VictorJuiz/thesis huggingface dataset:
The Transport of Chemicals and Biota into Coastal Rivers and Marine Ecosystems

Coastal rivers link terrestrial and freshwater systems to oceans. River networks drain watersheds, delivering freshwater, nutrients, sediment, chemicals, and biota to estuaries and coastal ecosystems. These influences can negatively and positively affect downstream receiving water bodies. Effects of rivers on oceans depend on rates of transport and export of river-borne materials from channels versus rates of in-channel processing: degradation, storage, or biological uptake of those materials. In California, under a Mediterranean climate, biotic transformations slow and fluxes increase during the winter months, which coincide with higher river flows./nI studied effects of two river-borne substances on coastal oceans: pyrethroid insecticides and riverine algae. Pyrethroids are in widespread use in both agricultural and urban environments in California. In upstream reaches of the Salinas River, in Central California, sediment samples collected in agricultural and urban creeks were found to be toxic to a common test species, and the mass of pyrethroids present in all these sediments could explain the measured toxicity. While compositional differences in sediment pyrethroid mixtures between the agricultural an urban land uses were not dramatic, movement of pyrethroids short distances from the areas of terrestrial application to downstream waterways was confirmed./nSuspended sediments sampled from three coastal rivers during storm events showed that pyrethroids were routinely discharged from these rivers. Sediments in estuaries and downstream reaches of the rivers contained concentrations of pyrethroids above those expected to be toxic. However pyrethroid residues were not detected in bed sediments of the continental shelf or in the deep sea, presumably due to dilution or degradation./nCoastal rivers can also transport nutrients, organic matter, or biota. We collected algal drift in the Eel River as it entered the estuary of the Eel in Northern California. The major component of this drift during summer base flows was benthic macroalgae which had detached from upstream aquatic habitats, while a winter storm delivered more terrestrial material. Marine and freshwater macroalgae were fed to interstitial estuarine invertebrates, both in an experiment examining preferences of free-swimming benthic isopods and amphipods, and in an experiment examining consumption rates of enclosed amphipods on various types of algae. These experiments showed the quick consumption and preference for freshwater algae. The flux of freshwater algae into the estuary and its quick consumption suggest that fluxes of riverine algae into marine ecosystems are likely to disappear rapidly due to preferential grazing, and would be easy to overlook as potentially important trophic subsidies for estuarine or coastal marine ecosystems.

Advisor: Power, Mary E
Weston, Donald P
Supporting Generative Thinking about Number Lines, the Cartesian Plane, and Graphs of Linear Functions

This dissertation explores fifth and eighth grade students' interpretations of three kinds of mathematical representations: number lines, the Cartesian plane, and graphs of linear functions. Two studies were conducted./nIn Study 1, I administered the paper-and-pencil Linear Representations Assessment (LRA) to examine students' understanding of the three representations. The LRA had an experimental component that compared performance on routine problems to non-routine problems (problems not amenable to routine solution procedures). I administered the assessment to Grade 5 students (n=126) who had no formal instruction involving function graphs, and I compared their performances with those of Grade 8 students (n=131) enrolled in Algebra 1. A repeated measures ANOVA revealed students in each grade performed better on routine problems compared to non-routine problems, suggesting that routine problems may falsely indicate greater competence. Paired samples t-tests indicated no differences in performance between Grades 5 and 8 students on number line items, though Grade 8 students outperformed fifth graders on Cartesian plane and function graph items. Videotaped interviews with a subset of Grades 5 and 8 students revealed that students in each grade approached tasks across representations in similar ways, suggesting persisting misconceptions. Interviews also revealed patterns unique to each grade./nIn Study 2, I examined the efficacy of a tutorial intervention. The intervention introduced written definitions to support principled understandings of the number line, the Cartesian plane, and function graphs. A repeated measures ANOVA that compared pre/posttest scores of Grade 5 students (n=20) to a matched control group (n=20) revealed significant gains from pre- to posttest in the experimental group, with no detectable gains in a control. At posttest, Grade 5 tutorial students performed significantly better on non-routine LRA problems than Grade 8 students who did not receive the tutorial. Video analysis revealed a correlation between tutorial students' appropriate uptake of definitions and gains from pretest to posttest./nAnalyses across the two studies indicate that instruction that supports students' coordination of linear and numerical units can support students' learning with understanding. Potential applications include the development of curricula to support students' learning with understanding related to these representations and teacher professional development interventions.

Advisor: Saxe, Geoffrey
Stream, for solo violin with variable ensemble

Stream is a composition for solo violin with variable ensemble. The score consists of a fixed part for solo violin along with a collection of one-page parts for the variable ensemble. This includes parts for flute, oboe, saxophone, clarinet, percussion, piano, violin/viola, cello, contrabass and a multi-channel electronic part, to be performed using a program designed for performance in Max/ MSP./nThis piece addresses an assortment of compositional practices, thereby blurring the lines between them. Elements of the notation vary in specificity, creating an ambiguity of constrained improvisation and detailed instruction. Similarly, the relationship between soloist and accompaniment suggests a simultaneously fixed composition, improvisation and open-form work. The variability of the ensemble is an extension of this modular, open-form practice./nStream was written for the sfSound ensemble and premiered on August 28, 2011 at ODC Theater, San Francisco, using a subset of six instrumental parts. The sfSound ensemble is comprised of musicians who specialize in both improvised music and meticulously notated scores. It was written with their abilities in mind, but also with the ability to be approachable to ensembles of non- improvisers.

Advisor: Bedrossian, Franck
Direct Observation of Colloidal Nanocrystals by Using Liquid Cell Transmission Electron Microscopy

Colloidal semiconductor and metal nanocyrstals receive attention from studying their physical properties to application in biology, electronics, optics, and catalyst. In addition, colloidal nanocrystals as artificial building blocks construct assemblies in solution phase and on substrate to exploit coupled properties of individual nanocrystals. A facile control of physical properties by tuning size, shape, and composition of nanocrystals can be achieved in solution phase synthetic protocols and now we have a library of literatures about them./nHowever, most of nanocrystal synthesis and their use are developed empirically, perhaps in a lack of fundamental understanding. Growth kinetics during synthesis, motion and behavior of nanocrystals in liquid and at interfaces include many questions which await mechanistic studies./nThis dissertation explores direct observation of nanocrystals in liquid by using liquid cell transmission electron microscopy. Growth of nanocrystals from molecular precursor in solvent requires observation in atomistic resolution of a single particle level. Chapter 1 describes single particle growth trajectories of metal nanocrystals investigated by using graphene liquid cell in transmission electron microscopy. This cell is employed to achieve high-resolution imaging of colloidal platinum nanocrystal growth. The ability to directly image and resolve critical steps at atomistic resolution provides new insights into colloidal nanocrystal growth./nControl of nanocrystal interaction and drying condition of solvent determines the final morphology of nanocrystal self-assembly. Chapter 2 presents direct imaging of nanocrystal motions in solution and real-time formation of two-dimensional nanocrystal superlattices by using liquid phase transmission electron microscopy. Nucleation and growth processes are introduced accompanying with detailed mechanistic steps and single particle trajectories. The important role of solvent fluctuation for self-assembly of nanocrystals is explored in experiment and coarse-grained lattice gas modeling./nConcluding remarks are presented in Chapter 3.

Advisor: Alivisatos, Armand P
Making Place and Nation: Geographic Meaning and the Americanization of Oregon: 1834-1859

Abstract/nMaking Place and Nation: Geographic Meaning and the Americanization of Oregon: 1834-1859/nby/nMacKenzie Katherine Lee Moore/nDoctor of Philosophy in History/nUniversity of California, Berkeley/nProfessor David Henkin, Chair/n"Making Place and Nation: Geographic Meaning and the Americanization of Oregon: 1834-1859" examines the ways colonists worked to counteract the problem of Oregon's complicated geographic situation in order to naturalize the territory's membership in the nation between the first American missionary settlement and admission as the union's thirty-third state. Driven by their desire for national inclusion, colonists ascribed national meanings to local actions while also adapting national narratives to fit their immediate experience. This study uses two key concepts to spatially reconstruct the colonial experience: mental maps and vernacular geography. Colonists relied on mental mapping to navigate and to organize geographic knowledge, and this cognitive practice became part of the spatially focused community discourse dubbed vernacular geography. Locally produced geographic discourse united under one rubric the twin objectives that defined the conquest of Oregon: to civilize the landscape and eliminate the Indian presence therein, and to concurrently rewrite the map of the United States with Oregon squarely within its borders. Thus, "Making Place and Nation" asserts that the conquest of Oregon is best understood as a recursive process of making both place and nation./nThe dissertation relies on a wide variety of documentary materials, including personal and official letter correspondence, diaries and travelogues, pioneer reminiscences, petitions to local and federal government entities, newspapers, and official reports to agents of the central government. These sources reveal that colonists read both the physical transformation of Oregon's environment and the amount of independence enjoyed by native groups as indicators of the territory's potential for national incorporation/n/nThe following chapters reinterpret a series of key events in the history of Oregon's colonization. Chapter One traces the role of mental mapping in establishing an American colony. Chapter Two explores colonists' conceptual tools to manage anxiety about sharing territory with independent Indian groups and their destruction in the 1847 Whitman Massacre. Chapter Three scrutinizes the production of local geographic knowledge as a method of wresting spatial control from Indians during the California and Southwest Oregon Gold Rush (1848-1853). Chapter Four analyzes the territorial dimensions of a colonial program of ethnic cleansing toward Indians in the Rogue River War (1855-56). Chapter Five investigates the extinguishment of Indian title and its relationship to the uneven implementation of the Oregon Donation Land Act during the era of removal (1856-1859).

Advisor: Henkin, David M
Examining and Supporting Agricultural Interventions to Reduce Deforestation in Brazil

The title of this dissertation is "Examining and Supporting Agricultural Interventions to Reduce Deforestation in Brazil." It is a collection of three research chapters. Each is a case study that stands alone and directly complements the other cases. Chapter One examines the international politics of targeting agriculture to Reduce Emissions from Deforestation and Forest Degradation (REDD) and how the ideas, approaches, and insights of an epistemic community of scholars has helped to frame the debate. Chapter Two explores whether in the absence of decisive multilateral actions, Brazil can effectively protect its forests without indirectly harming those of the rest of the globe. Chapter Three examines scientific, regulatory, and enforcement elements to reduce the risks of implementing a policy like the one I examine in Chapter Two. Taken together, these cases provide a cross section of normative, theoretical, empirical, regulatory, and political dimensions of emerging efforts to intervene in agriculture to prevent deforestation. Insights from each chapter and from the broader dissertation are intended to inform governance of the land use change process and to contribute to environmental social science scholarship that examines and informs these efforts.

Advisor: O'Neill, Kate M
Development of Stimuli-Responsive Elastin-like Polypeptide-based Nanocomposite Biomaterials

Smart biomaterials that can actively respond to and interact with their environment are sought after for regenerative medicine, therapeutic delivery, sensing, and actuation. Polymer-nanoparticle hybrids are a promising class of smart materials, but thus far the choice of polymers has predominantly been chemically synthesized ones. In contrast, natural tissues commonly utilize proteins to interface with nanoparticles and provide smart functionalities. Inspired by nature, this dissertation describes the development of genetically engineered, protein-based polymers (PBPs) for use as components of smart, polymer-nanoparticle hybrids. Specifically, elastin-like polypeptides (ELPs), a class of thermoresponsive PBPs, were utilized to functionalize two nanoparticles./nFirst, an improved method for synthesizing PBP genes was developed. Crafting new PBPs is limited by the ease with which their genes can be engineered. The new method utilizes a specific architecture of restriction enzymes to address some of the drawbacks of previous methods and was used to efficiently and accurately produce ELP genes./nNext, ELPs were engineered to display biomimetic, bone mineral-binding peptides and their effect on therapeutic bone cements was investigated. Bones are mechanically robust, composites composed predominantly of proteins and nanocrystalline mineral. In contrast, bone cements are brittle and do not contain organic materials. Composites of mineral-binding ELPs and cement had significantly improved strength. Furthermore, the injectability and washout resistance of cements were improved as a result of the ELP's thermoresponsive behavior./nFinally, photoresponsive composites were created by engineering ELPs to display graphene-binding peptides. Graphene-derived nanoparticles (GNs) exhibit unique mechanical, electrical, and optical properties but are difficult to integrate into biological systems due to their hydrophobic nature. The engineered ELPs non-covalently bound to GNs and the resulting ELP-GN hybrids exhibited increased colloidal stability and a reversible temperature-controlled aggregation behavior. The ability of GNs to convert near-infrared light to heat was exploited in order to remotely induce aggregation of ELP-GN hybrids in solution and to induce rapid, site-specific actuation of ELP-GN composite hydrogels. Finally, cell adhesion on ELP-functionalized graphene was enhanced by genetic addition of integrin-binding peptide motifs./nThese studies demonstrate that PBPs can be tailored to interact with nanoparticles of choice and can provide stimuli-responsive and bioactive properties to biologically relevant nanoparticles. Hybrid materials of PBPs and nanoparticles are, therefore, well suited for biotechnological applications which require smart behavior.

Advisor: Lee, Seung-Wuk
Reclaiming Native Soil: Cultural Mythologies of Soil in Russia and Its Eastern Borderlands from the 1840s to the 1930s

This dissertation explores the cultural topos of soil in Russian and early Soviet culture. Centered on the Soviet project of land reclamation in Central Asia in the 1930s, this dissertation traces the roots of Soviet utopian and dystopian fantasies of soil to the ideological and discursive traditions of the 19th century. It considers how Soviet cultural, scientific, and political figures renovated and adapted 19th-century discourse in order to articulate for their own age the national, revolutionary, and utopian values attached to soil. The intersection of national soil and national identity in this discourse is examined, along with the persistent fear that Russian identity and utopian aspirations are threatened by "Asian" land, both within and beyond Russia's borders./nProviding an overview of selected high points in the discursive history of soil in Russia, this study begins with romantic and materialist discourses of soil from the 1840s to the 1860s, tracing organicist concepts of native soil from German philosopher Herder to literary critic Vissarion Belinskii and thence to the symbolic uses of Russian pochva in the writings of the Slavophiles, the pochvenniki, and others. A case study follows on German chemist Justus Liebig and the transfer of scientific metaphors of soil into the cultural domain, concluding with a discussion of Liebig's influence on Marx's theory of social metabolism and its far-reaching influence on Soviet ideology./nThe study moves to its core discussion of Soviet poetics and ideologies of land use in the 1920s and 1930s. First, I examine writer and land reclamation engineer Andrei Platonov's novella Dzhan in the context of Soviet technological utopianism and the campaign to transform the sands of Central Asia into fertile soil. The following chapter extends the discussion of Soviet land reclamation to the dystopic themes of the Asiatic mode of production and "reforging" in the novels of Platonov, Bruno Jasienski, and Boris Pil'niak. This study closes with a discussion of the revival of organic conceptual metaphors of nationality and national soil in the context of the smychka, or union, between the Soviet center and its Asian periphery in the films of Vertov, Turin, Kalatozov, and Iarmatov.

Advisor: Paperno, Irina
Low Mach Number Simulation of Core Convection in Massive Stars

This work presents three-dimensional simulations of core convection in a 15 solar mass star halfway through its main sequence lifetime. We examine the effects of two common modeling choices on the resulting convective flow: using a reduced domain size and using a monatomic, or single species, approximation. We compare a multi-species simulation on a full sphere (360 degree) domain with a multi-species simulation on an octant domain and also with a single species simulation on a full sphere domain./nTo perform the long-time calculations, we use the new low Mach number code MAESTRO. The first part of this work deals with numerical aspects of using MAESTRO for the core convection system, a new application for MAESTRO. We extend MAESTRO to include two new models, a single species model and a simplified two-dimensional planar model, to aid in the exploration of using MAESTRO for core convection in massive stars. We discuss using MAESTRO with a novel spherical geometry domain configuration, namely, with the outer boundary located in the interior of the star, and show how this can create spurious velocities that must be numerically damped using a sponging layer. We describe the preparation of the initial model for the simulation. We find that assuring neutral stratification in the convective core and reasonable resolution of the gravity waves in the stable layer are key factors in generating suitable initial conditions for the simulation. Further, we examine a numerical aspect of the velocity constraint that is part of the low Mach number formulation of the Euler equations. In particular, we investigate the numerical procedure for computing β0, the density-like variable that captures background stratification in the velocity constraint, and find that the original method of computation remains a good choice./nThe three-dimensional simulation results show that using a single species model actually increases the computational cost of the simulation because the single species system takes longer to reach quasi-steady state convection. This is due to the fact that a single species model cannot effectively model mixing at the convection zone boundary, where fluid of a differing composition is pulled into the convective region./nSimulations in an octant yields flow with statistical properties that are within a factor of two (or less) of the full sphere simulation values. Both the octant and full sphere simulations show similar mixing across the convection zone boundary that is consistent with the turbulent entrainment model. However, the global character of the flow is distinctly different in the octant simulation, showing more rapid changes in the large scale structure of the flow, leading to a more isotropic flow on average. Thus, for studies of more rapid dynamics that could depend sensitively on anisotropy in the flow, such as simulations of the helium flash or oxygen shell burning, performing simulations on a reduced domain is questionable.

Advisor: Bell, John B
McKee, Christopher F