VictorJuiz/thesis huggingface dataset:
Biophysical characterization of the entry mechanisms of enveloped viruses

Enveloped viruses are a diverse group of agents that pose a threat to global health and economic stability. An enveloped virus consists of a lipid bilayer surrounding the particle, surface glycoproteins involved in entry, and a viral genome necessary for replication. To infect a host, the virus must interact with a host membrane and undergo membrane fusion in order to release its genome for replication. Because of the conserved nature of this process, understanding virus entry at the molecular level is critical. While virus infection and entry have been extensively examined over many decades, the molecular mechanism(s) of entry and critical membrane components remain poorly characterized for many enveloped viruses due in part to the convolution of binding and membrane fusion in many cellular based assays, the requirement for receptor identification and reconstitution, and the extreme heterogeneity of the glycocalyx surrounding the cell membrane. Model membrane systems provide a platform to examine these complex mechanistic questions surrounding virus entry. This dissertation develops model membrane platforms using single particle measurements to examine mechanistic processes of virus entry for several enveloped viruses. The Boxer lab pioneered the development of DNA-lipids as membrane tethers and recently demonstrated that DNA-lipids can be used to bind influenza to a target membrane without altering lipid mixing kinetics. This dissertation expands this receptor-agnostic platform towards novel enveloped viruses which do not require a host receptor for fusion and explores the tunability of receptor agnostic platforms. Controlled complexity is introduced into a model membrane platform in the effort to reconstruct essential components of the glycocalyx to understand its role in Influenza entry. This dissertation seeks to examine the mechanism of virus entry with the least number of confounding variables while still reconstructing critical host components. These single virus measurements deconvolve viral binding and membrane fusion to identify previously obfuscated components in each process

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Cui Bianxiao
Kim Peter
Birds of a feather : designing feathered morphing wings for soft aerial robots

Gliding birds morph their wings through continuous planforms to attain robust flight performance and maneuverability. These seamless shape changes are enabled by soft overlapping feathers moving in a coordinated fashion within the wing. While individual flight feathers are flexible, separate elements that connect only at their bases, together they form an avian wing capable of powering nimble flight. By understanding how feathers are coordinated within an avian wing, key biological findings can inspire designs of wings for morphing flexible paneled robotic wings. Conversely, biohybrid robotic designs used to make biological measurements that might not be possible can elucidate new biological insights. The integrative work presented in this dissertation combines biomechanical measurements and robotic design covering multiple morphological levels of organization in feathered wings. We measure the wing feather and bone kinematics, investigate adjacent feather interactions, and examine feather microstructures. These experiments update the previous hypothesis of feather "friction" from the mid 1900's and provide quantitative evidence that feathers act as directional probabilistic fasteners. The biological discoveries inform the bio-inspired design of underactuated robotic morphing wings validated through wind tunnel testing. Feathered morphing wings are incorporated into a biohybrid robot that is capable of continuous morphing during outdoor flight, pushing aerial robotics towards more robust and maneuverable flight. This dissertation contributes to both aerial robotics and biology, applying techniques including motion capture, computerized tomography, and 3D imaging. We take a multi-scale approach to gain insight into the underlying mechanisms that coordinate flight feathers, measuring feather interactions at different hierarchical levels of organization from the avian wing at the organismal level down to the feather microstructures at the cellular level. These biological measurements provide the foundation for the design of biohybrid aerial robots, enabling successful wing morphing and demonstrating that feathers of a bird stick together

Keywords: Mechanical Engineering.
Advisor: Lentink David
Cutkosky Mark R. 
Okamura Allison
Black hole superradiance signatures of ultralight vectors

The process of superradiance can extract angular momentum and energy from astrophysical black holes (BHs) to populate gravitationally-bound states with an exponentially large number of light bosons. We analytically calculate superradiant growth rates for vectors around rotating BHs in the regime where the vector Compton wavelength is much larger than the BH size. Spin-1 bound states have superradiance times as short as a second around stellar BHs, growing up to a thousand times faster than their spin-0 counterparts. Using measurements of rapidly spinning BHs in X-ray binaries as well as those of supermassive BHs, we can use these fast superradiance rates to exclude a wide range of masses for weakly-coupled spin-1 particles. We also explore routes to detection of new vector particles possible with the advent of gravitational wave (GW) astronomy. The LIGO-Virgo collaboration could discover hints of a new light vector particle in statistical analyses of masses and spins of merging BHs. Vector annihilations source continuous monochromatic gravitational radiation which could be observed by current GW observatories. At design sensitivity, Advanced LIGO may measure up to thousands of annihilation signals from within the Milky Way, while hundreds of BHs born in binary mergers across the observable universe may superradiate vector bound states and become new beacons of monochromatic gravitational waves

Keywords: Physics.
Advisor: Dimopoulos Savas
Graham Peter (Peter Wickelgren) 
Michelson Peter F.
Black holes, baby universes, and random matrices

There is a lot of evidence that black holes follow the usual rules of quantum mechanics, and exhibit all of the fundamental properties of quantum systems such as a discrete set of energy levels. However, many of these properties are difficult to see directly in gravity; there is an apparent tension between the gravitational description of black holes in terms of smooth geometry and the discrete 'quantum' aspects of quantum mechanics. In this work we focus on understanding certain probes of the discreteness of the black hole energy spectrum which exhibit this tension, such as an averaged version of the two-point function of operators widely separated in time outside of a black hole in AdS space. The chaotic dynamics of black holes indicates that its energy levels should have random matrix statistics, and its energy eigenstates should obey the Eigenstate Thermalization Hypothesis. These expectations allow us to make precise predictions for the behavior of our probes. We find strong evidence that contributions from spacetime geometries with nontrivial topology, and even arbitrary numbers of disconnected components, are responsible for reproducing the expected behavior of our probes. Physically, these contributions correspond to including effects from the absorption and emission of closed 'baby' universes from the black hole spacetime. These processes have a small amplitude, but may provide the dominant contribution to the transitions between very distinct states of the black hole

Keywords: Physics.
Advisor: Shenker Stephen Hart
Hartnoll Sean
Susskind Leonard
Blood and Treasure, but Mostly Blood: Electoral Accountability and the All-Volunteer Force

In the wake of the American military’s transition to an all-volunteer force, scholars and military leaders alike cautioned that the Armed Forces defending the nation would disproportionately draw from the least advantaged and least politically powerful populations. Should that be the case, certain communities would pay higher costs of war while others would be relatively untouched, leaving the president free to command with little public accountability. This thesis adopts an experimental statistical counterfactual approach to examine the geographic casualty distribution across states during the post-9/11 wars had there been a conscripted force employed. The data presented suggest that the conventional logic is partially correct: an all-volunteer force is not egalitarian. It disproportionately burdened certain states—predominantly in the South and Midwest— with higher casualty rates than would have a conscripted force. However, many of the states that shouldered the costs of war under an AVF also carry disproportionate political gravity as electoral swing states. These findings suggest that a President who chooses to use force is more likely to face electoral backlash for his or her decisions under an all-volunteer force than under a conscripted force. This finding runs contrary to the popular contention that a conscripted force is inherently more democratic and will lead to better electoral accountability for use of force.

Keywords: Center for International Security and Cooperation
Electoral accountability for war
use of force
U.S. politics
post-9/11 wars
U.S. Presidents
All-Volunteer Force
Conscription
Thesis
Advisor: Schultz Kenneth
Bridging the gap between design and analysis when making inference using observational HIV data

The human immunodeficiency virus (HIV) is still one of the main leading causes of death in the world. Depending on the geographic area of interest, different challenges around HIV remain to be addressed. The overall goal of this dissertation was to use different statistical and epidemiologic designs to address some current HIV-related issues, namely, i) morbidity and mortality of African HIV-exposed uninfected infants; ii) adherence and immunological outcomes among adult People Living with HIV in the United States of America ; iii) The use of transportability methods to improve causal inference among understudied subgroups in the context of HIV research. Chapter 1 of this dissertation is an original manuscript published in AIDS, "Breastfeeding mitigates the effects of maternal HIV on infant infectious morbidity in the Option B+ era". The goal of this chapter was to assess whether HIV-exposed uninfected infants were at a higher risk of infectious disease morbidity and mortality when compared with HIV-unexposed infants in African settings with good prevention of mother-to-child transmission and good exclusive breastfeeding rates using a prospective cohort study. I led the conceptualization, the analysis, the writing, and the preparation of the manuscript. Chapter 2 studied the relationship between adherence to Antiretroviral therapy (ART) and immunological and virologic outcome in a large population of adult People Living With HIV (PLWH) initiating ART at Kaiser Permanente Northern California (KPNC). In this chapter, an algorithm that estimates longitudinal adherence using pharmacy records over multiple six-month intervals was first developed. We then, assessed what variables were associated with longitudinal adherence and modeled the association between adherence and future CD4 counts and adherence and future viral load. Chapter 3 is a methodological paper that was informed by the limitations of chapters 1 and 2 as well as the lack of representativeness in current HIV clinical trials. Chapter 3 assessed how violations in the transportability methods' assumption affect the average treatment effect (ATE) estimation in the target population. This chapter also illustrates how we can use transportability methods and empirical Bayes to design a more efficient hybrid trial. Finally, we conclude that chapter by exploring how reconciling adaptive trial designs and the transportability framework can help us identify sources of violations in the transportability assumptions and improve our understanding of the Heterogeneous Treatment Effects(HTEs) within different subgroups in the target population

Keywords: Epidemiology and Population Health.
Advisor: Baiocchi Michael
Desai Manisha
Maldonado Yvonne A.
Sainani Kristin
"Can I contribute here?" Exploring how interpersonal treatment and mindset affect women's sense of fit in organizations

What does it mean to belong and feel included in a work setting? In this dissertation, I theorize that a core question that people ask themselves as they enter new work settings whether they are able or allowed to contribute towards shared work goals. In Chapters 2-5, I focus on interpersonal treatment, termed microinclusions, and find evidence that people are attuned to treatment from others that directly welcomes them as respected work partners, recognizes them as able to contribute to shared goals, and supports them in doing so. In Chapter 2, employees at a real-world technology company anticipated greater fit in a work group described by microinclusive treatment; however, this effect was greatest for women. Chapters 3-4 replicated the gain in fit with microinclusive treatment among female college students considering a job in a technology company, showed that it arose regardless of the numerical representation of women at the company, and that a microinclusion from a man (but not from another woman) led women to anticipate greater fit for another woman. Finally, using a laboratory paradigm, Chapter 5 shows that microinclusive treatment increased women's, but not men's, quantitative performance in a stereotype threat context. In Chapters 6-7, I take these findings explore whether a mindset intervention about growth in opportunities in contributions for new employees at a large technology company can also improve employees' experiences. Unexpectedly, the intervention led to lower higher employment terminations and lower belonging. Implications for psychological interventions are then discussed

Keywords: Psychology.
Advisor: Walton Gregory M. (Gregory Mariotti)
Markus Hazel Rose
Steele Claude
Can Smartphone Apps Address Loneliness Among College Students? Case Study and Viewpoint

Loneliness among college students is pervasive and is associated with lower social adjustment to college, poorer physical and psychological health, and greater likelihood of college drop-out. Interventions to reduce loneliness have traditionally focused on older adults; much less attention has been paid to prevention of loneliness in young adulthood, a life stage that currently intersects with the growing population of digital natives. Although technology has often been attributed to the rise of loneliness, it may be a critical part of the solution. The purpose of this viewpoint paper is to describe the emerging landscape of research using technology to address loneliness in young adults. It draws insights from a case study on Nod, a smartphone app that incorporates positive psychology, cognitive behavioral skill-building exercises, and mindfulness-based self- compassion to help college students build social connections. Six in-depth qualitative user experience interviews were conducted with first-year college students to identify how app features may be enhanced to promote behavior change. Integrating participatory design insights from these interviews, this paper seeks to provide perspectives on how to design for social connectedness. Leveraging smartphone app technology is a promising strategy to support social connection and impact modifiable cognitive and behavioral risk factors for loneliness during young adulthood — how this can be achieved and designed for is a complex task and warrants further research.

Keywords: loneliness
young adult
college
smartphone app
transformative technology
Thesis
Capacity, community, and consolidation : ransformative mentoring for formerly incarcerated young adults in reentry

Reentry is a challenging and often-forgotten transition from a period of incarceration back into communities. Mentoring programs may offer a promising approach to support young people in reentry. However, research on mentoring typically focuses on outcomes and not processes, limiting our understanding of mentoring in context, specifically with formerly incarcerated youth. The aim of my research is to understand in detail the social processes and practices -- both the formal aspects of the programs and the relational dimensions -- that support positive mentoring outcomes. This dissertation examines the case of Community and Youth Outreach (CYO), a community-based organization in Oakland, California, where staff engage in transformative mentoring, a specific approach to mentoring designed to support formerly incarcerated young adults in the process of reentry. To unpack and understand this process, I observed 21 weekly group mentoring classes, conducted 20 one-on-one semi-structured interviews with adult staff and young adult participants, and reviewed 10 organizational documents for triangulation. I used qualitative analyses with open coding to develop inductive codes through grounded theory alongside deductive coding with a priori codes from the literature. My observations and interviews revealed a system of strategies and pedagogical practices that together offered young people emotional, practical, and resiliency-building support. Analytically, these clustered into three broad constructs: Capacity, community, and consolidation. Mentoring should be conceptualized as a complex process requiring deep expertise from those with lived experience, distributed mentoring among a community of support, and a bidirectional relationship between these two components. This dissertation enhances our understanding of mentoring theory, provides insights for practical future applications of the process, and has implications for policies that support mentoring programs

Keywords: Education.
Advisor: Barron Brigid 
Damon William
Garcia Antero 
Ginwright Shawn A.
Capturing and Identifying Background Internet Radiation Events

Analysing traffic captured on darknets is a useful way to find patterns in network scanning, denial-of-service backscatter, and other internet phenomena known collectively as background internet radiation. However, the most recent large-scale analysis of such patterns was conducted in 2014. Since then, the nature of actors and threats on the internet has changed dramatically. In this thesis, we develop a darknet analysis system that can analyse darknet traffic both retrospectively and in real-time to highlight trends in background internet radiation. We then use this system to examine the modern scanning landscape by analysing scan traffic captured in March 2020. We present profiles of common scan targets, scan origins, and pattern variation in differently-sized scans. We find that scanning has changed significantly in the past six years and note the impact of the Internet of Things on scanning trends.

Keywords:  Department of Computer Science
scanning
darknet
internet telescope
background internet radiation
Thesis
Cardiovascular disease (CVD) in women: literature overview and medical database mining for reproductive risk factors and CVD in women aged 18 to 50

The goal of this non-comprehensive literature review is to provide a structured high level summary of both the cardiovascular risks and the types of cardiovascular diseases (CVD) specific to women, as well as to raise key questions, such as whether there might be a link between the types of cardiovascular disease encountered in young women and risk factors related to pregnancy complications.
The key findings from the medical database analysis of women aged 18-50 are:
Women with reproductive and pregnancy related conditions have a comparable risk of early cardiovascular disease (CVD) to women with diabetes.
Preeclampsia or preterm labor, even in the absence of diabetes mellitus, are higher risk factors for early CVD than gestational diabetes followed by early diabetes.
In women with a history of preeclampsia but no prior risk factors, about 8.6% had a form of cardiovascular disease while still aged 18-50. Compared to all women aged 18-50, the preeclamptic women with no prior risk factors had a higher rate of all types of hypertension (4.70% essential hypertension), angina, ischemic heart disease and atherosclerosis.
The black and “other” race (mostly Latino) women aged 18-50 seem to be at higher risk of developing hypertension after preeclampsia; the proportion of black women with preeclampsia and subsequent hypertension almost quadruples, at 11% compared to the general proportion of blacks in women 18-50 in this data- base.
A sizable proportion of women aged 18-50 with a history of preeclampsia also had a history of gestational diabetes (at least 22%), preterm labor (at least 19%) or poor fetal growth (at least 14%).
Compared to preeclamptic women with no cardiovascular disease aged 18-50, preeclamptic women with subsequent cardiovascular disease aged 18-50 had significantly higher rates of the following reproductive/pregnancy conditions: ear- lier menopause, PCOS, teenage preeclamptic pregnancy, gestational diabetes, uterine fibroids, preterm labor, poor fetal growth.

Keywords: Cardiovascular disease (CVD)
young women
pregnancy complications
female reproductive conditions
Thesis
Advisor: Stefanick Marcia
The causal effects of online ratings on buyer and seller behavior

This dissertation explores how online ratings influence the actions of buyers and sellers. It begins by analyzing the causal effects of increases in star ratings on demand for products in an e-commerce market, and how those effects vary across different products, sellers, and customers. After finding significant responses from buyers to rating increases, it confirms that there is no pricing response from sellers in the same market to this demand shock. This dissertation concludes by finding that the relative pricing responses of high and low reputation sellers depends on the competition faced by the sellers

Keywords: Economics.
Advisor: Wolak Frank A. 
Larsen Bradley J. 
Reiss Peter C. (Peter Clemens)