VictorJuiz/thesis huggingface dataset:
Discovery and Investigation of Small Molecule Inhibitors of Sulfate Assimilation Pathway as Novel Anti-Latent Tuberculosis Therapy

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the single most deadly pathogen. An estimated 2 billion people are currently infected and 2 million die each year as a result of the disease. However, only 10% of the cases are symptomatic. Majority of the infections are latent, which is characterized by non-replicative, slow metabolic, and dormant Mtb surrounded by a plethora of immune called the granuloma in the lungs./nThe nonreplicating persistent state of infection poses a great challenge to the efforts to eradicate TB. The frontline drugs, which were discovered almost half a century ago, are primarily efficacious against actively dividing or metabolically active bacilli. To ensure the latent infection would not transition into active infection, in a process called reactivation, the drugs are to be administered up to 9 months. The long regimen leads to high non-compliance rates and directly fuels the appearance of multiple drug-resistant (MDR), extensively drug-resistant (XDR), and just recently, the discovery of totally drug-resistant (TDR) TB. To complicate matters, the co-infection with HIV promotes the progression to AIDS and animate dormancy to active infections. Unfortunately, due to the lack of financial incentive, TB research in pharmaceutical industry has largely been absent. The responsibility falls in the hands of academic labs to discover new drugs that can target Mtb in the latent phase to eliminate the episode of reactivation, shorten the regimen, and increase compliancy./nThis thesis presents the utilization of high-throughput screening in an effort to identify small molecule inhibitors that target the sulfate assimilation pathway, which is believed to be critical during the latent phase of TB infection. Chapter 1 reviews the molecular pathways that govern the sulfate assimilation pathway. Chapter 2 discusses the efforts of devising an assay amenable to high throughput screening, target production, library selection, and quality control. Chapter 3 presents follow-up studies that encompass the confirmation of hit compounds, the elimination of aggregate formers, and elucidation of the binding mechanism. In addition, structure activity relationship was investigated by testing compounds similar in structure to the most potent compounds. Finally, chapter 4 explores the in vivo activity of the lead compounds in growth inhibition of Mycobacterium tuberculosis, Escherichia coli, and Bacillus subtilis, as well as toxicity profile against mammalian cell line.

Advisor: Bertozzi, Carolyn R
Light-matter Interaction in Deep Sub-wavelength Nano-photonic Structures

This dissertation focuses on the use of deep sub-wavelength(sub-) nano-photonic structures to enhance radiation of optical emitters. The deep sub-wavelength designs are based on high permittivity contrast of materials involving either purely dielectric interfaces or metal. The optical properties of metal at infrared and optical frequencies enable optical structures that can confine light to dimension smaller than the wavelength. The building blocks of these nano-photonic system are non-resonant, broadband waveguides with dramatic field confinement in the nano-scale low permittivity region. Strong interaction and enhanced radiation leads to efficient coupling into the primary optical mode of the structures which improves fluorescence brightness, saturation, speed, emission efficiency, single photon fidelity at a single emitter-single photon level and holds promise for solid-state lighting, molecular sensing, and quantum information processing application./nThe first part of the dissertation explores deep sub-wavelength waveguiding structures as non-resonant optical component that enhances radiation and collects emitted photon with high fidelity. The last part explores the design of small resonator that is constructed from a subwavelength waveguide for use as addressing optical emitters. The benefits of non-resonant design are highlighted throughout.

Advisor: Zhang, Xiang
Effective Field Theory Techniques for Resummation in Jet Physics

In this thesis, we present several new techniques for the resummation of observables relevant to jet physics at the LHC using effective field theory techniques. Specifically, we first derive the factorization theorem and calculate the generic soft function for N-jet threshold resummation. This allows for dynamic threshold resummation at hadron colliders, where parton distribution functions may enhance threshold effects. Then we develop a new metric to gauge the importance of threshold resummation in a process-independent manner. This also allows us to determine the relevant scales for threshold resummation without the introduction of an arbitrary procedure. Next, we present a new subtraction technique for the calculation of soft functions with complex phase space boundaries. This technique is especially useful in calculations involving eta-phi jet algorithms, which are common at hadron colliders. Finally, we discuss a new regularization scheme for real emission diagrams and present an example of said scheme.

Advisor: Bauer, Christian W
Hall, Lawrence J
Evidence to Policy: Do Voucher Programs Improve Maternal Health in Developing Countries?

Maternal mortality has been one of the most daunting public health problems facing developing countries for several decades. The average lifetime risk of maternal death in least developed countries is 1 in 22 compared with 1 in 8000 in industrialized countries. Such vast regional differences demonstrate how available and accessible resources can completely change the picture. Even in low-resource settings, it has been shown that basic district health systems can deliver the services needed to save women's lives. But women face many barriers to accessing care including distance, transportation, cost, perceived poor quality or actual poor quality. One mechanism that researchers and policy makers have been experimenting with to address several of these barriers is a voucher. Within a health voucher program, a woman can purchase a voucher for a fraction of the cost of services or receive it for free and redeem it an accredited health facilities (public or private) for specific services. Facilities are reimbursed for the care they deliver through government or development aid. Voucher programs aim to give patients the economic power to demand high-quality healthcare, to target aid to high-risk or low-income patients for critical services and to increase utilization rates within these populations./nFunders and policymakers have already shown support for this concept but more evidence is needed in order to evaluate if these programs should be taken to greater scale. This dissertation aims to address gaps in evidence and to work towards building stronger and more evidence- based policy around maternal health vouchers./nThe first component of this dissertation is a systematic review of the literature on voucher programs for health goods and services in developing countries. The review aims to assess whether the evidence for voucher programs thus far has shown that they are achieving their objectives and examines contextual factors associated with program success. The second component is an evaluation of how a reproductive health voucher programs impacts the job satisfaction of management and frontline health care providers in Uganda. The third component is a qualitative assessment of the experiences of women who are eligible to receive a reproductive health voucher in Cambodia and assesses facilitative and inhibitive factors that affect voucher use./nAs a result of this dissertation experience, next steps for improved policymaking around vouchers have been identified and include the need to focus efforts on evaluating if policy makers should use health voucher to support broader health system strengthening and how program implementers can use the experiences of beneficiaries (providers and patients) to tailor voucher programs to the local context while maintaining program fidelity.

Advisor: Potts, Malcolm
Complex Assessments, Teacher Inferences, and Instructional Decision-Making

The purpose of this study is to understand how teachers make sense of data from a complex set of reading assessments and how inferences they derive from the data affect decisions about instruction. There are two key research questions - 1) How does a teacher's developing expertise with a complex set of assessments (assessment literacy) affect the quality of the inferences they make about student learning?; and 2) How does the extent of a teacher's Pedagogical Content Knowledge affect the range and quality of instructional decisions made upon the basis of assessment results?/nSix English teachers from a middle school and a high school in Northern California administered a set of reading assessments constructed from various core elements in the reading domain. The data generated from the assessments were organized to facilitate analysis of the progress of teacher thinking about each of the different reading dimensions and with assessment and instruction. Measures of assessment literacy, a series of coded interviews and professional development with the teachers provided data about the development of their Pedagogical Content Knowledge (PCK) of reading. Their ability to make sense of this complex set of student reading data to make instructional decisions was examined over time./nIt was found that the skill and sophistication of the teacher's PCK of reading and interpretation of the assessment evidence increased as they delved deeper into close analysis of both the reading measures and the individual student data. The results have implications for a teacher-based "community of judgment" as a key element in effective school accountability systems.

Advisor: Wilson, Mark
Emotion Regulation and Culture: The Effects of Cultural Models of Self on Western and East Asian Differences in Suppression and Reappraisal

How and why do Westerners and East Asians differ in their use of emotion regulation processes? In the present dissertation, I describe five studies that test whether differences in the self-models of Westerners and East Asians lead to culture-specific patterns of emotion regulation. In Study 1, I conduct comparisons between and within cultures to test whether differential exposure to Western and East Asian culture is associated with divergent use of two emotion regulation processes--expressive suppression and cognitive reappraisal. In Study 2, I use an experimental design to prime American versus East Asian cultural identity in bi-cultural East Asian Americans, testing whether there is a causal link between cultural self-models and emotion regulation. In Studies 3 and 4, I present evidence that these cultural differences in emotion regulation are not due to methodological artifacts associated with global self-reports. In particular, I show that similar culture effects emerge when emotion regulation in a specific self-disclosure context is rated by independent judges (Study 3), and when emotion regulation is rated by peers from an individual's real-life social network (Study 4). In Study 5, I test whether Western and East Asian cultural differences in emotion regulation can be explained by two specific cultural mechanisms, namely the interdependent and independent cultural models of self. Findings are consistent across all five studies and show that Westerners use less suppression (but not less reappraisal) than individuals of East Asian cultural origin. In terms of mechanism, these differences seem to be due to the strong emphasis on independence and authentic self-expression in Western cultures, rather than to the strong emphasis on interdependence and interpersonal harmony in East Asian cultures.

Advisor: John, Oliver P
Space-based observations of NO2: Trends in anthropogenic emissions

Space–based instruments provide routine global observations, offering a unique perspective on the spatial and temporal variation of atmospheric constituents. In this dissertation, trends in regional–scale anthropogenic nitrogen oxide emissions (NO + NO2 ≡ NOx) are investigated using high resolution observations from the Ozone Monitoring Instrument (OMI). By comparing trends in OMI observations with those from ground–based measurements and an emissions inventory, I show that satellite observations are well–suited for capturing changes in emissions over time. The high spatial and temporal resolutions of the observations provide a uniquely complete view of regional–scale changes in the spatial patterns of NO2. I show that NOx concentrations have decreased significantly in urban regions of the United States between 2005 and 2011, with an average reduction of 32 ± 7%. By examining day–of–week and interannual trends, I show that these reductions can largely be attributed to improved emission control technology in the mobile source fleet; however, I also show that the economic downturn of the late 2000's has impacted emissions. Additionally, I describe the development of a high-resolution retrieval of NO2 from OMI observations known as the Berkeley High Resolution (BEHR) retrieval. The BEHR product uses higher spatial and temporal resolution terrain and profile parameters than the operational retrievals and is shown to provide a more quantitative measure of tropospheric NO2 column density. These results have important implications for future retrievals of NO2 from space–based observations.

Advisor: Cohen, Ronald C
Operators on k-tableaux and the k-Littlewood-Richardson rule for a special case

This thesis proves a special case of the $k$-Littlewood--Richardson rule, which is analogous to the classical Littlewood--Richardson rule but is used in the case for $k$-Schur functions. The classical Littlewood--Richardson rule gives a combinatorial formula for the coefficients $c_{\mu\nu}^{\lambda}$ appearing in the expression $s_{\mu}s_{\nu} = \sum_{\lambda} c_{\mu\nu}^{\lambda}s_{\lambda}$ for two Schur functions multiplied together. $k$-Schur functions are another class of symmetric functions which were introduced by Lapointe, Lascoux, and Morse and are indexed by and related to $k$-bounded partitions. We investigate what occurs when multiplying two $k$-Schur functions with some restrictions. More specifically, we investigate what happens when a $k$-Schur function is multiplied by a $k$-Schur function corresponding to a partition of length two. In this restricted case we are able to provide a combinatorial description of the $k$-Littlewood--Richardson coefficients that appear in the expansion of the product as a sum of $k$-Schur functions. These $k$-Littlewood--Richardson coefficients can be computed in terms of the number of $k$-tableaux with a certain property we call $k$-lattice. Furthermore, we conjecture that the result holds for any $k$-Schur functions, even when no restrictions are imposed. The proofs presented rely on a class of operators on $k$-tableaux which we introduce that are similar to the crystal operators on classical tableaux, but we provide a specific example that implies they are not actually crystal operators on $k$-tableaux. In addition to this, we also provide numerous examples and dedicate a chapter to examples of computation for some $k$-Littlewood--Richardson coefficients.

Advisor: Haiman, Mark
Gendered Racial Socialization in Black Families: Mothers' Beliefs, Approaches, and Advocacy

The purpose of this study was to explore Black mothers' beliefs about socializing their children to negotiate gendered and racial contexts. Sixteen Black mothers were individually interviewed about their gendered racial socialization beliefs and experiences. The process of gendered racial socialization is defined as the ways by which parents socialize their sons and daughters to issues of race. To understand how and why mothers socialize their adolescents to racial issues, the research questions of interest were: (1) What are similarities and differences among mothers' beliefs regarding socializing their sons and daughters to issues of race? (2a) What informs mothers' decisions to prepare children for bias or not? (2b) Do mothers consider preparation for bias messages to be beneficial or harmful to children's well being? (3a) What types of racialized experiences do children encounter that prompt mothers' racial socialization efforts? and (3b) In what ways do mothers respond to these incidents?/nGuided by grounded theory, the findings indicate that mothers had some gender-neutral concerns, yet they also had distinct concerns for their sons and daughters. Specific concerns for sons included physical safety and fair treatment, and concerns for daughters included acceptance of their physical beauty. Mothers' gender-neutral concerns included sons' and daughters' sense of self-worth and racial pride. The findings also suggest two primary approaches to discussions of racial bias with children: proactive and moderate. Whereas mothers with a proactive approach prepared children for bias because they believed that awareness of discrimination was beneficial to children's well being, mothers with a reactive approach chose not to give preparatory messages in order to avoid the psychological consequences of children knowing that they are in a stigmatized group. Additionally, results show that mothers' racial socialization messages were prompted by children's encounters with peer-related, teacher-related, and police-related racialized experiences. Furthermore, mothers' responses to these incidents took the form of direct communication with children and advocacy on children's behalf./nAs most of the research on racial socialization examines the frequency of messages and practices, the current study extends the literature by gathering more contextual and process-oriented data to help explain how and why mothers discuss race with their sons and daughters. This work is important because it sheds light on the factors contributing to mothers' racial socialization decisions. Complementing research that examines what parents do, the present study analyzes why parents make particular parenting choices. Instead of viewing racial socialization as static and unidirectional, the methodological and analytical approaches used in this study reposition the processes of racial socialization as dynamic and interdependent. The findings contribute to a deeper understanding of Black parenting, family processes, and adolescent development.

Advisor: Suad Nasir, Na'ilah
Essays on Microeconomics

This dissertation consists of two essays on microeconomics./nThe first chapter explores leadership within hierarchical organizations./nFor each hierarchy, I consider a dynamic signaling game/nin which each player observes only the actions of his direct/nsuperiors before choosing his action./nAt the top of the hierarchy are the leaders, who learn the state from nature./nThe hierarchy controls the flow of information and the timing of the game,/nand determines the equilibrium output and welfare./nI show that the welfare-optimal hierarchy is the chain, because/nit maximizes the incentive of players to ``lead by example'' for their/nsubordinates. The chain remains optimal even in the presence of verifiable/nor unverifiable costly information acquisition by the leaders./nLastly, I characterize optimal hierarchies when the number of layers or/nthe number of leaders is limited. Applications to fund-raising are also discussed./nThe second chapter studies the optimal way to select projects or agents in environments where/ninformation arrives in well defined rounds. Examples include academic/nenvironments where review periods are set by policy, aptitude tests such as/nthose given by software developers to programmers applying for jobs, venture/ncapital protocols where the rounds of funding may be stopped before the/nproject is complete, and FDA testing, where drugs can be dropped at well/ndefined junctures. Sequential rounds of elimination reduce the cost of/nselection, but also reduce the average quality of surviving projects. I/ncharacterize the nature of the optimal screening process with and without/n"memory." The second chapter is based on joint work with Suzanne Scotchmer.

Advisor: Shannon, Chris
Fairness for Whom? Regulating Banana Production through Voluntary Certification and Labeling

This study examines the role of Fairtrade certification and labeling in mediating the socio-ecological relations of banana production. Bringing to bear ideas from literature on agro-industrial development and restructuring, agrifood governance, agrarian change, agricultural labor relations, and sustainability, it examines how banana farmers, workers, and their communities are affected by participation in Fairtrade commodity networks under conditions of market liberalization. It concludes that, while, under certain conditions, Fairtrade can benefit some farmers and workers, it fails to address the broader social and ecological conditions of banana production. It attributes the challenges facing the Fairtrade system to the internal dynamics of its consumer-driven, market-based, and developmental model. Specifically, I argue that Fair Trade actors' focus on the terms of exchange fails to address the imperatives of growth and accumulation inherent in capitalist commodity production, which shape outcomes for banana farmers, workers, and environments./nThe analysis is based on research conducted at two key sites in the banana sector: Ecuador's South Coast and the Urabá region of Colombia. These regions have played an importation role in the expansion of Fairtrade banana supply, albeit under different conditions. In Ecuador, Fairtrade protection has primarily been extended to small farmers under the Fair Trade Labelling Organizations (FLO) Small Producer Organization standards. Meanwhile, the majority of Urabá's producers are certified under FLO's Hired Labor standards. Drawing on in-depth interviews with farmers, workers, administrative and technical staff of Fairtrade-institutions, as well as labor representatives, I find that Fairtrade certification generates uneven outcomes for different groups participating in the system. Activists and researchers have critiqued the expansion of certification to plantations and to the enrollment of transnational agribusiness companies, which they argue has undermined the position of small farmers within the Fairtrade system. Yet these critiques overlook significant socio-ecological complexity and differentiation in Fairtrade banana production. They also obscure the critical role of hired workers on small and large farms alike. The study, thus, attempts to reframe the mainstreaming debate, to place workers at the center of the Fairtrade banana story. In so doing, it argues that international Fair Trade actors must engage more fully with banana unions and labor solidarity movements in order to achieve their purported goals of supporting social and environmental justice in the global banana economy.

Advisor: Walker, Richard