VictorJuiz/thesis huggingface dataset:
Revolutionary competition : coalitions, labor, and the birth of French antitrust, 1791-1864

In 1791, The revolutionary French National Assembly enacted the Le Chapelier Law, abolishing all corporate bodies and collective economic associations. The old guilds were the embodiment of ancien régime privilege and a scourge to economic liberty and social progress. Though the law was primarily concerned with the regulation of labor, the animating principles behind it revealed a much broader and more sweeping anti-corporatist social vision. In introducing his proposal, Isaac Le Chapelier declared emphatically, "Corporate bodies no longer exist in this country. There exists only the particular interests of every individual and the general interest." But just what an economy lacking corporate "intermediary interests" was supposed to look like—and how it was supposed to function—remained an open question. The Napoleonic Penal Code of 1810 cleaved the Le Chapelier Law's anti-corporatist prohibitions into separate labor and antitrust statutes. Articles 414, 415, and 416 prohibited "coalitions" of workers and employers, while Article 419 prohibited business "coalitions." Despite their conceptual similarities and overlapping terms, these provisions governed different activities and different parties within the economic system. The Penal Code's creation of separate but related and coevolutionary bodies of law encouraged both workers and businesses accused of coalition to be opportunistic in the way they defended themselves, glomming on to developments in one area of the law to support their cause or defend their actions in the other. This dissertation traces the nineteenth-century history of the Le Chapelier Law, from its enactment in 1791, to its bifurcation in the 1810 Penal Code, to its effective abolition following the 1864 Ollivier law. It shows how, when French courts ruled that companies could not be guilty of coalition under Article 419 if they acted in parallel and charged similarly predatory prices—but did not explicitly agree to work in concert to put a competitor out of business—workers opportunistically began to defend their own collective actions in similar terms, as consciously parallel but not part of a concerted agreement. Similarly, when Articles 414, 415, and 416 were amended in 1864 to remove the prohibition of peaceful, non-violent coalitions, producers and legal commenters immediately argued that the amendment applied equally to business coalitions, effectively nullifying Article 419

Keywords: History.
Advisor: Baker Keith Michael
Daughton J. P. (James Patrick)
Kessler Amalia D.
Riparian Avifauna of the San Francisco Bay Region: Population Dynamics and Future Outlooks with Anthropogenic Climate Change

Anthropogenic climate change is predicted to drive widespread avian population declines, range contractions, and global extinctions in the coming century. Recent research has largely focused on identifying past trends and phenological disruptions; however, relatively little is known about how climate variation impacts the ultimate drivers of population change: demographic rates.
Throughout my project, I worked to expand this area of research by establishing two new bird banding stations for monitoring demographics and conducting analyses of existing banding data from the Coyote Creek Field Station in Milpitas, CA. I built demographic models in a Bayesian framework to evaluate the effects of growing-season precipitation, spring mean temperature, and mean winter minimum temperature on the adult apparent survival and reproductive success for nine songbird species from 1995–2018. One study species – the San Francisco common yellowthroat (Geothlypis trichas sinuosa) – is of immediate conservation concern. I simulated possible population trajectories for the period 2020–2100 using my estimated parameters and the predicted local climate from two global climate/circulation models under three future greenhouse gas emissions scenarios.
The demographic rates for six of these species were significantly affected by local climate variation. Reproduction was highest in years with the most growing-season precipitation and warmest spring mean temperatures. In contrast, adult apparent survival was lowest in years with the highest growing-season precipitation. There were several interesting exceptions to these general patterns as well. Among the study species, climate variation most impacted the survival and reproduction of the San Francisco common yellowthroat. Simulations with projected climate change suggest that this population will decline over the next 80 years.
To my knowledge, this is the first study to simulate population trajectories for a North American songbird species under future climate scenarios. The models show that immigration may buffer climate effects, which suggests metapopulation management of this species will be beneficial. This study highlights how population demographics can be applied to conservation and demonstrates the need for expanded research in this area.

Keywords: School of Earth Energy &amp; Environmental Sciences
bird banding
songbirds
passerines
population dynamics
avian demographics
climate change
common yellowthroat
Thesis
Advisor: Dirzo Rodolfo
Hadly Elizabth
The rise of entrepreneurship in China : modernity, social mobility, and entrepreneurialism

This dissertation investigates the social-psychological motivations to pursue entrepreneurship in the context of post-reformed China. Using an inductive in-depth interview approach tapping into individual motivations, it argues that rather than pure economic calculations, people pursue entrepreneurship as a project of self-making and that such a project is towards an aspired future self, informed by one's past and by the collective meaning of entrepreneurship. To further examine how public representation of entrepreneurship may impact people's decision to pursue entrepreneurship, I use a survey experiment to randomly assign members of the general public to one of the treatment conditions where the framing of entrepreneurship is manipulated. My findings establish that public representation of entrepreneurship can promote entrepreneurial intention and behavior. However, its impact is heterogeneous for different audiences and operates via mechanisms un-identified by existing theories. Contributions and avenues for future research are discussed

Keywords: Sociology.
Advisor: Granovetter Mark S.
Jiménez Tomás R. (Tomás Roberto)
Walder Andrew G. (Andrew George)
Robust causal inference and machine learning with clinical applications

As healthcare data becomes increasingly ubiquitous, improving data-driven biomedical research is timely and important. There is a rush to learn from these new sources of data, and to implement research findings into clinical practice. While machine learning methods provide compelling examples of recognizing sophisticated patterns in data, their impact rests heavily on their ability to use data to influence decision making, especially in healthcare. The relationship between machine learning and decision making becomes particularly clear through the lens of causal inference. In general, the harm and benefit attributed to a medical decision depends on the causal treatment effect of the decision in the appropriate population, beyond their baseline risk of poor outcomes. In precision medicine research, the goal is to develop treatment decisions for individual patients by considering the sub-population of individuals with similar covariates to each patient. This thesis advances methodology and practice for applying machine learning to learn better decision-making rules that influence clinical practice, and understanding the fundamental possibilities and limitations of using data to learn to make optimal decisions. First, we develop an approach for personalized treatment effect estimation based on the relative ratio of treatment outcomes. Second, we study when we can trust causal results learned from data, and develop a sensitivity analysis for conditional and average treatment effects to bound the bias created from unobserved confounding. Third, noting that treatment benefit is highly correlated with baseline risk for preventative treatments for atherosclerotic cardiovascular disease (ASCVD), we use machine learning approaches to improve ASCVD risk predictions from longitudinal cohort data that affect clinical prescribing practice, particularly among under-represented minorities

Keywords: Electrical Engineering.
Advisor: Tian Lu 
Duchi John
Van Roy Benjamin
Robust dynamic wireless power transfer based on parity-time symmetry

Wireless power transfer offers users the ability to access power provided by the electrical grid without the hindrance of power cables. The technology is gaining importance with the increasing number of mobile battery-powered devices we use in our everyday lives. Already, wireless inductive charging pads are commercially available for many devices, from electric toothbrush to smart devices and even electric vehicles. In many of these conventional wireless power transfer setups, their power and efficiency performance is sensitive to the relative movement of the device receiving power with respect to the power source. Thus, at present, wireless power transfer is largely restricted to the scenario of stationary charging. The ability to deliver robust and efficient dynamic wireless power transfer should open new application opportunities, from dynamic charging of electric vehicles travelling on roadways to powering electronic devices on the move. In this Thesis, we present our recent efforts in the development of a robust dynamic wireless power transfer scheme based on the concept of parity-time (PT) symmetry. In our PT scheme, power is provided to the system through an amplifier on the power source pad. This amplifier provides gain to the electromagnetic energy inside the system in balance with the loss contributed by the device's energy draw. This construction enables the system to reach a steady state where the electromagnetic field in the system oscillates at the steady state frequency that corresponds to the maximum transfer efficiency regardless of the transfer distance. The result is robust wireless power transfer that automatically self-adjusts as the transfer distance varies such that high transfer efficiency is maintained without the need of any external tuning circuit

Keywords: Electrical Engineering.
Advisor: Fan Shanhui
Fan Jonathan Albert 
Vuckovic Jelena
The role of ecophysiology and paleoenvironmental dynamics in the Ediacaran biostratigraphic record

The Ediacaran Period (635 to 539 million years ago; Ma) represents one of the most dynamic periods in Earth History. Terminating the Neoproterozoic Era, the Ediacaran begins immediately after the second of two Snowball Earth global Glaciations, the Sturtian (717 to 560 Ma), and the Marinoan (640 to 635 Ma), which among other things had profound impacts on the global carbon cycle. Upon the final melting of the Marinoan Glaciation, a period of over 50 million years (Myr) passed in the early Ediacaran with no evidence of complex macroscopic eukaryotic or animal life. Bookending this interval is the continental-scale Gaskiers Glaciation (580-579 Ma) which shows up in deep-marine glaciogenic strata in Newfoundland and England today. Several hundred meters above these deposits are the earliest macroscopic eukaryotes and purported animals to appear in the fossil record, known as the Ediacara biota. These deep-water communities, identified as 'Avalon Assemblages' initially appear only in deep-marine slope and basinal environments for some 15 Myrs before radiating up into the continental shelves worldwide ca. 560 Ma. However, the basins in which they appear have no equivalent shallow-water facies, making it impossible to discern whether this pattern is a genuine evolutionary pattern, or the product of bias in the stratigraphic record. By cs. 555 Ma, the shallow-water 'White Sea Assemblage' became the most diverse interval in the Ediacaran, and records newly emerging 'Cambrian-style' fauna including mobile bilaterians and increasingly complex trace fossils. These groups continue into the terminal Ediacaran, known as the 'Nama Assemblage' ca. 550-539 Ma when all Ediacara biota go extinct at the Ediacaran-Cambrian boundary. The circumstances that surround the timing and drivers of this initial diversification however are unclear, and hypotheses have focused primarily on the role of environment, including global reorganization of marine redox conditions, changes in primary productivity, ecological escalation, and climate stability following the end of Snowball Earth glaciations. As a result, the interval remains actively studied by geologists and paleontologists, however, there remain critical unanswered questions regarding the timing and spatial evolution of the Ediacara biota

Keywords: Geology.
Advisor: Sperling Erik
Graham S. A. (Stephan Alan)
Payne Jonathan L.
Somero George N.
The role of host arginine metabolism in murine malaria

Infection disrupts host metabolism, but it is not well-known how the nature and magnitude of metabolic disruption relates to the severity of infectious disease. In this dissertation, I describe our efforts to uncover new links between metabolism and disease severity in murine malaria. To more closely model disease in a diverse population like that of humans, we infected eight genetically diverse, inbred mouse strains with Plasmodium chabaudi and tracked their symptomatic, pathological, immunological, and metabolic responses to acute infection. In chapter 2, we describe a wide range of disease severity and metabolic phenotypes in the eight strains. We use supervised and unsupervised techniques to identify metabolic biomarkers for severe disease that change in both murine and human Plasmodium infection. With this approach, we uncover arginine depletion as a specific indicator of P. chabaudi-induced liver damage. Given the established importance of arginine in malaria, chapters 3 and 4 describe how host enzymes that catabolize arginine affect infection severity. In chapter 3, we test the hypothesis that liver damage causes plasma arginine depletion by releasing hepatic arginase-1 into circulation and examine the role of host arginase-2 in limiting infection severity. In chapter 4, we characterize the role of nitric oxide synthases in P. chabaudi infection and find that host endothelial nitric oxide synthase promotes host tolerance to P. chabaudi infection. Collectively, this work leverages phenotypic diversity and genetic tools in inbred mice to improve our bioinformatic and mechanistic understanding of relationships between metabolism and infectious disease severity

Keywords: Microbiology and Immunology.
Advisor: Schneider David (David Samuel)
Jagannathan Prasanna 
Monack Denise M.
Sonnenburg Justin
Spormann Alfred M.
The role of TET1-mediated 5hmC in skeletal development and disease

Cartilage, a mostly avascular tissue, is composed primarily of extracellular matrix proteins (ECM), in which resident cells, called chondrocytes, are embedded. Despite our knowledge about the biomechanical properties of cartilage, we still know relatively little about the identities of the chondrocytes embedded in the ECM matrix, and how they change with aging, injury, and chronic joint disease. The work described within this dissertation touches on two aspects of the molecular identities of these resident cells. First, in chapter 2, I describe work using cytometry by time-of-flight to characterize subpopulations of chondrocytes in human cartilage, and how these populations change with disease. I identify two new subpopulations, termed the Inflammation-Amplifying and Inflammation-Dampening cells, and demonstrate that drug modulations to their activities can alter disease progression. In chapters 3 and 4, the work switches to considering the epigenetic code that establishes cell identity. This work focuses on a chemical modification to the cytosine base, known as 5-hydroxymethylcytosine (or 5hmC), which marks the gene bodies of actively transcribed genes. In Chapter 3, I look at the role of this modification during cartilage development, and specifically how it primes the chromatin landscape for the transcription factor SOX9, allowing chondrocyte-specific genes to be expressed. In Chapter 4, I look at the role of 5hmc in disease progression of osteoarthritis

Advisor: Bhutani Nidhi
Chan Charles (Charles M.) 
Wang Kevin K. W.
Wu Joy
Van Rechem Capucine
The role of the P53-P21 pathway in metabolic stress-induced ferroptosis

Ferroptosis is a form of iron-dependent, non-apoptotic cell death that occurs due to the collapse of the glutathione peroxidase antioxidant system and the lethal accumulation of lipid peroxides. Selectively inducing ferroptosis in cancer cells represents a promising therapeutic strategy. However, it remains unclear how canonical tumor suppressors and oncogenes influence cell susceptibility to ferroptosis. The p53 tumor suppressor gene is the most commonly mutated gene in human cancers and serves as a master regulator of cell stress responses, metabolic adaptation, DNA damage repair, and cell death. Using a time-lapse microscopy system to study cell death kinetics over time, I found that activation of wild-type p53 suppresses the onset of ferroptosis in human cancer cells, and that deletion of p53 results in heightened ferroptosis sensitivity. The transcriptional activity of p53 is required for this function, in part through transactivation of CDKN1A (encoding p21). Activation of the p53-p21 pathway suppresses the accumulation of lipid peroxides and promotes the conservation of glutathione, an essential antioxidant required for the reduction of lipid peroxides. p53-p21 pathway activation results in decreased expression of the enzyme ribonucleotide reductase (RNR), which uses glutathione as a cofactor in the reduction of ribonucleotides to deoxyribonucleotides. Genetic and chemical inhibition of RNR is sufficient to suppress ferroptosis and conserve glutathione similar to chemical activators of the p53-p21 pathway. These results suggest that the ability of the p53-p21 pathway to downregulate RNR may allow cells to conserve glutathione and direct it towards the management of lipid peroxides during ferroptosis. This work supports the known role for wild-type p53 in regulating cell survival under conditions of metabolic stress and identifies nucleotide metabolism as a new regulator of ferroptosis in cancer cells. These findings have important implications for the development of ferroptosis-based therapies for human disease

Advisor: Dixon Scott James
Attardi Laura 
Brandman Onn
Sage Julien
The roles of virus-host interactions in the pathogenesis of Dengue and Zika viral infections

Dengue virus (DENV) and Zika virus (ZIKV) infections are threats to global health. However, the viral and host determinants underlying disease pathogenesis are incompletely understood. To study the host immune responses to dengue infection we aimed to elucidate mechanisms of disease pathogenesis and identify biomarkers predictive of severe dengue (SD). To capture tissue heterogeneity, we developed a single-cell transcriptomic platform that quantifies viral RNA abundance and the host transcriptome in thousands of single cells, and used it to monitor the host response to natural infection in adults' PBMC samples from a Colombia dengue cohort that we established. We showed large heterogeneity in the host response to dengue in a cell subtype specific manner. We discovered that naïve B cells are the predominant cell type associated with viral RNA and that their interferon response genes are upregulated relative to bystander or control uninfected cells. We revealed cell-type specific alterations in gene expression levels prior to progression to SD, such as upregulation of MX2 in naïve B cells and CD163 in CD14+CD16+ monocytes. In parallel, to capture real-world heterogeneity, we used a multi-cohort analysis framework that integrates heterogeneous datasets to identify robust host gene signatures that are generalizable across cohorts, and discovered a 20-gene set predictive of SD using publicly available dengue datasets. The prognostic power of this gene set to distinguish uncomplicated from SD early in the course of illness was validated in silico and prospectively in our dengue cohort. Another flavivirus infection associated with significant morbidity whose pathogenesis is poorly understood is ZIKV. The recent ZIKV epidemic has been associated with microcephaly in neonates as well as Guillain-Barre syndrome and encephalitis in adults. ZIKV infection causes cell death in neuro-progenitor cells, and increased expression of p53, a major regulator of cell death. Here, we evaluated the role of the ZIKV protease (NS2B3) in activating the p53 apoptotic pathway. Our studies showed that NS2B3 alone can trigger apoptosis and identified several novel NSB23 binding partners, including MDM4, an inhibitor of the transregulatory functions of p53, which is a candidate substrate of the protease activity, and two E3 ubiquitin ligases COP1 and CARP2, which lead to p53 degradation by the proteasome. Our data suggests that NS2B3 may inhibit the function of p53 regulatory proteins thereby increasing its protein expression and upregulating p53 target gene transcription leading to apoptosis. Together, these studies have shed light on the roles of virus-host interactions in the pathogenesis of flaviviral infections and provide potential translational avenues for targeted diagnostic and therapeutic interventions for these globally important viruses

Keywords: Microbiology and Immunology.
Advisor: Einav Shirit
Maecker Holden
Attardi Laura 
Carette Jan
Sarnow P. (Peter)