VictorJuiz/thesis huggingface dataset:
Using X-ray scattering and transient absorption to probe global and local structural dynamics of the bimetallic photocatalyst [Ir2(dimen)4]+2 [electronic resource]

Mechanistic pathways of inorganic homogeneous catalyts are determined not only by the reactive electronic structure but also the precise arrangement of the atoms within the catalyst. Furthermore, without knowing precisely how nuclear structure and electronic structure affect each other, computational methods may not be able to accurately portray the behavior of certain inorganic complexes. Ir2(dimen)4{+2} (dimen = 1,8-diisocyano-p-menthane) is such a system. X-ray crystallography has long supposed that this particular d8-d8 dimer has two thermally accessible minima on the same ground state and more recent temperature dependent solution spectra support this but, so far, computational efforts have not been able to recreate a double minimum potential energy surface. However, a simple quasi-empirical mechanical spring model has been proposed in the literature which features two minima with a shallow barrier. Herein, a combination of transient absorption (TA) and time-resolved X-ray diffuse scattering (XDS) is used to determine that the potential energy surfaces of ground and excited state follow this model. When exciting extremes of the HOMO-LUMO band which have been inferred to correspond to each ground state minima, we are able to use vibrational wavepacket analysis to qualitatively confirm that the ground state possesses two minima while the excited state has only one, as predicted in the literature model. Furthermore, we are able to observe ground state interconversion in real-time, occuring the in ~10ps regime, confirming that interconversion is thermally accessible but with a barrier height over five times larger than predicted. Furthermore, a combination of XDS and Born-Oppenheimer Molecular Dynamics is used to produce a global picture of Ir2(dimen)4{+2} in solution in which a detailed molecular solvent response is characterized for the excited state. Using this approach, it was found, both computationally and experimentally, that he methyl groups prefer to coordinate to the ground state and recoordinate via the nitrile group in the excited state which is quite unexpected and could not be predicted by continuum models or electrostatic arguments.

Keywords: Chemistry.
Advisor: Gaffney Kelly primary advisor. Thesis advisor
Bucksbaum Philip H. advisor. Thesis advisor
Fayer Michael D. advisor. Thesis advisor
Utilizing C. elegans as Environmental Metal Biosensors to Determine the Effect of Weak Metal-Chelators in the Presence of Heavy Metals

Glyphosate, originally patented as a metal chelator, is a primary active ingredient in many herbicides used worldwide. While glyphosate alone is thought to be non-toxic, the possibility that its metal-chelating properties could contribute to its toxicity in vivo has not been tested. Normally, strong chelators cause bound metals to be inert, and therefore easy to dispel. However, a weaker chelator such as glyphosate could allow metal ions to pass into the body until the complex reaches a region with low pH, which can lower the stability of the metal-chelator complex in vitro. With a weaker metal-chelator bond, the complex may dissociate, leaving the heavy metal ions in the tissue, potentially causing toxicity. However, there is a lack of in vivo systems to test this hypothesis. Because of their responsiveness to metal stress, C. elegans have proven useful as environmental biosensors. For this work, a collection of transgenic GFP (green fluorescent protein) reporter strains was generated utilizing CRISPR/Cas9 to study the hypothesis. Each strain bears GFP (green fluorescent protein) under the regulation of genes involved in the metal stress response pathway and exhibit dynamic metal- and dose-dependent GFP induction. The strains were then exposed to varying conditions of both metal and chelating agents at low and high pH. The results show an ability to quantify modest and dose-dependent changes in metal response in living animals, and hence to evaluate conditions under which the weak chelator might potentiate effects seen with metal-only conditions. This work establishes a technical foundation for further study of chelation-dependent effects of metal deposition and toxicity. Future research may provide valuable insight into the potentially toxic interactions of the widely-used herbicide ingredient, glyphosate, and demonstrates the need for further investigation.

Keywords:  Department of Biology
Biology
Transgenic C. elegans
GFP reporter
metal stress response
weak chelators
CKDu glyphosate
Thesis
Advisor: Fire Andrew
Mudgett Mary Beth
Utilizing consumer technologies to design accessible medical training and imaging tools [electronic resource]

The development of modern medicine has led to an unfortunate, but popular assumption: that advanced medical technologies are exorbitantly expensive and almost exclusively relegated to big hospitals. This work aims to subvert this assumption by providing a new model for carrying over the ten-fold reductions in cost and size found in the consumer space to the medical world. It accomplishes this task by outlining three key steps to incorporating consumer technologies into medical devices: modularization, simplification, and recycling. This work is then grounded in two novel systems which utilize the proposed framework to drastically reduce their cost and size relative to current options. The first is a handheld volumetric ultrasound system that is portable and can be produced for 10% of the cost of current volumetric ultrasound systems. The second is a virtual reality surgical trainer that packs flat, runs on a phone or tablet, and can be produced for 1% of the cost of current surgical trainers. The low-cost and portability of these new devices serve to not only make the current level of care more accessible, but also to open up entirely new applications.

Keywords: Mechanical Engineering.
Advisor: Leifer Larry J. primary advisor. Thesis advisor
Salisbury J. Kenneth primary advisor. Thesis advisor
Srivastava Sakti
VCAM1 is upregulated by an aged systemic milieu and regulates hippocampal neurogenesis through brain endothelial cell-mediated interactions

Brain structure and function are known to decline steadily with age, and recent models of aging implicate the circulatory environment in this process. Experiments in which young mice are exposed to aged blood demonstrate that pro-aging factors in the blood of old individuals induce hallmarks of brain aging, such as increased neuro-inflammation and a decline in neurogenesis. The inhibitory factors present in aged blood are still being identified, and whether these factors cross the highly selective blood brain barrier or act primarily through peripheral interaction with brain endothelial cells (BECs) remains unknown. In this study, we aimed to elucidate the mechanisms underlying regulation of Vascular Adhesion Molecule 1 (VCAM1), an adhesion molecule upregulated in BECs in response to aged blood and systemic inflammation, and assess whether Vcam1 deletion can rescue the decline in adult neurogenesis. We show that brain endothelial VCAM1 increases in expression in vitro and in young mice exposed to aged plasma. Additionally, while it has previously been shown that injection of aged plasma inhibits hippocampal neurogenesis in young mice, here we demonstrated that genetic deletion of Vcam1 prevents these inhibitory effects of aged plasma on hippocampal neurogenesis, suggesting that activated BECs inhibit neuronal regeneration through VCAM1-mediated peripheral interactions. Collectively, our results indicate that VCAM1 is involved in the regulation of adult neurogenesis in response to age-related systemic inflammation, making the adhesion molecule a therapeutic target for ameliorating the decline in brain function characteristic of old age.

Keywords:  Department of Biology
VCAM1
brain endothelial cells
hippocampal neurogenesis
systemic inflammation
neurodegeneration
aging
biology
Thesis
Advisor: Wyss-Coray Tony
Fernald Russell
Violence, justice, and reconciliation [electronic resource] : the politics of transitional justice in societies recovering from war

Serious human rights violations committed during civil war erode the political and social fabric in decisive ways. In addition to the physical violence and tremendous emotional trauma, they also fundamentally change the way in which citizens view their state -- the very entity whose existence is premised on protecting and securing the safety of its citizens. This dissertation explores how post-conflict governments respond to such war crimes, crimes against humanity, and other serious human rights violations committed during internal armed conflict. Why do some governments aggressively punish perpetrators of human rights abuse, while others embrace a policy of truth-seeking or even forgiveness? What impact do these policies have on the relationship between the state and its citizens? Combining formal theory with econometric techniques and case studies from Sub-Saharan Africa and Latin America, this dissertation seeks to explain the diversity of government uses of transitional justice policy. Further, original experimental evidence from Guatemala casts light on the long-lasting consequences of these policy choices on the political perceptions of citizens affected by war.

Keywords: Political Science.
Advisor: Magaloni Beatriz primary advisor. Thesis advisor
Blaydes Lisa
Laitin David D. advisor. Thesis advisor
Virtual Reality: Worth The Investment?

This essay will walk one through the history, current state and future of Virtual Reality technology. It will include a detailed analysis of Virtual Reality in comparison to the Smartphone along with a detailed illustration of some of the major applications of Virtual Reality Technology: Education, engineering, health care, live events, military, real estate, retail, sports and Video Games. Similarly, it will outline some of the most recent hardware and software developments. And finally, it will address the constraints and limitations of the technology and how these shortcomings could act as hurdles to the success of Virtual Reality. Through its entirety one will be able to gain a comprehensive understanding of the technology- what it does, what it will do and why it is worth investing in. Beyond its monetary value, the conclusion of this piece will touch on the important role that Virtual Reality can have in creating a more empathetic and skilled society.

Keywords:  Department of Communication.
Virtual Reality
Stanford University
Department of Communication
Media Studies
Thesis
Advisor: Hamilton James
Visual computational sociology [electronic resource] : computer vision methods and challenges

Targeted social and economic policies require an understanding of a country's demo- graphic makeup. Thus, countries like the United States spend more than 1 billion dollars a year gathering survey based census data such as race, education, occupation and unemployment rates. In this work, we explore the use of publicly available digital imagery to measure demographics without the high costs incurred by surveys. These results can then be inputs to critical socioeconomic policies. In particular, we apply computer vision methods to 50 million Google Street View images from 200 cities and show that a wide range of characteristics such as income, education levels, voting patterns, race, CO2 emission per capita and other market research results can be accurately inferred from these images. We specifically use fine-grained image recognition techniques to detect and classify approximately 21.8 million cars and use them to predict demographics. One can imagine using multiple objects such as trees, clothes, houses or people themselves to further extend this analysis and improve its accuracy. However, scal- ing these methods to other objects such as trees, clothes, houses or other objects using current supervised methods is infeasible. Fine-grained datasets are notoriously expensive to collect and it is not possible to annotate images of objects in every pos- sible form they can appear in the world. We present scalable methods of collecting synthetic fine-grained datasets and present an attribute based fine-grained domain adaptation method to perform data efficient classification.

Keywords: Electrical Engineering.
Advisor: Li Fei Fei
Ermon Stefano advisor. Thesis advisor
Gill John T.
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning [electronic resource]

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. Here, we propose a novel similarity-learning framework, SIMLR (single-cell interpretation via multiple kernel learning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization applications. Benchmarking against state-of-the-art methods for these applications, we used SIMLR to re-analyse seven representative single-cell data sets, including high-throughput droplet-based data sets with tens of thousands of cells. We show that SIMLR greatly improves clustering sensitivity and accuracy, as well as the visualization and interpretability of the data.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Curtis Christina advisor. Thesis advisor
Kundaje Anshul
Visualization and evaluation tools of quantitative MRI in an ACL-injured population [electronic resource]

Osteoarthritis (OA) is a degenerative whole joint disease that affects 27 million US adults and has societal health care expenditures of close to

Keywords: Electrical Engineering.
Advisor: Hargreaves Brian Andrew primary advisor. Thesis advisor
McWalter Emily Jane
Gold Garry E.
Nishimura Dwight George advisor. Thesis advisor
Volume reconstruction and resolution limits for three dimensional snapshot microscopy [electronic resource]

Three-dimensional snapshot microscopy refers to any technique capable of performing volumetric imaging of microscopic samples using information captured in a single photographic exposure. Unlike scanning microscopes, which collect volumetric information over time, 3-D snapshot microscopes can capture volumes at speeds limited only by the frame rate of the image sensor. Synchronous imaging is made possible by encoding depth information in the shape of the microscope's point response function (PRF). Each position in the volume produces a different, distinctive light intensity pattern on the camera sensor, and these patterns can be recognized by a computer algorithm and used to computationally reconstruct a full volume. In this work we explore two different 3-D snapshot microscopes for imaging of weakly scattering, fluorescent specimens. The first, the light field microscope, employs an array of microlenses to decompose light into different angular projections of the volume in a manner similar to computed tomography. We present an optical model for light field microscopy based on wave optics and a 3-D reconstruction method which we solve using a GPU-accelerated iterative algorithm. Theoretical resolution limits for the light field microscope are discussed and compared with experimental measurements using a USAF 1951 resolution target, pollen grains, and fluorescent beads. We also summarize our application of light field microscopy in neuroscience where we have used it to perform 3-D calcium imaging. Using this technique, we have recorded the activity of thousands of neurons in the brains of awake, behaving animals. Our second approach to 3-D snapshot imaging uses phase masks, rather than a microlens array, to encode volumetric information. We have designed a ``helical focus'' phase mask that generates a PRF that rotates as the microscope is defocused. This PRF contains a single lobe that does not change in size or shape as it rotates, thereby enabling imaging with consistent resolution over a configurable depth range of up to hundreds of micrometers. Further, we propose a design for a 3-D snapshot microscope that uses two such masks (in different light paths, but with simultaneous acquisition using two frame synchronized cameras) to capture volumetric information. Our optical simulations suggest that this microscope is capable of performing 3-D imaging at resolutions exceeding that of light field microscopy when imaging sparse volumes. We show these results and compare the two techniques.

Advisor: Levoy Marc primary advisor. Thesis advisor
Horowitz Mark
Wetzstein Gordon advisor. Thesis advisor
Voting Determinants of Brexit: How Trade and Immigration Affected the Vote Share for Brexit across the UK

On June 23rd, 2016, the UK shocked the world when 52% of voters decided the country should leave the EU. The referendum results reverberated through the country, the EU, and around the world. Prime Minister David Cameron stepped down in the referendum’s wake and the UK political elite has found itself having to almost exclusively focus on Brexit. As a string of surprising election results shock the globe, it becomes clear that a new trend of voter behavior appears to be emerging in many countries. This paper hopes that analyzing the determinants of the Brexit Referendum can illuminate this new trend in voter behavior. The hypothesis presented is that within a Local Authority District, the ‘Leave’ vote share is more related to subjective feelings towards immigration than objective hardships faced due to unemployment from immigration and trade vulnerability. Further, the flow of immigrants will have a heterogeneous effect across regions of the UK, with increased immigration increasing the Leave vote share in
England and Wales, while decreasing the Leave vote share in Scotland. These hypotheses are confirmed by the data analysis and regressions, as there are positive relationships between both the change in the foreign-born population share and the trade integration level and the Leave vote share across the UK. However, in Scotland alone the relationship between the change in the foreign-born population share and the Leave vote share is negative.

Keywords:  Department of Economics
Stanford Department of Economics
Brexit
referendum
voter behavior
immigration
trade
trade vulnerability
unemployment
economic adversity
rational ignorance
European Union
United Kingdom
Scotland
England
Wales
Greater London
Thesis
Advisor: Bagwell Kyle
"Wait for it" [electronic resource] : toward optimal emergency department wait time prediction

This thesis explores two problems in the field of Healthcare Operations Management, specifically in the emergency department (ED) setting. We first study the problem of how to accurately estimate the wait times of incoming patients to an ED. We introduce the Q-Lasso method for wait time prediction, which combines statistical learning with fluid model estimators. We implement Q-Lasso on an external website and in a partner ED's triage room, and observe that it achieves over 30% lower mean squared prediction error than would occur with the best rolling average method. Next, we study the problem of how to quantify and mitigate the extra waiting imposed on high-acuity patients by low-acuity patients in an ED, or "ExWAH." We find that an arriving low-acuity patient on average increases the subsequent aggregate wait times of high-acuity patients by 55 minutes. We investigate what operational mechanisms drive this effect, and propose managerial interventions EDs can use to reduce it.

Keywords: Business.
Advisor: Bayati Mohsen primary advisor. Thesis advisor
Plambeck Erica L. primary advisor. Thesis advisor
Xu Kuang advisor. Thesis advisor
We Do The Best We Can: Implementation of the McKinney-Vento Act by San Francisco Social Workers

Subtitle VII-B of the McKinney-Vento Homeless Assistance Act (MVA) was designed to ameliorate the negative academic and social effects experienced by homeless students. While researchers agree the MVA has created policies and programs that are beneficial to homeless youth, there is little evidence on the actual or perceived implementation of the program’s provisions within schools. This study recorded the perceptions of San Francisco Unified School District school social workers on their perceived implementation of certain MVA mandates in their respective schools. The results indicate that school social workers play a critical role in identifying and supporting homeless students, but their perception of the level of implementation of certain MVA provisions within their school varies. Overall, San Francisco school social workers agreed that the District has MVA-related policies in place to work with homeless students, but disagreed when it comes to the effectiveness and availability of these policies at a school level.

Keywords: McKinney-Vento Act
homeless youth
social worker
San Francisco
Thesis
"What are you doing here?" [electronic resource] : stylistic variation in the construction of a preaching woman persona

This study establishes the importance of persona in structuring variation in discourse. It examines the speech of African American preacher Dr. Claudette Copeland, as she speaks to an audience of several thousand women at a national conference for Women in Ministry. Dr. Claudette engages her audience in the well-known African American speech event, having church. This particular event is well known as a site for complex, multi-layered African American preaching, thus it provides the opportunity to examine the use of variation in stylistic performance. Dr. Claudette constructs a unique authoritative persona as a preacher, by combining the resources of pre-existing personae: the saintly woman, the seminary-trained preacher, and the black folk preacher. Each of these personae contributes a particular kind of authority and authenticity in the church. But her particular style profits from the inclusion of an additional, non-church persona, sistah-friend. This persona adds authenticity and solidarity as an equal and a sister, providing solidarity and authority with the particular trials, tribulations and interests of women in the church, allowing her to speak from a position of familiarity, strengthening her argument and legitimating her critique. I examine three quintessential features of African American Vernacular English (AAVE): (ay) monophthongization, rhoticity, and zero copula as they occur throughout the speech event. I compare alternative models of discursive organization as constraints on the use of these variables. I compare earlier models of black sermon structure as predictors of variation with the structure of persona structure. Specifically, the four personae that constitute Dr. Claudette's style are interspersed throughout the speech event, precluding a linear analysis. Employing Polanyi's Linguistic Discourse Model, I break the sermon down into Basic Discourse Units, and assign a persona to each unit based on criteria independent of the variation under study. Using regression analyses combining linguistic constraints with discourse models, I show that while the linear structure of the sermon does account for some patterns, the persona structure provides a more robust analysis overall.

Keywords: Linguistics.
Advisor: Eckert Penelope primary advisor. Thesis advisor
Rickford John R.
Podesva Robert advisor. Thesis advisor