VictorJuiz/thesis huggingface dataset:
Tree animation and modeling via analytic simulation and image-based reconstruction

Botanical trees are ubiquitous in many real-world environments, and they are consequently also pervasive in the virtual environments created for film special effects, games, virtual reality, etc. The motion of these trees ranges from subtle swaying that is easily overlooked to dramatic deformation in extreme weather conditions. The geometry of these trees is highly intricate, with features including bark, knots, intricate networks of fine twigs and branches, and at times leaves, fruits, and flowers. This dissertation presents a set of frameworks for modeling a tree's motion via artist-directed simulation and its geometry via image-based reconstruction. First, we address the challenge of efficiently simulating tree motion for complex tree models. Efficient simulation of tree movement is difficult due to the many degrees of freedom needed to represent a high fidelity tree; this challenge is further compounded by the typically stiff material properties of a tree, making it difficult to simulate at interactive frame rates using standard time integration techniques. To address these issues, we present an algorithm with linear time complexity that simulates trees as articulated rigid bodies with as-stiff-as-desired rotational joints by taking the analytic solution to an approximated problem. Our method supports a variety of effects including wind, fictitious forces, collisions, plasticity, and leaf and fruit fracture, and it can be used to interactively parameterize tree models, run tree simulations using a game engine on a commodity tablet, simulate and render high quality trees with thousands to millions of rigid bodies, etc. Second, we address the challenge of reconstructing high fidelity, simulation-ready geometry of a tree from the real world. Beginning with a set of drone-mounted cameras, we acquire image data and apply traditional structure from motion and multi-view stereo techniques, then use the resulting point cloud data to build a simulatable representation of the tree's trunk and major branches. To reconstruct smaller twigs, we present an image annotation approach and subsequent improvements to simplify or automate parts of the annotation process using stereo correspondence information and a trained network for semantic segmentation of tree images. Finally, we combine the resulting model with our simulation framework to animate the reconstructed tree geometry.

Advisor: Fedkiw Ronald P.
Bohg Jeannette
Khatib Oussama
TREM1 and TREM2 in the Maladaptive Microglial Inflammatory Response in Alzheimer's Disease

Alzheimer's disease (AD) is a debilitating neurodegenerative disease currently afflicting millions for which no disease-modifying treatments exist. Neuroinflammation has been heavily implicated in AD progression and is a potential therapeutic target. In addition to the neurotoxicity caused by amyloid beta (Aβ) and tau, microglial activity causes secondary toxicity and may exacerbate Aβ and tau pathologies. Triggering receptor expressed on myeloid cells 2 (TREM2) promotes phagocytosis and has been identified as a risk variant associated with AD using genetic approaches, but its role is not fully understood. TREM1 signals via the same pathway, and it has been identified as a potent amplifier of toxic immune responses in acute inflammatory settings but remains relatively unexplored in AD. Using immunohistochemistry, we examined microglial activity and TREM1 and TREM2 expression in mouse brain tissue with intracerebroventricular Aβ delivery. We measured microglial activity by examining process length, number of processes, and CD68, a phagocytosis marker. We also developed and verified a monocyte-derived, microglia-like cell (MDMi) model to provide more direct evidence of the microglial response to Aβ. We carried out an Aβ-dosing study where we examined the response of TREM1 and TREM2 in MDMi cells with exposure to escalating levels of Aβ. We additionally developed an IHC protocol to examine human brain tissue from AD patients and confirmed TREM1 expression. Our results support increased microglial activity upon exposure to Aβ, as well as an increase in TREM1 and decrease in TREM2 with Aβ. These data have led us to propose a model whereby TREM1 activity promotes the maladaptive immune response by decreasing expression of protective TREM2. With further exploration, the regulatory roles of TREM1 and TREM2 in development of pathologic inflammation could be fully revealed and hold clinical and therapeutic relevance.

Keywords:  Biology
Biology
Neurology
Alzheimer's Disease
microglia
inflammation
TREM1
TREM2
Thesis
Advisor: Andreasson Katrin
Luo Liqun
Sapolsky Robert
Trust in a Digital Age: Overcoming Systemic Difficulties in Returning Unclaimed Property

Each year, in California alone the state government takes in almost 9 billion dollars of unclaimed property from its residents. Unclaimed property can be defined as any property that is left to a specific person without their knowledge, most likely money given to an individual based on a will or a old bank account that had been closed. The process of identifying the owners of unclaimed funds as well as claiming funds once the owner has been found has been notoriously difficult with little changes made by the government to make the process easier for citizens to claim their property.
In this paper, I will examine the history of unclaimed funds and ways in which the government has systematically made it difficult for this property to be returned to its rightful owner. I will acknowledge the reasons that people’s lack of trust in government leads them to avoid searching for their funds on their own. I will also describe the ways in which modern financial scamming has only increased the difficulty for citizens to find these funds while navigating the online financial scams that exist.
Finally, I will propose an alternative method of reaching out to individuals who have unclaimed property, describing a business model that people can trust to help them get this money back. By relying on some psychology, I will focus on the trust that people inherently have in charities to describe a partnership with my business and charities in order to effectively return this unclaimed property back into the hands of its rightful owner.

Keywords:  Department of Communication.
Unclaimed Funds
Thesis
Advisor: Hamilton James
Tumor establishment requires tumor autonomous and non-autonomous decoupling of EGF signaling from apoptosis

In homeostasis, robust mechanisms enforce a balanced equilibrium between cell division and death. Nascent tumors must destabilize tissue-level homeostatic controls to subvert cell equilibrium for cancerous growth. Though central to understanding how new tumors become established, the mechanisms underlying these destabilizing events are poorly understood. One of the best characterized mechanisms for cell equilibrium is that of the adult Drosophila intestine. In this organ, division is coupled to death because Rhomboid, a protease that cleaves mitogenic epidermal growth factors (EGFs) for secretion, is induced in cells undergoing apoptotic elimination6. In Drosophila, as in mammals, intestinal stem cells give rise to adenomas following loss of adenomatous polyposis coli (APC). Examining Drosophila APC-/- tumorigenesis, we find that pre-tumor cells destabilize cell equilibrium by uncoupling rhomboid from apoptosis, which creates feed-forward amplification of EGF signaling for tumor establishment. Prior to tumor formation, APC-/- cells induce rhomboid in surrounding cells via activation of the stress signal JNK. During subsequent growth, APC-/- tumors induce rhomboid within the tumor itself via loss of E-cadherin and consequent activity of p120-catenin. Chronic induction of rhomboid in both tumor and surrounding cells leads to constitutive activation of EGFR and is essential for tumors to progress. Thus, incipient tumors combine non-autonomous and autonomous strategies to deregulate rhomboid and destabilize cell equilibrium. Since Rhomboid, EGFR, and E cadherin are associated with colorectal cancer in humans, our findings may shed light on how human colorectal tumors progress.

Keywords:  Department of Biology 2019
Biology
Molecular and Cellular Physiology
Thesis
Advisor: O'Brien Lucy
Luo Liqun
Tunable enzymatic synthesis of the immunomodulator lipid IVA to enable structure-activity analysis

The Lipid A family of glycolipids, found in the outer membranes of all Gram-negative bacteria, exhibits considerable structural diversity in both lipid and glycan moieties. The lack of facile methods to prepare analogs of these natural products represents a major roadblock in understanding the relationship between their structure and immunomodulatory activities. Here we present a modular, cell-free multi-enzymatic platform to access these structure-activity relationships. By individually purifying 19 Escherichia coli proteins and reconstituting them in vitro in the presence of acetyl-CoA, UDP-N-acetylglucosamine, NADPH, and ATP, we have developed a system capable of synthesizing Lipid IVA, the first bioactive intermediate in the Lipid A pathway. Our reconstituted multi-enzyme system revealed considerable promiscuity for orthologs with distinct substrate specificity, as illustrated by swapping enzymes from distantly related cyanobacterial and Pseudomonas species. Analysis of the agonistic and antagonistic activities of the resulting products against the THP-1 human monocytic cell line revealed hitherto unrecognized trends, while opening the door to harnessing the potent biological activities of these complex glycolipid natural products.

Keywords: Chemical Engineering.
Advisor: Khosla Chaitan
Monack Denise M. 
Sattely Elizabeth
Tuning and probing initial stages of lithium deposition for lithium metal battery anodes

Rechargeable lithium-ion batteries have become ubiquitous energy storage devices in society, functioning as power sources for electronics ranging from personal devices to electric transportation to grid-scale energy storage. However, in order to meet fast-growing demands for increased range of electric vehicles and longer times between charging of devices, higher energy density batteries with next-generation chemistries need to be developed. High capacity electrode materials like lithium metal are ideal candidates for advanced batteries, but suffer various problems which remain unsolved. Much research has been dedicated to elucidating and mitigating the safety and performance problems of lithium metal research, but bringing practical lithium batteries to market has still been impossible. In Chapter 1, the background and problems of lithium metal anodes are introduced, along with some discussion about current strategies for enabling their use. In Chapter 2, initial studies on the nucleation of lithium metal during electrodeposition are discussed and put into context the importance of the initial states of lithium metal growth. Chapters 3 and 4 introduce some examples of soft polymeric protective coatings developed to prevent performance decay of lithium electrodes, in addition to studies of standard polymers and determination of polymer properties which are critical to functional coatings. Chapter 5 introduces microelectrodes as a tool for high rate studies of lithium metal kinetics during deposition and stripping, and demonstrate the growth of highly faceted lithium metal particles during these high rate deposition experiments. Finally, lithium metal is put into context for future use as a practical anode material, and considerations related to the manufacturing and production of lithium metal-containing cells are discussed. Ultimately, it will be the combination of both advances in battery technology through research like what is presented here and the advent of new manufacturing techniques compatible with lithium metal that will enable a new paradigm in lithium-ion anode technology.

Keywords: Materials Science and Engineering.
Advisor: Cui Yi
Bao Zhenan 
Chueh William
Turning the page : image and identity in U.S. lesbian magazines

"Turning the Page: Image and Identity in U.S. Lesbian Magazines" is the first scholarly consideration of the visual culture in lesbian magazines in the United States. The photographs, drawings, paintings, posters, prints, diagrams, and cartoons by leading and little-known lesbian artists, both contemporary and historical, helped create and define lesbian existence in social, political, racial, and sexual dimensions during the second half of the 20th century. Paying close attention to the images created for and circulated in lesbian magazines reveals how lesbian identities were formed and supported. These magazines encouraged collaboration and creative expression and functioned as exhibition spaces for lesbian art and artists. The magazines that comprise this dissertation's case studies—"The Ladder" (1956-1972), "Cowrie" (1973-1974) and "Dyke: A Quarterly" (1975-1978), "On Our Backs" (1984-2006), "Onyx: Black Lesbian Newsletter" (1982-1984) and "Aché" (1989-1993), and "LTTR" (2002-2007)—supported and showcased both historical and contemporary artists and warrant recognition as sites for the creation and distribution of lesbian images. As women, these artists put pressure on social constructions of gender and, as homosexuals, these artists questioned the institution of compulsory heterosexuality. Thus, analyzing the content of these mostly overlooked periodicals offers access to a broader history of lesbian culture and expands the conversation on feminist and queer art. Examining these publications and the contributions of these artists make clear that the visual content was vital in defining and supporting a lesbian identity. As culture changed over time, so too did the visual images—beginning with simple line drawings, moving to photographic representations, and then more sexually explicit representations, abstraction, and different media. This is not to assert a linear progression or evolution of lesbian art in these magazines but rather to argue that these images responded and added to the thinking of their times. The magazines were not simply a repository for images but rather sites of engagement and interaction. Artists could debut their work, and readers saw themselves reflected, often for the first time, in the pages of these magazines. Moving from one magazine to the next and turning from cover to cover offer an overview of lesbian life and its evolution as well as its successes and failures in supporting and reflecting a variety of lesbian identities through images.

Keywords: Art and Art History.
Advisor: Meyer Richard
Freedman Estelle B.
Lee Pamela M. 
Nemerov Alexander
TweetCheckr

TweetCheckr is a web application that walks users through the steps to verify the information they find in posts on Twitter. Built for journalists, but available for everyone, TweetCheckr's process is based on First Draft News' Social Media Verification training course.
When breaking news occurs, many people turn to Twitter to share it. However, it is also very easy to share and spread misinformation quickly via the platform. Increasing numbers of reporters spend much of their time on Twitter, promoting their work, collaborating, and finding leads.
But most Twitter-using reporters are also aware of the pitfalls of using Twitter as a source of information for their reporting, despite the fact that there is a lot of legitimate newsworthy information being shared. Based on user research, most Twitter-using reporters don’t have a methodology for verifying the information they find on the platform.
Existing educational resources that help reporters verify online information require that they visit many different websites and online tools, and that they remember all the available resources and ways that information might be invalid.
TweetCheckr’s mission is to help stem the tide of misinformation being spread via social media, by providing an easy and accessible process to debunk falsified content, and educating Internet users (and journalists in particular) about how to spot a suspicious post.

Keywords:  Department of Communication
Department of Communication
Journalism
social media
news
verification
misinformation
Thesis
Advisor: Tumgoren Serdar
Ultrafast structural dynamics in layered transition metal dichalcogenides

This work focuses on visualizing and manipulating atomic-scale structural changes in transition metal dichalcogenide (TMD) materials, with the goals of understanding fundamental light-matter interactions in these materials and modulating material properties at an ultrafast time scale. Tungsten ditelluride is a layered TMD that crystallizes in a distorted hexagonal net with an orthorhombic unit cell (Td phase). The lack of inversion symmetry in this phase leads to a predicted new topological semimetal hosting the so-called type-II Weyl points. Here, we use a single THz pulse to trigger a structural phase transition to a centrosymmetric phase, and probe the switching using an ultrafast electron diffraction technique. These findings serve as the first direct evidence of a THz field induced structural transition in a two-dimensional material, and offer a new promising way to optically control the topological properties of solids. Additionally, we present a new non-destructive method for probing heat transport in nanoscale crystalline materials using time-resolved x-ray measurements of photo-induced strain. This technique directly probes time-dependent temperature changes in the crystal and the subsequent relaxation across buried interfaces by measuring changes in the c-axis lattice spacing after optical excitation. This work is motivated by the need to understand the fundamentals of nanoscale heat propagation, particularly at buried interfaces in functional devices.

Keywords: Chemistry.
Advisor: Heinz Tony F. 
Lindenberg Aaron Michael 
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Ultrasound neuromodulation : optimization, mechanisms, and confounds

Ultrasound neuromodulation has recently gained attention as a novel brain stimulation technology. There are several obstacles that ultrasound neuromodulation faces before the technology is ready for clinical use, including the need for optimizing ultrasound parameters, understanding of the unknown mechanism, and characterizing potential stimulation confounds. In this dissertation, I will present research addressing several of these challenges. I investigated the frequency dependence of ultrasound neuromodulation in the mouse model, with results suggesting an inherent tradeoff between spatial focusing and stimulation efficacy. In collaboration with the Baccus lab, we found evidence supporting a radiation force hypothesis for the mechanism of neuromodulation. Finally, I hypothesized that ultrasound was causing stimulation confounds via either the vestibular system or the tactile sensory system. Experiments using a vestibulotoxin mouse model suggest that stimulation of the vestibular system may play a significant role in ultrasound-elicited motor responses. Future work is still needed to address questions regarding optimal parameters, the mechanism, and stimulation confounds as ultrasound neuromodulation techniques mature.

Keywords: Bioengineering.
Advisor: Pauly Kim Butts (Kim Rosemary Butts)
Baccus Stephen A. 
Pelc Norbert J.
Unconventional housing, unprecedented amounts of fear challenge Bay Area census efforts

National changes to the 2020 census, such as response forms going online, cuts to the Census Bureau budget, and the possible addition of a citizenship question, complicate efforts to count California's Bay Area. Locally, census officials must contend with challenges to enumerate many Bay Area residents who live in unconventional housing and/or are immigrants.

Keywords:  Department of Communication
Communication
Journalism
2020 census
unconventional housing
Bay Area
trusted messengers
Thesis
Advisor: Zacharia Janine
Migielicz Geri
Unconventional superconductors and interplay with spin-orbit coupling, magnetism, and electronic interactions

It can be said that a lot of present day research on superconductivity is focused on unconventional superconductors. That is not surprising given that any non-s-wave superconductor is strictly speaking unconventional, from the high-Tc cuprates to heavy fermion superconductors, among many classes. As such, interesting, unsolved puzzles are often found in unconventional superconducting systems. For example, there is still no consensus on why the superconducting dome in SrTiO3 exists, or what the symmetry of the pairing state in Sr2RuO4 is. In this thesis, we will study various examples of unconventional superconductors and how their behaviors are driven and affected by interactions such as spin-orbit coupling, external magnetic fields, and atomic electronic interactions. While our main focus will be on unconventional superconducting systems, we will also delve a bit into the half-filled Landau level problem towards the end. The first part of this thesis focuses on how spin-orbit coupling and atomic interactions interplay to affect the kinds of on-site superconducting pairing states that are allowed by symmetry. Using group theory and mean field equations, we deduce the conditions under which spin triplet, orbital singlet on-site pairing states can be stabilized in multi-orbital d-electron based systems. Having theoretically studied one of the effects of spin-orbit coupling on superconductivity, we then switch our setting to the laboratory where we discover that spin-orbit coupling can be a significant energy scale -- of the order of the superconducting gap -- in epitaxially grown strontium titanate. The strength of the spin-orbit scattering rate leads to surprising behavior of the superconducting tunneling spectrum. Next, we turn to an entirely separate class of unconventional superconductors -- the uranium based heavy fermion superconductor UCoGe where we again apply group theory and Landau theory analyses to make predictions on the phase diagram of this system. The phase diagram of UCoGe permits coexistence of superconductivity and ferromagnetism. We study the nature of the phase transitions between the superconducting, ferromagnetic, and coexisting phases. In the final part of this thesis, we switch gears entirely and study the quantum oscillations near the half-filled Landau level in a two dimensional electron gas under a period electric potential. We uncover surprising results regarding the relationship between relativistic and non-relativistic theories for the half-filled Landau level.

Keywords: Physics.
Advisor: Raghu Srinivas
Hwang Harold Yoonsung
Kivelson Steven
Uncovering dynamic behaviors of the adult drosophila intestine using novel imaging techniques

A major goal of modern biology is to observe and dissect dynamic behaviors. However dynamic biological behaviors occur over a vast range of timescales. Short-term (second to hour) events at the molecular and cellular scale often compound to drive long-term (days to years) processes making it inherently difficult to understand the full range of behaviors with a single technique. In addition, many organs of interest are encased within an opaque outer layer, making it challenging to monitor these dynamic processes in vivo. In this dissertation, I present two works that further the goal of monitoring dynamic biological behaviors within the intestines of living adult organisms. First, I will share a novel, intravital imaging technique called Bellymount. Using this technique, we performed the first longitudinal tracking experiments in the adult Drosophila intestine. With Bellymount we tracked stem cell lineage development and microbiota colonization in the same individual over multiple days. Second, I use an existing short-term continuous imaging technique along with fixed tissue analysis to understand how cell cycle progression may regulate adult stem cell fate outcomes.

Advisor: O'Brien Lucy Erin
Fuller Margaret T.
Kingsley David M. (David Mark) 
Nusse Roel