VictorJuiz/thesis huggingface dataset:
Regulation of Form in Multicellular Choanoflagellates and the Evolutionary Cell Biology of Morphogenesis

Proper morphogenesis requires the regulated interplay between cellular behaviors and physical constraints. Studies of physiology and morphogenesis in protist and animal systems with respect to this interplay have led to important mechanistic insights. Comparatively little work, however, has studied how morphogenetic processes evolve in the context of physical constraints. Choanoflagellates, the closest living relatives of animals, can form multicellular colonies of various shapes and sizes. This diversity and the simplicity of multicellular forms in conjunction with their important phylogenetic position makes choanoflagellates an ideal system for studying the evolution of morphogenesis. Because most work has focused on genetics and genomics, little is known about the cellular and biophysical mechanisms underlying the regulation of multicellular form in choanoflagellates/nHere, I quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta. I find that rosettes reproducibly transition from an early stage of 2D growth to a later stage of 3D growth, despite the underlying stochasticity of the cell lineages. I postulate that the extracellular matrix (ECM) exerts a physical constraint on the packing of proliferating cells, thereby sculpting rosette morphogenesis. Perturbative experiments coupled with biophysical simulations demonstrate the fundamental importance of a basally-secreted ECM for rosette morphogenesis. In addition, this yields a morphospace for the shapes of multicellular colonies, consistent with observations across a range of choanoflagellates. Overall, this biophysical perspective on rosette development complements previous genetic perspectives and thus helps illuminate the interplay between cell biology and physics in regulating morphogenesis./nI also present the previously undescribed species Choanoeca flexa, a splash pool choanoflagellate that forms cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cGMP pathway. Inversion is mediated by cell shape changes requiring actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior. C. flexa thus rapidly converts sensory inputs directly into multicellular contractions. In this respect, it may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.

Advisor: King, Nicole
Hallatschek, Oskar
Speculative Statecraft: Logistical Media and the Culture of Chinese Cold War, 1945-1978

My dissertation explores the ways the media industries of the Chinese Nationalist Party turned Taiwan and Hong Kong—the Nationalist’s industrial home-front and informational hub—into what I call a regime of logistics after 1949. As one of the greatest human migrations in modern history, the mass exodus of millions of Chinese people to Taiwan and Hong Kong upon the triumph of the Communist party has been relatively understudied. The movement of military personnel, intellectuals, technocrats, and business communities represented a singular mode of migratory culture, as they were not only victims displaced by the Chinese Civil War but also a powerful cluster of human resources with which the Nationalist regime engineered the image of a “Free China” with the support from the United States. In this context, I ask how military, industrial, and commercial logistics forged a propaganda media infrastructure that both circulated and represented the movement of labor, information, and affects in the supply-chain capitalism during the Cold War./nMy dissertation inquiries into the specific ways state-sponsored cinema and literature turned the narratives of displacement into narratives defined by postwar developmentalism. It is my contention that in the process of being relocated and downscaled from a continental sovereignty to an exiled island-state, the Nationalists’ pursuit of a techno-utopia forged a series of media environments from which new cinematic and literary aesthetics emerged within the intertwined milieu between warfare and development. How did Taiwan and Hong Kong reshape the Nationalists’ narratives of nation-building and military logistics with their own aesthetic strategies? What do these strategies tell us about the relations among militarism, migration, and environment? To map out the interconnected conduits of aesthetic transformation between propaganda discourses and creative freedom, I read audiovisual images and literary texts against four principal enterprises for Nationalists’ mobilization—military science, agricultural campaigns, transportation networks, and architectural planning. Each of these medium/environment clusters is centered around a state-run enterprise—transplanted from China to either Taiwan or Hong Kong—and its correlated technocratic discourses. In aggregate, these images and texts provide the basis for a new narrative of Taiwan and Hong Kong’s Cold War culture.

Advisor: Jones, Andrew F.
Essays in Information Frictions and Financial Markets

Frictions affecting information demand play an essential role in equilibrium outcomes of financial markets, and the behavior of investors, managers, and regulators. Demand-side information frictions can be the result of costly information acquisition or psychological factors, and can interact with various behavioral biases resulting in outcomes that would be puzzling in traditional, entirely rational models./nThe first chapter models the learning and trading decision of investors in an economy with regular public announcements and costly information. Scheduled public announcements affect the information acquisition decision of traders, who in equilibrium focus their learning on stocks with upcoming announcements. When learning is endogenous, public announcements have a significant effect on information acquisition, price movements, and price informativeness. Using quarterly earnings announcements as regular and major information events, I document a number of patterns consistent with rational allocation of limited learning capacity. In the time-series, I show that costly information acquisition results in lower learning and price movements before announcements on busier weeks. In the cross-section of stocks, I find that learning and price movements are lower when other announcing firms are more valuable to learn about. The results suggest that learning plays a significant role in pre-announcement market movements, previously mainly attributed to leakage of insider information./nIn the second chapter, I propose a new approach to model the role of regret and rejoice in dynamic stopping problems; where past outcomes the agent chose not to reach act as reference points. An agent with regret induced reference points exhibits history dependent behavior, and if the stopping decision affects the set of available information, a regret agent is more likely to continue (stop) than a fully rational decision maker when regret level is sufficiently high (low). I show that this approach to regret and rejoice can provide a unified explanation for various previously analyzed phenomena in investor and CEO behavior, such as the disposition effect, the sunk cost fallacy, and the escalation of commitment. In an equilibrium asset pricing framework, regret generates asymmetric price reaction to news, where good information is reflected in prices to a lower extent than bad news.

Advisor: Sraer, David
Imagined Asia: Archaeology and Museum Anthropology of the Chinese Diaspora and the Ainu

Archaeological sites and ethnographic museums preserve materials, and the human lives to which they connect, in different ways. Sites preserve evidence of peoples’ everyday lives in the form of their material contents, but by their nature as buried and often fragmented artifacts and features they also indicate some degree of loss or even erasure during the process of the site’s formation. Ethnographic museums, by contrast, purposefully preserve both material and documentary evidence of people’s lives. However, they also maintain the context of the collection’s creation, the agencies of the original owners, collectors, and institutions involved in their assembly./nThis dissertation examines an archaeology site and museum collections in tandem to discern their shared context in transpacific interactions between the United States and East Asia in the late nineteenth century. First, I use a combination of oral history and historical archaeology to understand the lives of Chinese immigrants living at the Arboretum Chinese Quarters at Stanford University in California between 1876 and 1925, the era of both widespread Chinese diaspora and increasing racialization and discrimination against immigrants in the United States. Second, I examine ethnographic museum collections initially created during this same time period between the 1870s and 1920s. These collections of material culture from the Ainu, the Indigenous people of Hokkaido, Sakhalin, and the Kurile Islands, share a social context with the archaeological remains of the Chinese diaspora beyond their contemporaneity. Both the site and the collections formed as they did due to the racialization of Asian ethnic groups in the nineteenth century United States. Through uniting these material remains with historical documentation, oral histories, and records of oral traditions, I explore this shared context, the evidence they both provide about everyday lives shaped by colonial policy, and present ways that objects, both archaeological and ethnographic, continue to matter for descendent and other stakeholder communities today.

Advisor: Wilkie, Laurie A.
Topics in Conditional Inference

The modern data analysis process is rarely one-step, but instead paved with iterative exploratory data analyses and choices. Often data analysts are tempted to peek at the data before choosing the hypotheses to be tested. In other times, the vast amount of data is screened and not all information is accessible to the analysts. In either case, data analyses have to be carried post-selection, as a consequence of even the most innocuous exploratory data analyses. A particular method to conduct post-selection inference is conditional inference, with a few instances detailed in this work./nChapter 2 — based on Hung and Fithian (2019a) — explores a scenario where the choice of null hypothesis is dependent on the very same data used in the test. Using conditional inference, we provide a test that adapts to the data, for whichever hypothesis is most sensible. As a consequence of the adaptivity, our test is also much more powerful than the classical approaches./nChapter 3 — based on Hung and Fithian (2019b) — describes a meta-analysis where the data itself has been selected, but meaningful inference is nonetheless desired. Through conditional inference, we modified classical methods to provide post-selection inference./nFinally in Chapter 4, I present unpublished work investigating an optimal method of combining information from a post-selection original experiment and a replication experiment, a current common concern in experimental psychology.

Advisor: Fithian, William
Aldous, David
Understanding the Link between Myopia and Glaucoma- Clues from Intraocular Pressure and Optic Discs

Myopia (near-sightedness) has become a significant public health concern, as its prevalence continues to increase in the United States and around the world. Further, myopia is also linked to potentially blinding ocular disease. Growing evidence from a number of studies links myopia with an increased risk of glaucoma, a leading cause of irreversible blindness. Eyes with primary open angle glaucoma typically exhibit high intraocular pressure (IOP) and altered diurnal IOP rhythms. The structural organization of the lamina cribrosa (LC) of the optic nerve head may also render eyes more vulnerable to nerve fiber damage, the origin of vision loss in glaucoma. One or more of these factors may also contribute to the increased risk of glaucoma in myopic eyes./nIOP could play a role in normal ocular “growth” (enlargement), by exerting a stretching influence on the scleral wall of the eye. During myopia development and progression, scleral remodelling is upregulated, rendering it more susceptible to the stretching influences of IOP, with eye enlargement accelerating as a consequence. The converse that ocular elongation can be slowed by decreasing IOP and so the tension experienced by the sclera was tested in a set of experiments using a topical ocular hypotensive drug, specifically latanoprost. Its effects on both normal and “myopic” ocular growth in guinea pigs undergoing monocular form deprivation were examined, and treatment-induced ultrastructural changes in the sclera were quantified./nWith advances in high-resolution imaging and electron microscopy, we were able to characterize the effects of the above ocular hypotensive drug on the microarchitectural changes in the sclera and optic nerve head, including the LC./nOur results demonstrate that daily topical latanoprost is effective in both lowering IOP and slowing myopia progression in myopic guinea pig eyes. It also seems to protect the myopic scleral remodelling. These findings will open the opportunities to explore lowering IOP as a myopia control treatment option that may also reduce any future risk of glaucoma in myopic children.

Advisor: Wildsoet, Christine F
Design of Spectral Filtering Wireless Transmitters

A frequency-flexible radio-frequency (RF) front end has long been desired, but faces a myriad of obstacles to its realization. In recent years, the use of switching power amplifiers (PA) as part of digital PAs and RF digital-to-analog converters (RFDACs) has become more common. The primary motivation of these RFDACs is to directly convert from digital baseband bits to RF output. This is useful in the realization of a frequency-flexible RF front end, but this is prevented by the generation of significant spectral emissions in the form of harmonics and quantization noise by RFDACs. These issues are both typically remedied with the usage of high-order fixed filters which are inherently not frequency flexible./nIn this dissertation, we will discuss an approach to implement a frequency-flexible digital PA-based transmitter using programmable integrated filtering to suppress spectral emissions without the use of external filters. Two filtering techniques will be discussed, as well as their requirements and limitations. Additionally, design automation of core blocks within the transmitters using the Berkeley Analog Generator (BAG) framework will be discussed in detail. We will demonstrate two prototypes implemented in 65nm and 28nm processes achieving state of the art filtering performance at a peak power level of > 23 dBm across at least a 1 GHz - 2 GHz frequency range.

Advisor: Alon, Elad
Sound Works: Model Listeners in Soviet Art, 1929-1941

This dissertation explores the emergence of Soviet sonic culture––a concept I define as a set of practices, expectations, understandings, and preconceptions surrounding audible phenomena––during the early years of the Stalinist era (1929-41). On a global level, twentieth–century sound reproduction technologies enacted a dramatic shift in listeners’ conceptions of attention, space, and community, and I contend that these technologies had a distinct impact on Soviet literature and cinema. Unlike their Western counterparts who aimed to capture, commodify, and sell sound, many artists in the USSR saw sound reproduction as a vital tool for the construction of state socialism. In case studies that investigate the work of Dziga Vertov, Valentin Kataev, Viktor Shklovsky, Yuri Tynianov, Evgenii Cherviakov, and Andrei Platonov, I suggest that we can interpret these artists’ depictions of monumental construction, industrial development, and reformative incarceration as the imagination of new listeners for a new country. Accordingly, this dissertation problematizes an enduring binary in the Slavic academic field that associates official, state-sponsored art with Stalin’s repressive censorship, and which charts unofficial, unpublished art as a more legitimate site of artistic innovation. Contrary to a common narrative of the Soviet state’s ideological rigidity, sonic culture’s enthusiasm for incorporating sound into Soviet art suggests that Stalin’s uncompromising push for technological modernity led to officially sanctioned innovations in artistic form and expressivity. Ultimately, I argue that Soviet sonic culture significantly shaped the development of Soviet literature and film./nWhile critical in its assertions, this work is at its core a cultural history, and I have intentionally based my research on newspapers, rarely-cited technical publications, and memoirs from Soviet sound designers, inventors, critics, filmmakers, and writers. The project integrates a media archaeological approach into its method, but I expand upon the possibilities of media archaeology by exploring how technology is limited or emboldened by ideology. This analysis of Soviet sonic culture and the listeners it produced––both real and imaginary––offers more than a new lens for the Soviet ‘30s: it is a paradigm for determining how media technologies within non-capitalist modernity both established and overturned the relationships we may expect to find between art, culture, and power.

Advisor: Naiman, Eric
Exploring Children’s Experiences in a Targeted Compassion-Based Intervention

Psychologists have become increasingly interested in the concept of compassion and its role in promoting psychosocial wellbeing. As individuals experience compassion for others, compassion from others, and self-compassion, they set in motion a series of physiological processes that support emotion-regulation and prosocial interactions. There has also been a rise in the development of individual and group interventions that guide participants to develop greater compassion for the purposes of improving their mental health, prosocial behaviors, and physiological responses to stress. Meta-analytic findings of compassion-based interventions with adults show significant, moderate effects on compassion, self-compassion, mindfulness, depression, anxiety, psychological distress, and wellbeing. Preliminary evidence suggests compassion-based, group interventions may be effective targeted strategies for supporting youth who are at-risk for developing internalizing disorders. In this dissertation, I present a study examining the experiences of five fourth-grade students in a compassion-based, group intervention targeting internalizing symptoms. Guided by interpretive phenomenological analysis, semi- structured interviews were used to examine participants’ emotional experiences of the intervention and to elicit participant feedback on the helpfulness and usefulness of the intervention. Children’s artwork from the intervention was analyzed collaboratively to gather detailed descriptions of participants’ thoughts and emotional states during the creation and presentation of their art projects. Finally, audio recordings of group sessions were used to gather information on children’s interactions and field notes were analyzed to examine my own experience of facilitating the intervention.

Advisor: Worrell, Frank C
The Illusion of America: Seriality Across Media in Italian Cinema from Fascism to the Economic Miracle (1932-1968)

This dissertation explores the relationship between Italian cinema and the United States’ imagery and bodily practices in the years between the fascist regime and the Italian “economic miracle.” I analyze objects such as magazines, consumer goods and design furniture, the conditions of their consumption and production, and their presence in Italian films – from Mario Camerini’s What Scoundrels Men Are! (1932), to Alberto Lattuada’s Without Pity (1948), and Elio Petri’s The Tenth Victim (1965). Across different historical contexts and cultural products I examine the arc from Italy’s infatuation with “America,” to disillusionment. These two extremes are epitomized by the emulation of Hollywood stars during the fascist ventennio, as embodied by women’s magazines, all the way to the rejection of serial design furniture on the part of students protesting against American designers at a Milan Triennale exhibition in 1968. In between these two periods, the end of World War II and the Allies’ “liberation” brought about the physical exchange and contact between Italian civilians and US soldiers and consumer goods, partly thanks to the Marshall Plan. I argue that seriality – a mode of production and consumption, as well as an aesthetics – binds together the periods under analysis, is the engine for this exchange, and acts upon the portrayal and interpellation of women (actresses, readers and spectators) according to a precise visual grammar and narrative, rooted in Hollywood’s spectacle./nThanks to the exploration of films, magazines, and archival material, I observe the clear-cut break between fascist cinema (the so-called “telefoni bianchi”), and the “year zero” of neorealism under the lens of consumption and the presence of the United States. I then advance a hypothesis of continuity between the two periods, and between the aftermath of fascism and World War II, and the economic miracle. Framed by a new idea of continuity, the work of directors such as Camerini, Lattuada, and Petri, as well as Pier Paolo Pasolini and Michelangelo Antonioni, sustains my larger claim about Italian art and film’s historiography. These directors are joined, during the years of the economic miracle, by visual artists such as Ettore Sottsass and Giosetta Fioroni, mapping the birth of a specialized branch: industrial design. Following its heyday in the early and late 1960s, the new industry deflated on its own premises by the beginning of the next decade, carrying along, and away, the myth of America.

Advisor: Spackman, Barbara
Tidal and Seasonal Observations of Stratification and Water Temperature in Lower SouthSan Francisco Bay

San Francisco Bay sits within a highly urbanized community and is home to endangered species and fish nurseries. The surrounding dense population creates large wastewater effluent resulting in high nutrient levels in the estuary. Scientists wonder why there have not been annual phytoplankton blooms as observed in other estuaries with lower nutrient levels such as the Chesapeake Bay \cite{Boynton:1995}. Some have hypothesized it is due to high turbidity levels and tidal breakdown of stratification creating nonideal environments for phytoplankton growth. However, decadal-trends show that the estuary is becoming less turbid, and with changes in climate patterns, there is potential for persistent stratification./nThis dissertation breaks down the mechanics responsible for observed development of stratification over the ebb tide and destratification at the end of ebb to mid flood tides. Results reveal longitudinal mechanics are primarily responsible for development and destruction of stratification at times of high velocity. During tide transitions, lateral exchange allows for the interaction of perimeter-shoal waters. Seasonal differences in salinity and water temperature are observed in order to develop an understanding of how the estuary responds to various climates. Seasonal trends indicate changes in precipitation lead to high variability of the magnitude and range of salinity, magnitude of stratification, and perimeter water temperature. Salinity and temperature observations are used to calculate residence time and longitudinal dispersion rates for Lower South San Francisco Bay. Present-day conditions reveal stratification is broken down on each tide, but further research should be done applying these observed salinity and temperature gradients with adjustments for potential future climate conditions.

Advisor: Stacey, Mark