VictorJuiz/thesis huggingface dataset:
Emancipatory Digital Archaeology

As archaeologists integrate digital media into all stages of archaeological methodology it is necessary to understand the implications of using this media to interpret the past. Using digital media is not a neutral or transparent act; to critically engage with digital media it is necessary to create an interdisciplinary space, drawing from the growing body of new media and visual studies, materiality, and anthropological and archaeological theory. This dissertation describes this interdisciplinary space in detail and investigates the following questions: what does it mean to employ digital media in the context of archaeology, how do digital technologies shape inquiry within archaeology, can new media theory change interpretation in archaeology, and can digital media serve as a mechanism for an emancipatory archaeology? To attend to these questions I address digital media created by archaeologists as digital archaeological artifacts, understood as active members of a network of interpretation in archaeology. To give structure to this understanding I assemble three object biographies that identify the digital archaeological artifact's context, the authorship of the artifact, the inclusion of multiple perspectives involved in its creation, and evaluate the openness or ability to share the artifact. The three object biographies that constitute the body of this work are a digital photograph taken of a teapot at Tall Dhiban in Jordan, a digital video of an unexpected excavator participating at Çatalhöyük in Turkey, and a 3D reconstruction of a Neolithic building excavated at Çatalhöyük within the virtual world of Second Life. In these object biographies I weave together narrative, imagery and rigorous, theoretically informed analyses to provide a reflexive investigation of digital archaeological artifacts. Drawing from this research, I advocate a critical making movement in archaeology that will enable archaeologists to use digital media in an activist, emancipatory role to highlight inequity, bring the voices of stakeholders into relief, de-center interpretations, and to make things and share them.

Advisor: Tringham, Ruth
Careless Engagements: Literature, Science, and the Ethics of Indifference in Early Modernity

This project offers a new interpretation of the beginnings of experimental science in seventeenth-century England, arguing that an emergent interest in states of muted feeling enabled the epistemological breakthroughs of Francis Bacon's "great instauration." I propose that ethical reflection on peaceful "nonchalance" (to use Michel de Montaigne's term) catalyzed scientific innovation: Baconian intellectuals (a category that includes theologians, essayists, and poets, as well as natural philosophers) advocated a state of heightened receptivity predicated on effortless serenity of mind, suggesting that cognitive freedom (from Aristotelian dogma and the prejudicial illusions of common sense) could only be achieved by surrendering the teleology of desire, especially the desire for certainty. By aligning Baconian experimentalism with neo-Stoicism, previous scholars have evaded the paradox at its heart. In fact, experimentalists differentiated their own brand of casual indifference from Stoic obstinacy, favoring the leisurely attention of carelessness over the arduous self-discipline of sheer dispassion. By promoting the cultivation of an experience defined by its uncultivated nature, experimentalists created a practical quandary. I explore the capacity of literary form to solve that problem: new literary genres made it possible for readers to experience the sensory awareness and cognitive flexibility on which the new science depended./nMy argument shows that the motifs of "progress" and "method" that organize discussions of seventeenth-century intellectual history, with their suggestion that scientific modernity took its bearings from the imposition of instrumental reason on philosophical inquiry (both its experimental procedures and its manner of accumulating data over time), grossly misrepresent the ethos of experimentalism. Andrew Marvell's self-portrait as a "careless" natural philosopher who "languish[es] with ease" while inspecting and transforming his surroundings with the help of "multiplying glasses" captures the actual interest of scientists like Robert Boyle in risky states of subtle pleasure in which the mind wanders from its habitual course--an errancy John Milton's Son exemplifies. A better understanding of the origins of modern science requires an attention to waywardness and lapses of discipline, antitypes of "progress" and "method" that reframe the latter as fantasies of order that obscure a history in which scientists and likeminded intellectuals savored the disorder of experience and placed their trust in its capacity to yield insight.

Advisor: Kahn, Victoria
Achieving Novel Magnetic States in Perovskite Oxides through Heteroepitaxy

This dissertation is focused on controlling the spin state and long-range magnetic order in cobaltites by heteroepitaxial thin-film growth. I explore the growth of two different cobaltite materials, LaCoO3 and PrCoO3, on lattice-mismatched substrates to determine the role of epitaxial strain in giving rise to long-range magnetic order. This magnetic order is not found in the bulk cobaltite material and warrants the detailed investigations carried out in this work. I investigate changes in structure and stoichiometry that influence the electronic structure and the long-range magnetic order in these materials./nIn the LaCoO3 system, I explore the changes in structure in the films under tensile strain and compressive strain by growth on SrTiO3, LaSrAlTaO3, and LaAlO3 substrates and film growth between 8 nm -133 nm thick. Substrate-dependent oxygen vacancy ordering in the films is found using microstructural characterization, presumably related to the amount of stress in each of the films. By carrying out a study of the effects on the film structure from the oxygen growth pressure, I find an overall increase in the out-of-plane lattice parameter with lower oxygen growth pressures./nThese structural and stoichiometry changes in the LaCoO3 films to trends appear to be related to the stabilization of long-range magnetic order. Highest moment is found in the films in tension (which also have the most defects) on SrTiO3 and LaSrAlTaO3 substrates and the lowest moment is found in films in compression on LaAlO3. Element-specific X-ray absorption techniques reveal contributions from Co in different spin and valence states. I show how strain affects the electronic structure and distribution of these different states and relate these observations to trends observed in the magnetism. Strained films in tension have the highest amount of high spin Co3+ and high spin Co2+, while relaxed films appear to have mostly low spin Co3+ at 25 K. I present some scenarios to explain how these different Co ions combine to give rise to long-range ferromagnetic order in LaCoO3 films./nIn the PrCoO3 system, I explore whether long-range magnetic order can be observed using heteroepitaxial synthesis similar to the efforts in the LaCoO3 thin film system despite PrCoO3 having a more stable low spin state configuration in the bulk. The PrCoO3 films in tension are ferromagnetic, similar to the LaCoO3 system. Thus, epitaxial strain dominates the effects of chemical pressure which stabilize a low spin state. The strained films have more high spin Co3+. The implication of Co sublattice ordering on the ordering of the Pr sublattice is explored using X-ray magnetic circular dichroism. A rare ordering of the Pr ions anti-parallel to the orientation of the moments on the Co sublattice appears to occur in this system. These studies demonstrate the power of heteroepitaxial synthesis to give rise to new magnetic functionality in perovskite oxide systems.

Advisor: Suzuki, Yuri
Study of Ubiquitinating Enzymes Essential for Cell Proliferation

Ubiquitination is a form of post-translational modification of proteins, in which the 76-residue ubiquitin polypeptide is conjugated to the lysine residues of either the substrate protein or the preceding ubiquitin molecule. Ubiquitination requires the sequential action of three types of ubiquitin enzymes: the ubiquitin activating enzyme (E1), the conjugating enzyme (E2) and the ligase (E3). In human genome, there are two different E1s, ~40 E2s and more than 600 E3s. Ubiquitination regulates a variety of cellular processes, including cell cycle progression, induction of inflammatory response, or intracellular protein trafficking. The anaphase-promoting complex/cyclosome (APC/C) and the SCF are two important E3 ligases regulating cell cycle progression. Understanding how they recognize their substrates and how their enzymatic activity is regulated will provide valuable clues for inhibiting unchecked cell proliferation such as in cancer. The objective of this dissertation is twofold: 1) Chapter 1: understanding how APC/C forms ubiquitin chains on its substrates. We found that APC/C preferentially uses lysine11 of ubiquitin to assemble ubiquitin chains on its substrates. By recognizing the same motif present in both the substrates and ubiquitin, APC/C switches from initial modification of the substrate to processive chain elongation, leading to the rapid turnover of its substrates. 2) Chapter 2 to 5: identifying Cul3Klhl12, a structural relative of SCF, as an essential ubiquitin ligase in embryonic stem cells (ESCs). In an siRNA screen, we found that Cul3Klhl12 affects cell adhesion and proliferation of ES cells by regulating COPII-mediated protein trafficking. Cul3Klhl12 ubiquitinates Sec31A, a coat protein of COPII vesicles, and causes the enlargement of the vesicles. This enables the COPII-dependent transport and proper deposition of collagen, a major component of extracellular matrix (ECM).

Advisor: Rape, Michael
The role of attention in cortical and subcortical spatial mapping

Perceiving objects' positions is one of the fundamental purposes of vision and is crucial to day-to-day life. Much work has been devoted to finding and characterizing spatial maps in the brain, but we still know strikingly little about how these maps support perceptual localization. The experiments in this thesis employ a combination of functional brain imaging and visual psychophysics, drawing on a body of behavioral literature on spatial perception and visual attention, to ask how position coding in the brain adapts to support the demands of the task at hand./nThe experiments in Chapter 2 ask how and where perceived object positions are represented in the brain. Perceived position depends on many factors such as attention, frame of reference, adaptation, and motion. At what stage of visual processing is this information integrated into the brain's retinotopic maps? By measuring variability in perceived position alongside variability in the multivariate pattern of neural responses in a host of visual areas, we identify a percept-centered reference frame in high-level object-, face-, scene-, and motion-selective regions./nThe experiments in Chapter 3 ask how the visual system achieves improved spatial resolution with focused attention. Attention is known to boost the amplitude of neural responses, but it might also sharpen position tuning at the neural population level, making the activations produced by adjacent objects more distinct within the cortex. Employing a combined imaging and modeling approach, we find that attention narrows the spatial spread of the fMRI BOLD response in early visual cortical areas, including V1. This narrowed population position tuning is an efficient means of achieving visual resolution improvements./nThe experiments in Chapter 4 ask how the brain suppresses distracting visual input in order to limit its negative impact on performance. During a selective attention task, we measure the BOLD response in the pulvinar nucleus of the thalamus, an area whose damage appears to lead to distractor filtering deficits. We find that while attended items are represented with high spatial and featural precision in the pulvinar, ignored items are gated out, leaving no discernable trace in the pattern of response in the pulvinar. These results suggest that the spatial maps in the pulvinar may serve as an interface in which distracting visual input is filtered out./nCollectively, the findings presented here speak to a remarkable flexibility in the way the brain represents spatial information. The brain's visual maps adapt on a moment-by-moment basis to support the demands of the task at hand.

Advisor: Whitney, David
Hyperpolarized Xenon Magnetic Resonance Imaging of Combustion Processes

There is considerable interest in new methods to probe the chemistry and thermodynamics of enclosed combustion processes. Hyperpolarized xenon gas magnetic resonance imaging enables sensitive and noninvasive analysis of chemical composition and velocity within enclosed and opaque samples. By taking advantage of both the temperature sensitivity of the chemical shift as well as the inertness of xenon-129, temperature and velocity distribution images of an enclosed flame can be acquired. Previous attempts to analyze high-temperature combustion reactions using nuclear magnetic resonance employed two-dimensional exchange spectroscopy of hyperpolarized xenon and proton single-point imaging. In the present study, a homebuilt, water-cooled probe was fabricated, including electronics that are able to withstand high temperatures (approaching 2000 K). Hyperpolarized xenon is premixed with a combustible gas (methane or dimethyl ether) and meets with pure oxygen at an enclosed diffusion flame centered within a 15-mm (diameter) by 25.4-mm (height) insulated coil. A spin echo pulse sequence with velocity and acceleration compensated phase-encodes, is used to generate temperature-weighted, three-dimensional chemical shift images as well as velocity maps of the flame region. This technique can be applied to studying confined combustion processes such as microturbine engines on microelectromechanical systems devices.

Advisor: Pines, Alexander
Towards an Ultra-Low Energy Computation with Asynchronous Circuits

Emerging biomedical applications would benefit from the availability of digital processors with substantially improved energy-efficiency. One approach to realize ultra-low energy processors is to scale the supply voltage aggressively to near or below the transistor threshold, yet the major increase in delay variability under process, voltage and temperature variations combined with the dominance of leakage power makes robust near- and sub-threshold computations and further voltage scaling extremely challenging./nThis research focuses on the design and implementation of robust and energy-efficient computation architectures by employing an asynchronous self-timed design methodology. A statistical framework is first presented to analyze the energy and delay of CMOS digital circuits considering a variety of timing methodologies. The proposed analysis framework combines variability and statistical performance models, which enables designers to efficiently evaluate circuit performance, and determine the optimal timing strategy, pipeline depth and supply voltage in the presence of variability./nTwo asynchronous self-timed designs are then implemented. First, a low-energy asynchronous logic topology using sense amplifier-based pass transistor logic (SAPTL) is presented. The SAPTL structure can realize very low energy computation by using low-leakage pass transistor networks at low supply voltages. The introduction of asynchronous operation in SAPTL further improves energy-delay performance without a significant increase in hardware complexity. The proposed self-timed SAPTL architectures provide robust and efficient asynchronous computation using a glitch-free protocol to avoid possible dynamic timing hazards./nSecond, an asynchronous neural signal processor is presented to dynamically minimize leakage and to self-adapt to process variations and different operating conditions. The self-timed processor demonstrates robust sub-threshold operation down to 0.25V, while consuming only 460nW in a 65nm CMOS technology, representing a 4.4X reduction in power compared to the state-of-the-art designs. The proposed asynchronous design approach enables CMOS circuits to fully benefit from continued technology scaling and realize ultra-low voltage operation, without incurring the leakage and variability issues associated with conventional synchronous implementations.

Advisor: Rabaey, Jan M
The Role of Mitochondrial Deacetylase SIRT3: Delivering Benefits of Calorie Restriction and Promoting Adult Stem Cell Function

With the increase in the aging population, there has been a growing interest in/nunderstanding the process of age-related physical decline and increased disease risk./nResearch in model organisms has shown that aging, far from being a spontaneous/ndevelopment, is actually a controlled process, with molecular mechanisms that can alter/nthe pace of cellular and tissue decline. The aim of this dissertation work was to gain/ninsight into the molecular mechanisms that can control this aging rate./nWe found that SIRT3, a mitochondrial NAD+-dependent deacetylase, performs a vital role/nduring calorie restriction in mice to decrease oxidative damage in tissues. These results/nled us to identify superoxide dismutase 2(SOD2) as a target protein of SIRT3, and/nconfirmed that SIRT3 can deacetylate SOD2 at two critical lysine residues (K53 and K89)./nDeacetylation of these residues on SOD2 leads to an increase in SOD2 detoxification/nactivity. Furthermore, SOD2 is more deacetylated in the tissues of mice on calorie/nrestriction, but this effect is abrogated in mice that are deficient for SIRT3. These results/nled us to develop a model whereby calorie restriction upregulates SIRT3 expression and/nactivity, leading to an increased deacetylation of SOD2. The increased activity level of/nthe deacetylated SOD2 has the effect of decreasing oxidative damage in tissues./nConcomitantly, we found that SIRT3 is required for the switch to fatty acid utilization during/ncalorie restriction. SIRT3 KO mice on calorie restriction have reduced beta- oxidation, lower/nlong chain-acyl CoA dehydrogenase activity (LCAD), and a preference for glucose uptake/nand carbohydrate metabolism. Our findings indicate that other molecular adaptations that/noccur during calorie restriction are insufficient to compensate for a SIRT3 deficiency in this/nmetabolic context./nWe also present our findings that SIRT3 is highly expressed in hematopoietic stem cells/n(HSCs) as compared to differentiated hematopoietic cells, which led us to explore the role/nSIRT3 was playing in this stem cell population. Our results indicate that SIRT3 is required as a stress-responsive protein that can protect stem cell function during conditions of/noxidative stress. These conditions can include serial transplant, chemical treatment, or/nthe increased oxidative stress associated with aging. Furthermore, we show that SIRT3/nexpression is decreased in HSCs from aged mice, and enforced expression of SIRT3 can/nimprove the function of aged HSCs, suggesting the potential for rejuvenation of aged/nHSCs./nOur studies confirm the role that SIRT3 plays in protecting cells and tissues from oxidative/nstress, as well as offer. Although to date, no lifespan data has been published on SIRT3/nKO mice, the results presented here indicate that a relatively shortened lifespan or/nhealthspan would not be unexpected. These findings also open avenues for/nunderstanding the role of SIRT3 in stem cell biology, both other stem cell types, and/npotentially in human stem cell systems.

Advisor: Chen, Danica
Rural electrification, climate change, and local economies: Facilitating communication in development policy and practice on Nicaragua's Atlantic Coast

I explore the role of information and communication in the world of institution-led development. Through a series of case studies from the Atlantic Coast of Nicaragua, I present several projects and their implications for uncovering information that may lead to greater local benefit from externally-planned development projects. In order to construct policies and implement projects, development institutions collect, analyze, and simplify information, collapsing messy physical and social realities into narrow sets of metrics. In addition, local stakeholders often aren't privy to the analysis and assumptions of the "expert" planners. An evolved set of methods for dialogue and planning, which focus on sharing available information, can help facilitate outcomes that are more beneficial for targeted groups./nCarbon abatement cost curves provide a clear example where the relations of complex social, economic, and environmental systems are reduced to a narrow set of metrics, specifically the cost of carbon mitigation and the total tons reduced. When the carbon abatement cost curve is applied to the community level, it reveals information and allows for conclusions obscured by aggregated national level studies. I show that there are opportunities for augmenting the limited metrics of these cost curves to include those that relate to welfare, beginning to highlight how costs and savings are distributed among stakeholders. In particular, the benefits to the most marginalized groups are heavily dependent on planners taking a pro-poor approach./nHowever, planners typically remain blind to the priorities, capabilities, and values of the target stakeholders. There is a dearth of methods that effectively open up the development expert's black box of project designs, allowing their proposed solutions to be transparent to the target beneficiaries. I address this challenge through the presentation of a participatory modeling process that was utilized with groups of artisanal fishers. Participatory modeling places a greater emphasis on understanding processes, rather than just focusing on outcomes. The process facilitated the detailed exploration of local realities through the creation and playing of a board game that modeled their local fishing economy. Participants were able to look closely at the causal relations between several potential development interventions such as a cooperative-owned fish businesses and local ice production, gaining insights into possible costs and benefits.

Advisor: Kammen, Daniel M