VictorJuiz/thesis huggingface dataset:
Rapid, inducible degradation of CENP-C suggests novel roles for CENP-C in centromere assembly and maintenance
Keywords:  Department of Biology
biology
biochemistry
centromere
kinetochore
cenp-c
cenp-t
cenp-k
Thesis

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.
Rateless lossy compression via the extremes [electronic resource]
Keywords: Electrical Engineering.

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.
Rateless wireless networks [electronic resource]
Keywords: Electrical Engineering.

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.
Realm of the unseen [electronic resource] : devotional practice and sufi authority in the Kunta community
Keywords: Religious Studies.

This dissertation investigates the relationship between Sufi friendship with God and devotional religious practice as it emerges from the works of the first two leaders of the Kunta community, Sīdi al-Mukhtār and Sīdi Muḥammad al-Kuntī. These two scholars rose to prominence in the Southern Saharan desert in the late eighteenth century and came to exert considerable influence over the development of Sufi and Islamic culture in the region. This study argues that the Kunta argued for their authority as Sufi friends of God based on their privileged interaction with what they called "the realm of the unseen, " and their resulting access to powerful practices. These practices, which they called "the sciences of the unseen, " included the creation of amulets, communication with the jinn, the recitation of litanies, and the use of magical charts and tables to effect tangible, material changes in the world. The Kunta leaders were aware that other Muslim scholars might consider these practices to be acts of sorcery, but they argued strenuously that they should be considered legitimate Muslim practices. Moreover, they not only argued in favor of these practices but provided explicit prescriptive instructions for how to perform them. This study seeks to situation this discussion of the sciences of secrets relative to both the devotional religious landscape of the Southern Sahara desert and the larger Sufi and Islamic intellectual framework developed by the Kunta scholars. In the process, I argue that any understanding of West African Islamic history must consider the changing relationship between Sufi friendship with God and devotional religious practice.
Reconceptualizing the teaching of Mexican American contributions in U.S. history [electronic resource] : a case study on Mendez v. Westminster
Keywords: Education.

This research considers how Mexican American history becomes part of the curricular canon, and what their inclusion tells us about popular conceptions of Mexican Americans. At a time of increasing presence of Latina/o students in K-12 classrooms, it is important to consider how we depict their experiences in U.S. history. To address this concern, this research is comprised of two interrelated studies regarding Mendez v. Westminster, a case about 1940s Mexican American school segregation. The first study considers how high school curricular materials frame the Mendez narrative and the role they play in how students construct the historical significance of the Mendez case. I argue that Mexican American inclusion into the U.S. history curriculum is contingent on their story being analogous to the Black experience. Mendez is taught as if it were Brown v. Board of Education but with protagonists of a different skin color. Consequently, students learn a linear story of racial progress, shorn of nuance and erasing the variegated experiences of Mexican Americans and other people of color. The second study is based on a Mendez curricular intervention. Through a combination of primary and secondary sources, students learned about Mexican Americans' claim to legal Whiteness to gain access to better schools. The curriculum also highlighted how the Mendez decision upheld existing racial school segregation and language-based segregation. The findings suggest that there is value in using historical inquiry to help students evaluate evidence that focuses on anti-essentialist content that aims to avoid reductive notions of race/ethnicity that assumes that all people of color are the same. The findings also revealed that students' understanding of how racial categories, racial constructs, and White privilege function in the present allowed them to empathize with Mexican Americans in the 1940s who identified as legally White to gain access to better schools. Yet, when it came to language segregation, students' present understanding of language education interfered in them understanding that language segregation was a proxy for racial/ethnic segregation. Thus, Mexican Americans, and other Latinas/os may see history through multiple lenses: One as a racialized group that identifies with other historically disenfranchised people of color; and another, an English dominant group that does not align itself with language minorities or racialized linguistic discrimination. Collectively, these manuscripts are part of a broader research agenda that aims to challenge the education field to rethink diversity in a way that is more inclusive of Latinas/os and goes beyond thinking about race relations as a Black-White binary.
A reconfigurable switched-capacitor DC-DC converter for millimiter-scale energy harvesting sensor nodes [electronic resource]
Keywords: Electrical Engineering.

Wireless sensor nodes are the key building blocks for realizing the Internet of Everything (IoE). Conventionally, batteries have been utilized to power IoE-type devices; however, batteries have a limited lifetime and therefore need to be re-placed or recharged. They also increase the size and cost of the sensor node. Therefore, batteries do not offer a viable solution to power billions of IoE devices in the future. An alternative approach to power wireless sensors is ambient energy harvest-ing. In an ambient energy harvesting sensor node, a transducer converts a form of ambient energy such as light, vibration, or temperature difference to electrical en-ergy. Then, a power management circuit converts the volatile electrical power generated by the harvester to a regulated supply for sensor circuits. This talk presents the design, implementation and measurements of a power management IC for mm-scale energy harvesting wireless sensor nodes. Our pow-er management IC uses the series-parallel switched-capacitor architecture and has the following characteristics. First, to support the wide input voltage range of the energy harvester, the converter is designed to be reconfigurable: It adjusts its voltage gain dynamically to regulate the output voltage of the converter within a target window. Second, our design automatically adjusts its operating frequency based on the current consumption of the load circuits to achieve high efficiency. This power management IC has been fabricated in a 0.25-μm CMOS process and operates with an input voltage ranging from 0.6 V to 2.4 V, from which the con-verter generates a regulated 1.2 V output rail with a maximum load current of 100 μA. The maximum power conversion efficiency is 78% and remains above 60% across a wide range of input voltages and load currents.
Regulation of Natural Killer Cell Ligand Expression by Epstein-Barr Virus
Keywords:  Department of Biology
Biology
Immunology
Epstein-Barr Virus
EBV
Latent Membrane Protein 1
LMP1
Natural Killer Cell
NK Cell
PTLD
flow cytometry
HLA-E
HLA-A/B/C
CD48
MICA
MICB
ULBP1
ULBP2/5/6
Nectin-2
CD8+ T Cell
Stanford University
Biology Department
Thesis

Latent Epstein-Barr Virus (EBV) infection plays a significant role in the onset of lymphoproliferative disorders (LPDs), like post-transplant lymphoproliferative disorder (PTLD). EBV+ LPDs are characterized by uncontrolled proliferation of B lymphocytes driven, in part, by the viral oncogene latent membrane protein 1 (LMP1). Emerging evidence suggests natural killer (NK) cells, which help protect against malignancies and viruses, may play an important role in the immune response to EBV. We hypothesize that NK ligand expression by B cells, the host cell of EBV, may be regulated by EBV via LMP1 to circumvent immune responses during development of EBV-related LPDs. We compared expression of nine NK cell ligands in EBV-infected B cells to uninfected autologous B cells by flow cytometry. We also investigated the role of LMP1 in regulating NK ligand expression using a signaling-inducible LMP1. We found, in accordance with published findings, that the NK activating ligand CD48 is upregulated by EBV infection. We also found EBV infection, in contrast to published findings, downregulates expression of the NK inhibitory ligands HLA-A,B,C and HLA-E. Furthermore, we show that LMP1 upregulates both HLA-A,B,C and HLA-E. These seemingly contradictory findings suggest a larger regulatory system involving other viral factors on the part of EBV that controls NK cell ligand expression and may be involved in coordinating immune evasion by EBV. Understanding such regulation may yield several potential therapeutic targets for treating EBV-related PTLDs.
Rehabilitated ruins [electronic resource] : development, democratization, and UNESCO World Heritage in Turkey
Keywords: Anthropology.

Based on two years of multi-sited ethnographic research with bureaucrats, academics, and heritage professionals in Turkey and in Paris, France, this dissertation traces the global shift in heritage from a politics of responsibility to one of opportunity. It is the story of an international heritage program, guided by the UNESCO Convention Concerning the Protection of the World Cultural and Natural Heritage (World Heritage Convention), and of the field that this program offers Turkey and other nation-states for political and economic maneuvering. It traces how the Turkish state strategically deploys heritage to position itself in an increasingly transnational political, economic, and social order. This study details how global notions of cultural heritage touch down in Turkey, where there is often a gap between the Western principles of World Heritage and local practices. It explores how local actors negotiate this gap to advance their political agenda at the national and the transnational levels. The major argument of this dissertation is that the Turkish government uses the forum provided by the World Heritage Convention domestically to support development initiatives and shape the political field. Internationally, the Turkish state uses the Convention to affirm its commitment to liberal ideals and to expand Turkey's global influence. This study details, ultimately, that non-European states are not merely subject to the World Heritage Convention but empowered by it. In light of this dissertation, it is clear that new global ideas about heritage are entangled with states' global pursuit of capital and prestige. It is an entanglement that binds World Heritage to the archaeological record, the state, and the global economy, providing a clear vantage from which to understand how local histories shape global futures.
Re-Imagining Urbanity: Performance and Collective Disruption in Our Cities
Keywords: Stanford University
Department of Urban Studies
Urban Society and Social Change
performance
civic engagement
incarcerated youth
community-engaged theater
participatory theater
Thesis

I investigated community-based performance as a means of centralizing the experiences of marginalized people in urban political discourses. While community-engaged city planning takes heed of citizens’ experiences in order to create more equitable cities, community-engaged art has the potential to steal through the cracks in regimented and exclusive institutions, transforming them in quiet but commanding ways. I argue that performance works to elevate the voices of oppressed communities in three major ways: it invites unlikely participants to remember and act upon their citizenship, allows those participants to experiment with modes of resistance against oppressive institutions, and finally, allows for the envisioning of new social fabrics through the act of collective imagination. I approached community-engaged performance through three primary channels. Firstly, I worked as stage manager for a multi-city, audience-participatory play called City Council Meeting: Performed Participatory Democracy, which is based upon actual transcripts of city legislative meetings and reflects and scrutinizes the way city governments address the issues that affect their residents’ lives. Secondly, I co-facilitated the creation of dance and spoken word performances with incarcerated youth at Hillcrest Juvenile Hall as the teaching assistant for a Stanford course called “Dance in Prison”. Finally, I drew from my personal experiences with organized political protest, understanding public demonstration as a form of cooperative performance. This research spanned the course of September 2013 through May 2015.
Relating Protein Structure and Scalar Couplings: Improving the Karplus Relation
Keywords:  Department of Biology
Biology
scalar
coupling
karplus
NMR
molecular dynamics
Department of Biology
Stanford
Thesis

Intrinsically disordered proteins (IDPs) are implicated in an increasing number of neurodegenerative diseases, including Parkinson's, Alzheimer's, and Huntington's disease. While our knowledge of protein structures in the crystalline phase is advanced, IDPs do not readily crystallize, and the tools we have to study protein structure in solution are more limited. In this project, we integrated X-ray crystal-structure data from the PDB repository, solution-phase NMR spectroscopy data from the BMRB database, and molecular dynamics simulations to improve the accuracy of the Karplus Relation, an especially important but dated tool used towards solving the structures of solution-phase proteins. Improvement of the Karplus Relation would advance our understanding of protein dynamics and aid in small-molecule drug design.
Relations between information and estimation [electronic resource] : a unified view
Keywords: Electrical Engineering.

Measures of information, such as entropy, mutual information, and relative entropy play important roles in various domains: underlying algorithmic procedures in machine learning, characterizing operational quantities in communication, storage and inference, and characterizing the likelihood of large deviations events in statistics and probability, among others. Such information measures also turn out to give a quantitative understanding of several estimation theoretic notions - such as the costs of causality and mismatch, and the benefit of lookahead - via relations between information and estimation. This thesis presents a new framework for understanding the rich interconnections between information and estimation for a variety of widely applicable observation models. Many of these relations can be viewed as identities between expectations of random quantities. This dissertation presents these identities and their generalizations in new light. The first part of this thesis focusses on two canonical observation models: The additive Gaussian channel and the Poisson channel. For both these models, we dispense with the expectations and explore the nature of the pointwise relations between the respective random quantities. Our results recover and generalize previously known identities involving mutual information and minimum mean loss in estimation. Classical estimation and information theoretic quantities emerge with new and surprising roles. In the second part of the thesis, we introduce a natural family of Levy channels where the distribution of the output conditioned on the input is infinitely divisible. This family includes, as special cases, both the Gaussian and Poisson channels. For Levy channels, we establish new representations relating the mutual information between the channel input and output to an optimal expected estimation loss, thereby unifying and extending previously known results. Corollaries of our results include new formulae for entropy and relative entropy. The unified framework extends to continuous-time stochastic processes as well, where we introduce and study these connections for semi-martingale channels, which include the well-known white Gaussian channel and the multivariate point process channel. In the third, and final part of this dissertation, we revisit the white Gaussian channel and study the problem of estimation with finite lookahead. We look at the properties of finite lookahead minimum mean squared error and investigate connections between this quantity and mutual information.
Remote sensing and statistical analysis of the lightning-ionosphere interaction [electronic resource]
Keywords: Electrical Engineering.

Lightning is an extremely frequent phenomenon and an important part of the global electrical circuit with an average of 2000 active storms globally every day and an average flash rate of 40-50 flashes per second. Each lightning stroke radiates an intense electromagnetic pulse (EMP) in the VLF/LF frequency band (300 Hz---300 kHz). This EMP propagates efficiently in the earth-ionosphere waveguide and can be measured long distances away on the ground, in excess of several thousand kilometers. The upwardly directed part of the EMP interacts with and heats plasma in the Earth's ionosphere. Some of this energy propagates through the ionosphere where it enters the magnetosphere as a whistler-mode wave which may resonantly interact with energetic electrons in the Earth's radiation belts. Intense lightning EMPs may produce brief optical flashes known as ``elves'' in the lower part of the ionosphere ($\sim
RNA secondary structure inference and functionalized virus-like particles for tumor cell detection and enumeration [electronic resource]
Keywords: Chemical Engineering.

In the new biotechnology age, a rich understanding of the properties of biological macromolecules allows chemical engineers to precisely manipulate these materials for a desired application. This body of work focuses on two areas of molecular understanding research, the development of tools to study the structure and functions of RNAs and the engineering of virus-like particles for the purpose of detecting circulating tumor cells. Single nucleotide resolution tools like selective 2'-hydroxl acylation by primer extensions (SHAPE) provide a facile method to probe the solution states of RNAs. We benchmarked SHAPE-directed RNA structure modeling on six molecules and determined that the error rates of SHAPE were comparable to previous benchmarks of other chemical probing methods. To address the limitations identified from our benchmark, we introduced the mutate and map method. Using high throughput RNA structure probing, we generated an information rich matrix that can be used to improve RNA structure determination. Coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from several structured RNAs. It was determined that this new method reduced the error rates. Combining this method with the Rosetta/FAFAR algorithm, we were able to produce a nucleotide-resolution three-dimensional model of the double-glycine riboswitch. Virus-like particles made from the protein shell of viruses constitute a versatile nanoparticle platform with tunable properties while remaining non-infectious. In this work, we first examine general rules and methodologies to functionalize virus-like particles. Using this obtained intuition, we have synthesized cancer cell-specific luminescent nanoparticles for tumor cell detection and enumeration. We explored a series of peptide tags and solution conditions to improve the conjugation efficiency of various ligands to the Hepatitis B core virus like particle. These improved methods and design principles then enabled the advancement of technology for circulating tumor cell detection. We have developed a filter-plate assay to immobilize and decorate these rare cells with cancer cell-specific luminescent nanoparticles. A charge-coupled device system provided enough resolution to see individual spots reflective of single cells. We find that the total light intensity correlate with the number of marked cells spiked into a mixture of unmarked cells. These new protocols allow for a rapid, non-laboratory based procedure that can be readily performed and interpreted by physicians. We envision that such protocols will provide real-time analysis to oncologists by noninvasive cancer monitoring and enable more effective cancer treatment.