VictorJuiz/thesis huggingface dataset:
Chromatin-mediated regulation of neighboring genes in mammalian synthetic circuits
Keywords: Bioengineering.

In mammalian cells, genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding the dynamics of this transcriptional regulation is important for natural processes, such as heterochromatin spreading during development, aging, and disease, and for designing synthetic gene regulation circuits. In this work, we systematically dissect this spreading behavior in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that with the Kruppel associated box (KRAB), a repressive domain associated with histone methylation, silencing spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by polycomb repressive complex 2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. We find that gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Lastly, our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment
Chronic Smoke Exposure Burden: Impact on the Immune System of Firefighters
Keywords:  Department of Biology
Biology
Firefighter
Wildfire
Environmental Pollution
Heavy Metals
Air Pollution
Occupational Health
Immunology
Text
Thesis

Firefighters are exposed to significant levels of smoke during their careers. Long-term smoke exposure has been associated with chronic diseases and cancers in firefighters. Furthermore, smoke exposure has been associated with the long-term accumulation of heavy metals (e.g., lead, arsenic), which have toxic effects. Despite these known risk factors, the impact of this pollutant burden on the immune system of firefighters remains largely unknown. The goal of this study was to characterize the immune dysfunction caused by chronic smoke exposure and identify possible associations with heavy metals in firefighters versus controls.
We profiled peripheral blood mononuclear cells (PBMCs) utilizing cytometry time of flight (CyTOF) and measured heavy metal levels in the cells during CyTOF by utilizing available heavy metal channels in a cohort of San Francisco firefighters (n=9; 21-52 years;) and healthy controls (n=9; 26-58 years) with a similar level of baseline pollution exposure. FlowJo was used to identify cell populations.
The firefighter group had a lower frequency of CD45- CCR7+CD27- NK cells in the live cell population (p<0.02) and in the NK cell population (p=0.016). Lower cell counts (p<0.05) were found in the firefighter group compared to control in B cells that were positive for Cd 106, Pb 204, and W 182 and CD4+ cells that were positive for Pb 204 and Pb 208. These results suggest chronic smoke exposure may alter the frequency of CD45- CCR7+CD27- NK cells and accumulation of certain heavy metals compared to healthy controls.
This study expands our current knowledge of potential mechanisms of immune dysfunction associated with smoke exposure and heavy metals in firefighters.
Civil rights and nation building in a multiethnic borderland : Lwów and Galicia 1918-1939
Keywords: History.

This dissertation is a microhistory of civil rights in the newly founded Polish Republic, as seen through the lens of violence between the state and its citizens during the twenty-year period between the world wars. Focusing on the city of Lwów and the surrounding Eastern Galicia, this dissertation focuses on Poland's two largest minorities, Jews and Ukrainians (who together represented a quarter of the country's population) and employs an approach merging comparisons and connections to analyze the mechanisms of the conflict between the state and the citizens whose civil rights were denied. The chapters of this dissertation are focused on four distinct episodes of violence: the 1918 pogrom of Lwów's Jews by the Polish Army and local Polish population, the 1922 trial of Józef Piłsudski's failed Ukrainian assassin Stepan Iaroslav Fedak, the 1930 "pacification" of Galicia's Ukrainian countryside, and the 1936 workers' protest where fourteen Lwowians of all three ethnicities were shot and killed by the Polish State Police. This work defines the four crucial elements of the conflict between the state and its minority citizens for full civil rights: the gap between the letter of the law and the willingness of state organs to enforce it; the existence of a clearly defined root of the majority group's supposed superiority (discourses on culture, civilization, race); a projection of the dominant group's (by extension, the state's) own entitlement onto the minority groups and the condemnation of their demands for rights as demands for supposed privileges; and defining the non-dominant identities as inherently "political" and therefore anti-state. The proposed model is applicable in wider contexts regarding minorities and civil rights and is the work's contribution towards a global history of civil rights, now including East Central Europe
The civil-military politics of war termination
Keywords: Political Science.

Civilian leaders interpret the value of war in terms of political ends, while military leaders often pursue victory itself as war's object. An empowered military can therefore make war harder to end. Estimates from international conflict data show that termination of a war short of victory is more likely when civilian leaders become more politically dominant. However, civil-military consequences for war termination arise from more than outright shocks to political power. Survey experimental evidence demonstrates that senior U.S. military leaders can use typical political activities to recruit public support for persisting in wars and create costs for elected leaders who want to end them. Finally, qualitative analysis of the U.S. post-9/11 wars and text analysis of a new data set of congressional testimony yield evidence of military dissent and its influence on presidential policy decisions. Altogether, this dissertation moves beyond war termination's civil-military problem, which is about whether and how to stop fighting, and sheds light on the problem of its civil-military politics, which is about how to define war's end but also how to resolve competing claims
Clock atom interferometry for precision measurements in fundamental physics
Keywords: Physics.

Recent technological advances have enabled the development of new precision atomic sensors for tests of fundamental physics. In this thesis, I will introduce the concept of clock atom interferometry, a hybrid of atomic clocks and atom interferometry that is particularly suited for gravitational wave detection and ultralight dark matter searches. I outline the experiment we built to cool and trap strontium atoms for prototyping this concept and demonstrating our initial atom interferometric results. I will then discuss the first realization of large momentum transfer (LMT) clock atom interferometry using single-photon interactions on the strontium 689 nm transition, implementing Mach-Zehnder interferometers and gradiometers with state-of-the-art momentum separation to enhance their sensitivity. Furthermore, using amplitude modulated pulses, I demonstrate Floquet atom optics as a tool to allow symmetric evolution of two states at equal and opposite detuning and allows high pulse efficiencies greater than 99% for all detunings, in particular even when the detuning is on the order of the Rabi frequency. Applying this technique, I extend the visibility of an atom interferometer out to a record momentum transfer in excess of 400 photon momenta. I conclude by demonstrating how this technique can be further advanced to allow for 601 photon momenta of separation, as well as a discussion of the new measurement opportunities made possible with these techniques in the fields of high-precision inertial sensing and fundamental physics detection
Coherent control of Angstrom-wavelength laser pulses for ultrafast physics
Keywords: Physics.

In 2009, the Linac Coherent Light Source (LCLS) generated Angstrom wavelength x-ray pulses with femtosecond pulse duration. This marked the advent of the first Angstrom wavelength x-ray laser in history. The ultrafast, ultrabright and highly coherent x-ray pulses opened up new opportunities to catch a glimpse of the bizarre and fascinating world of atom dynamics. To explore these dynamics at the natural spatial and temporal scale of atoms and molecules, new x-ray optics systems are required to precisely manipulate the x-ray laser pulse. This is the focus of my research. In this thesis, I summarize my effort of developing an efficient numerical simulation platform for the time-dependent behavior of Bragg crystal optics, and the design and experimental demonstration of a dispersion-free ultra-stable optical system to split, delay and recombine hard x-rays in a manner that will enable a new generation of high sensitivity ultrafast measurements. In the end, I present a future-oriented conceptual study that applies these techniques to the well-known chirped pulse amplification (CPA) process that has revolutionized high power optical lasers and show how this could be achieved at Angstrom wavelengths to deliver over a terawatt of x-ray power
Collaborative artificial intelligence (AI) for idea generation in design teams
Keywords: Mechanical Engineering.

Engineering design teams are critical for innovation and in solving the increasingly complex problems we encounter. As Artificial Intelligence (AI) systems are providing capabilities that enable humans to perform well beyond what they might have been able to, an understanding of how engineering design teams can leverage AI systems is critical. We have seen these AI capabilities for example in human-AI art generation; software development where computers write a significant portion of code; and even in radiology where AI identifies patterns that humans cannot. This work takes the position that collaborative human-AI teams are the next frontier, and explores this in two studies. The first one involved a voice/text AI collaborator by developing, then testing various vocabularies. It concluded by highlighting gaps in the current models and datasets, which need to be resolved in order to implement such voice/text AI collaborators. The second involved a sketching AI, and used an open source app. Though it worked well as a divergent ideation collaborator, we identified gaps in the variety of suggestions that the AI presented. In addition to this, it demonstrated that when given a prompt to design for, human-AI teams generated more ideas on average, as well as more that were rated higher by two trained research assistants. By demonstrating that Human-AI teams can outperform Human-Human teams on a design task, we provide empirical evidence of AI's potential in design teams. As we enter to the next phase of human-machine collaboration, this work contributes towards a conceptual design of a new class of AI systems that observe humans and come up with suggestions in real time, enabling researchers to design and test new concepts. Others can apply the methods we have demonstrated to explore different environmental contexts such as distributed teams or mixed reality; as well as other modes of interactions during collaboration such as gestures and non-verbal cues
Collective dynamics of high brightness electron beam compression and manipulation
Keywords: Applied Physics.

High brightness electron beams have revolutionized accelerator science and enabled a large range of high impact applications such as X-ray free electron lasers(XFEL), inverse Compton-scattering, plasma wakefield accelerators and future linear colliders. In pursue of higher beam brightness, collective effects become key limiting factors. Those collective effects happen during the beam generation, acceleration, compression and transport, including coherent synchrotron radiation, space charge and resistive wall wakefields. As people are entering the new parameter regime — such as the generation of ultra-short electron bunches or ultra-high peak current — collective effects can play a dominant role and classical theories of wakefield can break down. In this work we describe our efforts in understanding and controlling the collective dynamics of high-brightness electron beams. In the first half of the thesis, we focus on one of the most challenging beam dynamics problems in accelerator physics — coherent synchrotron radiation (CSR) and introduce a novel computational model of 2D/3D CSR in relativistic beams. The model achieves both accurate and efficient simulations of CSR in the regime that conventional 1D models become invalid, which can be crucial for the design of next generation accelerators. In the second half, we switch gear to techniques that enable better control of the collective effects. Specifically we examine laser shaping techniques both in spatial and temporal domains as a powerful beam manipulation tool. We first discuss in detail the numerical and experimental studies using Laguerre-Gaussian mode laser in the laser heater to improve the microbunching instability suppression in XFEL drivers. Then we introduce temporal laser shaping to achieve flexible longitudinal phase space manipulation and apply it as an active out-coupling method for cavity-based free-electron lasers
College Student Elasticity: The Impact of Job Openings on College Major Decisions
Keywords:  Department of Economics
human capital investments
higher education
field of study
labor market information
vacancy data
expected demand
postsecondary school
mismatch employment
Text
Thesis

Over time, there has been a shift in the demand for different college majors and skills, particularly engineering and science majors. Understanding how college students decide their major is important for future employment outcomes. This paper studies the effect of shifts in job opening availability on college major choice. I use a novel job openings dataset and a record of degrees conferred in the United States from 2007 to 2019. I use lags and fixed effects to estimate exposure to change in job openings by region and identify the effect on college major choice. I find that a 25 percentage point increase in job openings for a given industry leads to a 1 percentage point increase in the fraction of degrees in that industry. The results are similar for public colleges and community colleges. Students who attend small colleges and majority undergraduate colleges are more responsive to changes in job openings. In addition, students in the fields of business and humanities are more responsive to changes in job openings than other industries.
College Students Aren’t As Liberal As You Think: Evidence for Political Moderation Within Homogeneous Groups
Keywords: Polarization (Social sciences)
Politics and government
Political parties
ideological polarization
group polarization
Psychology
symbolic systems
affective polarization
Text
Thesis

As America grows ever more polarized, a question arises: are productive discussions even possible anymore? Due to the rising phenomenon of partisan sorting, more and more Americans are living in enclaves that share not just demographic features but are politically homogeneous (Brown and Enos 2021). A set of famous findings in the literature offers little hope: the widely-accepted universal law of group polarization states that homogeneous groups always become more extreme after discussion (Sunstein 2002). Groups that enter a conversation leaning towards one perspective come out ever more ensconced in opinions more radical than previously held (Friedkin 1999). If this law really is universal, it poses a serious problem for the efficacy of political conversations in the United States. This thesis aims to disprove the universality of this law by considering a study, “Shaping Our Future” from the Stanford Center for Deliberative Democracy, undertaken with a group of highly homogeneous college students (n = 541, where 75% of the sample identified as or leaned towards the Democratic Party, compared to just 11.5% for the Republican Party). College students are a perfect population for this question as they tend to be highly liberal and are the subject of a current political battleground between the left and the right. By examining opinion change using a pre- and post-study survey method, this thesis demonstrates that this homogeneous group moderated (decrease in ideological polarization) on a majority of proposals as well as grew warmer (decrease in affective polarization) towards the other side. In particular, this group of liberal college students became more conservative on economic issues. T-tests are used to prove statistical significance. Overall, I find that this group, despite its makeup, did meaningfully reduce polarization through discussion. I therefore offer a potential counterexample to the universal law of group polarization as well as a hopeful note for future conversations in the college campus climate and around the nation.
Combating noise and uncertainty in biophysical models
Keywords: Applied Physics.

Noise and uncertainty are ubiquitous in biological systems, and robustness to these effects may be a crucial piece of understanding biological design. In small biophysical systems, thermal fluctuations can be of the order of the energy difference between system states, and these fluctuations are an important operational consideration for systems at the mesoscale. At the behavioral level, organisms constantly confront an unpredictable world and must make decisions that achieve their goals but are also sensitive to risk. In this work we discuss two projects that attempt to provide insight into robust biophysical models at two very different scales. At the smallest scale, we investigate theoretical bounds on the accuracy of single cellular sensors and how this is limited by energy dissipation. We then move to the behavioral scale and apply large deviation theory to risk-sensitive reinforcement learning in order to generate variance-constrained policies
Combining electroanalysis and nanoscale characterization to understand battery electrolytes
Keywords: Chemistry.

Development of batteries with higher energy density than conventional Li-ion batteries can facilitate electrification of passenger vehicles, aeronautics, and long-range transportation. Metallic lithium is the ideal anode for maximizing energy density, but insufficient rechargeability limits its widespread adoption. The reactivity of Li with electrolytes and growth of filamentary "dendritic" Li morphologies during charging underly its poor rechargeability. Electrolyte engineering can simply and effectively mitigate these problems; however, the mechanistic basis for the dependence of Li passivation and morphology on electrolyte chemistry remains poorly understood. In this dissertation, I discuss how it is now possible to understand the complex multiscale relationship between electrolyte chemistry and rechargeability by using the complementary strengths of electroanalysis and cryogenic transmission electron microscopy. First, I discuss the electrochemical and structural evolution of a passivation film on Li called the solid electrolyte interphase (SEI) in select electrolytes. The results refine our understanding of SEI structure and growth and suggest control of electroplated Li morphology is key to prevent corrosion of Li during calendar aging. Next, I will discuss the current and electrolyte dependence of Li plating pathways and kinetics to reveal the main factors controlling Li morphology. The results first show that fracture of the SEI and exposure of fresh Li-electrolyte interfaces -- as opposed to mass transport limitations alone -- are responsible for dendritic Li plating during fast charging. I then discuss a new electroanalytical method using ultramicroelectrodes that can probe the charge-transfer kinetics at fresh Li-electrolyte interfaces after SEI fracture. The kinetics deviate from classical Butler-Volmer models and provide insight into how solvation and interfacial structure tune reaction rates in batteries. Correlating the kinetics in many electrolytes to rechargeability suggests that the equilibrium potential of Li/Li+ redox and surface energy -- thermodynamic factors modulated by the strength of Li+ solvation -- underly trends of Li morphology across distinct classes of electrolyte
A compact reader for wireless passive sensors
Keywords: Electrical Engineering.

The demand for continuous, long-term wireless sensing is growing in applications where tethered links cannot be used. Achieving a complete sensing solution requires innovations both in the reader and the sensor to make them easy-to-manufacture, small, safe, disposable, and yet sufficiently functional. Fully passive sensors (FPS) which consist of only a resistive-capacitive-inductive (RLC) tank are widely used as a simple and inexpensive alternative to their active counterparts. Although great effort and progress have been made in developing such sensors, the reader design remains a bottleneck. Existing solutions rely on forced excitation which makes the implementation inherently more complex. Self-oscillation circumvents these limitations. We show that a nonlinear negative resistance which exhibits a step-like current-voltage characteristic enables self-oscillation to automatically find and lock to the sensor value. Moreover, use of a non-resonant reader coil or unidentical tank topologies in the reader and sensor results in distance dependency of measurement results. We investigate the sources of distance variations and suppress their effects by optimizing the tank topology and employing a closed-loop mechanism which locks to the point of operation with minimum variation. Both improvements allow for a simple reader sticker (5.4cm by 3.4cm) which is wirelessly powered using near-field communication signals and achieves < 0.16% variation over a distance of 1.6cm for a 1.2kOhm sensor resistance. This simple reader solution advances the field of continuous, ubiquitous, and long-term sensing, paving the way for widespread deployment in daily applications, such as food safety, structural, and health monitoring