VictorJuiz/thesis huggingface dataset:
The Saga of Light-Matter Interaction and Magneto-optical Effects. Applications to Atomic Magnetometry, Laser-cooled Atoms, Atomic Clocks, Geomagnetism, and Plant Bio-magnetism

The quest to expand the limited sensorial domain, in particular to bridge the inability to gauge magnetic fields near and far, has driven the fabrication of remedial tools. The interaction of ferromagnetic material with a magnetic field had been the only available technique to gauge that field for several millennium. The advent of electricity and associated classical phenomena captured in the four Maxwell equations, were a step forward. In the early 1900s, the model of quantum mechanics provided a two-way leap forward. One came from the newly understood interaction of light and matter, and more specifically the three-way coupling of photons, atoms' angular momenta, and magnetic field, which are the foundations of atomic magnetometry. The other came from magnetically sensitive quantum effects in a fabricated energy-ladder form of matter cooled to a temperature below that of the energy steps; these quantum effects gave rise to the superconducting quantum interference device (SQUID). Research using atomic magnetometers and SQUIDs has resulted in thousands of publications, text books, and conferences. The current status in each field is well described in Refs. [48,49,38,42] and all references therein. In this work we develop and investigate techniques and applications pertaining to atomic magnetometry. [Full text: eric.corsini@gmail.com]

Advisor: Gawlik, Wojciech
Budker, Dmitry
Culture as Talk: American Literature and the Ethnography of Utterance, 1880-1945

Accounts of the American literary field at the turn of the twentieth century often emphasize its fascination with everyday speech, explaining this fascination in terms of a widespread popular interest in folk cultures. This dissertation, working between literary history and the history of anthropological linguistics, argues that we can reverse the direction of these accounts, using the literary representation of speech to explain the history of the culture concept. It's well known that anthropologist Franz Boas and his students relativized the idea of culture during this period, championing a new pluralistic theory of difference. What's less well known is that this theory owed many of the particulars of its elaboration to the practical obstacles ethnographers faced in transcribing folk speech. "Culture as Talk" links these productive difficulties of ethnographic method to features of literary form by viewing them as aspects of a single technical problem, the textual representation of "talk"--a term adopted here for its connotation of discourse that is socially embedded and that stands at a slant angle to the standard. If these pragmatic and vernacular qualities make talk key to writing about ethnic affiliation and alterity, they also make it a complex object to entextualize. How does one inscribe both the social universe indexed by a given speech act and, at the same time, the tonal idiosyncrasies of the particular voice that produced it? In the literary field, this questions play out across a wide range of genres and traditions, as the project demonstrates through close readings of John Oskison's Indian Territory fiction, Helen Keller's memoirs, F. Scott Fitzgerald's The Great Gatsby, and Claude McKay's dialect poetry. Drawing on social-scientific theories of transcription, these readings qualify the commonplace opposition in literary studies between cultural studies and formalism by showing that, from the late nineteenth century on, the history of the culture concept has been, in part, a record of the formal effects produced when texts hit their limits at the object of talk.

Advisor: Hale, Dorothy J
Policy Analysis 2.0 - Structured Collaboration Using Projected Outcome Matrices from the Eightfold Path

The Eightfold Path is a methodology for policy analysis taught at the Goldman School of Public Policy, at the University of California, Berkeley. At the center of this methodology is a matrix in which each cell represents the projected outcome of the policy alternative corresponding to the cell's row, as measured by the criterion corresponding to the cell's column. Policy analysts use this methodology to explore complex policy problems, consider the tradeoffs between different alternatives, and orient decision makers as to the choices they face. A similar methodology has been developed for the analysis of competing hypotheses (ACH) regarding intelligence assessments of streams of evidence. The ACH method, also based on a matrix, represents evidence, hypotheses, and analyst's assessments of the consistency of a particular piece of evidence with a given hypothesis. The ACH methodology has been implemented as open source software that enables collaboration between intelligence analysts and contributes to more robust analysis. This dissertation starts with the open source implementation of ACH, and adapts it to fit the Eightfold Path methodology. Debates from a 2009 Congressional hearing on sunsetting provisions from the USA PATRIOT Act are then used as a case study to demonstrate that benefits from the ACH system can also be captured by policy analysts using the Eightfold Path.

Advisor: Nacht, Michael
Sensing and Responding to Stress Stimuli in Caenorhabditis elegans: Implications for Aging and Immunity

Animals have evolved sophisticated mechanisms to perceive stress or even anticipate it before it has caused damage. Ideally, stress responses are controlled to ensure that they are specific and not excessive lest they cause collateral damage to the host. Here I describe my work in Caenorhabditis elegans examining the initiation and consequences of stress responses. In chapters 2 and 3, I examine the mechanisms of initiation of C.elegans immune responses to Pseudomonas aeruginosa, focusing on pathogen recognition. In chapters 4 and 5 I describe a project that was initiated within the realm of host-pathogen interactions, but evolved to focus on age as a context determining the outcome of both biotic and abiotic stress responses./nDespite extensive knowledge of conserved signaling pathways in the C.elegans immune response, a question that has remained elusive is whether C.elegans can directly recognize pathogens, or if alternatively, they detect cellular damage caused by infection. I have shown that the immune response to P. aeruginosa can be dissociated from colonization and that potential damage from secreted molecules cannot induce a marker of the early immune response; in contrast, a non-pathogenic Pseudomonad can. This suggests that the response can be initiated at least in part by structural features of the bacteria. Furthermore, I have identified a family of genes in C.elegans encoding LysM domain proteins which are known to participate in recognition of microbial envelope components. Genetic and functional analyses suggest a potential role for family members in pathogen recognition in C. elegans./nIn the second half of this dissertation, I show that while the C.elegans JNK homolog KGB-1 is stress-protective during development, its activation in adults compromises stress resistance as well as general lifespan. I go on to show that this phenomenon is mediated in part by KGB-1's age-dependent antagonistic modulation of the conserved FOXO transcription factor, DAF-16. Genome-wide analysis of the KGB-1 transcriptome revealed that KGB-1 regulates several genes in an age-specific manner, and pointed to another conserved transcription factor, FOS-1 as a mediator of KGB-1's effects. Interestingly, the phenomenon of the same protein having opposite effects dependent on age is reminiscent of the Antagonistic Pleiotropy theory for the evolution of aging. Our results shed light on molecular mechanisms underlying this long-standing theory.

Advisor: Shapira, Michael
Architecture and Biogenesis of the Human Telomerase Holoenzyme

Telomerase adds simple sequence repeats to the ends of linear chromosomes to counteract the loss of end sequence inherent in conventional DNA replication. Telomerase is a ribonucleoprotein (RNP) whose catalytic activity arises from the cooperation of the telomerase reverse transcriptase protein (TERT) and the telomerase RNA (TER), which provides an integrated template for DNA repeat addition. TERs vary widely in sequence and structure but share a set of motifs required for TERT binding and catalytic activity. Species-specific TER motifs play essential roles in RNP biogenesis, stability, trafficking, and regulation. Human TER, or hTR, contains a motif shared with a large family of H/ACA RNAs that directs a pathway of RNP maturation./nI have investigated the RNA and RNP architecture of the hTR H/ACA domain and defined the sequence and structural elements required for RNA accumulation and RNP assembly. I have shown that, like other eukaryotic H/ACA RNAs, hTR recruits two sets of H/ACA core proteins despite a noncanonical spacing of conserved elements in its 5' H/ACA hairpin (Chapter Two). I have found that an hTR-specific BIO box motif within the 3' H/ACA loop stimulates H/ACA core RNP assembly in a manner required for hTR accumulation in vivo (Chapter Three). Finally, I have generated stable cell lines expressing tagged hTR and TERT to enable RNA-based and protein-based affinity purification of telomerase complexes in order to identify hTR-interacting factors and investigate telomerase multimerization (Chapter Four).

Advisor: Collins, Kathleen
Friend and foe: The early Ottoman reception of Ibn 'Arabi

Abstract/nFriend and foe: The Early Ottoman Reception of Ibn `Arabi/nby/nAhmed Zildzic/nDoctor of Philosophy in Near Eastern Studies/nUniversity of California, Berkeley/nProfessor Hamid Algar, Chair/nThe legacy of the great Muslim Sufi master from the XII century, Muhy al-din Ibn al-`Arabi left broad, profound, lasting and polarizing impact on the development of Islamic mysticism in the centuries after his death. The underlying principles of Sufism such as the ideas of the transcendental unity of being, the Perfect Man, the sealhood of the Mu-hammadan sainthood in their final form and ultimate interpretation are usually, both fa-vorably and unfavorably, associated with the name of Ibn `Arabi./nThis dissertation is a historical inquiry into the pathways through which the influence of Ibn `Arabi, as well as that of his works, disciples and ideas was inherited and incorpo-rated into the intellectual milieu of the Ottoman learned class represented here by two groups: religious scholars, and members of the imperial administration. This dissertation follows the continuities of the textual and interpretative community of Ibn Arabi, stretch-ing through a series of Ibn Arabi's disciples from the time of his sojourn in pre-Ottoman Anatolia until the first scholarly figures and institutions of the Ottomans whereby Akbari teachings were propelled into the nascent Ottoman scholarly circles./nThe tumultuous historical events of the first decades of the XVI century, namely the Ot-toman conquest of the Arab world and the resulting defeat of the Mamluks and the Sa-favids, provided an opportunity for the evaluation of the well-established Akbari teach-ings in an Ottoman context. A notable XVII century Ottoman commentator of the Fusus, Abdullah el-Bosnevi in his famous Sharh proposed that the advent of the Ottomans into the Arab world reinvigorated, or more precisely for the first time launched heated debates concentrated around the question of the acceptability of IbnArabi's beliefs in Ottoman realm. The abundant amount of primary sources originating from that period shows in-tensive activities focused at attacking and defending Ibn `Arabi, his views and his follow-ers, and that fact appears to bear out el-Bosnevi's assumption. Based on primary manu-script sources and an array of secondary literature this dissertation attempts to follow those debates in two textual corpuses: in imperial discourse represented here by a short, anonymous and obscure treatise titled Al-Shajara al-nu`maniyya fi `ulama' al-dawla al-`uthmaniyya, and in legal discourse represented by a selection of fatwas issued by some of the most illustrious Ottoman scholars and shaykh al-islams from that period.

Advisor: Algar, Hamid
The Photometric Properties of Nearby Type Ia Supernovae

Type Ia supernovae (SNe Ia) are the final brilliant explosion of a carbon-oxygen white dwarf accreting mass from a companion star. At peak brightness, a SN Ia can outshine an entire galaxy of billions of stars. Most SNe Ia have a standardizable luminosity, ideal for use as an extragalactic distance indicator. Measurements of a large sample of SNe Ia over a range of distances enables the estimate of cosmological parameters to help determine the mass-energy content of the Universe (Riess et al. 1998; Perlmutter et al. 1999; Riess et al. 2004; Astier et al. 2006; Riess et al. 2007; Wood-Vasey et al. 2008; Kowalski et al. 2008; Hicken et al. 2009a; Amanullah et al. 2010; Sullivan et al. 2011a; Suzuki et al. 2012)./nThe cosmological application of SNe Ia is predicated upon relationships between the intrinsic luminosity and light-curve properties. Despite the successful measurement of cosmological parameters using SNe Ia, our understanding of SNe Ia themselves is surprisingly lacking. The SN Ia progenitor system has never been directly observed, making it unclear how many different channels exist to make a SN Ia. The physical nature of the relationship between light-curve parameters and luminosity is also not well understood, and it remains to be seen whether other correlations exist to improve SN Ia distance estimates./nThe goal of this dissertation is to shed light on the physics of SNe Ia and search for new correlations to improve distance estimates to SNe Ia by analyzing a large sample of well-observed, high-quality SN Ia light curves. I have collected, reduced, and analyzed optical photometric data for 165 nearby SNe Ia as part of the Lick Observatory Supernova Search (LOSS). These data represent a significant contribution to the existing sample of nearby SN Ia light curves./nAfter giving a general overview of SNe Ia in Chapter 1, I present the methods used to obtain and reduce the LOSS data in Chapter 2. In Chapter 3, I use the LOSS data in an analysis of the earliest photometry epochs to understand the explosion physics governing the initial rise of the SN Ia light curve. These early data points also provide a means of testing models to constrain the nature of the binary companion star. I do not find evidence for interaction between SN ejecta and a companion star, ruling out theories requiring a red giant as a companion in most cases. In Chapter 4, I combine the data presented in this thesis with other samples in the literature to place constraints on cosmological parameters. I reject a non-accelerating Universe with 99.999% confidence. In Chapter 5, I present a study of an individual peculiar SN Ia that is unlike any previously published object, bucking the relationships normally observed in SNe Ia. Studying extreme SNe Ia may provide insights into understanding the physics of normal SNe Ia.

Advisor: Filippenko, Alexei V
Control Strategies for a Minimally Actuated Medical Exoskeleton for Individuals with Paralysis

Over 265,000 individuals in the United States have a spinal cord injury. The wheelchair is currently the most prescribed mobility option for this population. Robotic exoskeleton devices are a promising alternative means of mobility that enable a paraplegic user to regain the physical and emotional health benefits of standing and walking. This dissertation will discuss novel gait strategies that were designed for a minimally-actuated medical exoskeleton device./nTwo novel stance control strategies will be presented that are designed to propel the exoskeleton and pilot forward out of double-stance. The first stance strategy relies on the movement of the pilot's torso as a means to dynamically propel the system forward through a step. Second, a more advanced strategy that propels the user forward while stabilizing their torso will also be proposed. Through the manipulation of lower extremity kinematics, the user can be propelled forward out of double-stance with an exoskeleton that only has actuation at the hips. Sequential methods of trajectory generation will be described for both strategies. Experimental results will be presented that support the efficacy for these stance strategies./nIn addition, this dissertation proposes an original sequential swing phase model. This model is used to produce a gait trajectory for the swing leg that dynamically controls an unactuated swing knee. A method for swing phase hip trajectory generation will be presented. Experimental results will be shown that validate the efficacy of the swing phase trajectory at producing a natural human-like swing phase from a swing leg that has no actuation at the knee./nExtensive pilot testing of the medical exoskeleton in both structured and unstructured environments was completed. The results from these tests support the efficacy of the control algorithms and show great promise in the minimally actuated exoskeleton paradigm. This work enables a reduction in exoskeleton hardware complexity, reduced weight, and anticipated lower costs for end users so that more spinal cord injury patients may have greater access to this technology.

Advisor: Kazerooni, Homayoon
Investigation into Utrafast Dynamics of Organometallic Compounds with Transient Resonance Infrared Spectroscopy and Growing String

Two systems were studied using either a pump-probe spectroscopic technique or a density functional theory computational method. Ultrafast time-resolved infrared spectroscopy has been used to investigate the reactivity of V(CO)5, a doublet species, with silicon-hydrogen and carbon-hydrogen bonds. Using a ultraviolet pump pulse, a carbonyl was dissociated from V(CO)6 while dissolved in triethylsilane; subsequently, a broad bandwidth infrared pulse interrogated the system. On timescales less than 1 ns, vanadium pentacarbonyl does not appear to react. The second study used the Growing String Method incorporating density functional theory to examine the possible reaction mechanisms for the fluxional rearrangement of Fe3(CO)12 and Ru3(CO)12. Fluxional mechanisms have structurally identical reactants and products; the atoms swap positions with other atoms of the same element. The concerted bridge-opening, bridge-closing mechanism for the Fe3(CO)12 was calculated to have the lowest barrier of those tested at 0.777 kcal/mol; in this mechanism, all twelve carbonyl change position and the final structure is equivalent to the initial structure. At 4.285 kcal/mol, the next lowest energy barrier was calculated for the Cotton's Merry-Go-Round mechanism.

Advisor: Harris, Charles B
Building for Oil: Corporate Colonialism, Nationalism and Urban Modernity in Ahmadi, 1946-1992

Located at the intersection of oil and space, this dissertation highlights the role of oil as an agent of political, social and cultural change at the level of the everyday urban experience by introducing the oil company town as a modern architectural and urban planning prototype that has been largely neglected in the Middle East. Using the Kuwait Oil Company (KOC) town of Ahmadi as a case in point this article offers a new history of oil, architecture and urbanism in Kuwait since 1946. Apart from oil dictating Ahmadi's location and reason for being various actors were complicit in the creation and playing out of Ahmadi's urban modernity: British KOC officials, the company's architectural firm Wilson Mason & Partners, nationalism, the process of Kuwaitization, Ahmadi's architecture and urbanism, and, especially, the town's residents. I argue that Ahmadi's colonial modernity which was initially targeted at the expatriate employees of the company during the 1950s, was later adopted by KOC's Kuwaiti employees after the country's independence in 1961, and in turn mediated a drastically new lifestyle, or urban modernity, during the 1960s and 1970s. The memory of this urban modernity coupled with its gradual erosion ever since have rendered Ahmadi a nostalgic city in the nation's collective imagination.

Advisor: AlSayyad, Nezar
I Will be VIP!: The Cultural and Political Strategies of Peripheral Abidjanais Men

This dissertation examines the livelihoods and lifestyles of men in Africa's urban informal economy. I look at the relationship between masculinity, work and globalization from the perspective of two groups of peripheral men who symbolize the political and economic dimensions of the crisis in Abidjan, Côte d'Ivoire: street-level political propagandists (orators) for former President Laurent Gbagbo and mobile street vendors, respectively. My analysis is premised on the fact that adult masculine identity in Côte d'Ivoire is predicated on formal work and marriage, two criteria the men I studied were unable to meet. I include analyses of public spaces where these men frequent to explore the relationship between urban informality and masculine identity./nIn what I term "complicit nationalist masculinity," the orators used narratives of Ivoirian exceptionalism and invested in the ruling regime to ensure their livelihoods, gain status, and secure their post-crisis futures. Moreover, denouncing Franco-Ivoirian neocolonial relations they blamed the unemployment crisis on a "Francophone" reliance on the state bureaucracy. They advocated an "Anglophone" pro-business state and imagined themselves as patriotic entrepreneurs at the country's helm. In what I term "complicit global masculinity," the vendors had no ties to the state and were targets of informal state extraction and harassment. In seeking self-affirmation they bypassed the state and identified with media images of black masculinity from the African diaspora. They were complicit because, rendered redundant as non-productive men, they inserted themselves into the neoliberal economy through consumption-oriented identities popularized in mainstream media and corporate advertising./nIn both strategies, peripheral men's relationship to the global economy has transitioned from exploitation to exclusion; men thereby respond not by resisting but by seeking to belong. In short, I argue that unable to be producers and providers via the formal economy, peripheral Abidjanais men search for political or cultural alternatives wherein they may incorporate into local and global society.

Advisor: Ray, Raka