VictorJuiz/thesis huggingface dataset:
Synthesizing high-quality and controllable tennis animation from real-world video collections
Keywords: Engineering.

Demonstrations of human performance are important for creating realistic virtual characters. However, collecting high-quality demonstrations via motion capture can be costly in both time and monetary cost, because it requires expensive environment setup and skilled performers to be present at the capture location. In contrast, there is an abundance of video capturing expert-level human performances. Given this observation, this thesis seeks to answer the question: how can we harvest information from internet videos to create realistic virtual human characters? In particular, online videos of athletic events provide a rich sampling of in-activity motion data which encompass the full spectrum of skills an athlete must perform in a sport. The challenge is that compared to the high quality of motion capture data, demonstrations extracted from monocular real-world videos will exhibit errors due to limitations of current machine perception algorithms, and source video deficiencies like occlusions and motion blur. This thesis centers its focus on a specific sports domain: tennis, and demonstrates that it is possible to use large-scale observations of athlete performance obtained from real-world video collections to create controllable, high-quality tennis animations of virtual characters playing singles tennis points. These characters successfully conduct tennis rallies, carry out realistic decision-making, and appear photorealistic. Specifically, this thesis shows that a fairly simple state machine designed given the domain knowledge of tennis, is sufficient to provide structure for building complicated tennis controllers from unstructured video demonstrations. Next, this thesis contributes a system for learning a motion controller from real-world video demonstrations that is capable of precisely controlling a physically simulated character to play tennis points using a diverse set of skills. Finally, this thesis shows that macro-level behavior and player appearance information can be extracted from videos to enhance the realism of synthesized virtual characters. Overall, this thesis creates realistic virtual characters that can be effectively controlled to play singles tennis points involving a diverse array of strokes (serves, forehands, and backhands), spins (topspins and slices), and playing styles (one hand vs. two hand, left hand vs. right hand), as well as macro level behavioral choices that reflect player specific styles, such as shot selection choices. In the limited case of 2D sprite animation generation, it also demonstrates that appearance data from the videos can be employed to yield characters that are photorealistic in their appearance.
Synthetic polyelectrolyte models for understanding partitioning in polyelectrolyte complex coacervates
Keywords: Humanities and Sciences.
Chemistry.

Polyelectrolyte complex coacervates (PECs) are liquid-like droplets that are formed from mixing oppositely charged polyelectrolytes and are important in biology, food science, and personal care products. Since the first observation of coacervation almost a century ago, there have been several efforts to understand what molecular features affect coacervate stability. However, the physical rules for how PECs selectively partition species remains an unresolved question. In this thesis, I used dye-labeled polyelectrolytes prepared by RAFT polymerization and ICP-MS to understand the partitioning of added divalent salt and its effect on polyelectrolyte partitioning. In the third chapter, I used dye-labeled polyelectrolytes prepared from ATRP, RAFT, and NCA ring-opening polymerizations to understand how the molecular weight of polyelectrolytes affects their partitioning in the coacervate phase. I also used fluorescence microscopy to understand the replacement dynamics of PECs and PECs with an added enzyme. These studies shed light on our understanding of the physical rules for partitioning of components in PECs.
Systematic characterization of gene regulatory interactions with high-throughput CRISPR screens
Keywords: Medicine.
Genetics.

Chapter 1: Hundreds of thousands of cis-regulatory elements (CREs) have been identified across a myriad of cell types and conditions, but relatively few have been empirically characterized. Here, we present a scalable, phenotype-driven CRISPR screen to identify hundreds of essential regulatory elements in K562 cells by perturbing 7,500 DNase hypersensitive sites (DHS) around the top 400 essential genes in K562. In addition to distal enhancers, we identify promoter-overlapping enhancers that selectively regulate multiple genes. Using orthogonal CRISPR systems with narrow or broad perturbative windows, we demonstrate that fine-mapping screens can resolve and characterize core transcription factor binding sites (TFBSs) within enhancers, highlighting the advantages of complementary CRISPR systems to investigate CREs. Lastly, we use our results to further interrogate how transcription factor binding sites hierarchically interact to drive enhancer function at the CBFA2T3 locus. This study demonstrates a scalable CRISPR screening framework for identifying and dissecting CREs that regulate selectable phenotypes. Chapter 2: The ENCODE consortium's encyclopaedia, containing millions of non-coding CREs has advanced our understanding of gene regulatory landscapes. Nonetheless, few CREs have been functionally characterized directly; determining the regulatory effects on gene expression is a critical next step, and pooled, non-coding CRISPR screens have emerged as a valuable tool to endogenously characterize the function of CREs. However, these screens' design, execution, and analysis have been highly heterogeneous. Here, we present the ENCODE CRISPR screen database: the largest, multi-center, standardized collection of non-coding screens to date. We evaluated the most common design and analysis platforms and observed that functional elements are enriched at DHS/H3K27ac sites, while the strongest sgRNAs target the DHS summit. Additionally, we discovered a subtle, previously undescribed target DNA strand-bias for CRISPRi in transcribed regions. Our dataset represents a broad resource for the community, establishes a standardized data format, provides guidelines for screen implementation, and uncovers fundamental insights into gene regulation
A systematic study of GaN static induction transistors (a.k.a. vertical FinFETs) for RF applications
Keywords: Engineering.
Electrical Engineering.

Silicon has played a crucial role in the advancement of electronics, but it has limitations in high-power, high-temperature, and high-frequency applications. These limitations have led to the emergence of wide-bandgap semiconductors such as gallium nitride (GaN) as alternative materials. GaN, particularly in the form of AlGaN/GaN high electron mobility transistors (HEMTs), is now commercially utilized. Despite their excellent high-frequency and high-power performance, GaN HEMTs face inherent issues associated with their lateral device structure, including DC-RF dispersion, due to its horizontal channel with electrons confined to a thin sheet near the interface. In recent years, there have been efforts to replace GaN HEMTs with vertical transistor structures for applications where the weaknesses of GaN HEMTs become more pronounced than their strengths. One such structure is the static induction transistor (SIT), which is also called the vertical FinFET. During my time as a Ph.D. student in Professor Srabanti Chowdhury's group, my primary objective was to demonstrate the advantages of this device over HEMTs. To achieve this, I developed a TCAD model to design, analyze, and comprehend the device. The major focus of my work was establishing the complete fabrication process at Stanford. Throughout this phase, numerous challenges arose, stemming from the unique nature of the device structure as well as practical issues encountered in the cleanroom. However, I tackled these challenges systematically, addressing them one by one. Notably, I developed and refined various fabrication techniques, including an accurate sidewall patterning technique, etching of the high aspect-ratio fin structure using alternative mask materials, and plasma-based ohmic contact for low thermal budget processing. The fabricated devices exhibited desirable characteristics such as DC-RF dispersion-free behavior and hysteresis-free operation. The implementation of the new ohmic contact technique resulted in the achievement of the lowest on-resistance in published GaN SIT devices. These achievements represent significant strides towards the realization of next-generation RF electronics.
Systems approach to unravel lymphoid development in human bone marrow
Keywords: Medicine.
Microbiology and Immunology.

Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (BM) are the source of life-long replenish of immune cells in the humans. Among multiple lineages, T cell, B cell, NK cell, and Innate lymphoid cell (ILC) are classified as lymphoid cells, based on their morphology and developmental origin. However, mainly due to the limited experimental manipulations for human hematopoiesis studies, lymphopoiesis in human bone marrow still remains elusive. To overcome the experimental limitations, we leveraged the systems approach to analyze healthy human BM HSPCs. We conducted a highly multiplexed single-cell proteomic screen to construct a comprehensive protein expression map of human BM HSPCs. From there, we identified several lymphoid progenitor populations by their lymphoid specific functional protein markers. The target populations were assessed for their epigenetic priming for lymphoid lineages by chromatin accessibility. Furthermore, we utilized the protein expression information to identify surface markers to enrich for the target population, prospectively isolated, and functionally validated their lymphoid potentials ex vivo. This multi-omic study exemplifies the integration of a high-dimensional single-cell study with experimental validations. Moreover, we provide a fine-mapped human lymphopoiesis landscape in human hematopoiesis.
TaleStream: Supporting Story Ideation with Trope Knowledge
Keywords: Siu, Alexa
Dernoncourt, Franck
Storytelling
Tropes
Recommender systems
Knowledge graph
Creativity Support Tool
Text
Thesis

Story ideation is a critical and creative part of the story-writing process. It is challenging to support it computationally due to its exploratory and subjective nature. Tropes, which are narrative elements recurring across stories, are essential in stories as they shape the structure of narratives and our understanding of them. In this paper, we propose to use tropes as an intermediate representation of stories to approach narrative design. We present TaleStream, a canvas system that uses tropes as building blocks of stories and provides steerable suggestions of story ideas in the form of tropes. Our suggestion methods leverage data from the tvtropes.org wiki. We find that 97% of the time, trope suggestions generated by our methods provide better story materials than random tropes. Our system evaluation suggests that TaleStream can support writers’ creative flow and greatly facilitates developing stories. Tropes, as a rich lexicon of narratives with available examples, play a key role in TaleStream and hold promise for story ideation.
Targeting extracellular and membrane proteins for degradation via lysosome targeting chimeras
Keywords: Humanities and Sciences.
Chemistry.

Targeted protein degradation (TPD) is a promising strategy to remove deleterious proteins for therapeutic benefit and to probe biological pathways. The past two decades has witnessed a surge in development of technologies that rely on intracellular machinery to degrade challenging cytosolic targets. However, these TPD platforms leave the majority of extracellular and membrane proteins untouched. To enable degradation of these classes of proteins, we developed lysosome targeting chimeras (LYTACs) as a general strategy to degrade both secreted and membrane-anchored targets as introduced in Chapter 1. The first lysosome targeting chimeras (LYTACs) targeted extracellular and membrane proteins for degradation by bridging a target protein to the lysosome trafficking receptor, cation-independent mannose-6-phosphate receptor (CI-M6PR). Because CI-M6PR has broad tissue distribution, harnessing a receptor with tissue-restricted expression could mitigate off-target effects and allow tissue-specific degradation. In Chapter 2, we developed "GalNAc-LYTACs" that engage the asialoglycoprotein receptor (ASGPR), a liver-specific lysosomal targeting receptor, to degrade extracellular proteins in a cell type-specific manner. Site-specific conjugation and development of homogeneous LYTAC ligands improved the pharmacokinetic profile of GalNAc-LYTACs in vivo. GalNAc-LYTACs represent an avenue for cell-type restricted protein degradation, and additional discovery of recycling receptors with distinct and exclusive localization would expand the range of tissues or cells that LYTACs can target with selectivity. To address this need, we generated a comprehensive map of receptors that traffic from the plasma membrane to the lysosome across different tissues in mice in Chapter 3. Although extracellular degrader technologies have recently expanded the scope of potential therapeutic targets, no prior work has identified cellular features which enable or inhibit membrane protein degradation. Development of LYTACs as therapeutics would greatly benefit from insight into the factors that govern their activity. In Chapter 4, we conducted a genome-wide CRISPR screen to identify modulators of LYTAC-mediated membrane protein degradation. Our findings inform new design strategies for LYTACs with enhanced degradation activity and elucidate fundamental insights of receptor occupancy and trafficking
Tatanka Awicagli na Mahpiya Ile Win: An Intergenerational Story of Buffalo Restoration and Lakota Futures
Keywords: Indigenous peoples > Social conditions
Indigenous peoples > Politics and government
Indigenous Public Health
Native American Health
Public health
Bison
Bison restoration
Buffalo
Buffalo restoration
Lakota Indians
Cheyenne River Sioux Tribe of the Cheyenne River Reservation
futurism
cultural revitalization
Storytelling
life story
intergenerational
Decolonization
historical trauma
Indian reservations
Text
Capstone
Thesis
Student project report

This thesis explores the potential of Buffalo restoration to lead the Lakota people to a healthful Lakota future. Through background and socio-cultural context, storytelling and the intergenerational life-story analysis of the author and her father, and a discussion of medical anthropology and radical hope, this thesis aims to assert Buffalo restoration as mechanism towards realizing a radical reconceptualization of Lakota public health.
Technologies for mapping the spatial architecture of complex tissues
Keywords: Medicine.
Biochemistry.

Single-cell RNA sequencing (scRNA-seq) is generating an expanding wealth of comprehensive single cell expression profiles of tissues in health and disease, however spatial information is missing and specific cell classes may be systematically under-represented because of difficulty in viably isolating them. The next major challenge is to map how RNA expression is spatially organized, which has been termed spatial transcriptomics. Here, we report a simple strategy to efficiently and inexpensively map inferred cell types based on single-cell sequencing data back into a 3D volume of tissue, a process we call "back-mapping." Our approach begins with a machine-learning algorithm that identifies a minimal panel of moderate to highly expressed transcripts that in combination distinguish every cell type in a scRNA-seq dataset. The target tissue is then fixed and embedded in a physically durable hydrogel that is stained for proteins of interest prior to multiplex in situ hybridization for the transcript panel. These tissues are optically imaged in 3D, single cell profiles generated in an automated fashion, then scRNA-seq classes inferred and displayed in 3D. In many cases it is possible to visualize the cytoplasmic volume of cells to display cytological features based on RNA expression. As a demonstration, we "back-map" the Tabula Muris lung dataset into intact mouse lung and illustrate candidate ligand-receptor interactions between neighboring cells. Using our strategy, biologists can easily and affordably take their single-cell RNA sequencing dataset of their healthy or diseased tissue and generate a map at single-cell resolution map, merely by staining for tens of transcripts
Temporal regulation of DNA replication at the G1/S transition of the cell cycle
Keywords: Medicine.
Chemical and Systems Biology.

A fundamental challenge in cell division is replicating genomic DNA once and only once each cell cycle, such that daughter cells faithfully inherit their genome. In eukaryotes, duplicating DNA precisely once is critically dependent on separating DNA replication into two distinct stages: "origin licensing" during G1 phase, and "origin firing" during S phase. During origin licensing, cells demarcate future sites of DNA synthesis by loading inactive MCM helicases onto origins of replication. At the start of S phase, cells begin origin firing, whereby replication factors are recruited to the inactive helicases to form the active CMG helicases and replication forks that duplicate DNA. Critically, licensing is inhibited once DNA synthesis starts, such that newly synthesized DNA cannot be re-licensed. Failure to coordinate these processes can lead to re-replication of DNA, in which DNA is copied more than once within a single cell cycle, causing DNA damage and genome instability and ultimately can produce the mutations underlying diseases such as cancer. This dissertation describes work done to understand the regulation and signaling which coordinates G1 phase origin licensing and S phase origin firing. In human cells, inhibition of licensing in S phase centers around inhibition of licensing factor CDT1 starting from S phase entry. However, the E3 ubiquitin ligase CRL4Cdt2 only starts to degrade the licensing factor CDT1 after origin firing, raising the question of how cells prevent re-replication before CDT1 is fully degraded. Using quantitative microscopy and in vitro reconstituted human DNA replication, we show that CDT1 inhibits DNA synthesis during an overlap period when CDT1 is still present after origin firing. CDT1 inhibits DNA synthesis by suppressing CMG helicase progression at replication forks, and DNA synthesis commences once CDT1 is degraded. Thus, in contrast to the prevailing model that human cells prevent re-replication by strictly separating licensing from firing, licensing and firing overlap, and cells instead separate licensing from DNA synthesis.
Testimonial Advertisements and Willingness to Pay: The Role of Gender and Presentation
Keywords: Advertising
Willingness to pay
Sex
Text
Thesis

This paper investigates the impact of video and text testimonials on willingness to pay
(WTP). An experiment is run eliciting WTP for three different ungendered products
where participants see a photo of the product and either a male or female video testi-
monial, a text testimonial, or no testimonial. We find that the female video testimonial
significantly decreases WTP, while the male video testimonial and the text testimonial
have approximately no effect. Additionally, the text testimonial leads to a significantly
higher retention of factual information presented as compared to the video testimonial
treatment. These results support the hypothesis that consumers’ engagement in video
testimonials is more focused on the presenter than the product.
The Afternoon Fun Economy
Keywords: WFH
Geospatial data
Alternative data
Leisure
Consumption (Economics)
Text
Thesis

Using GPS data gathered from 2019 to 2022, this paper analyzes the effect Covid-19 and
Work from Home (WFH) had on consumption decisions, specifically in relation to golfing
activity. Integrating thousands of geospatial polygons with vehicular and mobile GPS data, this
paper finds strong growth in golfing throughout Covid-19 and subsequently after. Similarly, the
temporal and daily distribution of golfing trips underwent significant changes, exhibiting growth
midweek and midday. To contextualize these trends against WFH, I conducted a regression over
a fixed panel of golfers active from 2019 to 2021 to identify the effect income and remote job
postings had on golfing growth. Based on the evidence presented in this paper, I find WFH to be
the likely culprit behind the growth in golfing and the change in weekly and daily patterns.
The concept of music in the Shakespearean corpus: an exploration of neoplatonic ideas of music in Shakespeare (1996)
Keywords: Shakespeare, William, 1564-1616
Neoplatonism in literature
English drama > Early modern and Elizabethan
Music imagery
Musicology > Philosophy
Text
Thesis

Part One surveys the major musical concepts of the English Renaissance and their relationship to the Platonic tradition. The main body of the thesis (Part Two) consists of a systematic presentation of Shakespeare’s ideas on music under the Boethian categories of musica mundana, musica humana, and musica instrumentalis. In Part Three, after tracing Shakespeare’s indebtedness to the Platonic tradition, an attempt to synthesize his ideas on music under major Neoplatonic themes is made. The present thesis comes to the conclusion that the wealth, extent, and use of musical allusions in the Shakespearean Corpus allow the definition of Shakespeare’s concept of music as predominantly Neo-Platonic, and centering on the notion of “harmony.” M.Phil. (by research) thesis, University of Liverpool, 1996.
The Cost of Imperialism: Designing a Model of Reparations to Laos from the U.S. for the Secret War Bombing
Keywords: Reparations for historical injustices
Imperialism
Laos
Vietnam (Democratic Republic)
Cambodia
Secret War
Vietnam War (1961-1975)
Indochinese War (1946-1954)
Laotian Civil War
Laotian Americans
Laotian Americans > Cultural assimilation
Laotian Americans > Political activity
Laotians > Social conditions
Southeast Asia
Transitional justice
International Center for Transitional Justice
Decolonization
Solidarity
International Solidarity Movement
Text
Thesis

During the Secret War concurrent with the Vietnam War era, the U.S. dropped over 270 million cluster bombs on Laos, making it the most bombed country per capita in the world. To this day, approximately 80 million unexploded ordinances remain in Laos. America’s Secret War on Laos continues to impact the livelihood and well-being of Laotian citizens today, yet there has been little conversation regarding what justice looks like for these people. In my thesis, I argue that the U.S. is culpable for wartime damage to Laos, that there is both legal and moral justification for transitional justice in the region and that reparations are the most appropriate transitional justice mechanism. My research seeks to answer the question: Based on the material needs of the Laotian people, what model of reparations is most appropriate and feasible? In other words, what form should these reparations take, to whom should they be directed, and how should they be administered? Through interviews with Laotian citizens, I hope to provide a snapshot of the war's continued impact on the Laotian people and their visions of justice and reparation for the Secret War. My interviews inform the design of a comprehensive model of reparations specifically tailored to address the needs of the Laotian people as they pertain to the lasting consequences of the war. I also evaluate the political feasibility of reparations through a comparative analysis of reparations implementation in other international case studies. Ultimately, I hope to establish a design precedent that encourages the pursuit of ambitious justice processes, especially for those peoples who continue to struggle against imperialism and its enduring impact.