli known as distracters. In my thesis research, I studied how the ability of chickens to attend to and identify a specific target was affected by the presence of a distracter at various locations. Behavioral tests, measured by gaze direction and reaction times, quantified shape discrimination. Three birds were trained to discriminate between squares and X’s: two birds were trained to report X stimuli as targets and to ignore square stimuli as distracters, while one bird was trained to report square stimuli as targets and to ignore X stimuli as distracters. When the target and distracter were in the same left or right hemifield, the birds were generally less accurate in choosing the target as opposed to when the target and distracter were in opposite hemifields. There was a large difference in the performance between different elevations. Data varied depending on visual field quadrant and the behavior of the bird itself. These data can provide implications about attention to stimuli, potentially leading to neural recordings that show the importance of the midbrain selection network for comparing the relative strengths of competing stimuli and selecting the one with the greatest importance for attention. An understanding of mechanisms underlying the brain’s ability to attend is needed to develop targeted therapies for psychiatric disorders, including ADHD, schizophrenia, bipolar disorder, and autism, for which there are no known cures.

Keywords:  Department of Biology
Biology
Neurobiology
Behavior
Attention
Competitive Selection
Birds
Chickens
Thesis
Advisor: Fernald Russell
Knudsen Eric I.
Effects of pH on the Growth, Herbivory, and Chemical Defenses of Macrocystis pyrifera Apical Meristems

Ocean acidification has the potential to reshape the structure of kelp forest communities dominated by giant kelp (Macrocystis pyrifera). Whereas decreasing pH has been shown to enhance the growth of kelp, acidification may also influence the grazing activity of common herbivorous species that feed on kelp. The shift in balance between changes in the rate of growth and herbivory can determine whether a phase shift from a kelp-dominated to a turf algae-dominated ecosystem will occur. This study investigated the effect of pH on the growth rate of M. pyrifera apical meristems as well as how alterations in their chemical defenses due to acidification influence the rate of herbivory. Although prior studies have documented increased algal growth under low pH conditions, few have examined whether changes in blade palatability govern the amount of grazing. Moreover, little is known about how the apical meristems, which are responsible for the vertical growth essential to the survival of kelp in their light-limited environment, are affected by changes in seawater pH. We exposed apical meristems to two different pH treatments – naturally acidified upwelled seawater from Monterey Bay, for which pH oscillated between pH 7.6 and 7.9, and a control treatment around pH 8.01 – in outdoor flow-through aquaria and measured the rate of blade growth and the polyphenol concentration to quantify chemical defense at one week intervals. Reciprocal transplant herbivory experiments were run with juvenile purple sea urchins (Strongylocentrotus purpuratus) and brown turban snails (Chlorostoma brunnea) to determine how the rate of herbivory of these two ecologically important invertebrates was influenced by pH. Kelp growth was found to be elevated under low pH conditions, while herbivory and polyphenol levels were not significantly altered. The varied response of kelp to pH highlights the dynamic balance between algal growth and herbivory and has long-term implications for the health, recruitment, and ecological underpinnings of kelp forest ecosystems as the ocean continues to acidify.

Keywords:  Department of Biology
apical meristem
biology
growth
herbivory
Macrocystis pyrifera
marine ecology
ocean acidification
phase shift
polyphenols
Thesis
Advisor: Micheli Fiorenza
Somero George
Effects of shock strength, confinement, and geometric perturbations on shock boundary layer interactions [electronic resource]

Shock boundary layer interactions (SBLIs) occur in many supersonic flows, including supersonic combustion ramjet (scramjet) engines. The successful operation of a scramjet depends on a series of oblique shock waves in the inlet and isolator sections that set up the correct supersonic conditions at the inlet to the combustor. The blockage associated with shock induced boundary layer separation can initiate unstart, a common failure mode for these engines. This Ph.D. thesis describes the effects of confinement and shock strength on three-dimensional SBLI flows in low aspect ratio ducts. SBLIs are generated in two test geometries using sub-boundary layer height compression ramps and investigated using particle image velocimetry (PIV) measurements. The two cases show significant qualitative and quantitative differences, including regular vs. Mach reflection of the incident shock and the size and strength of boundary layer separation. The sensitivity of the SBLI features to many different small perturbations in the inlet boundary conditions is also documented. Small perturbations placed in a sensitive region cause large changes in the downstream flow, whereas the flow is insensitive even to larger perturbations outside this region. Quantitative metrics for comparison of the different flow fields are developed. The datasets are well suited to CFD validation. A new framework for approximately quantifying biases in PIV measurements of high speed compressible flows is established, and its utility for performing validation of CFD results using PIV data is demonstrated.

Keywords: Mechanical Engineering.
Advisor: Eaton John K. primary advisor. Thesis advisor
Cappelli Mark A. (Mark Antony) advisor. Thesis advisor
Iaccarino Gianluca advisor. Thesis advisor
Efficient reinforcement learning with value function generalization [electronic resource]

Reinforcement learning (RL) is concerned with how an agent should learn to make decisions over time while interacting with an environment. A growing body of work has produced RL algorithms with sample and computational efficiency guarantees. However, most of this work focuses on "tabula rasa" learning; i.e. algorithms aim to learn with little or no prior knowledge about the environment. Such algorithms exhibit sample complexities that grow at least linearly in the number of states, and they are of limited practical import since state spaces in most relevant contexts are enormous. There is a need for algorithms that generalize in order to learn how to make effective decisions at states beyond the scope of past experience. This dissertation focuses on the open issue of developing efficient RL algorithms that leverage value function generalization (VFG). It consists of two parts. In the first part, we present sample complexity results for two classes of RL problems -- deterministic systems with general forms of VFG and Markov decision processes (MDPs) with a finite hypothesis class. The results provide upper bounds that are independent of state and action space cardinalities and polynomial in other problem parameters. In the second part, building on insights from our sample complexity analyses, we propose randomized least-square value iteration (RLSVI), a RL algorithm for MDPs with VFG via linear hypothesis classes. The algorithm is based on a new notion of randomized value function exploration. We compare through computational studies the performance of RLSVI against least-square value iterations (LSVI) with Boltzmann exploration or epsilon-greedy exploration, which are widely used in RL with VFG. Results demonstrate that RLSVI is orders of magnitude more efficient.

Keywords: Electrical Engineering.
Advisor: Van Roy Benjamin primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Johari Ramesh
O'Neill Daniel
Electrical activity and cell fate specification in the normal developing brain and in neuropsychiatric disease [electronic resource]

Mutations in CACNA1C, the gene encoding the L-type voltage gated calcium channel (LTC) Cav1.2, have been associated with autism, schizophrenia, and bipolar disorder. In this thesis, I investigated the role of activity through the LTC Cav1.2 on the generation of excitatory projection neurons in the developing cortex. LTCs such as Cav1.2 convert electrical activity into calcium signals that activate programs of gene expression in the developing nervous system. A gain of function mutation in an alternatively spliced exon of Cav1.2 causes Timothy Syndrome (TS), a multisystemic disorder characterized by cardiac arrhythmias and autism. Using an induced pluripotent stem cell (iPSC) platform, our lab previously reported that neurons from TS patients have altered gene expression suggesting a change in the abundance and laminar identity of early-born cortical projection neurons. As part of my thesis work, I demonstrated that Cav1.2 is expressed in the developing cortex in the mouse and human brain, and that GABA depolarization-induced calcium rises in NPCs and immature neurons can be completely blocked by pharmacological inhibitors of LTCs. I then found that splicing of Cav1.2 is dynamically regulated during mouse embryonic brain development and in human iPSC-derived cells. The exon containing the TS mutation is predominantly expressed in immature cells, and the TS mutation causes subtle alterations in Cav1.2 mRNA splicing, resulting in overabundance of the mutant exon in Cav1.2 transcripts. Through a series of in utero electroporation experiments mimicking TS, I found that over-expressing TS or wild type Cav1.2 in vivo recapitulates the differentiation defects reflected by our gene expression studies in iPSC-derived TS neurons, resulting in reduced SATB2-expressing putative callosally projecting neurons and increased CTIP2-expressing subcortically projecting cells. Over-expressing a channel that cannot carry calcium eliminates this effect, supporting the idea that excess calcium signaling may underlie differentiation defects observed in TS patient cells. In utero loss of function of Cav1.2 has the opposite effect, resulting in an overabundance of SATB2-expressing cells in the cortical plate. In a collaborative project exploring another genetically defined form of autism caused by deletion of the 16p11.2 genomic locus, we also observed a reduction in SATB2-expressing cells, suggesting the possibility of common cortical differentiation defects across ASDs. Together, this work indicates that altered expression of Cav1.2 can bidirectionally regulate the differentiation of early-born cortical projection neurons and seeds the idea that the abundance of SATB2 and CTIP2-expressing cells may be a point of convergence for multiple psychiatric disorders.

Advisor: Dolmetsch Ricardo E. primary advisor. Thesis advisor
Palmer Theo primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
McConnell Susan K. advisor. Thesis advisor