VictorJuiz/thesis huggingface dataset:
Cortical neural population dynamics for flexible motor control and motor learning

Animals have a remarkable capacity to learn new motor skills while maintaining existing ones. Motor learning encompasses a wide range of phenomena, from relatively low-level mechanisms for calibrating movement parameters, to making high-level cognitive decisions about how to act in a novel environment. Yet the neural mechanisms of these behavioral phenomena, in particular their underlying neural population dynamics, remain largely unknown. Precise motor control and flexible motor learning involve distributed brain regions, among which motor cortex is a key brain hub involved in the control of skilled movements. The neurophysiological studies (Chapters 2 and 3) and the tool-development project (Chapter 4) presented in this dissertation aim to address the roles of neural population activity in motor cortex underlying different behavioral phenomena during movement control and motor learning. In the neurophysiological studies, we recorded hundreds of neurons simultaneously with high-density electrodes while monkeys were learning one or multiple motor skills. To investigate the neural population data, we used techniques based on the dynamical systems theories and applied different dimensionality reduction methods. In the tool-development project, we demonstrate a new imaging platform in behaving monkeys that was able to monitor the same neural population across weeks and could provide us a potential avenue for studying long-term motor learning. In Chapter 2, I first address the question of how neural population activity in rhesus macaque motor cortex changes when learning new arm movement from dynamic force perturbations. Chapter 3 reports the neural population activity patterns during interference and learning of multiple different skills. Chapter 4 demonstrates the development of chronic in vivo two-photon calcium imaging for rhesus macaques generating arm movements and the implementation of an optical brain-computer interface (oBCI), as well as the capability to combine functional and structural imaging of the motor cortical neural population

Keywords: Biology.
Advisor: Shenoy Krishna V. (Krishna Vaughn) 
Clandinin Thomas R. (Thomas Robert)
Luo Liqun 
Newsome William T.
Shen Kang
Counterexamples in digital system verification, channel coding, and electro-neural interface design

This thesis contains chapters on several different topics. Chapter 2 explores hardware Trojan detection, by considering attacks that can be implemented when fabrication of the integrated circuits (ICs) is not trusted. Many other works focus on Trojan detection during IC testing or pre-silicon verification, but these cannot detect all attacks. We present a system architecture using randomized error-detection codes, which can detect any hardware Trojan on any digital IC, in real-time, during both testing and system operation in the field. It cannot produce false positives. In addition, it prevents a large variety of reverse-engineering attacks during chip design and fabrication. Chapter 3 explores channel coding a bit further. While channel capacity captures fundamental limits on communication under a transmit energy constraint, it fails to account for processing energy. Using VLSI complexity models from computer science, we analyze total power for regular-LDPC codes and iterative message-passing decoders. This specific code family is selected for analysis, based on its use in many real (wired and wireless) communication standards. We establish many counterexample scenarios, where it is actually more energy-efficient to use uncoded transmission than coding. Some post-layout circuit simulations of decoders help corroborate the theoretical results, at short communication distances on the order of 1m. Chapter 4 presents a proof-of-concept design of an invasive, electro-neural interface for neural recording and information telemetry in some sensory applications. The communication distance required is on the order of 1cm. Yet, even though the power constraints are solely transmit power constraints (unlike the counterexample scenarios of Chapter 3), it is not currently feasible to use capacity-approaching codes due to thermal and area constraints associated with implantation of the sensors in-body. We design a wireless, distributed, modular, and miniaturized opto-electronic system, that easily meets thermal and ocular safety limits. Chapter 5 provides conclusions for each chapter, future work, and a discussion of some follow-up works in the recent literature

Keywords: Electrical Engineering.
Advisor: Prabhakar Balaji
Le Binh Q. (Binh Quang) 
Van Roy Benjamin
Coupling single cell RNA sequencing with crispr perturbation and using single cell RNA sequencing to profile musculoskeletal injuries and disease

Single cell RNA sequencing (scRNAseq) has changed the way we understand cellular heterogeneity and overall tissue behavior. Using scRNAseq, we addressed three questions here, one technical, two biological. For the first question, we wanted to assess if Clustered regularly interspaced short palindromic repeats (CRISPR) perturbation information can be coupled with transcriptomic information in the drop-seq setting through direct capture of the small guide RNA (sgRNA). While capturing sgRNAs on drop-seq beads was achieved, we found that our downstream signal was scrambled. The first biological question we addressed was looking at an Hsl knockout mouse with faster fracture repair. Initial experiments suggested osteoimmunological causes behind the faster repair. Using scRNAseq, we found that pre-osteoclasts were the most perturbed cell type suggesting they may play a role in the improved fracture repair. Furthermore, pre-osteoclasts were some of the few cells in our dataset that expressed Pparg for which Hsl makes ligands. The second biological question we addressed was looking at tendon progenitor cells (TPCs) derived from either tendinopathic or normal patellar tendon. In our mechanical stress experimental system we found substantial differences between normal and tendinopathy TPCs. This dissertation illustrates the potential of scRNAseq applications to address a number of important biological questions while still have room to be further expanded

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Qi Lei (Professor of Bioengineering) 
Alizadeh Ash
Oro Anthony
Wu Joy
Cracks in the Sanctuary Walls: The Effects of Local Immigration Enforcement on Trust in the Police

Secure Communities is a national immigration enforcement program that allows U.S.
Immigration and Customs Enforcement (ICE) to gain access to the fingerprints of all suspects booked at local jails. Upon receiving the fingerprints, ICE can request that the jail hold a suspect until they can be transferred into ICE’s custody. From 2009 to the present day, Secure Communities has led to the deportation of hundreds of thousands of immigrants and has garnered criticism for threatening to compromise the relationship between local law enforcement and the communities they serve. This thesis provides one of the first empirical examinations of the effects of the program on individuals’ trust in local law enforcement. I use millions of calls for service before and after the implementation of Secure Communities in Seattle, Washington as a proxy for residents’ trust in local law enforcement. Using this call for service data, I employ a difference-indifferences design to estimate the causal relationship between the implementation of the program and trust in local law enforcement. In particular, I examine whether we observe a decrease in calls for service in higher-density Hispanic areas compared to lower-density Hispanic areas postimplementation. Contrary to expectations, I find no significant effect of the programs’ implementation on rates of calls for service, in general, or on domestic violence calls, in particular. In light of these findings, I remark on the possibility that Seattle’s sanctuary policies may have provided a buffer against the potential negative consequences of Secure Community’s implementation on Hispanic residents’ trust in local law enforcement.

Keywords:  Fisher Family Honors Program in Democracy
Political Science
Center for Democracy Development and the Rule of Law
immigration
Secure Communities
police
Thesis
Advisor: Jefferson Hakeem
Thompson Dan
Crafting cosmologies : buddhist cartography and the spatial imagination in Medieval China

This dissertation traces written and visual discourses mapping the Buddhist cosmos in medieval China. This study is grounded in sixth- to eleventh-century Chinese manuscripts and murals preserved at the Mogao Grottoes, a bustling Buddhist cave complex in the Dunhuang region. I expand this localized focus with analysis of texts, images, and maps whose productions range from the Six Dynasties (220--589) to the Song Dynasty (960--1279), from sand-swept caves of Dunhuang to elite temples of central China, and from the hands of anonymous local scribes to imperially sponsored scholar-monks. Each chapter examines a unique method of crafting cosmologies in medieval China. These methods are demonstrated inductively, grounded in three distinct bodies of materials, each evincing a particular pursuit in the production. Chapter One highlights the method of crafting cosmologies through visual transformation, examining wall murals at Mogao that engage in the artistic pursuit of turning a Mainstream text into a collection of graphic narrative maps of two distinct universes and one micro-cosmos. Chapter Two uncovers the creative method of textual appropriation, examining two new texts added to the Lotus Sūtra which I identify as having been made from at least one pre-existing cosmology. Chapter Three explores an element of material culture, examining one cohesive manuscript in order to illuminate possible practical pursuits involved in the creation of a meta-cosmology through the practice of textual compilation. Throughout, this study strives to demonstrate the foundational role cosmology played in medieval Chinese Buddhist ontology and soteriology

Keywords: Moerman, D. Max (David Max) degree committee member.
Religious Studies.
Advisor: Kieschnick John
Harrison Paul M. (Paul Maxwell)
Wigen Kären
Creating the Kibbutz Family in the 1920s: Between Revolution and Tradition

Labor Zionist kibbutzniks faced a dilemma in the 1920s with the birth of their first children in Palestine. As Socialists, they saw the bourgeois Jewish family as an outdated way to control women and property. In fact, according to Socialist critique by Engels and Bebel, the bourgeois family was destined to disappear with the abolishment of capitalism. But as Jews and Zionists, they understood that the family was important for preserving tradition and building the Jewish nation. This thesis aims to shed light on the tension between Zionism and Socialism through an analysis of the family question on the early kibbutz.

Keywords:  Department of History
anat peled
kibbutz
labor zionism
kibbutz family
socialism
a.d. gordon
moshav
shtetl
jewish family
jewish families
kadish luz
the family question
degania
dgania
zionism
nahalal
second aliya
Thesis
Advisor: Naimark Norman
Mancall Mark
Critiquing counter-terror : the impact of security policy on American, British, and French publics post 9/11

In this thesis, "Countering Counter-Terror: The Impact of Security Policy on American, British and French Publics Post 9/11", I reframe counter-terrorism law as performance; I argue it is a scenario or blue-print for military and civilian interactions in the public sphere. As evidence of how counter-terrorism is a form of performance, I explore the intersections between security policy in the United States of America, the United Kingdom, and the fifth French Republic and immigration practices, indeterminate detention, torture, and mass surveillance. More specifically, I demonstrate how the U.S. Patriot Act (2001), UK CONTEST (2007 -- 2019), and France's SILT law (2017) have significantly reduced peoples' privacy, impacted peoples' right to freedom of movement and of speech, and escalated racial, class, religious and ethnic divides. Though particular emphasis is placed on the violence perpetrated against disenfranchised Muslim and/or Arab communities, this dissertation argues that national security discourses are broadly betraying the democratic values and institutions they purport to protect

Keywords: Theater and Performance Studies.
Advisor: Elam Harry Justin 
Menon Jisha
Alduy Cécile 
Holloway D. J.
Cryo-EM study of ATP induced conformational heterogeneity in archaeal chaperonin mmCpn

Proteins must fold into their correct three-dimensional conformations to function properly. Aberrant folding has been linked to a rapidly expanding list of pathologies, including Alzheimer's disease (AD) and Parkinson's disease (PD). However, the vast majority of cellular proteins are unable to reach their native state spontaneously. The correct folding of these proteins requires the assistance of a complex cellular machinery of proteins known as molecular chaperones. Among the chaperones, chaperonin is a highly conserved subgroup that consists of two stacked seven- to nine-membered rings. These chaperonins bind nonnative polypeptides in their central cavity and use energy from ATP to mediate the polypeptide folding. So far, ATP induced conformational changes in chaperonins are considered to be coordinated in time and space by complex allosteric regulation. However, the current models employed to describe allostery in chaperonin do not distinguish allostery in ATP binding from that in ATP hydrolysis. Here I use cryo-EM to study the ATP occupancy and distribution in each ring of the archaea Methanococcus maripaludis mmCpn chaperonin complex. By exploring the nucleotide distribution in hundreds of thousands of mmCpn subunits, I find that ATP binding to chaperonin mmCpn is statistically random both within the ring and across the ring. The quarternary structure of mmCpn differs from particle to particle and the lid closing of the two rings is found to be uncorrelated to each other. Our observation of a high subunit conformational and compositional heterogeneity in each ring of mmCpn complex suggests that intra-ring subunit conformational change is non-concerted and the existence of intermediate states may help explain chaperonin's ability to fold very large protein substrates

Advisor: Chiu Wah 
Frydman Judith 
Wakatsuki Soichi
Cultural competence in teaching immigrant-origin youth : the ethic of Cariño

This dissertation documents the elements that characterize the perspectives and practices of four high school teachers identified as highly effective educators working with immigrant-origin Latina and Latino students in urban settings. They are distinguished in consistently taking into account their students' cultural backgrounds and personal narratives. Using portraiture methodology, this study examines the development of their cultural competencies and the myriad ways each one promotes, supports, and celebrates the learning of their immigrant-origin Latinx students. Data sources include semi-structured interviews with the teachers, administrators, and members of the community, classroom observations and audio files, extensive field notes, and demographic data about the local context of the school where the four teachers have been teaching. The teachers' commitment to serve immigrant-origin students was manifested in their persistent efforts to get to know their students well, to build strong relationships and to validate their voices. With rigor and thoughtfully planned lessons, they engaged their students in Socratic discourse about controversial current political issues and debates. These teachers demonstrated cariño, an ethical and moral foundation of teaching and education more generally. The ethic of cariño is explored and further conceptualized throughout this work. Eight emergent themes were found to demonstrate the ethic of cariño—four focused on perspectives and four on practices. The four perspectives that drove these teachers ranged from critical consciousness and equity-driven perspectives to embracing a reflective ethos viewing their students wholistically. The practices they manifested included curricular rigor and building relationships with students as well as engaging them and developing relevant curricula. The four perspectives and practices were not fixed categories, and all four teachers illustrated them in different degrees. The data sources revealed a fluid and dynamic relationship between the teacher practices and the teacher perspectives—a cyclical process that was generative in nature and informed the teacher's instructional choices. What was the same was how these eight themes combined in their teaching to illustrate the ethic of cariño that teachers used in approaching their immigrant-origin students. The portraits of the four teachers affirm existing research on the potential equity and culturally responsive contributions that teachers who work with immigrant-origin Latinx youth can provide in their classroom context. This work raises questions to the field about how teachers understand and make sense of the lived experiences of immigrant-origin youth and how they might develop their teaching craft to promote equity and social justice in their approaches to culturally and linguistically diverse students

Keywords: Education.
Advisor: Lotan Rachel A. 
Valdés Guadalupe
Martínez Ramón
Cytometric and genomic dissection of normal and neoplastic stem cell hierarchies

Multicellular tissues are hierarchically organized into distinct cell types with intrinsic differences in function and developmental potential. Residing at the apex of this complex organization is the stem cell—the master orchestrator of tissue development, maintenance, and regeneration. Stem cells carry the unique property to indefinitely divide and differentiate into specialized cells. As best demonstrated in the blood system, a single hematopoietic (blood-forming) stem cell (HSC) can repopulate all the blood and immune cells of an organism. The regenerative potential of stem cells and their ability to become any cell type in the body has inspired numerous biological studies on how cell decisions are made and tissues are organized. These insights have influenced clinical applications in cell replacement therapy, disease modeling, and even the treatment of cancer, where stem cells that promote tumor growth, metastasis, and recurrence can be targeted. Here, I describe the identification of stem cell populations in various normal and neoplastic tissues, including the mouse bone marrow, human skeleton, and human breast cancer. In the first part, I find a new marker expressed on the surface of mouse HSCs, Neogenin-1 (Neo1), that stratifies HSCs into two subpopulations—one that is more active and biased towards producing myeloid cells and another that is more dormant and capable of producing all blood lineages equally. Next, I demonstrate how analysis of single cell RNA-sequencing data from the human fetal growth plate enabled me to identify surface markers to isolate a highly regenerative population of human skeletal stem cells. Finally, I show how I leveraged a simple measure of transcriptional diversity in single-cell RNA-sequencing data to build a computational tool, CytoTRACE, that predicts the ordering of cells based on differentiation status and reveals genes associated with candidate human breast cancer stem cells. In summary, these studies highlight both functional and computational approaches for the identification of novel stem cell populations

Advisor: Newman Aaron (Biomedical data scientist) 
Weissman Irving L.
Chan Charles (Charles M.)
Dark, dreary mines : bituminous coal in the United States, 1865-1900

In 1900, the bituminous coal industry was highly competitive—a fact that set it apart from many other industries. Both miners and the people who operated the mines believed that too many miners and too many mines produced too much coal. The competition made the industry dysfunctional; miners regularly had too little work to do. This dissertation focuses on the groups that caused this problem and those who tried to fix it. It answers questions about how labor unions came to be considered monopolies at the same time that bituminous coal had no monopoly. Railroads caused mines to open because they needed traffic. Highly speculative, very expensive, and politically connected new railroads in the southern Appalachian Mountains were particularly desperate to recoup their costs. Coal provided a solution. Railroads offered preferential freight deals to those to whom they owed money and pursued other means of influencing the coal market. As a result, railroads expanded the scope of the coal market and intensified competition within and among coal-mining regions. The steel industry also contributed to the dysfunction. Andrew Carnegie, the nation's largest steel producer, developed a close partnership with Henry Clay Frick, the nation's largest producer of metallurgical coal. The close partnership seemed to portend stability for Frick's coal company. The steel industry was remarkably stable—exactly the opposite of the bituminous coal industry. Carnegie, by investing deeply, helped Frick quickly grow his business beyond even Carnegie's demands for coal. While Frick wanted to use his excess capacity to bring stability to the coal industry, Carnegie wanted to use Frick's excess capacity to control his competitors. Carnegie, who always had the upper hand, always won out, and the coal industry suffered as a result. Coal mine operators made slim or sometimes no profits. Coal miners suffered even more. In what was known as the Central Competitive Field, miners and operators teamed up to try to bring stability to the industry in a series of Joint Conferences of Miners and Operators. They looked to maintain power against the railroads by forming democratic associations to fix wages and ensure profits to operators. They had measured success in the 1880s and 1890s. But by the end of the century, changing tactics and decreasing attention to democracy led them to more closely resemble a trust

Keywords: History.
Advisor: Campbell James T.
White Richard
Hobbs Allyson Vanessa