VictorJuiz/thesis huggingface dataset:
Loop-Mediated Isothermal Amplification for the Mapping of Microbes: An Anti-Capitalist Approach

The field of microbial ecology is hindered by our general inability to map microbes on a geographical scale. This is in part due to technical limitations posed by current DNA detection reactions. This dissertation presents the application of Loop-Mediated Isothermal Amplification (LAMP) for the purpose of amplifying DNA from pollen grains; down to a single grain and with a resulting fluorescence signal to indicate the presence or absence of the particular DNA fragment in question. Three academic papers outlining this method comprise the bulk of the work and are bookended by a brief survey of microbial detection efforts to date and future applications of our method./nBeyond technical limitations there are social and political priorities embedded within the biological sciences that are implicit in our inability to map microbes. Therefore, any advance in the resolution of microbial mapping must also challenge these priorities. In place of the centralized research conducted by experts in universities and corporations, and ultimately for the purpose of capital accumulation, we propose a distributed and horizontally organized mapping network antagonistic to capitalist biology./nPollen grains are our choice of microbe because they are the vector of reproduction for flowering plants and thus an important source of contamination of transgenic DNA from transgenic plants. The growing rejection of transgenic crops across the globe points to a strong desire to identify their location, utilizing microbial mapping methods, and eliminate their spread./nThe technical advances presented here, alongside our social and political commitments, aim to assist in that effort.

Advisor: Chapela, Ignacio H
Homological mirror symmetry for open Riemann surfaces from pair-of-pants decompositions

Given a punctured Riemann surface with a pair-of-pants decomposition, we compute its/nwrapped Fukaya category in a suitable model by reconstructing it from those of various pairs/nof pants. The pieces are glued together in the sense that the restrictions of the wrapped/nFloer complexes from two adjacent pairs of pants to their adjoining cylindrical piece agree./nThe A infinity-structures are given by those in the pairs of pants. The category of singularities/nof the mirror Landau-Ginzburg model can also be constructed in the same way from local/nane pieces that are mirrors of the pairs of pants.

Advisor: Auroux, Denis
Design of control algorithms for redundant neuroprosthetic brain-machine interfaces

Dexterous control of upper arm movements is integral to activities of daily living. This important ability may be lost due to neurological injury or disease, yet brain-machine interfaces (BMIs) or neuroprosthetics may offer the ability to restore motor function by bypassing damaged neural circuitry. Though tremendous progress has been made in BMI performance and robustness, additional gains are needed to improve the clinical utility of BMI systems. Of particular importance is the need to scale BMI performance beyond the simple 2-D reaching paradigm typically studied and extend to the multi-degree-of-freedom (multi-DOF) case. We explored methods and design considerations for redundant multi-DOF BMIs and examine the neuroprosthetic control mechanisms engaged by subjects./nIn this work, healthy non-human primate subjects controlled a variety of virtual and physical actuators using neural signals recorded from electrode arrays implanted in the motor cortex. We analyzed 2-D natural arm movements and developed a fast method to extract sparse components of hand kinematics during point-to-point reaching. We then analyzed neuroprosthetic control of a computer cursor in which neural decoding is performed using a Kalman filter (KF). We discovered several links between KF parameters and control performance of the overall BMI system, including the ability to manipulate the speed-accuracy tradeoff of neural cursors. Building from hypotheses of model based control in natural motor control, we examine BMI cursor control for evidence of model-based and feedforward control./nWe then proceeded to develop an architecture for BMI control of a redundant actuator. Subjects learned BMI control of a redundant four-link virtual “arm” which was confined to move in a two-dimensional plane. When controlling this redundant arm, performance improved when subjects made use of the redundant control dimensions. Furthermore, redundant control signals were critical to escaping manipulator singularities, similar to how redundant control signals are used in robotic systems. These results suggest the utility of using neural signals in conjunction with standard robotic path planning methods to control endpoint-redundant aspects of a robotic prosthesis. Altogether, the work of this dissertation contributes progress toward BMI control of highly redundant prosthetic systems for clinical use.

Advisor: Carmena, Jose M
Water temperature modeling in streams to support ecological restoration

Water temperature is a critical water quality parameter that affects salmonid survival by influencing its metabolism and growth at all life stages. Stream temperature is an especially important parameter in California rivers where it frequently limits the range of salmonids. Anthropogenic activities have increased stream temperature and degraded spawning, holding, and rearing habitats, and this has contributed to declines in salmonid populations in California. Fisheries managers have a range of analytical and empirical tools available to assess and quantify elevated stream temperature conditions, but many of these tools do not focus on water temperature conditions at the spatial and temporal scales important to salmonids. My research focuses on assessing water temperature at the watershed and upwelling hyporheic scale which are critical to salmonid survival as stream temperature approaches thermal tolerances./nI developed a model to calculate water temperature at locations throughout a watershed to provide a method to evaluate the availability and connectivity of suitable thermal habitat throughout a stream network. The model used a linear weighted average of the maximum and minimum air temperatures of the current and 4 prior days. The weighting parameter is dependent upon upstream drainage area enabling the application of the model to both small tributaries and large mainstem streams. I used historical data from the Sonoma Creek, Napa River, and Russian River watersheds to develop, test, calibrate, and partially validate the model. Model results from Sonoma Creek and Napa River indicated it was generally able to estimate daily average water temperature within 1.5 degrees C of the observed water temperature. Data from the Russian River highlighted the model was limited to streams without significant hydrologic modifications or geologic constraints that forced groundwater to the surface./nA 1-D advection dispersion heat transport model was developed to quantify the upwelling hyporheic temperature that provides cold water thermal refugia along a streambed for salmonids. I analyzed hyporheic temperature measured at five sites in a previous research program across sixteen kilometers of Deer Creek near Vina, California, to test, calibrate, and partially validate the model. At three sites, I found the 1-D advection and dispersion were the dominant heat transport mechanisms with model root mean square error less than 0.6 degrees C. At two sites, the model was not applicable because modeling results indicated that surface flow rate variations, solar radiation, and multi-day flow paths also influenced the upwelling hyporheic temperature. Modeling was valuable for highlighting the contribution of these additional processes from that of 1-D advection dispersion. The availability of monitoring data over the summer-fall period was essential for modeling upwelling temperature dynamics along a semi-natural channel.

Advisor: Hunt, James R
The Government of the Senses: Aesthetic Subjectivity and the Rule of Taste in Britain, 1660-1760

The Government of the Senses is a study of how the changes in aesthetic culture that occurred in the wake of empiricism operated as regulating social processes. Tracking the rise of a new concern with tastefulness as well as various approaches to aesthetic detachment, I describe how these critical discourses translated into different styles of subjectification. Each chapter identifies figural representations in literature and visual culture that reflect what it felt like to participate in the new aesthetic culture. Chapter One describes the new interest in ideas of taste and “gust” in John Milton’s work and models of aesthetic detachment in John Dryden, showing how Lord Shaftesbury and Joseph Addison developed these models of aesthetic behavior into a comprehensive social program. Chapter Two argues for a continuity between the cultivation of pleasure in the Restoration libertine discourse of Lord Rochester and George Etherege and the eighteenth-century cultivation of aesthetic pleasures. I show the importance of the fop character type in the transition to socially acceptable enjoyments: at the center of ambivalence about cultural consumption, the fop is the first figure that condenses the experience of modern aesthetic subjectivity. Chapter Three follows the inner sense tradition, arguing that Daniel Defoe’s Robinson Crusoe narrates an aesthetic self-fashioning by testing the limits of detachment from social life. This wildly popular novel shows how culturally relevant the new aesthetic culture had become beyond the stratified elites. Chapter Four studies the emergence of a socially intelligible figure of the person of taste between Jonathan Richardson’s theory of connoisseurship and the major statements on the standard of taste in the 1750s. It shows that the methods, tensions, and models of authority associated with the new aesthetics were most fully exemplified in the literary career of Alexander Pope. Methodologically, this project studies the regulating effects of aesthetics using Michel Foucault’s late theory of “governmentality” and it describe aesthetics as a self-sustaining social process using the theory of Niklas Luhmann. The chapters also include discussions of the Cartesian theory of pleasure, Hobbesian psychology, the theory of the je ne sais quoi of Dominique Bouhours, the models of conduct in Baltasar Gracián and the Chevalier de Méré, John Locke on secondary qualities and self-education, inner sense theory in Ralph Cudworth and Francis Hutcheson, Adam Smith on self-regulation, William Hogarth on utility, and the theories of taste in Edmund Burke, Alexander Gerard, and David Hume. I show that the first phase of modern British aesthetics fashioned a coherent model for the conduct of conduct using the intensities of the sensitive body.

Advisor: Turner, James G
Wayreading Chamorro Literature from Guam

Wayreading Chamorro Literature from Guam/nThis dissertation maps and navigates contemporary literature by indigenous Chamorro authors from the Pacific island of Guam. Because Guam has experienced more than three centuries of colonization by three different imperial nations, Chamorro language, beliefs, customs, practices, identities, and aesthetics have been suppressed, changed, and sometimes completely replaced. As a result of these colonial changes, many anthropologists and historians have claimed that authentically indigenous Chamorro culture no longer exists. Similarly, literary scholars have argued that contemporary Chamorro literature is degraded and inauthentic because it is often composed in a written form as opposed to an oral form, in English as opposed to Chamorro, and in a foreign genre (such as a novel) as opposed to an indigenous genre (such as a chant). This discourse of inauthenticity, I suggest, is based on an understanding of Chamorro culture and literature as static essences that once existed in a "pure" and "authentic" state before colonialism, modernity, and globalization. Countering these arguments, I view Chamorro culture as a dynamic entity composed of core, enduring values, customs, and practices that are continually transformed and re-articulated within various historical contexts and political pressures. Relatedly, I contend that Chamorro literature is a dynamic phenomenon comprised of an aesthetic genealogy that has also been transformed by colonialism and re-articulated by every successive generation of Chamorro authors. To understand these complexities, I enact a literary methodology that I term "wayreading," which involves tracking how the primary themes (the content) of Chamorro literature express the survival and vitality of Chamorro language, customs, values, and practices, as well as how the primary narrative structures (the forms) of Chamorro literature embody Chamorro aesthetics, technologies, and ecologies. While the first chapter of this project launches into a discussion of Chamorro cultural identity and literary authenticity, the subsequent chapters focus on representations of important Chamorro cultural symbols—including land, housing, navigation, and storytelling—in a wide range of contemporary Chamorro literary expressions. In the Conclusion, I assert that Chamorro literature is a symbolic decolonial act and a pragmatic decolonial tool in ongoing decolonization, demilitarization, and sovereignty movements in Guam. This dissertation is significant because it highlights a relatively unknown indigenous literature, thus contributing to the intellectual traditions of Pacific Islander, Native American, and Global Indigenous Cultural and Literary Studies. Beyond the realm of the indigenous, this study also contributes to the fields of Hispanic, American, Post-colonial, and Comparative Ethnic Cultural and Literary Studies.

Advisor: Piatote, Beth
Secondary receptors of the Shh pathway

The Sonic Hedgehog signaling pathway is central in vertebrate development and in several human disease states. Our current understanding of the pathway outlines a straight-forward mechanism whereby the Shh ligand is perceived by the nine-pass transmembrane receptor Ptch1. In its active state Ptch1 represses Smo, a GPCR like protein, which acts as the ultimate on and off switch of the Shh pathway. When Shh binds Ptch1, Ptch1 becomes inactivated and Smo becomes activated, subsequently leading to the downstream activation of the Shh response./nDespite this framework our understanding of how Ptch1-Shh binding leads to Smo activation remains rudimentary. To understand this crucial step of the pathway one must consider that Ptch1 exists within the Shh receptosome. The Shh receptosome, consists of several membrane bound and transmembrane proteins, which bind Shh. Delineating the function of these proteins is important for understanding how receptosome-Shh interactions lead to Shh pathway activation. Boc, Cdo and Gas1 are secondary receptors of Shh that are known agonists of the pathway. Furthermore, all three proteins are suspected to interact with Ptch1 and there collective presence is necessary for activation of the Shh pathway. Ptch2, a paralogue of Ptch1, is dispensable for development, but has been documented to act as a repressor of the Shh pathway./nWe sought to further characterize the function of Ptch2, Boc, Cdo, and Gas1 in the context of Ptch1. Through in vitro experiments we have determined that Shh binding to Ptch1; or Boc, Cdo and Gas1 alone is insufficient to potentiate positive Shh signaling, however, Shh binding to Ptch1 alone is sufficient to cause Smo localization to the primary cilia, an event associated with active Shh signaling. Additionally, we have found that Ptch2 functions as a repressor of the Shh pathway in the absence of Ptch1, further suggesting that Ptch2 and Ptch1 share overlapping functions. Moreover, the distinct possibility remains that like other proteins of the Resistance Nodulation Family, Ptch1 and Ptch2 may interact. Thus, the simple model of Ptch1 mediated Shh reception needs to be revised to include the collective activity of Ptch2, Boc, Cdo and Gas1.

Advisor: Roelink, Henk
Health Services Utilization of Older Adults with Depression and Comorbid Chronic Health Conditions: Evidence from China

This study examines the health services utilization of older adults in China with depressive symptoms and chronic health conditions. In older adults with chronic conditions, depression has shown to be associated with greater severity of medical illness, poorer health status and quality of life, and increased mortality. Studies in western industrialized societies have shown that individuals with depression use a higher number of physical health services. However, there have been no studies identified to date that have looked at this question for China, including for Chinese older adults in particular. The healthcare utilization patterns of Chinese residents with depression may show differential patterns from those of individuals living in western industrialized countries due to differences in culture, available forms of help, existing service systems, and policy contexts, including the rapid expansion of healthcare coverage in China in recent years due to healthcare reform./nThis study employs logistic regression to analyze the relationships between depression, chronic health conditions, and health services utilization among Chinese older adults. It uses nationally representative survey data from the 2011-2012 China Health and Retirement and Longitudinal Study (CHARLS) (n=17,708). The study also presents a profile of service users based on a cluster analysis of health conditions and health services used./nAfter controlling for sociodemographic and health characteristics, depression was found to be positively associated with outpatient service utilization but not significantly associated with inpatient service utilization for the general sample of older adults in China. Among the sample of older adults with chronic conditions, also having depression was significantly associated with greater outpatient service use. Those with both chronic conditions and depression were 1.53 times more likely to use outpatient services than those who only had chronic conditions with no depression. There was no significant relationship between chronic conditions and depression with inpatient service use./nResults of a cluster analysis indicate that depression levels and levels of ADLs and IADLs appear to be positively associated with both outpatient and inpatient service utilization. High utilizers of outpatient services tend to be less uninsured and to have the most Urban Employee and New Cooperative insurance, and the least Urban Resident and Government insurance relative to moderate and low users of outpatient services. High users of outpatient services are more likely to be female and rural residents. High users of inpatient services tend to be more rural and to have lower levels of social support than both moderate and low users. Findings on the healthcare usage patterns of this population have implications for improving health policy and interventions related to the treatment and prevention of depression among this population of vulnerable older adults.

Advisor: Chow, Julian
Singing as an Israeli Woman: Musical Personae in a Cosmopolitan Society

Israel in the 21st century is an intensely multicultural society where several types of cosmopolitanism vie with regional and ethnic forms of expression, a phenomenon that plays out in musical life. I propose that such a society offers a variety of possibilities for what a woman is, what she can do, and how she can work. This dissertation is an ethnographic study of four female singer-songwriters that examines the ways they negotiate and sometimes challenge socio-cultural norms in creating their careers and constructing their artistic personae, or the version of themselves that they present as musicians./nThe artists I focus on straddle four major rifts in Israeli society, between Arabs and Jews, Mizrahim and Ashkenazim, Russian-speaking immigrants and native Israelis, and Orthodox and non-Orthodox communities. In using their ethnic heritage as cultural capital to corner a unique market niche, these artists become enmeshed in social politics that include tensions between ethnic and religious groups, conflicting gender roles, and struggles over belonging. I argue that as they create legible personae to meet the demands of the music industry, their liminality between mainstream society and a minority sector challenges the discourse around those identities. The success of their careers thus depends both on how their particular ethnicity is positioned in relation to more powerful models of Israeliness that are reproduced by public discourses, the state media and the entertainment industry, as well as how they meet commercial criteria for mainstream pop music. In working to satisfy this dual set of demands they engage with the canon of Israeli music, revealing and expanding its boundaries./nTo illuminate how the artists define and challenge discourses of Israeliness, I analyze their songs, how they perform them, and what people say about them. The radio airtime their music receives and the venues where they perform further reveal how they are positioned within Israeli culture. Thus while the strategies they use in marking themselves as foreign are common to artists cross-culturally, the challenges they encounter offer a window onto changing social patterns in contemporary Israeli society.

Advisor: Brinner, Benjamin E
Nuclear Excitation by Electronic Transition of U-235

Nuclear excitation by electronic transition (NEET) is a rare nuclear excitation that is theorized to occur in numerous isotopes. One isotope in particular, U-235, has been studied several times over the past 40 years and NEET of U-235 has never been conclusively observed. These past experiments generated conflicting results with some experiments claiming to observe NEET of U-235 and others setting limits for the NEET rate./nThis dissertation discusses the latest attempt to measure NEET of U-235. If NEET of U-235 were to occur, U-235m would be created. U-235m decays by internal conversion with a decay energy of 76 eV and a half-life of 26 minutes. A pulsed Nd:YAG laser operating at 1064 nm with a pulse energy of 789 mJ and a pulse width of 9 ns was used to generate a uranium plasma. The plasma was captured on a catcher plate and electrons emitted from the catcher plate were accelerated and focused onto a microchannel plate detector. A decay of 26 minutes would suggest the creation of U-235m and the possibility that NEET occurred. However, measurements performed using a variety of uranium targets spanning depleted uranium up to 99.4% enriched uranium did not observe a 26 minute decay. Numerous other decays were observed with half-lives ranging from minutes up to hundreds of minutes. While NEET of U-235 was not observed during this experiment, an upper limit for the NEET rate of U-235 was determined. In addition, explanations for the conflicting results from previous experiments are given. Based on the results of this experiment and the previous experiments looking for NEET of U-235, it is likely that NEET of U-235 has never been observed.

Advisor: Norman, Eric B