VictorJuiz/thesis huggingface dataset:
The public impact of Latin America's approach to open access [electronic resource]

This study explores the extent to which research published in Latin America—where the vast majority of which is made freely available to the public—has an impact and reach beyond the academic community. It addresses the ways in which the study of research impact is moving beyond the counting citations, which has dominated bibliometrics for well over the last 50 years. As more of the world's research is made freely available to the public, there is an increasing probability that the impact and reach of research extends beyond the confines of academia. To establish the current extent of public access, this study explores who the users of Latin American research are, as well as their motivations for accessing the work by using a series of simple pop-up surveys, which were displayed to users of the two largest scholarly journal portals in Latin America. The results, after thousands of responses, indicate that traditional scholarly use makes up only a quarter of the total use in Latin America. The majority of use is from non-scholar communities, namely students (around 50% of the total use) and from individuals interested for professional or personal reasons (collectively around 20% of the total use). By linking the survey responses to the articles being read, it was also possible to identify points of convergence and divergence in student, faculty, and public interest groups. Finally, this study employed methods from a new field of inquiry, altmetrics, in an attempt to capture engagement with research on the social Web. The success of such methods for the Latin American case were limited due to low coverage levels, but the research nevertheless contributes to the understanding of nascent field of altmetrics more broadly. The study concludes with a discussion of the conceptual, political, curricular, and methodological implications of this new approach to scientific communication.

Keywords: Education.
Advisor: Willinsky John
McFarland Daniel (Daniel A.) advisor. Thesis advisor
Parigi Paolo
Stevens Mitchell L. advisor. Thesis advisor
Quantifying paleoclimate dynamics using isotopes in precipitation [electronic resource]

As anthropogenic emissions of greenhouse gasses continue to alter the Earth's climate, it becomes increasingly vital to understand how the Earth system has responded to high temperatures and pCO2 in the past. The Cenozoic era in particular offers unique insights into climate systems equilibrated with modern to near-future radiative forcing and comparable global geographic boundary conditions. Isotopes in precipitation ([delta] D and [delta] 18O) are one of the more ubiquitous tools used to investigate Cenozoic climate, as they are sensitive to a number of hydro-climatic factors including rainout patterns, terrestrial moisture recycling, evaporative source conditions, and atmospheric mixing by transient eddies. While this sensitivity allows for the potential characterization of large-scale hydrologic dynamics, separating out these disparate effects remains a major challenge for interpreting proxy records. This dissertation aims to address this challenge by using a reactive transport model of isotopes in precipitation to develop a framework for testing hypotheses of past conditions against proxy records. This framework is then applied along with other established methods to investigate a number of Cenozoic climate questions including: (1) migration of the Pacific storm track in response to changes in the structure of tropical Pacific SST's and initiation of Northern Hemisphere glaciation through the Plio-Pleistocene; (2) peak eustatic Pliocene sea level and East Antarctic Ice Sheet stability; and (3) global latent heat transport under Early Eocene hothouse climate conditions.

Keywords: Earth System Science.
Advisor: Chamberlain C. Page primary advisor. Thesis advisor
Diffenbaugh Noah S. advisor. Thesis advisor
Maher Katharine advisor. Thesis advisor
Quantitative image analysis reveals diet-driven changes in gut microbiota localization [electronic resource]

The community of commensal bacteria, viruses and eukaryotic microorganisms within our gastrointestinal tract, the gut microbiota, is a fundamental part of our biology. Foundational work has demonstrated that these organisms are required for proper development of the immune, circulatory and central nervous systems; and changes in the membership of this community are associated with pathologies such as obesity, colorectal cancer, type 2 diabetes and inflammatory bowel diseases. Though much research has focused on community composition assessed by pyrosequencing, emerging evidence suggests that many of these disease states are also associated with changes in bacterial localization within the intestines. However, standardized imaging and quantitation methods have not been established yet in the field. The work in this dissertation develops and validates such methods, and applies them to determine the effects of a low fiber diet on spatial organization of the gut microbiota. Chapter 1 contains a literature review of existing tools to study the microbiota, with a focus on the advantages and limitations of different imaging strategies. Chapter 2 includes the histological, imaging, and computational methods developed to develop a high-resolution imaging and quantification pipeline, using gnotobiotic and humanized mice on a polysaccharide-deficient diet as a test case. Chapter 3 further develops the work from Chapter 2, with a focus on host response to a low fiber diet. Chapter 4 contains perspectives and future directions for the applications of imaging to the gut microbiota field.

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Amieva Manuel advisor. Thesis advisor
Huang Kerwyn Casey
Schneider David (David Samuel)
A quantitative study of the axonal transport mechanics in neurons [electronic resource]

Neurons are highly polarized cells with their axon often extending over large distances away from the cell bodies (up to 1 meter in axonal length with a cell body less than 50 micrometer in diameter). Given that the majority of neuronal proteins and materials are synthesized in the cell body, such a long axon precludes effective diffusion of soma-produced proteins to their presynaptic destinations at the axonal terminals. As a result, neurons rely extensively on active axonal transport to deliver newly synthesized synaptic proteins, ion channels, lipids, and mitochondria to their axonal destinations via anterograde transport. On the other hand, retrograde axonal transport is responsible for carrying molecules and organelles destined for degradation from the axonal terminals back to the cell body. A highly efficient and tightly regulated machinery is thus required for a robust long-range transport of materials to ensure the neurons' proper growth, maintenance and survival. This thesis is a quantitative study of the underlying mechanism of axonal transport, with a specific focus on the retrograde axonal transport machinery in neurons. In our experimental setup, the axonal transport of cargos can be directly visualized in real-time using a neuronal microfluidic platform and fluorescence microscopy technique. We observe that cargos have high tendency to slow down their transport speed when crossing various obstacles along the axon such as non-moving cargos and stationary mitochondria. Single molecule study of retrograde nerve growth factor transport reveals that mechanical tug-of-war and intracellular motor regulation are complementary features of the near-unidirectional endosome directionality. Specifically, a stochastic mechanical simulation suggests that the endosomes are driven on average by 5-6 active dyneins and 1-2 down-regulated kinesins. This result is further supported by a study of the dynamics of endosomes detaching under load in axons, showcasing the cooperativity of multiple dyneins and the subdued activity of kinesins. Lastly, we present a quantitative characterization of the complex behavior of light-sensitive cryptochrome 2 (CRY2) protein under blue light. The results contribute to the understanding of the light-inducible CRY2 system and can be used as a guide to establish new optogenetic strategies to probe cellular processes in live cells.

Keywords: Chemistry.
Advisor: Cui Bianxiao primary advisor. Thesis advisor
Kool Eric T. advisor. Thesis advisor
Moerner W. E. (William Esco)
Quantum edge transport in topological insulators [electronic resource]

In the quantum Hall effect, electrons circulate in one direction around the edge of a 2D sample. The robustness of these states is protected by the topology of the band structure and scattering is only possible if thermally-activated 2D conduction provides a path across the bulk. However, the environmental conditions required for the effect (large magnetic fields and, usually, low temperatures) make it unsuitable for most practical applications. This dissertation discusses the implementation of two similar topological transport phenomena, in the absence of magnetic fields, using the class of materials known as topological insulators. First, it reports on investigations into the quantum spin Hall effect, a time-reversal-symmetric state with counterpropagating, spin-polarized edge channels. Mean free paths in this case are limited to only a few micrometers due to a scattering mechanism under investigation. Second, it reports on recent results on the quantum anomalous Hall effect demonstrating part-per-10,000 conductance quantization, arising from nearly perfect transport through one-way edge channels, in magnetically-doped thin films of 3D topological insulators. It shows that dissipation only occurs due to thermally-activated states that can be nearly eliminated via an unexpected magnetocaloric effect.

Keywords: Physics.
Advisor: Goldhaber-Gordon David
Cui Yi
Moler Kathryn A. advisor. Thesis advisor
Quaternion tools for mathematical prediction [electronic resource]

Existing quaternion neural network structures suffer from two key limitations: first, these structures are computationally expensive to train; and second, they do not perform all mathematical operations in the quaternion domain. Existing quaternion neural networks are limited by using a real-valued, nonlinear activation function independently on each quaternion dimension. The original contributions to knowledge in this work address both limitations. The computational limitations are addressed through the introduction of a version of quaternion Backpropagation that requires significantly fewer training cycles for convergence and is further addressed with the introduction of Direct Quaternion Error, an algorithm that performs equivalently to quaternion Backpropagation under certain conditions and requires considerably less computation per training cycle. As for performing mathematical operations in the quaternion domain, a new multi-valued quaternion neuron and neural network structure are proposed, wherein a discrete-valued activation function that operates simultaneously in all four quaternion dimensions is introduced. Since there are no standard datasets for the evaluation of quaternion neural networks, two applications are used to demonstrate the effectiveness of the proposed techniques. The problems of automated prostate cancer Gleason grading and chaotic time series prediction are investigated. Both of these are difficult prediction problems and are appropriate for benchmarking mathematical classification and prediction techniques. The high-speed quaternion neural network training techniques are shown to be effective in the Gleason grading experiments, and the new multi-valued quaternion neural network is shown to outperform both real-valued and other quaternion-valued neural networks in the chaotic time series prediction.

Keywords: Electrical Engineering.
Advisor: Agaian S. S.
Gill John T.
Smith Julius O. (Julius Orion) advisor. Thesis advisor
The queer chronotope [electronic resource] : the confessional return in the nineteenth-century fantastic

Rousseau claims that in writing The Confessions, he seeks to make himself completely transparent to his reader. And indeed, recourse to the confessional mode in eighteenth-century sentimentality often points to sympathy with another, or the desire for thoroughly open communication. With the turn to the nineteenth century, literary historians argue that psychological realism supplants the affective charge of sympathetic discourse all the while retaining the (now implicit) claim to total transparency. In other words, where the diarist once confessed, now the panoptic gaze of the dispassionate realist narrator unearths. But effusive expressions of love, care, and admiration between men, uneasily coexisting with paranoias born of fretful musings and intractable jealousies, continue to haunt the literature of terror in the nineteenth-century. And those expressions are still inscribed in a confessional mode. Therefore, this dissertation sets out to track the persistence of this discursive mode in the traditions of the fantastic in the British, French, and German novels. This dissertation examines how confession flows into a generic configuration called the queer chronotope, which replaces eighteenth-century sentimentality. But distinct to the male confessional plots of the queer chronotope is the denial of sympathy. The texts in question betray the affective mark of being cut off from the sympathetic other of sentimentality. Unlike their literary fathers, the neurotic heroes of male confessional plots no longer delight in unburdening through narrative. Instead, they find themselves trapped in a morose narrative body. The confessional mode in the queer chronotope, as this dissertation argues, becomes a solipsistic prison in which a weakened narrative ego confesses before an omnipotent super ego, deriving from the fear of losing paternal love. And therefore the male confessional plot rehearses the same frustration of satisfaction of the ego ideal, which means narrativizing hypochondria, melancholy, narcissism, self-loathing, and other male obsessional disorders. As a narrative poetics, confession turns into the repetition of an unpleasure.

Keywords: Comparative Literature.
Advisor: Cohen Margaret primary advisor. Thesis advisor
Greene Roland
Gumbrecht Hans Ulrich advisor. Thesis advisor
Saldívar Ramón advisor. Thesis advisor
Radical democratic action [electronic resource] : movement, institution, and the development of constituent power

Radical democracy is a project for Left-democratic alternatives to both state socialism and capitalist liberalism. It promotes expanding and enhancing the power of the people in the decisions and institutions that affect their lives. In this dissertation, I develop a theory of radical democracy as a mode of action aimed at developing constituent power. I then use this as a foundation for a strategy of social transformation that links movement and institution, simultaneously challenging barriers to democratization while meeting community-defined needs for critical goods and services. This is guided by three objectives: 1) to demonstrate the value of radical democracy as a meta-frame that is useful for bridging multiple struggles for social justice; 2) to provide a framework for analyzing how the "power of the people" or constituent power develops; and 3) to develop a strategy for a radical democracy movement that bridges the divide between movement and institution. In Chapter One, I introduce a basic framework for understanding movements and the role of institutions in facilitating movement activity. In Chapter Two, I define the vision for a radical democracy movement as an ongoing process of developing constituent power. I trace a history of radical democratic theory, distinguishing it from liberal and market-based approaches to democracy, while illustrating its affinity with new conceptions of socialism and communism. I then analyze radical democracy in terms of a disaggregated and developmental conception of constituent power, a framework to which I return in each of the subsequent chapters. In Chapter Three, I introduce three different approaches to contemporary movement work -- prefigurative politics, the party-form, and counter-institutions. While, each of these works to develop some elements of constituent power, they are inadequate individually. In the final two chapters, I propose a structure and action framework for a radical democracy movement, a strategy that integrates movement and institution. In Chapter Four, I present an institutional design of democratic counter-institution that builds on the movement structures discussed in the previous chapter. I draw on a number of existing experiments in democratic political economy, but propose a structure that embeds local, activist enterprises in participatory communities and support institutions. And in Chapter Five, I focus on the specific action of radical democracy movement-building -- transformative organizing. I link this organizing approach to democratic counter-institution and the development of constituent power. In both of these chapters, I address some of the challenges that these forms will face as they work to deepen democracy internally and expand a radical democracy movement into new spaces and new spheres of life.

Advisor: Cohen Joshua
Hardt Michael
McAdam Doug advisor. Thesis advisor
Rainbow Junction: South Africa’s Born Free Generation and the Future of Democracy

Fifty-five percent of South Africa’s population today is under 25 years old, born with no living memory of apartheid. By demography alone, this “born free” generation will play an increasingly central role in the nation’s civic and political life. Therefore I ask: What attitudes, values, and beliefs characterize the born free generation’s views on democracy and civic engagement in South Africa? And what do these imply for the country’s future? Given South Africa’s democratic transition, I initially hypothesized that the born frees would possess distinctive views; like many researchers and authors, I took the very term “born free” to suggest a different set of attitudes about democracy and a certain liberation from the fetters of apartheid. Yet my results indicate that at the national level, South African born frees do not possess uniform views on the psychological, political, and economic aspects of democracy and governance. Although the generation never lived through apartheid, its lived experience is historically freighted and differs tremendously along lines of race and class. My analysis also shows something else: deep, pervasive racial cleavages in the psychological, political, and economic attitudes of the born frees, and in South Africa more generally. In one urban Johannesburg neighborhood, my data indicate that its born frees, overcoming both racial stratification and planned gentrification, do possess distinctive values and beliefs on the hyper-local level: my ethnographic work shows that these young South Africans have developed numerous civic micro-practices that enable and are enabled by interpersonal trust and use difference as a political resource. Hyper-local civic interactions can percolate upward, a process essential to consolidating democracy in the Rainbow Nation.

Keywords:  Program in International Relations
Center on Democracy Development and the Rule of Law
Program on Urban Studies
Stanford University
South Africa
Born Free
Afrobarometer
Mixed Methods
democratic transitions
youth attitudes
ethnography
civic micro-practices
civic engagement
Rainbow Nation
Thesis
Advisor: Diamond Larry
Rapid, inducible degradation of CENP-C suggests novel roles for CENP-C in centromere assembly and maintenance

Chromosomes are segregated equally to each daughter cell during mitosis. A protein complex known as the kinetochore is responsible for linking chromosomes to spindle microtubules during mitosis. Mitotic assembly of the kinetochore requires a
specialized underlying region of chromatin called the centromere. Centromeres are epigenetically marked by the incorporation of the histone H3 variant CENP-A, which recruits the 16-subunit constitutive centromere-associated network (CCAN). The
organization of the CCAN, as well as how the CCAN recruits the kinetochore to promote proper chromosome segregation, remains unclear. Previous work has demonstrated a fundamental role for the CCAN protein CENP-C in recruiting the rest of the CCAN and the kinetochore protein Mis12. A detailed understanding of the role of CENP-C has been hampered by the inability to rapidly and efficiently degrade endogenous CENP-C. Here we have characterized a cell line expressing a selectively degradable form of CENP-C, allowing us to efficiently deplete endogenous CENP-C in as little as 45 minutes. Depletion of CENP-C did not result in defects in the localization of CENP-T and CENP-K shortly after depletion, but did result in defects after 72 hours. These results suggest that CENP-C may play separable roles in CCAN recruitment and maintenance, and they
highlight how fine temporal manipulation of protein levels can help us dissect these mechanisms.

Keywords:  Department of Biology
biology
biochemistry
centromere
kinetochore
cenp-c
cenp-t
cenp-k
Thesis
Advisor: Straight Aaron
Skotheim Jan
Rateless lossy compression via the extremes [electronic resource]

In the era of Big Data, the volume of data grows rapidly, and compression is becoming an increasingly important issue. Information theory, in particular, approaches this problem mathematically to find optimum compression algorithms. Such works often focus more on optimality of compression rate but tacitly ignore the complexity of algorithms. On the other hand, in the real world, various compression algorithms are developed for each different application. These algorithms provide low complexity but cannot guarantee the optimum compression rate. In this work, we try to achieve both the low complexity and optimality of the rate. More precisely, a new technique using successive refinement is proposed to reduce the complexity of algorithms that achieve the optimum compression rate.

Keywords: Electrical Engineering.
Advisor: Weissman Tsachy primary advisor. Thesis advisor
El Gamal Abbas A. advisor. Thesis advisor
Goldsmith Andrea
Rateless wireless networks [electronic resource]

Wireless networks rely on passive channel strength prediction or explicit receiver feedback mechanisms for rate adaptation on the physical (PHY) layer. In the MAC layer, current wireless protocols aim to avoid collisions either through passive exponential backing off or explicit handshaking protocols. However, all these mechanisms are either inaccurate or add significant control overhead especially with highly mobile clients or in networks with high contention. In this dissertation, we present the design of a Rateless Wireless Network where transmitters can transmit oblivious to the wireless channel state without sacrificing performance. This is achieved by designing novel PHY and MAC layer protocols : Strider and AutoMAC. Strider is a rateless code for wireless networks which adapts to varying channel strength at the physical (PHY) layer without explicit rate adaptation or channel strength feedback. The transmitter sends a stream of coded packets until the receiver successfully decodes and sends back an ACK. We then build on top of a rateless code in the PHY layer to design a MAC protocol (AutoMAC). AutoMAC uses the rateless code at the PHY layer to enable successive interference cancellation techniques. It can thus exploit collisions (instead of avoiding them) by decoding all component packets in a collision.

Keywords: Electrical Engineering.
Advisor: Katti Sachin primary advisor. Thesis advisor
Levis Philip advisor. Thesis advisor
Özgür Ayfer advisor. Thesis advisor