VictorJuiz/thesis huggingface dataset:
Towards a better understanding of water microbiomes from source to tap in a rapidly urbanizing area with a tropical climate

Access to safe drinking water remains a key concern across the globe. From the water source to the tap, many factors can influence microbial communities in water. This dissertation explores bacterial communities at various stages in the drinking water system serving the peri-urban region of Arraiján, Panama. First, the influence of land use and reforestation efforts on stream water bacterial communities was evaluated. Bacterial communities in the water column of four streams in the Panama Canal Watershed were assessed, each influenced by a different land use common in the Neotropics: mature forest, secondary forest, silvopasture and traditional cattle pasture. Land use was a key factor in microbial diversity and community composition. Streams influenced by forested areas exhibited diversity and community structure significantly different than streams influenced by lands with cattle. Reforested areas and agroforestry efforts such as silvopastures have the potential to protect water quality and significantly influence nearby water microbiomes./nMoving downstream in the drinking water system, the effects of water treatment and distribution were evaluated in the region of Arraiján, Panama, as well as the effects of intermittent water supply in a section of Arraiján’s drinking water distribution system. Treatment processes were determined to have varied effects on bacterial diversity and structure at the three different drinking water treatment plants surveyed. Water quality parameters such as chlorine concentration and temperature correlated with bacterial composition in treated drinking water. In the distribution system, bacterial diversity and structure varied spatially. Intermittent water supply significantly influenced microbial communities in drinking water, driving the proliferation of Pseudomonas and exhibiting higher number of unique bacteria that could result from intrusion or regrowth between supply cycles. Two key features of intermittent water supply were assessed in controlled laboratory bench-scale experiments: stagnation and drainage. Stagnation led to higher bacterial concentrations and significantly influenced bacterial diversity and structure. The effect of drainage was evident only in biofilm bacterial communities. The application of DNA sequencing to study source water and treated drinking water demonstrated the ability to characterize changes to the microbiome that would not have been evident through the use of traditional water quality parameters. This work provides helpful insights into drinking water bacterial communities in a tropical setting that could be useful for better managing water systems in similar settings.

Advisor: Nelson, Kara L
Lower Scalar Curvature Bounds for $C^0$ Metrics and Regularization by Ricci Flow

We use Ricci flow to create a class of local definitions of weak lower scalar curvature bounds that is well defined for $C^0$ metrics. We show the following: that our definitions are stable under greater-than-second-order perturbation of the metric, that there exists a reasonable notion of a Ricci flow starting from $C^0$ initial data which is smooth for positive times, and that the weak lower scalar curvature bounds are preserved under evolution by the Ricci flow from $C^0$ initial data. We also explain some applications of this approach to certain questions regarding uniform convergence of metrics with scalar curvature bounded below. Finally, we consider the relationship between this approach and some other generalized notions of lower scalar curvature bounds, and discuss some open questions.

Advisor: Bamler, Richard
Monumental Fragment, Reconstituted: Reproducing the Yuanming Yuan

This dissertation examines the multiple contexts in which the ruins of the Yuanming Yuan (Garden of Perfect Brightness) imperial garden-palace of the multiethnic Qing dynasty (1644–1912) are reconstituted through acts of copying. I consider the Yuanming Yuan as a site that has always been in cross-cultural translation, not only in its construction—its most famous section was designed in Sino-Baroque style by Jesuit court artists—but also in its destruction, when Anglo-French troops looted and burned it during the Second Opium War in 1860, leaving behind the marble ruins of the Sino-Baroque European Palaces. The dissertation shifts away from the original site in Beijing towards the garden’s reinterpretation and reconstitution in alternate spatial contexts from the early twentieth century to the present day. Because these reproductions are not exact copies, I consider them “translations,” in that they translate the Yuanming Yuan into new spatial contexts of international diplomacy, domestic theme park, museum gallery, and digital space; furthermore, by reconstituting a Qing imperial space that was looted and burned during the Opium Wars, these “translations” also serve as a means to reproduce—and challenge—national identities, cultural heritage, and appropriations of the past./nThe introduction establishes the Yuanming Yuan as a site of cross-cultural translation, a site of memory, and a site of fragmentation. Chapter one examines the architectural translation of the Haiyantang (Hall of Calm Seas) in the European Palaces (Xiyanglou) section of the Yuanming Yuan. In the aftermath of the Boxer Rebellion, Empress Dowager Cixi reconstructed a new Haiyantang in the Central Lake area of Beijing; I argue that the appropriation of the Yuanming Yuan’s European Palace-style served to create a mediated space for renewed Qing diplomacy with international powers. Chapter two turns to the reconstruction of the Yuanming Yuan as theme parks in Shenzhen, Zhuhai, and Hengdian and examines the parks’ strategies of selective reproduction and conflation of Qing imperial spaces. I argue that the microcosmic nature of the original Yuanming Yuan made it a suitable site to replicate within theme park imaginaries of the national future. Chapter three traces the journey of the looted bronze zodiac animal heads from the Haiyantang and argues that their potency as symbols of Yuanming Yuan’s looted objects comes from their physical form as decapitated heads. I further argue that the reinterpretation of the heads through acts of artistic creation and vandalism by contemporary artists and activists speak to present day concerns about cultural heritage, preservation practice, and national identities. The dissertation concludes with a meditation on the possibilities and limitations of digital reconstruction and preservation.

Advisor: Berger, Patricia
Effects of particle shape and fluid shear on the kinematics and mass transfer of large particles in turbulent flow

In this dissertation I set out to determine how shape and size influence the kinematics and mass flux of Taylor-lengthscale-sized particles in homogeneous isotropic turbulence. Through laboratory experiments, I investigated different sized and shaped flat particles to determine what happens with the spinning and tumbling of those particles in turbulent environments. The results of this first set of experiments showed dependence on size, but not shape. The size-dependent results from the flat particles agreed with the findings for fibers (Oehmke et al., 2021) and cuboids (Pujara et al., 2018)./nTo determine the mass flux of Taylor-lengthscale-sized particles, I developed a new particle to study dissolution in turbulence. This particle was made from a sugar-glass recipe and had the characteristics of being neutrally buoyant and shape-similar while it dissolved (Oehmke and Variano, 2021). Based on results from previous work that characterized motion (Pujara et al., 2018, Bordoloi and Variano 2017, Byron et al., 2015), I created rod- and disc-like particles and compared their surface area, volume, and surface-area-to-volume ratios. In all cases, the disc-shaped particles dissolved faster than the rod-shaped particles signifying that shape plays an important role in dissolution dynamics.

Advisor: Variano, Evan A
Investigating the Dynamics of Non-Equilibrium Behavior in Eukaryotic Transcriptional Regulation

Biological systems provide a rich environment for studying non-equilibrium phenomena, an exciting new frontier in physics. Of particular interest is the study of transcriptional regulation---the process by which transcription factors regulate the activity of mRNA production. Recent evidence suggests that in eukaryotes, organisms whose cells possess nuclei, transcription involves non-equilibrium effects such as energy expenditure. In this work, we undergo a systematic dissection of transcriptional regulation in eukaryotes and demonstrate the necessity for non-equilibrium models in the case of the developing fruit fly. We then investigate some theoretical ramifications of non-equilibrium models of chromatin accessibility that incorporate transient dynamics. Finally, we describe a novel experimental and computational framework for studying the entire transcription cycle---consisting of mRNA initiation, elongation, and cleavage---in order to investigate transcriptional regulation beyond that of simple regulation of initiation.

Advisor: Garcia, Hernan
On the Combinatorics of LLT Polynomials in Classical Lie Type

LLT polynomials were first introduced by Lascoux, Leclerc, and Thibon using the action of an affine Hecke algebra for S$_n$, and can be viewed as a $q$-generating function for both ribbon tableaux and tuples of semistandard Young tableaux. This definition has since been expanded to arbitrary Lie type, although with no combinatorial definition. We establish a combinatorial model for LLT polynomials in particular cases for Sp$_{2n}$ and further conjecture a similar model for the orthogonal Lie types. Our definition uses a new object we call an out-in tableau as well as a correspondence between oscillating tableaux and symplectic tableaux that we use to give a proof of a Cauchy identity for Sp$_{2n}$.

Advisor: Haiman, Mark
Health Equity at the Local Level

AbstractHealth Equity at the Local Level by Elizabeth Ambriz Doctor of Public Health University of California, Berkeley Professor Jason Corburn, Chair/nThis dissertation provides insight into Local Health Department (LHD) and county practice to engage in a health equity practice. The persistent health inequities pattered by race, class, and gender in the US call for a paradigm shift in public health practice with renewed approaches and skills. The more than 3,000 LHDs nationwide can play a central role in reducing health inequities by engaging in an intentional health equity practice that addresses the social, economic, and historical drivers of health inequities./nIn the first paper, Transforming LHD Practice to Address Health Inequities: A Systematic Review, I characterize the practices that comprise a LHD health equity practice to help LHDs gain a better understanding of LHD approaches to more effectively address health inequities. This paper identifies six practices that comprise a LHD health equity practice including (1) authentically engage communities and build their power, (2) address the social determinants of health (SDOH) through collaboration across sectors, (3) assess and influence the policy context, (4) build organizational and staff capacity, (5) demonstrate leadership, and (6) change the narrative./nIn the second paper, One LHD’s Journey Towards Health Equity, I critically analyze how one suburban LHD with large areas of rural farmland, the Monterey County Health Department (MCHD), is engaging in a health equity practice and the challenges they face. The MCHD is building community power through its Leadership and Civic Engagement Academy (EnLACE), building Staff capacity through its Health Equity Scholars Academy (HESA) and Government Alliance for Racial Equity (GARE) trainings, and collaborating across multiple sectors to address social determinants of health (SDOH) through its Health in All Policies (HiAP) initiative. However, the MCHD experiences barriers to implementing a health equity practice including funding cuts and inflexible funding, conflicting agendas and interests, a lack of a systemic approach to addressing inequities, and an intentional focus on vulnerable and highest need groups and places in MC./nFinally, in the third paper, Monterey County’s COVID-19 Response Through a Health Equity Lens, I focus on analyzing the context in which the MCHD operates by examining Monterey County’s COVID-19 response through a health equity lens. This study found that MC is addressing the immediate crisis and aims to implement a long-term approach to addressing inequities in the SDOH. However, it is imperative that MC shares decision making power with the communities most impacted by inequities.

Advisor: Corburn, Jason
Building RL Algorithms that Generalize: From Latent Dynamics Models to Meta-Learning

Building general purpose RL algorithms that can efficiently solve a wide variety of problems will require encoding the right structure and representations into our models. A key component of our generalization capability is our ability to develop an internal model of the world that can be used for robust prediction and efficient planning. In this thesis, we discuss work that leverages representation learning to learn better predictive models of physical scenes and enable an agent to generalize to new tasks by planning with the learned model under the framework of model-based RL. We cover two kinds of abstraction that can enable good generalization: state abstraction in the form of object level representations and temporal abstraction in the form of skill representations for hierarchical RL. By incorporating these abstractions into our models, we can achieve efficient learning and combinatorial generalization over long horizon, multi-stage problems. We also discuss the role of meta-learning in automatically learning the right structure for general RL algorithms. By leveraging large scale evolutionary based computation, we can meta-learn general purpose RL algorithms that have better sample efficiency and final performance over a wide variety of tasks. Finally, we cover how these internal models can be used to compute the RL objective itself and train general RL agents with complex behavior without having to design the reward function.

Advisor: Levine, Sergey
Red Sun, Red Star: Japanese Members of the Chinese People's Liberation Army, 1937-1958

From 1937 to 1958, thousands of Japanese soldiers, medical workers, and civilians collaborated with the Chinese Communist Party and Chinese People’s Liberation Army, some as volunteers and others as captives or conscripts. Many of these Japanese individuals became formal members of the PLA, received medals of distinction, and had their acts of sacrifice and heroism recorded in the official histories of the Chinese military divisions they joined. Japanese soldiers assisted the Chinese communist war effort during the Chinese Civil War and the Korean War, while Japanese nurses and doctors tended to Chinese patients, often on the front lines of battle, and helped establish and manage the earliest medical institutions and public health and inoculation campaigns of the PRC. Japanese filmmakers worked in the production of some of the early PRC’s most iconic films such as The White Haired Girl, and Japanese specialists in practically every field contributed their expertise to the establishment of the Chinese communist state and its civil infrastructure. The experience of membership in the PLA and of work in communist China was a profoundly transformative one for the former settlers of the Japanese empire. For many, it marked an awakening to an entirely novel worldview, an embrace of socialist ideals, the development of lifelong friendships and relationships, and the discovery of China as a ‘second motherland’. For the returnees, contact with Chinese communism proved to be a stigma when seeking entry into the Japanese home island workforce and society, while also serving as a bonding experience, creating a cohort of individuals unified by their extraordinary experiences on the continent.

Advisor: Barshay, Andrew
The Matter of Wu and Yue: Story Cycles in Early Chinese Historiography

This dissertation proposes that writings about the past in the classical era (323 BCE- 316 CE) are best viewed as rhetorical constructs, rather than history. Classical-era writers were interested in the past mainly because history provided useful examples, good and bad, for addressing sociopolitical problems in the present. In writing the histories of the kingdoms of Wu and Yue (sixth-fourth centuries BCE), classical-era writers, centuries removed in time, space, and customs from the southeast, took individual anecdotes and speeches associated with famous historical figures such as Wu Zixu and Fan Li, which were in oral and written forms, for didactic and even entertainment purposes. These anecdotes and speeches they inserted into a chronological order in order to “reconstruct” history” and repurpose it. By examining nine complete versions of the Wu-Yue legends from the received texts, “side-by-side.” this thesis attempts to show that the early empires' rhetorical needs shaped the structures and logics of the narratives that did develop. For that reason, characters and events central to one story version were sometimes omitted from other versions of the same story, and frequently rhetorical devices such as dramatic irony were employed to make the narrative arcs of the versions more memorable. For modern scholars writing histories of early China, this hypothesis has important implications for how we understand the unseen processes by which our sources were compiled and transmitted, which, in turn, suggests that scholars need to modify their current methodological approaches to the early histories, legends, and myths, given that the stuff of history was not usually intended primarily to convey reliable accounts of the remote past. As was the case with the “histories” of Wu and Yue, stories – even stories about the most famous historical figures from those regions – tell little about the inhabitants of those kingdoms over time, even the rulers of those kingdoms. Attention to the epigraphical evidence shows us that many rulers besides Goujian were unknown to the authors and compilers of Qin and Han. Even by Western Han, their strange-sounding names were only half-remembered in jumbled and confused king lists, and key events during their reigns tended to be forgotten or unremarked. Perhaps forgetting some part of the past allowed Goujian and other semi-legendary figures from the remote past to be “remembered” in a new way.

Advisor: Nylan, Michael
Everyday Corporations: Clubs and Civil Society 1688-1800

The explosive growth of British clubs over the 18th Century has been understood to have major implications for the histories of sociability, the public sphere, civil society, and masculinity. This dissertation looks at the history of clubs from another perspective, that of the history of organizations. To capture a robust narrative of club growth over the long term, a Digital Census of club activities was produced drawing from archive catalogues, contemporary newspapers, and secondary sources. Displaying these enumerations in data visualizations shows the steady growth in the per capita density of clubs over the long 18th Century. Clubs developed from marginal urban pastimes to inescapable cornerstones of everyday life. Clubs used minutes, democratic deliberation, and elected officers to maintain themselves: practices that were borrowed from the wider corporate world. This dissertation reframes the growth of civil society organizations like clubs as the spread of procedural, formal administration into everyday life. Corporate paperwork was used not only to make a rational organization but also to develop interested, embedded, local ties. The expansion of these corporate tools led to the development of a pluralistic civil society that included a huge range of increasingly specialized activities. A case study of change ringing, a form of English church bell ringing, shows how the pastime developed into a conspicuously complex amusement in order appeal to a niche of accurate middle-class men. But this civil society became specialized, fractured, and at times obscure. The fracturing of civil society came to a political crisis in the 1790s, with the French Revolution and the domestic British radical project for political reform. We have missed how this conflict was not just about reform against reaction, but also about the proper uses of civil society organizations. What resulted from the conflict was a conception of civil society as ‘neutral’, acting outside of the state or the market and limited self-interest.

Advisor: Laqueur, Thomas
Part I. Synthesis of delavatine A, incarviatone A, and fascaplysin natural products. Part II. Total synthesis of calyciphylline B-type alkaloids

This dissertation details work in two categories: (1) development of novel annulation strategies enabled by regioselective ring-opening of 2-pyrone derivatives and showcasing the utility of such transformations in total synthesis (Chapters 1–4). (2) total synthesis of calyciphylline B-type alkaloids and evolution of a novel methodology to access oxazaborinine heterocycles (Chapters 5–6). Chapter 1 is an introduction to known annulation reactions employing the versatile reactivity of 2-pyrone derivatives. This chapter provides a comprehensive summary of such strategies to highlight the key areas where further development is needed./nChapter 2 describes the evolution of our symmetry-inspired unified strategy for the synthesis of delavatine A and incarviatone A. Key features of our final synthetic route include an electrocyclization cascade sequence involving five transformations occurring in a single pot. This sequence was initiated by a regioselective 1,6-ring opening of a 2-pyrone derivative, which was synthesized by employing site-selective cross-couplings of 3,5-dibromo-2-pyrone./nChapter 3 details experimental and computational studies conducted to gain insight into the mechanism of the observed site-selective cross-coupling of 3,5-dibromo-2-pyrone. These insights may prove valuable in developing a more general understanding of the effects of solvents and additives on site-selective cross-coupling of other polyhalogenated heterocycles./nChapter 4 describes an extension of our interest in exploiting annulation strategies enabled by the regioselective ring-opening of 2-pyrone derivatives. Specifically, this chapter discusses the development of an annulation strategy that relies on 1,2-ring opening of N-heterocycle–pyrone adducts. The scope of this strategy was extended to access diverse N-fused heterocycles including pyrido[1,2-a]indoles. Additionally, the utility of this methodology was demonstrated in a concise formal synthesis of three fascaplysin congeners./nChapter 5 focuses on our early approach toward the synthesis of calyciphylline B-type natural products, a subfamily of the polycyclic Daphniphyllum alkaloids. While this strategy did not prove fruitful to access the target molecules, the approach revealed a wealth of interesting reactivity surrounding oxazaborinine heterocycles./nChapter 6 highlights our successful route to access calyciphylline B-type alkaloids. Specifically, the synthetic studies culminated in the first total synthesis of daphlongamine H, gave access to isodaphlongamine H, and also led to revision of the reported structure of deoxyisocalyciphylline B.

Advisor: Sarpong, Richmond