VictorJuiz/thesis huggingface dataset:
Forests, Water, and the Atmosphere in Northern California: Insights from Sap-Flow Data Analysis and Numerical Atmospheric Model Simulations

Evapotranspiration cools the land surface by consuming a large fraction of the net radiative energy at the surface. In forested regions, trees actively control the rate of transpiration by modulating stomatal conductance in response to environmental conditions, and species with different stomatal dynamics can affect the atmosphere in distinct ways. Using principal component analysis (PCA) and Markov chain Monte Carlo (MCMC) parameter estimation with direct, tree-level measurements of water use, we show that Douglas-firs (Pseudotsuga menziesii), a common evergreen needleleaf tree species in the Northern California Coast Range, decrease their transpiration sharply in the summer dry season in response to a dry root zone; and in contrast, broadleaf evergreen tree species, especially Pacific madrones (Arbutus menziesii), transpire maximally in the summer dry season because their transpiration is much less sensitive to a dry root zone and increases continually in response to increasing atmospheric evaporative demand. We scale up these tree-level observations to construct a bottom-up estimate of regional transpiration, and we use these regional estimates along with atmospheric models, one simple and one comprehensive, to quantify the potential impact of species transpiration differences on regional summertime climate. The atmospheric models suggest that these species differences in transpiration could affect the well-mixed atmospheric boundary layer temperature and humidity by 1-1.5 degrees C and 1 g/kg, respectively, and near-surface temperature and humidity by 1.5-2.5 degrees C and 2-3 g/kg, respectively. We further investigate the sensitivity of California climate to evapotranspiration by estimating the sensitivity of wind energy forecasts at a California wind farm to regional-scale perturbations in soil moisture using a regional atmospheric model. These tests show that forecasts at this particular farm are most sensitive to soil moisture in the Central Valley, and that changes in soil moisture on the order of previously-demonstrated errors in atmospheric reanalyses lead to wind energy forecast errors of 1-3 m/s, which can translate to differences in forecasted wind energy of 15-40% of a wind farm’s maximum rated power.

Advisor: Fung, Inez Y
The Rhetoric and Ritual of Celestial Signs in Early Imperial China

The Rhetoric and Ritual of Celestial Signs in Early Imperial China investigates the circulation of signs such as planets in retrograde motion, comets, oddly-shaped clouds, inclement weather, and rainbows in the Western Han (206 BCE–8 CE) and Eastern Han (25–220 CE) dynasties. Building on scholarship in the history of science and previous historical studies of omenology, the present work focuses on the rhetorical and ritual dimensions of celestial signs within broader political, literary, and technical networks. It examines technical treatises in the standard histories, manuscripts on astro-omenology from the tombs of the ruling family of Dai at Mawangdui (terminus ad quem 168 BCE), memorials to the throne, liturgical repertoires, poetic celestial journeys, and early exegetical works to illuminate how celestial signs both created discursive possibilities and were themselves shaped by generic contexts and performative goals. The dissertation argues that celestial signs became meaningful always in relation to surrounding contexts, as they were read against the constellations in which they appeared, historical circumstances, present conditions in the empire, and through the voices of the deities, supplicants, rulers, and ministers that invoked them. By examining a broad range of contexts in which celestial signs appeared, this dissertation contributes to a fuller and more balanced appreciation of the variegated roles celestial signs played in the shifting culture of early imperial China.

Advisor: Csikszentmihalyi, Mark
Efficient Foraging of Limited Resources in a Multi-Agent System

This dissertation examines a number of scenarios in multi-agent foraging. The first scenario examined looks at a group of agents seeking to forage from resources that have a known location, but unknown quality. Communication among the agents is limited by range, and resource sites are arranged so they are farther apart than the communication range of the agents. Agents seek to maximize their expected foraging rate over a given time horizon. Initially, agents must choose which site they are going to investigate first. After inspecting a site, the agents must choose to either continue foraging at the site they are currently at or to investigate one of the other sites. Agents can communicate their decisions to one another as well as their information about other food sites when they are within communication range. The optimal way of making decisions is shown mathematically for the case of two resource sites and multiple agents under certain assumptions as well as three resource sites and only one agent./nAnother scenario examined is one where discrete food pieces are generated on a grid and agents must compete with one another to forage the food pieces. Food pieces are generated from two distinct resource sites. The first case examined is when the other agents are visible and the food pieces are visible to the agent. In this case the agent moves to consume a piece of food if it can do so before any other agents. If it is not moving to consume a piece of food, then it moves to maximize its probability of consuming a piece of food in the future. Another case is examined when the other agents are not visible. In this case an agent must decide whether it thinks it can consume a food piece before other agents can. The agent also wants to move in order to maximize the probability of consuming future food particles, but in this case must make decisions based on how food particles are disappearing rather than directly observing other agents./nThe most complicated scenario examined is one where the other agents are visible to one another, but unconsumed food pieces are not visible. The only food locations known to an agent are the pieces that it consumes. Agents search for pieces of food based on probability maps that they generate. Probability maps are generated based on the agent's information it has about food it has consumed. The agents also make use of observations of the other agents in order to search for new food particles.

Advisor: Hedrick, Karl
Money, Sex, and Power: An Analysis of Relationship Power in the Context of Conditional Cash Transfer Interventions to Reduce Risky Sex in Tanzania

The success of Conditional Cash Transfer (CCTs) program in several health and social domains has led to recent experiments testing CCTs for sexual and reproductive health. However, this approach has yielded mixed results and has been understudied. My dissertation explores whether sexual relationship power - the power women have to decide if and when to have sex, with whom, and with or without a condom - influences the effectiveness of CCTs to reduce STIs, and additionally, if these CCTs influence relationship power. If we can answer these questions, researchers will be better able to design CCT interventions to reduce the spread of STIs and HIV./nMy overall hypotheses are: (1) CCTs given to women with high baseline relationship power are more effective at reducing STIs than CCTs given to women with low baseline relationship power (Chapter 1); and (2) that the CCT itself changes the relationship power of those enrolled in the intervention (Chapter 2). A relevant example of women’s power to negotiate safer sex is female sex workers’ interactions with their clients. Therefore, in chapter 3, I draw on theoretical models and previous literature related to the determinants of safer sex among commercial sex workers to analyze qualitatively how Female Sex Workers (FSWs) respond to a novel pilot study using CCTs to incentivize safe sex (Chapter 3)./nTo test these hypotheses, I conducted three studies: The first explores the effect modification of baseline relationship power on the impact of CCTs to reduce STIs; the second is an intent-to-treat analysis of the effect of the CCT on relationship power; and the third is a qualitative analysis of how female sex workers respond to a pilot CCT intervention to incentivize safe sex. Chapters 1 and 2 draw on data from the RESPECT study in Tanzania and Chapter 3 draws on data from the RESPECT II Pilot study to reduce STIs and HIV among female sex workers in Tanzania./nMy analysis reveals that women’s relationship power significantly modifies the effect of the CCT on STIs. In addition, I show that a CCT improved women’s relationship power, but whether or not women were eligible to receive a high, low, or no cash transfer had little relative impact on changes in their relationship power. Finally, I identify the salient domains of power for female sex workers that are necessary to meet the conditions of a CCT intervention./nTaken together, acknowledging and addressing both the degrees of relationship power and domains of relationship power that women experience when enrolled in a CCT will improve the outcomes of these interventions in the context of STIs and HIV.

Advisor: Fernald, Lia C.H.
Building Efficacy of Student Study Teams (BESST)

Minority students underperform academically when compared to their White counterparts. In response to this phenomenon, various prevention strategies have been implemented. Student Study Teams (SSTs) reflect one such strategy. SSTs are site-based proactive problem-solving teams, charged with marshaling systematic, evidence-based interventions and supports for struggling students. Yet, SSTs are vastly misunderstood, affecting efficacy of implementation. Indeed SSTs are often deficit-based and reflect disproportionality in terms of referrals and placement of minority students./nBuilding Efficacy of Student Study Teams (BESST) is a professional learning series created to improve SST practices by guiding middle school counselors through a reflective and iterative tool development process, resulting in the construction of an SST Handbook. Counselor engagement in the process and task of developing an SST Handbook was expected to enhance understanding of effective SSTs as strengths- based interventions and to raise awareness of effective implementation. Findings of BESST may assist in revealing important information to leverage SSTs as effective interventions for struggling students by increasing counselor awareness and expertise of essential elements of effective SSTs, including how to identify student strengths. This design study is centered on action research and includes two primary research elements, evaluation of the design outcome and assessment of the design process.

Advisor: Gifford, Dr. Bernard
Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes

A complex, spatially and temporally dynamic network of gene expression underlies proper metazoan development, yet methods have not previously existed to assay this network in an efficient, systematic manner. Brute-force application of in situ imaging has been used to painstakingly assay the network, but is impractical to apply to assay the complete gene expression network in multiple mutant conditions. Sequencing, in contrast, is fast and genome-wide, but is generally applied to homogenized tissues, discarding any spatial information./nIn the first phase of my research, I have developed methods for performing mRNAseq to globally profile gene expression in dissected subsets of single Drosophila embryos. The patterns I measure are consistent between replicates, and also faithfully reproduce patterns already known from in situ hybridization experiments. However, the global nature of this experiment also reveals spatial patterning in many genes that have not been successfully assayed, even in relatively large-scale projects. Furthermore, I demonstrate that this can be used across samples from different developmental time points to produce a genome-wide developmental atlas of zygotic gene activation./nBecause the small sample size of slices of single embryos limited the ability to use standard cDNA library preparation protocols, I next assayed a number of previously published protocols that were specifically designed for minute samples. Previous literature had not addressed whether these protocols would be suitable for reconstructing spatial patterns, and I was particularly concerned that pre-amplification steps would introduce unacceptable non-linearities in the data. Upon analyzing the results, however, I determined that all the protocols I tried were acceptable, and all approximately equally good. I also investigated a few modifications to one of the protocols that reduces the cost of library preparation such that it is no longer the primary limiting factor in terms of number of samples to be sequenced./nFinally, with these methods well refined, I have sliced and sequenced embryos with severe genetic perturbations to maternally provided factors at the head of the patterning network. Comparing embryos deficient in the key pioneer factor zelda, I have revealed that this lethal mutant is nevertheless able to correctly produce the majority of gene expression patterns in the wild-type embryo. Embryos lacking the maternally provided activator bicoid show a greater loss of proper patterning, including the surprising result of ubiquitous over-expression of a number of genes. Simple models of local action of bicoid cannot easily account for this change. Surveying bicoid over-expression mutants and hunchback knock-downs has also yielded a large number of unexpected patterning changes. All of these changes recapitulate previously measured patterning changes, but also highlight new avenues to investigate.

Advisor: Eisen, Michael B.
The Freedom of Despair: Modern Art and Political Violence in Baghdad, 1941-1979

This dissertation asks what the artwork could offer when other forms of action and expression had been foreclosed by political violence. It considers art practice in Baghdad during the nineteen-sixties and seventies, in relation to the collapse of liberal forms of politics and, later, the collapse of a form of anticolonial liberation struggle introduced by the Palestinian liberation movement, which subsequently provided a framework for leftist politics. My argument is that, during these years, the modern artwork underwent a transformation that reconstituted it as the site of a particular kind of speech, implicated in a particular kind of politics, neither liberal nor anticolonial. Following the eclipse of the public sphere in the aftermath of a coup by the Ba’ath Party in 1963, it came into interaction with an ancient tradition of mourning that precipitated a shift in art practice from a concern with representation to a practice of rhetoric. Over the nineteen-seventies, as the possibilities for political action narrowed, this practice of rhetoric evolved a distinctive critique of violence./nOrganized into three parts, the dissertation charts a trajectory of art practice, across which the artwork became a site of critique. Part One examines the establishment of a discursive foundation for the practice of modern art in Baghdad during the nineteen-forties and fifties, on the basis of a medieval history of manuscript illustration and in the context of a broader cultural renewal. It focuses on the artist Jawad Salim’s (1920-1961) discovery of Yahya al-Wasiti’s illustrations of the Maqamat of Hariri, and the ways in which that discovery shaped his conception of modern art. Part Two examines the transformation of art practice following the persecution of leftists by the Ba’ath Party in 1963. It focuses on how, in circumstances where neither an appeal to the law nor political action were possible, the artist Kadhim Hayder (1932-1985), in a series of paintings entitled The Epic of the Martyr [Mulhamat al-Shahid], set a new paradigm for art practice by introducing into the artwork a rhetorical form drawn from the mourning celebrations that commemorate the martyrdom of the Imam al-Husayn. Part Three traces the legacy of this rhetorical form in the practice of the artist Dia Azzawi (1939-). It focuses on a critique of violence he developed over the course of the nineteen-seventies, following the collapse of the Palestinian liberation movement.

Advisor: Pandolfo, Stefania
Power and the Pursuit of Connection: The Effects of Social Power on Social-Connection Seeking after Rejection

People have a fundamental need to feel socially connected to others -- in other words, a need to belong (Baumeister & Leary, 1995). This need is thought to operate according to a drive model, such that a threat to this need – in the form of social rejection or disconnection – motivates one to seek out means to restore the need, in the form of social acceptance or connection (Baumeister & Leary, 1995). The present dissertation examines social power as a factor that may enhance social-connection seeking in the wake of rejection. Social power – defined as the ability to control the resources and outcomes of others (Keltner, Gruenfeld, & Anderson, 2003) – has several consequences that may foster social-connection seeking, including greater resilience to rejection (Kuehn, Chen, & Gordon, in press), and greater goal pursuit (Guinote, 2007). The present work tested two specific mechanisms by which higher power may drive connection-seeking after rejection: greater expectations for acceptance and lesser concern with rejection./nIn the present work, Studies 1 and 2 examined whether power would enhance social-connection seeking after rejection. Study 1 manipulated power in a visualization paradigm and measured participants’ tendency to seek connection after a hypothetical rejection. Study 2 measured trait power in romantic partners and observed behavioral engagement with a partner after perceiving low responsiveness from that partner. Studies 3a and 3b examined whether power predicted our hypothesized mediators. Study 3a examined relationships between trait power, trait acceptance expectations, and trait rejection concerns. Study 3b manipulated power in a visualization paradigm and measured acceptance expectations and rejection concerns from a hypothetical partner. Study 4 tested the full mediation model, assigning participants to a role of high-power or low-power for a partner task, manipulating rejection by delivering accepting or rejecting feedback from the partner, and measuring acceptance expectations, rejection concerns, and behavioral and motivational social-connection seeking tendencies with a new social target./nStudies 1 and 2 demonstrated that greater power predicted greater social-connection seeking uniquely following rejection (and not following acceptance). Studies 3a and 3b demonstrated that power was associated with greater acceptance expectations and lesser rejection concern. Study 4, however, failed to replicate these effects, and failed to provide evidence for mediation. Potential explanations, limitations, and suggestions for future directions are discussed.

Advisor: Chen, Serena
Viral-induced global mRNA degradation influences viral mRNA abundance and host transcription rates

Lytic gammaherpesvirus infection restricts host gene expression by promoting widespread degradation of cytoplasmic mRNA through the activity of the viral endonuclease SOX. Though generally assumed to be selective for cellular transcripts, the extent to which SOX impacts viral mRNA stability has remained unknown. We addressed this issue using the model murine gammaherpesvirus MHV68 and, unexpectedly, found that all stages of viral gene expression are controlled through mRNA degradation. Using both comprehensive RNA expression profiling and half-life studies we reveal that the levels of the majority of viral mRNAs but not noncoding RNAs are tempered by MHV68 SOX (muSOX) activity. The targeting of viral mRNA by muSOX is functionally significant, as it impacts intracellular viral protein abundance and progeny virion composition. In the absence of muSOX-imposed gene expression control the viral particles display increased cell surface binding and entry as well as enhanced immediate early gene expression. These phenotypes culminate in a viral replication defect in multiple cell types as well as in vivo, highlighting the importance of maintaining the appropriate balance of viral RNA during gammaherpesviral infection. This is the first example of a virus that fails to broadly discriminate between cellular and viral transcripts during host shutoff and instead uses the targeting of viral messages to fine-tune overall gene expression./nWe also address some downstream consequences of viral-mediated mRNA decay for the host. We reveal that mammalian cells respond to this widespread cytoplasmic mRNA decay by altering levels of RNA polymerase II (RNAPII) transcription in the nucleus. Measurements of both RNAPII recruitment to promoters and nascent mRNA synthesis revealed that the majority of affected genes are transcriptionally repressed in SOX-expressing cells. The transcriptional feedback does not occur in response to the initial endonuclease-induced cleavage, but instead to degradation of the cleaved fragments by cellular exonucleases. In particular, Xrn1 catalytic activity is required for transcriptional repression. Notably, viral mRNA transcription escapes decay-induced repression, and this escape requires Xrn1. Collectively, these results indicate that mRNA decay rates impact transcription in mammalian cells, and that gamma-herpesviruses have incorporated this feedback mechanism into their own gene expression strategy.

Advisor: Glaunsinger, Britt A