VictorJuiz/thesis huggingface dataset:
Tumor establishment requires tumor autonomous and non-autonomous decoupling of EGF signaling from apoptosis
Keywords:  Department of Biology 2019
Biology
Molecular and Cellular Physiology
Thesis

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.
Tunable enzymatic synthesis of the immunomodulator lipid IVA to enable structure-activity analysis
Keywords: Chemical Engineering.

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.
Tuning and probing initial stages of lithium deposition for lithium metal battery anodes
Keywords: Materials Science and Engineering.

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.
Turning the page : image and identity in U.S. lesbian magazines
Keywords: Art and Art History.

"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.
TweetCheckr
Keywords:  Department of Communication
Department of Communication
Journalism
social media
news
verification
misinformation
Thesis

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.
Ultrafast structural dynamics in layered transition metal dichalcogenides
Keywords: Chemistry.

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.
Ultrasound neuromodulation : optimization, mechanisms, and confounds
Keywords: Bioengineering.

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.
Ultra-thin platinum : nucleation to application
Keywords: Mechanical Engineering.

The ability to deposit thin, conformal films is very important given the down-scaling of devices. Pt, in particular, has attracted considerable attention for thin film applications in micro and nano-electronic devices due to its chemical inertness, high work function, and excellent electrical properties, including a linear temperature coefficient of resistance (TCR), over a wide temperature range. However, the use of Pt in devices has been somewhat limited, both because of material cost and limitations caused by the directionality of conventional Pt deposition techniques. In this work, thin Pt films as thin as 3.7 nm were deposited using Plasma Enhanced Atomic Layer Deposition (PEALD), and electrical properties of thin Pt films were measured. In addition, some potential application areas for thin Pt films were explored. Chapters 3 and 4 of this dissertation discuss lowering the thickness limit of current Pt films, and how these films' electrical properties change according to thickness. Here in this work, by changing the nucleation layer to TiO2 from Al2O3, the non-ideal nucleation behavior of Pt was mitigated. With this change, the previous thickness limit of electrical continuous Pt, reported to be 8 nm, was pushed to 4 nm. The electrical properties of these thin Pt films, electrical conductivity and Temperature Coefficient of Resistance (TCR), were measured. While Pt films down to 5.7 nm followed the theoretical models very well, Pt films thinner than 5.7 nm deviated from the theory due to incomplete coverage. Nonetheless, Pt film with a thickness of 3.7 nm was deposited on TiO2 and showed good electrical conductivity and electrical stability; the results show that Pt films could be used for Resistance Temperature Detectors (RTDs) for next-generation micro/nano-electromechanical devices. Two potential application areas of thin Pt are discussed in the last two chapters of this dissertation: wearable and flow sensing applications. In chapter 5, thin Pt films' ability to be used as a flexible electrode was studied for wearable application. Pt deposited on flexible substrates had a similar electrical property and TCR as Pt deposited on rigid substrates, and also demonstrated remarkable stability during a bending test, showing within 1% drift in electrical conductivity after 1000 cyclic bending tests. In chapter 6, fabrication and testing of the first thinnest PEALD Pt anemometer is discussed. In addition, with U-Trench technique, novel corrugated beam design and its effect on anemometer performance is discussed. For 20 nm thick Pt sensing element, wind velocities between 1.5 - 18 m/s could be sensed by using as little as 3 mW with the response time of 3.74 ms. Moreover, when the sensing element was wide as 20 um, adding corrugation to the sensing element heated the sensing element more than the sensing element with no corrugation, thereby increasing the anemometer performance significantly. In summary, Pt showed remarkable performances for both applications, proving its potential importance for next-generation micro/nano-electromechanical devices.
Unconventional housing, unprecedented amounts of fear challenge Bay Area census efforts
Keywords:  Department of Communication
Communication
Journalism
2020 census
unconventional housing
Bay Area
trusted messengers
Thesis

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.
Unconventional superconductors and interplay with spin-orbit coupling, magnetism, and electronic interactions
Keywords: Physics.

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.
Uncovering mental structure through data-driven ontology discovery
Keywords: Psychology.

Psychological sciences have identified a wealth of cognitive processes and behavioral phenomena, yet struggles to produce cumulative knowledge. Progress is hamstrung by siloed scientific traditions and a focus on explanation over prediction. These issues are particularly damaging for the study of multifaceted psychological construct and our general understanding of psychology's practical utility. In this dissertation we use the construct of self-regulation as a case-study to develop a data-driven framework for psychological science. Self-regulation is a broad construct representing the general ability to recruit cognitive, motivational and emotional resources to achieve long-term goals. This construct has been implicated in a host of health-risk behaviors and has a rich and varied measurement tradition. Despite the intensive focus of many research programs and clear societal benefits, the psychological components of self-regulation remain poorly understood, and its practical utility as a psychological construct has not been systematically evaluated. In Chapter 3, we derive a psychological ontology from a large dataset of individual differences across a broad range of behavioral tasks, self-report surveys, and self-reported real-world outcomes. Though both tasks and surveys putatively measure self-regulation, they show little empirical relationship. Within tasks and surveys, however, the ontology identifies reliable individual traits and reveals opportunities for theoretic synthesis. In Chapter 4 we evaluate predictive power of the psychological measurements both for health behaviors normally associated with self-regulation, and individual ideological characteristics. We find that while surveys modestly and heterogeneously predict both health and ideological outcomes, tasks largely fail to predict health behaviors. We conclude that self-regulation lacks coherence as a construct, and should be abandoned in favor of a multiply-determined view of so-called self-regulatory outcomes. Finally, in Chapter 5 we introduce a method to extend the psychological ontology, opening the door for a truly cumulative quantitative framework for psychology.
Understanding adaptation and trade-offs in evolving yeast
Keywords: Biology.

Adaptation is a major driving force behind the observed bio-diversity in nature. Trade-offs as an essential concept in evolutionary biology, on the other hand, constrain the improvement of multiple traits simultaneously and thus limit the potential of adaptation. To understand how adaptation and trade-offs together shape the evolutionary processes, one needs to study the genetic and functional bases underlying both adaption and trade-offs, and how such genotypic and phenotypic changes affect organisms' fitness. Microbial experimental evolution approach offers an excellent framework to examine evolutionary processes under well-controlled conditions. However, existing techniques of characterizing adaptive events from experimental evolutions are often low-throughput and bias towards a subset of lineages with a high fitness and a high frequency in the population, preventing a comprehensive study of evolution. To overcome this limitation, a DNA barcode lineage-tracking system was previously developed in Saccharomyces cerevisiae, which enables the isolation and analysis of a large number of independently evolved adaptive clones. My work in graduate school has centered on combining the yeast lineage-tracking system, the experimental evolution approach, and the next-generation sequencing technique to investigate the evolutionary processes in a high-throughput and highly quantitative way. In Chapter 1, by measuring the fitness of thousands of evolved yeast clones and genome-wide sequencing hundreds of them, we constructed a comprehensive genotype-fitness map. Two major classes of adaptive events were observed in this serial transfer evolutionary condition, where cells experienced lag, fermentation and respiration phases within each growth cycle. In Chapter 2, we characterized the adaptive strategies of clones isolated in Chapter 1, by quantifying their fitness changes in physiologically distinct growth phases. Contrary to the common assumption that fitness benefits are acquired from an increased exponential growth rate, we instead showed that in batch serial transfer experiments, adaptive mutants' fitness gains can be dominated by benefits that are accrued in one growth cycle but not realized until the next growth cycle. In Chapter 3, we investigated whether and how yeast growth in physiologically distinct growth phases was constrained. We collected thousands of adaptive clones form multiple evolutionary conditions and measured their performance in different traits (phases of the growth cycle). The existence of an evolutionary inaccessible space was demonstrated between two pairs of traits, demonstrating the existence of trade-offs. Furthermore, by identifying the causative mutations of adaptive clones, we elucidated the underlying genetic basis of trade-offs