VictorJuiz/thesis huggingface dataset:
Bioengineering basics, biometrology, and biocivics with ganoderma lucidum
Keywords: Bioengineering.

Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on unicellular organisms or filamentous fungi in liquid bioreactors and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on aerobic solid-state fermentation (SSF) and wood-degrading fungi could enable more direct and sustainable means of manufacture, novel products, market pull for the biomaterials industry, reduced time to market, and reduced production costs. However, basic methods for cultivating wood-degrading fungi and the production of mycological materials are often ad hoc and not readily reproducible. Additionally, existing genetic engineering tools for wood-degrading fungi are not standardized or readily available. Furthermore, the global need for practitioners skilled in fungal biotechnology is outgrowing the available workforce at a time when civic engagement with the biological sciences by the general public is being poorly supported. To address the aforementioned needs, I have developed standard materials, measures, methods, and educational programs enabling bioengineering basics, biometrology, and biocivics with Ganoderma lucidum. Specifically, I developed standard materials, measures, and methods enabling simple laboratory culture of wood-degrading fungi. I established Ganoderma lucidum 10597-SS1 as a reference strain, PringlesTM as a regularized widely-available reference substrate, a simple plate-based assay for standardized radial extension measurements, and a relative extension unit framework for reducing extrinsic effects on measurements of growth that supports sharing of measurement data across locations. So established, I coordinated an interlaboratory study to enable community-based metrology for wood-degrading fungi in simple laboratory conditions and published a peer-reviewed paper describing our work. I co-authored a peer-reviewed White Paper to identify opportunities for reuse of materials, measures, and methods supporting reproducible science and reliable production with fungal biotechnology. Finally, I co-developed a culturally relevant education program, BioJam, to engage youth from underserved communities and nurture equity in biotechnology literacy and governance; and I also co-founded a public benefit organization, Xinampa, whose mission is to cultivate an equitable bioeconomy on the Central Coast of California and form nucleation points for practitioners from the community to develop public-interest biotechnologies that support their community. Taken together, my contributions should begin to advance distributed mycological production in support of all earthlings and the planet
Biomaterial-based approaches for vascularization in bone tissue engineering and regenerative medicine
Keywords: Chemistry.

The fields of tissue engineering and regenerative medicine hold great promise to advance the treatment of large-scale bone defects caused by trauma and disease. However, the development of engineered tissues is held back by the challenge of reestablishing functional vascular networks throughout large defect volumes. This dissertation explores two strategies to encourage the reconstruction of large bone defects through the design and synthesis of new biomaterials for use as scaffolds to support and guide new tissue growth. The first approach explored is to incorporate a major blood vessel surrogate within large tissue engineered constructs to surgically establish a supply of blood through the regenerating tissue. Current synthetic vascular grafts used in clinic display undesirable mechanical properties and scarce tissue remodeling. A new family of elastic polyurethanes was developed to better match the complex properties required for vascular compatibility. Gradual degradation of the material in vivo enables scaffolds to be replaced by native tissues. Porous, tough, and compliant vessel grafts were fabricated using a heat cure/porogen extraction molding technique. When implanted in rats, these grafts supported robust vascular tissue redevelopment and sustained blood flow for up to four months. The second approach explores a modification to the induced membrane technique for bone reconstruction. The induced membrane is a vascularized fibrous layer of tissue that forms around poly(methyl methacrylate) bone cement spacers as part of a foreign body reaction. This membrane provides a privileged environment for bone healing in subsequent reconstructive steps, but the mechanism by which the induced membrane promotes regeneration is poorly understood. Two preclinical models are presented here to evaluate the potential of synthetic engineered membranes as alternatives to the traditional biomembrane and to investigate the biological mechanism by which the spacer material induces membrane properties. By providing models to elucidate biomaterial effects on bone healing, we believe that improved bone tissue engineering therapies may be developed
Biophysical characterization of the entry mechanisms of enveloped viruses
Keywords: Chemistry.

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
Birds of a feather : designing feathered morphing wings for soft aerial robots
Keywords: Mechanical Engineering.

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
Black hole superradiance signatures of ultralight vectors
Keywords: Physics.

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
Black holes, baby universes, and random matrices
Keywords: Physics.

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
Blood and Treasure, but Mostly Blood: Electoral Accountability and the All-Volunteer 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

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.
Bridging the gap between design and analysis when making inference using observational HIV data
Keywords: Epidemiology and Population Health.

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
"Can I contribute here?" Exploring how interpersonal treatment and mindset affect women's sense of fit in organizations
Keywords: Psychology.

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
Can Smartphone Apps Address Loneliness Among College Students? Case Study and Viewpoint
Keywords: loneliness
young adult
college
smartphone app
transformative technology
Thesis

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.
Capacity, community, and consolidation : ransformative mentoring for formerly incarcerated young adults in reentry
Keywords: Education.

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
Capturing and Identifying Background Internet Radiation Events
Keywords:  Department of Computer Science
scanning
darknet
internet telescope
background internet radiation
Thesis

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.