VictorJuiz/thesis huggingface dataset:
Development of a Single Particle Analyzer of Mass and Mobility

Mass spectrometry (MS) is an important analytical tool for obtaining information about the identity, structure and function of molecules over a wide range of sizes, from small molecules up to large protein complexes. Conventional MS techniques work by measuring the mass to charge ratio (m/z) of an ensemble of ions, then using the spacing between different m/z peaks to find the ion charge states so that the masses can be determined. This approach can be difficult to use for samples with a molecular mass beyond ~1 MDa or made up of a heterogeneous mixture of molecules with similar masses, which are typically detected as a single broad, unresolved m/z peak for which the charge cannot be obtained. These samples can instead be weighed with single ion MS, in which the m/z and charge of each ion is measured individually, so other ions do not interfere with the mass measurement. The work described in this dissertation is focused on developing a new instrument for single ion MS that uses charge detection mass spectrometry (CDMS) to better analyze samples that are difficult to measure with conventional MS. New instrumentation and data analysis techniques to improve the precision of CDMS mass measurements and use CDMS for new types of measurements are demonstrated. In CDMS, ions are detected by the charge they induce as they fly through a conducting tube. A new type of CDMS detector with four detector tubes inside an ion trap is used to increase the number of measurements of each ion and reduce the uncertainty in the m/z and charge by signal averaging. A method to measure the ion energy during the trapping time from the signal pattern the ion produces was also developed. This enables the energy and mass of the ion to be determined after collisions with the background gas and after fragmentation events, as in tandem MS. The energy lost to collisions can be used to obtain information about the collision rate and size of the ions, as in ion mobility spectrometry. Monitoring the ion energy also makes it possible to normalize charge measurements for the effect of energy, improving the precision of mass measurements in CDMS.

Advisor: Williams, Evan R
Extended Formulation Lower Bounds for Combinatorial Optimization

Linear and semidefinite programs are fundamental algorithmic tools, often providing conjecturally/noptimal results for a variety of combinatorial optimization problems. Thus, a natural/nquestion is to understand the limitations of linear and semidefinite programming relaxations./nIn particular, the goal is to prove unconditional lower bounds on the size of any linear or/nsemidefinite programming relaxation for a given problem./nIn this dissertation, I will give two results of this flavor. First, I will show that any linear/nprogramming relaxation for refuting random instances of constraint satisfaction problems/n(e.g. k-SAT) requires super-polynomial size. This theorem can be understood as evidence/nthat refuting CSPs is hard, since it rules out a broad class of algorithms. Second, I will/nshow that any symmetric semidefinite programming relaxation for the matching problem/nin general graphs requires exponential size. Since there is a polynomial time algorithm for/nthe matching problem, this result provides an example of the limitations of semidefinite/nprogramming relaxations.

Advisor: Raghavendra, Prasad
Processing Speed in Girls with and without ADHD: Association with Longitudinal Outcomes in Symptoms and Academic Achievement

Theoretical models of ADHD often implicate executive function difficulties, particularly inhibitory control, as underlying ADHD symptoms. However, this theory has been challenged by studies showing that only a portion of children with ADHD have deficits in executive function. Processing speed has been suggested as a cognitive endophenotype of ADHD due to shared genetic and neurobiological etiologies with relevant symptom patterns. Indeed, children with ADHD often demonstrate slower processing speed than comparison children. It may be that “lower order” cognitive deficits in processes such as processing speed are crucial with respect to the long-term impairments of children with ADHD./nThe purpose of the present investigation was to examine (1) processing speed differences between ADHD presentations, (2) the relation between processing speed and ADHD symptomatology, (3) the relation between processing speed and academic achievement, and (4) the relation between processing speed and adult educational and occupational outcomes in a sample of girls with ADHD and their typically developing counterparts./nThe present study comprises secondary data analysis from 228 participants in a longitudinal investigation of females with and without ADHD (i.e., combined or inattentive presentations). Girls participating in the original study were between the ages of six and 12 years and participated in summer enrichment programs. In addition to the original data collection, three follow-up studies were conducted at five-year, 10-year, and 16-year follow-up intervals, with excellent subject retention, during which participants, caregivers, and teachers completed evaluations, including objective tests of academic performance./nIn conclusion, findings from the present study demonstrate an association between processing speed and concurrent inattentiveness in girls with ADHD. These findings also demonstrated a long-lasting association between slow processing speed in childhood and poor math performance from childhood through adulthood regardless of diagnostic status. Aside from the association with inattentiveness, slow processing speed does not seem to put girls with ADHD at particular risk for poor academic outcomes through childhood, adolescence, or adulthood. This may be attributable to sex differences in processing speed, such that females tend to have faster processing speeds than males. Indeed, this may be a protective factor of sorts for girls with ADHD. This may also mean that girls may benefit from targeted intervention in deficits other than processing speed. However, it was found that for all girls, regardless of diagnostic status, slow childhood processing speed predicts poor math performance through childhood, adolescence, and adulthood.

Advisor: Hinshaw, Stephen P.
Indigenous Literacies in the Techialoyan Manuscripts of New Spain

Though alphabetic script had become a prevailing communicative form for keeping records and recounting histories in New Spain by the turn of the seventeenth century, pre-Columbian and early colonial artistic and scribal traditions, including pictorial, oral, and performative discourses still held great currency for indigenous communities during the later colonial period. The pages of a corpus of indigenous documents created during the late-seventeenth and early-eighteenth centuries known as the Techialoyan manuscripts abound with vibrantly painted watercolor depictions, alphabetic inscriptions, and vivid invocations of community elders’ speeches and embodied experiences. Designed in response to challenging viceregal policies that threatened land and autonomy, the Techialoyans sought to protect and preserve indigenous ways of life by fashioning community members as the noble descendants of illustrious rulers from the pre-Columbian past. The documents register significant events in the histories of communities, often creating a sense of continuity between the colonial present and that of antiquity. What is more, they provide the limits of the territory within a depicted landscape using a reflexive, ambulatory model. Representations of place evoke ritual practices of walking the boundaries from the perspective of the ground, enabling readers to acquire different forms of knowledge as they move through the pages of the book and the envisioned landscape to which it points. The different communicative forms evident in the Techialoyans, including pictorial, alphabetic, oral, and performative modes contribute to understandings of indigenous literacies of the later colonial period by demonstrating the diverse resources and methods upon which indigenous leaders drew to preserve community histories and territories./nThe Techialoyans present an innovative artistic and scribal tradition that drew upon pre-Columbian, early colonial, and European conventions, as well as the contemporary late-colonial pictorial climate. The artists consciously juxtaposed traditional indigenous materials and conventions with those of the contemporary colonial moment to simultaneously create a sense of both old and new. Not only did the documents recount indigenous communities’ histories and affirm their noble heritages, they also proclaimed possession of an artistic and scribal tradition that was on par with that of their revered ancestors, thereby strengthening corporate identity and demonstrating their legitimacy and autonomy within the colonial regime.

Advisor: Olson, Todd
Trever, Lisa
Public Reason and Private Bias

Public reason theorists argue that it is permissible for the state to enforce political norms, such as laws or constitutional principles, when those norms are acceptable to “reasonable people.” Reasonable people are neither actual people, with all their flaws, nor are they perfect people; they are rather a partially idealized group – realistic in some ways and idealized in others. Each of the major public reason theorists – John Rawls, Gerald Gaus, Jonathan Quong, Joshua Cohen – idealizes reasonable people to a different degree, but they all share two claims: 1) Reasonable people hold diverse views of the good life. Nevertheless, 2) Reasonable people can all accept basic liberal political norms grounded in freedom and equality./nMy dissertation begins by arguing that theorists are not free to choose any level of idealization, but are constrained in this choice by the justifications of their theories. In particular, idealization is constrained by one essential part of public reason’s justification, which I call the “diversity argument.” The diversity argument explains the first element of reasonable people: why do they disagree about the good? The answers, I argue, attributes certain realistic qualities and tendencies to reasonable people, which therefore constrains how much we can idealize them./nIn chapters on the major public reason theorists, I argue that they all offer a diversity argument that does not match the level of idealization that they employ. As a result, they are unable to show that liberal norms are acceptable to reasonable people, appropriately idealized. In the final chapter, I argue that the mismatch in these theories goes even deeper, which we can see when we ask why we must accommodate disagreement at all. The answers that philosophers have given us – reasonable disagreement is the inevitable result of human reasoning, human psychology, or free conditions – also apply to irrational disagreement. Irrational influences such as implicit bias and motivated reasoning are also inevitable results of who we are and how we live, which means we must accommodate these realistic tendencies in political justification./nSo, if public reason theories must now accommodate disagreement among reasonable-but-sometimes-irrational people, what could be acceptable to all such people? I conclude by suggesting a new direction for public reason theories. People who disagree about the good life, but recognize their common biases, can still justify their views to each other by supporting institutions that mitigate those biases, such as non-discrimination laws and deliberative institutions. This requires a new kind of social contract theory – one that is grounded in the shared recognition of our limitations, rather than our shared reasons.

Advisor: Bevir, Mark
Recurrent Neural Network Models of Human Mobility

Locational data generated by mobile devices present an opportunity to substantially simplify methodologies and reduce analysis latencies in short-term transportation planning applications. Short-term transportation planning, such as traffic flow management or traffic demand management, requires accurate prediction of daily network congestion levels and the congestion contributors. The existing human mobility models using locational data have fo- cused on predicting next activities, and many models limited the prediction to only temporal features or only spatial features that they cannot be directly applied to such applications. In this dissertation, we propose Long Short Term Memory (LSTM) models for learning and predicting human mobility sequences using mobile locational data. The major contributions of this dissertation include the following: first, we developed the LSTM mobility models that are capable of learning and predicting the entire mobility sequences within a time window of interest; second, we developed the LSTM mobility models that are able to predict activity sequences with activity type choices and explicit spatial-temporal choices; third, the LSTM mobility models are able to capture long-term activity dependencies. The LSTM models can be applied for transportation demand forecasting problems, including typical-day activity prediction, medium-term activity prediction, and activity prediction with social-demographic information. We performed validation through micro-simulation and compared the simula- tion results to real-world traffic counts. The results showed high similarities between gen- erated traffic volumes and observed traffic volumes. The performance of LSTM models was also compared against baseline sequence models including Hidden Markov Models and near- est neighbour models. Using daily activity structure and daily travel distance as metrics, we observed better performance of LSTM models due to the capability of learning long-term activity dependencies. Lastly, we extended the LSTM mobility models for learning activ- ity sequences with contextual information. We demonstrated the capability of the LSTM models to handle both discrete and continuous contextual information.

Advisor: Pozdnukhov, Alexei
Experimental Methods in Transportation Pricing: Applications to Employee Parking

In this dissertation, we develop two experimental methods for the problem of pricing or incentivizing use of a transportation service and apply them to the pricing of employee parking at the University of California, Berkeley./nThe University of California, Berkeley, with 23,962 employees is the largest employer in the eastern half of the San Francisco Bay Area and has a problem with employee parking. The university wants to explore a daily parking cash-out program, named the FlexPass, to make employees more mindful of their parking consumption. We use a Randomized Controlled Trial(RCT) to reveal the causal power of the cash-out. The RCT is applied to 392 employees, representing 10% of the university employees driving alone and parking, over three months using an IT system able to collect daily parking consumption, weekly commute mode reports and location data. The FlexPass treatment reduced consumption by 6.1% with high significance./nOur second experiment is focused on measuring an incentive response curve. We use a repeated 2nd price reverse auction, in which 215 parking permit holders participate for 61 working days. Our method measures the incentive response curve for our subjects and we estimate the curve for the employee population using a quantile regression. We find the known and heavy overhead of repeated bidding can be removed by a lightweight IT system compressed of apps on iPhone and Android and a server in the cloud./nFinally, we build a two-stage signaling game and design a variable-rate daily incentive scheme, where the incentive changes based on weekday and weather. The variable-rate daily incentive outperforms the fixed-rate daily incentive on both parking cruising times and leftover parking spaces.

Advisor: Sengupta, Raja
The Regulation of CD8+ T Cell Fate by Transcription Factor Binding and Chromatin Accessibility

CD8+ T cells fight viral infections and other intracellular pathogens by identifying and destroying infected cells. CD8+ T cells, like all cells, take on different cell states which determine their behavior. This dissertation examines how epigenetic mechanisms such as chromatin accessibility and transcription factor binding regulate transcription, and consequently CD8+ T cell state. The particular CD8+ T cell states that I examine in this dissertation are: Naive (quiescent cells), Effector (cells actively fighting infection), Memory (cells that remain after infection is cleared, ready to fight recurrence of same infection), and Exhausted (cells with weakened cytotoxic function due to prolonged encounter with a particular antigen)./nChapter One introduces CD8+ T cells, regulation of transcription, and some of the high-throughput sequencing assays used later in the text to study CD8+ T cells. Chapter Two describes some of the computational tools I developed to process and infer useful information from high-throughput sequencing data. Chapter Three presents evidence that the chromatin of Exhausted CD8+ T cells differs from that of normal T cells, and demonstrates that these differences have functional consequences by validating an exhaustion-specific enhancer for PD-1, an important immunotherapy target. Chapter Four presents evidence that Batf and Irf4 work together to remodel chromatin and affect the binding of key CD8+ T cell transcription factors during the transition from naive to effector cell state.

Advisor: Yosef, Nir
Study of three dimensional Kiatev Honeycomb materials

Transition metal oxides are fascinating and complex materials that have puzzled condensed matter physicists for many years due to their many different electronically ordered ground states. Albeit separated by external or internal parameters, these nearly degenerate phases are sometimes intertwined in competition or coexistence, which can itself lead to further phase emergence./nA unique feature of the 5d iridium oxide materials is that spin-orbit and Coulomb interactions are of comparable strength and therefore compete vigorously. In a honeycomb structure, this competition gives rise to strong magnetic frustration due to their edge-shared bonding environment, in which quantum interference of the two exchange paths favors a strongly anisotropic, Ising-like exchange between neighboring spin-1/2 moments. Such an interaction couples different orthogonal spin components for the three nearest neighbors and, as a consequence, no single exchange direction can be simultaneously satisfied, leading to strong frustration described by the Kitaev Hamiltonian. This model results in the infinitely degenerate and extremely exotic quantum spin liquid state, whose excitations range from being Majorana-like to fractionalized fermionic excitations. In this thesis, I examine the magnetic properties of the three-dimensional Kitaev candidate materials in the Harmonic Honeycomb family, using a combination of thermodynamics and resonant x-ray scattering techniques.

Advisor: Analytis, James G
Estranged Comrades: Global Networks of Indonesian Communism, 1926-1932

Scholars have carefully studied the history of Indonesian communism from its inception in 1914 to its destruction after 1965 with a noticeable exception between 1927 and 1945. The justification is simple—the Dutch authorities crushed the Partai Komunis Indonesia (PKI) completely after its unsuccessful revolts in 1927 and exercised tight political control in the remainder of the Dutch colonial period. Communism also played an insignificant role under the Japanese occupation due to the effective military suppression of clandestine activities. Historians commonly describe Indonesian communism during this period as generating lasting impact on Indonesian politics by providing a useful ideological weapon for carrying on anti-colonial struggles, but it lost its organizational significance as a cohesive force to mobilize the masses and gather them under the common political banner. Such claims are problematic for two main reasons: First, historical writings concerning Indonesia’s wide array of anti-colonial struggles, communism included, have been mostly following a nation-state-based paradigm; The second is that current scholarship tends to equate the history of Indonesian communism to the history of the communist party (PKI)./nThis dissertation seeks to examine Indonesia’s ongoing communist movement beyond the colonial borders after the 1926/27 PKI revolts by focusing on its global connections. I argue despite the party’s collapse in the aftermath of the uprisings, Indonesian communism persisted internationally in three “worlds” of global networks, namely international fugitive networks, the international policing networks, and networks of the Comintern-dominated international communism. Specifically, the movement continued in the fragmented fugitive networks; yet, these groups took drastically different directions due to the split of the party leadership. Additionally, Indonesian communism existed as an existential threat throughout the remainder of the colonial period and loomed large in the world of international policing. Moreover, Indonesian communism remained marginal in the world of international communist revolution, but those stayed close with the course of the Comintern gained the authority in shaping the narratives concerning the PKI’s failure in the 1920s, which served as an essential source of legitimacy for reclaiming the party leadership in the 1940s.

Advisor: Zinoman, Peter
Hidden Lives: Asceticism and Interiority in the Late Reformation, 1650-1745

This dissertation explores a unique religious awakening among early modern Protestants whose primary feature was a revival of ascetic, monastic practices a century after the early Reformers condemned such practices. By the early seventeenth-century, a widespread dissatisfaction can be discerned among many awakened Protestants at the suppression of the monastic life and a new interest in reintroducing ascetic practices like celibacy, poverty, and solitary withdrawal to Protestant devotion. The introduction and chapter one explain how the absence of monasticism as an institutionally sanctioned means to express intensified holiness posed a problem to many Protestants. Large numbers of dissenters fled the mainstream Protestant religions—along with what they viewed as an increasingly materialistic, urbanized world—to seek new ways to experience God through lives of seclusion and ascetic self-deprival. In the following chapters, I show how this ascetic impulse drove the formation of new religious communities, transatlantic migration, and gave birth to new attitudes and practices toward sexuality and gender among Protestants. The study consists of four case studies, each examining a different non-conformist community that experimented with ascetic ritual and monasticism. Chapters two and three examine the prayer practices of two semi-monastic Protestant communities—the ‘Angelic Brethren’ led by the mystic Johann Gichtel and a circle of Quietists led by Charles Héctor Marquis de Marsay. These communities fused the ascetic, mystical teachings on self-renunciation and union with modern mystical traditions in creating their own withdrawn, mystical devotions in an attempt to separate themselves from the world and their own carnal wills. In chapter four, the familiar story of a Protestant cloister in North America, the Ephrata Cloister, is recast as a part of the broader ascetic revival in this dissertation. Particularly attention is given in this chapter to the prevalence of celibacy in Protestantism. The final chapter and conclusion examines the afterlife of ascetic theology and mysticism in the late enlightenment and romantic period which saw a fierce divide over the value and meaning of solitude. From northern Germany, Amsterdam, and across the Atlantic in colonial North America, these dissenters formed utopian communities that strove to keep their distance from civilization even as they engaged in the project of global European expansion, empire, and settlement.

Advisor: Sheehan, Jonathan