VictorJuiz/thesis huggingface dataset:
The Total Synthesis of Cycloprodigiosin and Synthetic Efforts Toward the Pentacyclic Ambiguine Class of Natural Products

The synthesis and absolute stereochemical determination of cycloprodigiosin has been completed. Chapter 1 discusses the historical, synthetic, and biological background of prodiginine natural products, specifically of prodigiosin and cycloprodigiosin. Chapter 2 details our synthetic attempts for the synthesis of cycloprodigiosin and the strategy used to determine the absolute stereochemistry at the C4’ position of this prodiginine. The syntheses of both enantiomers of cycloprodigiosin were completed in an efficient five step sequence utilizing a Barton-Schöllkopf-Zard pyrrole synthesis. Cycloprodigiosin was isolated from its parent bacterial source, Pseudoalteromonas rubra, by Tristan de Rond in a collaboration with the Keasling group at UC Berkeley. The natural isolate was determined to exist as a scalemic mixture in a ratio of 83:17 (R):(S) at C4’. The enzyme responsible for the final oxidative cyclization event from prodigiosin to cycloprodigiosin was identified as the alkylglycerol monooxygenase-like enzyme PRUB680./nThe second topic of this thesis details the first total synthesis of ambiguine P in 19 steps from (S)-carvone. The isolation, biosynthentic, and synthetic background of the ambiguine family of natural products is discussed in Chapter 3. The challenges associated with the synthesis of pentacyclic ambiguines are described in Chapter 4 and focus on the formation of the pentacyclic core in addition to the installation of the C12 quaternary center. The 1st generation synthetic approach to access the ambiguine pentacyclic core involves a key γ-enolate cross-coupling reaction to form the tetracyclic precursor. The intermediates in this approach were synthesized from indole and (S)-carvone using an intermolecular Nicholas alkylation. The 2nd generation synthetic route to access the key pentacyclic core involves an intramolecular Nicholas alkylation at C2 of indole, followed by Friedel-Crafts cyclization at C4 to successfully generate the pentacylic core./nChapter 5 describes the completion of ambiguine P; many strategies were explored to install the C12 quaternary center, and eventually a directed C–C bond construction utilizing formates was found that successfully formed the C–C bond on the desired α-face. The requisite vinyl group at C12 and the amide functionality at C11 were installed using an interrupted Peterson olefination strategy. Attempts are described to access ambiguine L from these late-stage intermediates using benzylic oxidation and hydration methodologies.

Advisor: Sarpong, Richmond
Understanding and Assessing Expertise in Culturally Agile Pedagogies (CAPs)

This study surveys the knowledge base of culturally responsive instruction (i.e., culturally relevant, responsive, sustaining, revitalizing, and reality pedagogies) and consolidates them under the term Culturally Agile Pedagogies (CAPs). CAPs are defined as theories, principles, and methods of teaching that require the mutual understanding, valuing, and use of teachers' and students' linguistic and cultural identities to inform instruction and optimize learning. This study engages teachers who have been identified by their principals as exceptionally culturally responsive and helps those teachers reconcile their practice with empirically supported instructional strategies. This study uses culturally responsive instruction literature, a teacher questionnaire, lesson observations, and teacher interviews to develop and present a tool that might be used to identify and assess expertise in CAPs. This tool is the CAPs Practices Expertise Scale. The tool development process measures the teachers' shift from an intuitive sense of justice in teaching toward a more formal knowledge of CAPs practices. This new teacher learning is then applied to refine the tool so it more accurately describes observable instructional practices in the classroom.

Advisor: Gifford, Bernard
Go with the Flow: Graphs, Streaming and Relational Computations over Distributed Dataflow

Modern data analysis is undergoing a ``Big Data'' transformation: organizations are generating and gathering more data than ever before, in a variety of formats covering both structured and unstructured data, and employing increasingly sophisticated techniques such as machine learning and graph computation beyond the traditional roll-up and drill-down capabilities provided by SQL. To cope with the big data challenges, we believe that data processing systems will need to provide fine-grained fault recovery across a larger cluster of machines, support both SQL and complex analytics efficiently, and enable real-time computation./nThis dissertation builds on Apache Spark, a distributed dataflow engine, and creates three related systems: Spark SQL, Structured Streaming, and GraphX. Spark SQL combines relational and procedural processing through a new API called DataFrame. It also includes an extensible query optimizer to support a wide variety of data sources and analytic workloads. Structured Streaming extends Spark SQL's DataFrame API and query optimizer to automatically incrementalize queries, so users can reason about real-time stream data as batch datasets, and have the same application operate over both stream data and batch data. GraphX recasts graph specific system optimizations as dataflow optimizations, and provides an efficient framework for graph computation on top of Spark./nThe three systems have enjoyed wide adoption in industry and academia, and together they laid the foundation for Spark's 2.0 release. They demonstrate the feasibility and advantages of unifying disparate, specialized data systems on top of distributed dataflow systems.

Advisor: Franklin, Michael
Stoica, Ion
The Rise of Educational Consciousness: Racial and Class Politics of the Detroit Public Schools, 1943-1974

This study examines the development of radical educational consciousness in Detroit, 1943-1974. This study draws on precepts of critical social theory to analyze archival data, memoir and biography, personal archival collections, extant oral history interviews, and 16 original oral history interviews conducted in Detroit. Utilizing a relational historical ethnography research design, this study asserts the emergence of radical educational consciousness was informed by a critique of capitalist relations of production and experiential knowledge of a geography of spatial racism. This radical analysis directly challenged racialized administrative control over the school system. In Detroit, a radical conception of community control of schools was articulated as a rejection of both racial liberalism and bourgeois cultural nationalism. By the late 1960s, radical educational consciousness conceptualized educational struggle as a front of broader liberation struggle.

Advisor: Perlstein, Daniel H
Context, Causality, and Information Flow: Implications for Privacy Engineering, Security, and Data Economics

The creators of technical infrastructure are under social and legal pressure to comply with expectations that can be difficult to translate into computational and business logics. This dissertation bridges this gap through three projects that focus on privacy engineering, information security, and data economics, respectively. These projects culminate in a new formal method for evaluating the strategic and tactical value of data: data games. This method relies on a core theoretical contribution building on the work of Shannon, Dretske, Pearl, Koller, and Nissenbaum: a definition of situated information flow as causal flow in the context of other causal relations and strategic choices./nThe first project studies privacy engineering's use of Contextual Integrity theory (CI), which defines privacy as appropriate information flow according to norms specific to social contexts or spheres. Computer scientists using CI have innovated as they have implemented the theory and blended it with other traditions, such as context-aware computing. This survey examines computer science literature using Contextual Integrity and discovers, among other results, that technical and social platforms that span social contexts challenge CI's current commitment to normative social spheres. Sociotechnical situations can and do defy social expectations with cross-context clashes, and privacy engineering needs its normative theories to acknowledge and address this fact./n/nThis concern inspires the second project, which addresses the problem of building computational systems that comply with data flow and security restrictions such as those required by law. Many privacy and data protection policies stipulate restrictions on the flow of information based on that information's original source. We formalize this concept of privacy as Origin Privacy. This formalization shows how information flow security can be represented using causal modeling. Causal modeling of information security leads to general theorems about the limits of privacy by design as well as a shared language for representing specific privacy concepts such as noninterference, differential privacy, and authorized disclosure./nThe third project uses the causal modeling of information flow to address gaps in current theory of data economics. Like CI, privacy economics has focused on individual economic contexts and so has been unable to comprehend an information economy that relies on the flow of information across contexts. Data games, an adaptation of Multi-Agent Influence Diagrams for mechanism design, are used to model the well known economic contexts of principal-agent contracts and price differentiation as well as new contexts such as personalized expert services and data reuse. This work reveals that information flows are not goods but rather strategic resources, and that trade in information therefore involves market externalities.

Advisor: Chuang, John
Mulligan, Deirdre
Civics English: Integrating Civics in Middle School English Language Arts Teaching

English Language Arts has historically been tied to the civic purposes of schools, and this qualitative study of a social design-based project (Gutiérrez & Vossoughi, 2010) examines the intersection of language and literacy learning and youth civic engagement, a problem space I call “Civics English.” In this dissertation, I describe and analyze the experimentation and inquiry process of a Professional Learning Community of English teachers in a diverse middle school as they integrated civic learning and action into their English teaching practices. The dissertation examines this teacher team’s development and shifts through various tensions and challenges that arise, analyzing through the lenses of Cultural Historical Activity Theory the ways their Professional Learning Community operated as an English teaching activity system attempting to integrate the cultural activity of civic engagement, leading to the teachers’ expansive professional learning (Engeström, 2001) about possibilities and challenges of Civics English./nThe English teachers implemented various civic action projects, including producing and sharing multimodal civic advocacy essays online, composing and presenting children’s storybooks about civics issues, and organizing and conducting a Town Hall with local leaders about civic dimensions of allyship and youth sports. This study looks at how, contextualized by these civics activities, they adapt and innovate customary English Language Arts practices, such as reading novels, writing in authentic genres with blended text types, and developing literacy and discourse. As the teachers encounter various tensions that arise in their attempts at Civics English, I present evidence of how these tensions emerge from the contradictions of two intersecting cultural activity systems, and what adaptations and innovations the teachers develop to overcome these tensions./nIntegrating civics causes shifts in the teachers’ practices of literary study, writing, and classroom discussion, as they orient students’ learning towards public audiences, collective action, and discursive models of political and professional discourse. I identify how reading literature creates an imaginative space for civic deliberation. And I demonstrate how the Town Hall civics project shifts various dimensions of literacy and language activity by recontextualizing them. The potentials and the constraints of these shifts are examined through studying the teachers’ work, students’ language and activity, and the civic event’s efficacy as an English teaching focal point.

Advisor: Gutiérrez, Kris D
Freedman, Sarah W
Aspects of Supersymmetric Surface Defects

Starting from type IIB string theory on an $ADE$ singularity, the $\cN=(2,0)$ little string arises when one takes the string coupling $g_s$ to 0. We compactify the little string on the cylinder with punctures, which we fully characterize, for any simple Lie algebra $\fg$. Geometrically, these punctures are codimension two defects that are D5 branes wrapping 2-cycles of the singularity. Equivalently, the defects are specified by a certain set of weights of $^L \fg$, the Langlands dual of $\fg$./nAs a first application of our formalism, we show that at low energies, the defects have a description as a $\fg$-type quiver gauge theory. We compute its partition function, and prove that it is equal to a conformal block of $\fg$-type $q$-deformed Toda theory on the cylinder, in the Coulomb gas formalism./nAfter taking the string scale limit $m_s\rightarrow\infty$, the little string becomes a $(2,0)$ superconformal field theory (SCFT). As a second application, we study how this limit affects the codimension two defects of the SCFT:/nwe show that the Coulomb branch of a given defect flows to a nilpotent orbit of $\fg$, and that all nilpotent orbits of $\fg$ arise in this way. We give a physical realization of the Bala--Carter labels that classify nilpotent orbits of simple Lie algebras, and we interpret our results in the context of $\fg$-type Toda. Finally, after compactifying our setup on a torus $T^2$, we make contact with the description of surface defects of 4d $\mathcal{N}=4$ Super Yang-Mills theory due to Gukov and Witten \cite{Gukov:2006jk}.

Advisor: Aganagic, Mina
Mechano-NPS and Visco-NPS: Microfluidic Approaches to Single-Cell Mechanics

The mechanical properties of cells provide valuable information regarding biological and clinically relevant cellular characteristics. In this dissertation, we demonstrate two new microfluidic platforms, mechano-node-pore sensing (mechano-NPS) and visco-node-pore sensing (visco-NPS), to characterize cellular mechanical behavior. Mechano-NPS is a multi- parametric single-cell-analysis method to quantify simultaneously cell diameter, resistance to compressive deformation, transverse deformation under constant strain, and recovery time after deformation. We define a new parameter, the whole-cell deformability index (wCDI), which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell types. The wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant, MCF-10A and BEAS-2B cell lines. We categorize cell recovery time and show that the composition of recovery types, which is a consequence of changes in cytoskeletal organization, correlates with cellular transformation. Through the wCDI and cell-recovery time, mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells. Mechano-NPS identifies mechanical phenotypes that distinguishes lineage, chronological age, and stage of malignant progression in human epithelial cells./nVisco-NPS is a new, electronic-based, microfluidic rheology platform that quantifies cellular viscoelastic properties under periodic deformation. We measure the storage (G’) and loss (G”) modulus of individual cells, which represent cellular elasticity and viscosity, respectively. By applying a wide range of deformation frequency, our platform quantifies the frequency dependency of viscoelastic properties. The measurement of G’ and G” shows that malignant breast epithelial (MCF-7) cells have distinctly different viscoelastic properties as compared to non-malignant breast epithelial (MCF-10A) cells. With its sensitivity, visco-NPS is able to dissect the individual contributions of different cytoskeletal components, i.e. actin filaments and microtubules, to whole-cell mechanical properties. Through G’ and G”, visco-NPS can also quantify the mechanical transitions—a consequence of changes in cytoskeletal organization and nucleus structure—that cells undergo as they traverse the cell cycle. visco-NPS identifies viscoelastic characteristics of cells, which can provide both a biophysical understanding of cellular behavior and a potential for clinical applications.

Advisor: Sohn, Lydia L
Adaptive and Diverse Techniques for Generating Adversarial Examples

Deep neural networks (DNNs) have rapidly advanced the state of the art in many important, difficult problems. However, recent research has shown that they are vulnerable to adversarial examples. Small worst-case perturbations to a DNN model's input can cause it to be processed incorrectly. Subsequent work has proposed a variety of ways to defend DNN models from adversarial examples, but many defenses are not adequately evaluated on general adversaries./nIn this dissertation, we present techniques for generating adversarial examples in order to evaluate defenses under a threat model with an adaptive adversary, with a focus on the task of image classification. We demonstrate our techniques on four proposed defenses and identify new limitations in them./nNext, in order to assess the generality of a promising class of defenses based on adversarial training, we exercise defenses on a diverse set of points near benign examples, other than adversarial examples generated by well known attack methods. First, we analyze a neighborhood of examples in a large sample of directions. Second, we experiment with three new attack methods that differ from previous additive gradient based methods in important ways. We find that these defenses are less robust to these new attacks./nOverall, our results show that current defenses perform better on existing well known attacks, which suggests that we have yet to see a defense that can stand up to a general adversary. We hope that this work sheds light for future work on more general defenses.

Advisor: Song, Dawn
Rethinking Recognition: Freedom, Self-Definition, and Principles for Practice

This dissertation argues that self-definition should be an important guiding value for the politics of recognition and identifies three principles essential to such a politics: self-definition, responsiveness, and internal contestation. Government officials and other authorities who seek to correct social and political inequality with policies of recognition should use the principles I propose to guide their efforts. We should expect injustice to persist even in the face of widespread, honest efforts to practice recognition as justly as possible, but we must still strive for just practices that support the positive potentials of recognition by respecting both equality and freedom. These principles are drawn from a detailed examination of three central examples of recognition in practice. I examine (1) the Canadian government’s 1988 apology for internment and dispossession of Japanese Canadians in the 1940s, (2) the development of the Canadian Museum of Civilization’s exhibits of Aboriginal history and culture from the 1980s to early 2000s, and (3) the development of the National Museum of the American Indian’s inaugural exhibits in the 1990s and 2000s. These practices of recognition illustrate the importance of self-definition and suggest the above principles practice. As a work of contextual political theory, this dissertation develops normative principles by bringing conceptual conversations in the theoretical world together with evocative contemporary political examples.

Advisor: Song, Sarah
Performance Characterization of Beams with High-Strength Reinforcement

A laboratory test and analytical research program was undertaken to characterize the performance of reinforced concrete beams with high-strength reinforcement subjected to reversed cyclic lateral loading simulating earthquake effects. The beams are representative of beams used in special moment frames. Four beams were tested in the laboratory test investigation, one with A706 Grade 60 reinforcement, one with Grade 100 reinforcement having tensile-to-yield strength ratio (T/Y) of 1.17, one with Grade 100 reinforcement with T/Y = 1.26, and one with A1035 Grade 100 reinforcement. In each beam, the noted reinforcement grade was used for both longitudinal and transverse reinforcement, except for beam with Grade 100 T/Y = 1.17 that had transverse reinforcement of Grade 100 with T/Y = 1.26. Overall, all beams achieved rotation capacity of at least 0.045 radians. The beams with A706 Grade 60 and Grade 100 (T/Y = 1.26) reinforcement failed by buckling of longitudinal bars over several hoop spacings. The other two beams with Grade 100 reinforcement failed by fracture of longitudinal bars at the maximum moment section. Strain gauges installed on longitudinal bars indicated that beams with higher T/Y achieved greater spread of plasticity compared to beams with lower T/Y./nIn the analytical study, the seismic performance of tall reinforced concrete special moment resisting frames with high-strength reinforcement was investigated through nonlinear dynamic analyses. Four 20-story reinforced concrete moment frames, three reinforced with Grade 100 steel and one with Grade 60 steel were designed in accordance with ASCE 7-16 and ACI 318-14 at a hypothetical site in San Francisco, California. All four frames had the same dimensions and concrete properties, resulting in identical design drifts. Frames with Grade 100 reinforcement were designed to have reduced amount of longitudinal reinforcement to provide equivalent nominal strength as was provided in the Grade 60 reinforcement model. Tests had demonstrated that frames with higher-grade reinforcement had greater strain penetration into beam-column joints, resulting in greater slip of reinforcement from connections. This effect combined with reduced reinforcement ratios caused the frames with Grade 100 reinforcement to be more flexible than the frame with Grade 60 reinforcement. In addition, some currently available types of Grade 100 reinforcement have lower tensile-to-yield strength ratio and lower uniform elongation compared with Grade 60 reinforcement. The reduced T/Y results in reduced strain-hardening, increased strain localization, and increased P-Delta effects. The effects of these local behaviors on overall frame performance are studied through the nonlinear dynamic analyses. The various types of reinforcement were found to result in minor differences in overall frame seismic performance.

Advisor: Moehle, Jack P