VictorJuiz/thesis huggingface dataset:
Nature As Discourse: A Co-Evolutionary Systems Approach to Art and Environmental Design

ABSTRACT/nNature As Discourse:/nA Co-Evolutionary Systems Approach to Art and Environmental Design/nby Susannah Hays/nDoctor of Philosophy in Interdisciplinary Studies University of California, Berkeley/nProfessor Galen Cranz, Chair/nTransdisciplinarity, an international education movement that explores pathways to a coherent epistemology beyond all disciplines, seeks to become a sustaining vital force in human development. To do so, it needs to be complemented by a branch of epistemology called epistemics or self-knowledge. Only if co-evolutionary phylogenetic principles of human-brain and autonomic nervous system functioning are included in transdisciplinarity’s model can individuals experientially evolve to the levels of reality the model entails. An actual, “true to life,” transdisciplinary education teaches isomorphic qualities intrinsic to perception, pattern mapping, language, and aesthetic (non-directive) skills. Curricula utilizing these educational tools will result in indispensable, creative learning environments. A trajectory not yet explored in other literature on Transdisciplinarity is an emphasis on cross-cultural research in human- brain and autonomic nervous system dynamics. Three key understandings that guide human biological evolutionary processes toward higher levels of consciousness are Paul MacLean’s triune-brain neuroethology, Stephen Porges’ Polyvagal Theory of emotions, and G. I. Gurdjieff’s three-centered self-study practice. Each chapter describes a non-profit organization whose goal is to raise humanity’s normative level of participation in environmental sustainability. These organizations demonstrate how Transdisciplinarity can recalibrate human evolution, if the educational movement synthesizes the autonomic/cognitive forces within Homo sapiens’ biological organization.

Advisor: Cranz, Galen
Establishing Planar Cell Polarity in an Edgeless Epithelium

Abstract/nEstablishing Planar Cell Polarity in an Edgeless Epithelium/nBy/nKatherine Ruth Lipari/nDoctor of Philosophy in Molecular and Cell Biology/nUniversity of California, Berkeley/nProfessor David Bilder, Chair/nIn all animals, organ function is dependent on two major processes that happen in the very beginning of embryonic development: differentiation and morphogenesis. In this study we focus on the process of morphogenesis, studying the planar cell polarity (PCP) pathway, a process that acts perpendicular to the apical-basal axis to orient the cell within the larger environment. From the elongation and closure of the entire central nervous system during neural tube closure, to the subtle orientation of hairs on the skin of a mammal, PCP dictates gross morphological events by first polarizing subcellular structures. Most of our knowledge about PCP derives from the Drosophila wing, where two well-characterized signaling pathways are currently known to regulate PCP: Fz/Vang PCP and Fat/Ds signaling. These two pathways have also been implicated in vertebrate PCP; despite vigorous investigation, there is a surprising paucity of data on how these pathways are shaping vertebrate organs, beyond the fact that they do. One major limitation is that PCP has been most deeply studied in organs with a fundamentally different topology than the tubules that make up the majority of animal organs. While planar polarization of proteins within the cells of the Drosophila wing align with the edge of the wing, causing elongation in the direction of polarization, vertebrate planar polarity proteins align perpendicular to later elongation and do not orient towards the edge of the tissue. Indeed, vertebrate tubular organs do not have similar edges to dictate orientation; they are ‘edgeless’ tissues. To study how planar polarization occurs in such structures we use the Drosophila egg chamber as a model. This tissue undergoes planar polarization perpendicular to the axis of elongation – similar to other tubule elongation – and depends upon the Fat2 cadherin for planar polarization and elongation. In this dissertation I show that planar polarization in this tissue is established early during development of the tissue – at the level of a few cells – by biased microtubule growth. This bias is then propagated by rotation of the entire tissue to create planar polarization of the overlying extracellular matrix to establish a persistent orientation as the tissue grows. I find novel genetic enhancers of the Fat2 mutant phenotype that identify genes involved in this early event and later morphogenetic events. I also study what cells within the epithelium itself are necessary for this rotation to occur. Overall, my thesis work has shown how planar polarization is established and propagated in edgeless tissues through tissue migration.

Advisor: Bilder, David
Household Drinking Water Treatment in Rural China: Microbiological Effectiveness and Socioeconomic Predictors

Across the world, well over one billion people lack access to safe drinking water. There are a variety of low cost household drinking water treatment technologies available, but hitherto none have achieved widespread adoption. Globally, boiling is the most common treatment method./nOver the last few decades, China has achieved historically unprecedented reductions in rural poverty and concomitant expansions of piped drinking water access. However, hundreds of millions of rural Chinese still lack reliable access to safe drinking water. Most households in rural China boil their drinking water, often using biomass or coal for fuel. Though boiling is microbiologically effective, once it cools boiled water is susceptible to recontamination, and the combustion of solid fuels for boiling creates hazardous air pollution./nThis research sought to evaluate the microbiological effectiveness of the household water treatment methods used in rural China, and to investigate the socioeconomic predictors associated with water treatment methods and preferences./nTo conduct this research, I collaborated with the National Center for Rural Water Supply Technical Guidance, an agency of the Chinese Center for Disease Control and Prevention, and their counterparts in Guangxi Province. In 2013 we collected survey and water quality data from 450 households across 15 villages. Household drinking water samples were analyzed for indicators of fecal contamination and physicochemical analyses were conducted for village drinking water sources. Data collection was repeated in a subset of villages over the 2013-2014 winter to address seasonality, and remote temperature sensors affixed to kettles and pots were used to corroborate household survey responses about boiling frequencies and durations./nAs far as I am aware, this was the first research study in China focused on household water treatment, and the first to quantify the advantages of boiling with electric kettles.

Advisor: Romm, Jeffrey M
Ray, Isha
Mechanisms of the Human Telomerase Catalytic Cycle

At the ends of every linear chromosome, genomic integrity is threatened by incomplete/nDNA synthesis by the replisome and the potential for inappropriate DNA break repair./nEukaryotic cells control these reactions through the function of telomeres. Maintenance/nof the characteristic DNA repeat tracts that form telomeres requires the specialized/nreverse transcriptase telomerase, with its active site in the protein subunit TERT and the/ntemplate for DNA synthesis in the integral RNA subunit. Many telomerases can extend a/nchromosome 3' end by processive addition of single-stranded repeats. This processive/ntelomeric repeat synthesis requires a specialized telomerase catalytic cycle, involving/nnucleic acid handling specificities not found in any other polymerase. Developing new/napproaches of subunit fluorescence labeling for single-molecule analysis, I show that/nhuman telomerase reconstitution generates mixtures of complexes of varying TERT/nsubunit stoichiometry but activity requires a complex containing only one TERT/nmolecule. This establishes conservation of active telomerase subunit architecture across/nphylogeny. Using TERT and RNA domain-complementation assays to sensitize for/nprimer-template duplex use by the telomerase active site and a direct footprinting assay/nfor telomerase association with product DNA, I uncover mechanisms by which TERT/ndomains and RNA motifs interact to specify telomeric repeat synthesis. This work/ndevelops a new model for specialized primer-template duplex sensing during the human/ntelomerase catalytic cycle.

Advisor: Collins, Kathleen
Interface Electronics for Ultrasonic Transducers

Ultrasound has long been used for medical imaging. Recent advances of miniaturized MEMS ultrasonic transducers new applications such as gesture recognition, personal fitness devices, and fingerprint sensors. These devices are considerably smaller than conventional transducers. To benefit from their lower excitation power requirements and address the reduced sensitivity requires the design of novel interface electronic circuits./nThe first part of this thesis describes new circuits capable of generating all the high voltage drive signals for MEMS transducers on-chip from a single low-voltage supply. A novel level shifter design lowers power dissipation by suppressing the crow-bar current of conventional designs. The techniques have been verified in a seven channel ASIC and applied to a personal fitness application./nThe second part of the thesis applies the new circuit ideas to the realization of an ultrasonic fingerprint sensor comprising over 6000 individual transducer elements in a 5x4 mm^2 area, each with drive and sense electronics. Unlike prevalent optical or capacitive fingerprint sensors, the ultrasonic solution is capable of recording both the surface and inner layers of the finger, resulting in reduced susceptibility to spoofing attacks.

Advisor: Boser, Bernhard E
Sparks to Signals: Literature, Science, and Wireless Technology, 1800-1930

“Going wireless” involves not only the elimination of wires but also the production of electromagnetic waves, a realization that had far-reaching implications for the cultural logics of German modernity. As a media archaeology of wirelessness, this dissertation situates the “discovery” of electromagnetic radiation and the “invention” of wireless transmission in a richer field of scientific, experimental, and aesthetic relations during the early and pre-history of national broadcasting. Before wireless transmission came to be synonymous with the mass distribution medium of radio or even the long-distance communication medium of wireless telegraphy, it was at the center of speculation about a variety of possible wireless futures. Understanding the rhetoric of the new media of radio and wireless telegraphy in the first chapter opens onto questions of continuity and change in the longue durée of the second chapter. The insights gained from this comparison of pre-modern cultural techniques and modern electronic technologies are crucial for understanding the “discovery” of electromagnetic radiation and the “invention” of wireless telegraphy examined in the third and fourth chapters with a focus on the immediate pre-history of national broadcasting in the late nineteenth and early twentieth century. The significance of this pre-historical period and the contingency of national broadcasting in the mid-twentieth century arguably only became apparent with the revival of wireless transmission at the turn of the twenty-first century, as the fifth chapter makes evident. As a contribution to the early and pre-history of national broadcasting, this dissertation suggests a new way of thinking about the order of wirelessness, from “wireless” as synonymous with the communication medium of telegraphy or the distribution medium of radio, to “wireless” as electromagnetic radiation and a medium of experimentation.

Advisor: Largier, Niklaus
Spectroscopic Studies of Physical and Electronic Structure in Transition Metal Oxide Photocatalysts

The complex relationship between electronic structure and physical structure in both molecular and solid state photocatalytic systems is examined. Ultrafast transient optical absorption spectroscopy and x-ray photoelectron spectroscopy are the main techniques used to investigate the underlying properties that affect the reactivity of various photocatalysts. The two respective spectroscopies are exceptionally suited to observing the ultrafast kinetics and interfacial behavior of these systems. In this dissertation, two systems are investigated-- one a vanadium-based organometallic complex and the other strontium titanate, a wide band gap metal oxide semiconductor. The relaxation dynamics of a chelated oxovanadium (V) ligand-to-metal charge transfer complex are measured by ultrafast transient absorption. A combination of theoretical and experimental work indicate that the observed excited state lifetime in this molecular complex, which is an order of magnitude longer than those of metal-to-ligand charge transfer iron compounds, is derived uniquely from geometric constraints on its radiative and nonradiative relaxation pathways. Transient optical reflectance measurements are also carried out on niobium-doped strontium titanate at the solid-liquid interface to identify midgap radical states that could be implicated in the water oxidation mechanism. The creation of localized radical hole species is determined to be a surface-site limited process, which is highly dependent on the in situ reaction conditions. The application of voltage is shown to induce a significant redistribution of holes to the surface from valence band hole species, highlighting the capacity of the surface to accommodate localized charge under different conditions. Additional x-ray photoelectron spectroscopic measurements are taken under ambient pressure conditions to investigate water adsorption on the strontium titanate (001) surface. The effects of different variables-- surface termination, dopants, and photoelectrochemical surface treatment--on the surface wetting behavior are considered. Further quantitative analysis of the x-ray photoemission data is currently underway; details of the data processing and analysis procedures as well as a description of how these sample variables might manifest in our x-ray spectra are discussed.

Advisor: Cuk, Tanja
Heterogeneity within Indian cities: Methods for empirical analysis

Abstract/nHeterogeneity within Indian cities:/nMethods for empirical analysis/nby/nKrishnachandran Balakrishnan/nDoctor of Philosophy in Landscape Architecture and Environmental Planning/nUniversity of California, Berkeley/nProfessor Louise Mozingo, Chair/nThis dissertation proposes new methods for analyzing the heterogeneity within Indian cities. The research focuses on developing methods which rely mainly on secondary datasets and demonstrates the application of the methods using data for Bangalore city. The dissertation is structured as a set of three papers, each of which focuses on a specific dimension of heterogeneity within Indian cities. The first paper uses data from the Census of India to generate sub-city typologies based on socio-economic attributes, housing quality, and access to water and sanitation infrastructure. The second paper proposes a predictive framework for high-resolution population density estimation in Indian cities. The method uses data on land-use, land-cover, street network, building height and asset ownership to predict population at a resolution of 30m. This paper also demonstrates the application of a new method for generating building height estimates at a city-wide scale using satellite stereo imagery. The third paper in this dissertation focuses on understanding heterogeneity in the volume of domestic piped water availability across parts of Bangalore city. It combines the high-resolution population mapping method of the second paper with data from the local water utility, to analyze domestic piped water availability. Using normative demand scenarios, it also estimates the deficit in domestic piped water availability and the extent of direct or indirect dependence on groundwater in a spatially disaggregated manner. The dissertation concludes with a discussion on the patterns of spatial inequality within Bangalore, as revealed by the three papers.

Advisor: Mozingo, Louise
Probabilistic Methods for the Inference of Selection and Demography from Ancient Human Genomes

Recently developed technologies for the recovery and sequencing of ancient DNA have generated an explosion of paleogenomic data in the last five years. In particular, human paleogenomics has become a thriving field for understanding evolutionary patterns of different hominin groups over time. However, there is still a dearth of statistical tools that can allow biologists to discern meaningful patterns from ancient genomes. Here, I present three methods designed for inferring past demographic processes and detecting loci under selection using ancient and modern hominin genomes. First, I describe an algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters - including drift times and admixture rates - for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. The method is implemented in a C++ program called `Demographic Inference with Contamination and Error' (DICE). Then, I present two methods for downstream analyses of paleogenomic samples, specifically tailored for detecting different types of positive selection. The first of these consists in a series of summary statistics for detecting adaptive introgression (AI). In particular, the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive pressures on introgressed haplotypes. The second approach for detecting selection is a composite likelihood ratio method called `3P-CLR', and is aimed at locating regions of the genome that were subject to selection before two populations split from each other. I use this method to look for regions under positive selection in the ancestral modern human population after its split from Neanderthals. I validate all of the above methods using simulations and real data, including present-day human genomes from the 1000 Genomes Project and several high- and low-coverage ancient genomes from archaic and early modern humans. I also recover potentially interesting candidate loci that may have been important for various phenotypic adaptations during recent human evolution.

Advisor: Slatkin, Montgomery
Regulation of Human Telomerase Assembly and Recruitment to Telomeres

Telomerase is the ribonucleoprotein complex that synthesizes telomeric repeats and maintains telomere length in cells where it is expressed. The telomerase holoenzyme is composed of many regulatory factors which instruct telomerase biogenesis and engagement with telomeres. Common themes of telomerase regulation in divergent organisms emerge in the form of telomerase RNA accumulation, trafficking among cellular compartments, and cell cycle dependent access to telomeres. My investigations have focused on human telomerase regulation./nI found that a key chaperone which localizes telomerase to Cajal bodies binds and releases telomerase in a cell cycle dependent fashion in coordination with the increased accessibility of telomeres during the replication phase (Chapter two). I also investigated the role of the canonical H/ACA small nucleolar RNA pathway in human telomerase maintenance of telomeres. I found that the H/ACA pathway was required for endogenous telomerase to assemble into active enzyme and that chaperone trafficking of telomerase to Cajal bodies regulated telomere length homeostasis, but was not a requirement for telomere maintenance (Chapter Three)

Advisor: Collins, Kathleen
How much water will we have by the end of summer? Progress and pitfalls along the path to prediction.

Seasonally dry climates exhibit annual swings in precipitation that strongly influence surface water availability. Reliable prediction and characterization of these resources are important for ecosystems and society, yet few hydrologic models and methods have been tailored to cope with the complexities of a non-stationary climate./nThis dissertation focuses on techniques to improve prediction and analysis of soil moisture, hillslope flow generation, and catchment scale flows in seasonally dry climates. It evaluates the performance of three new models for these hydrologic variables, which span the relevant range of scales for conservation and management purposes. It examines in fine detail a common mathematical model for the streamflow recession, the power law differential equation dq/dt = -aq^b, which is one of the simplest and most broadly used functions to describe the draining of a catchment. For seasonally dry watersheds that spend much of the year in a state of recession, the power law model is an important tool for streamflow modeling and analysis. The work here assesses some of the mathematical challenges associ- ated with application of the power law recession model, and quantifies uncertainty associated with determination of the power law parameters, a and b.

Advisor: Thompson, Sally E
'Women Know Their Place': Gender and the Politics of Public Health in Twentieth-Century Senegal

This dissertation examines how the politicization of women’s reproductive health/nand fertility presented new opportunities for women to assert themselves socially as well/nas politically. From colonial policies designed to encourage maternity births during the/n1920s and 1930s to contemporary efforts to promote the use of family planning and birth/ncontrol among Senegalese women, maternal and infant health initiatives transformed/nwomen’s relationship to the state. Using these interventions as a backdrop, this project/nexplores the ways that women have appropriated the language of development to make/nwider claims about their roles in Senegalese society. These findings challenge the/ncommon assumption that public health interventions impose hierarchies of race, class,/nand gender. Instead, they emphasize how Senegalese women transformed their positions/nof subordination into platforms for social and political change. By embracing rather than/neschewing their roles as wives and mothers, women thus carved out new spaces of/nauthority and power.

Advisor: Kanogo, Tabitha