VictorJuiz/thesis huggingface dataset:
Septin Self-Assembly: Plasticity and Protein Scaffolding

Septins are a conserved family of cytoskeletal proteins implicated in a wide array of cellular functions including cell cycle regulation, ciliogenesis, and cell motility. Two of the most basic functions of septins seems to be compartmentalization of membrane structures and protein scaffolding. Of the four cytoskeletal protein families that provide structure and organization to the cellular environment, septins are the most recently discovered and the least characterized. Like tubulin and actin, septins bind nucleotide (GTP/GDP) and assemble into filaments via interactions between nucleotide-binding domains. Like the intermediate filaments, septins contain coiled-coils essential for the formation of higher-order assemblies. What sets septins apart is their striking structural plasticity. Septin subunits form apolar heteromeric complexes, which self-assemble into filaments, paired filaments, rings, and gauzes. My work has sought to answer three questions about septin plasticity and protein scaffolding. How are distinct septin subunits arranged in heteromeric complexes? How does the arrangement and composition of subunits relate to distinct assembly states and cellular functions? How do the scaffolding properties of septins regulate cellular processes? Using electron microscopy and biochemical techniques to study the structure and function of the mitotic septins (Cdc3, Cdc10, Cdc11, Cdc12 and Shs1) in the budding yeast Saccharomyces cerevisiae, I have found that Shs1 substitutes for Cdc11 at the terminal position in septin octamers and promotes the formation of septin rings, instead of the paired filaments formed by Cdc11-capped octamers. The rings observed in vitro are similar in size as those found in vivo, and Shs1 is essential for the robust formation of the ring-like septin collar at the site of cytokinesis. In addition to subunit exchange, I provide evidence that phosphorylation regulates septin self-assembly. Different phosphomimetic mutations of Shs1 either prevent ring assembly or promote the formation of an alternate assembly, septin gauzes. The implications of these results are discussed. I also studied the molecular organization and self-assembly properties of Spr3 and Spr28, two septins expressed specifically during meiosis and sporulation, an alternate developmental pathway induced by nutrient starvation. I also examined the mechanism by which septins serve as a protein scaffold for the cell-cycle regulator Hsl1, an AMPK protein kinase that appears to act as sensor for septin assembly.

Advisor: Nogales, Eva
A Search for Physics Beyond the Standard Model using Like-Sign Muon Pairs in pp Collisions at sqrt(s) = 7 TeV with the ATLAS Detector

This dissertation presents a search for physics beyond the Standard Model using pairs of muons with equal electric charge. The search is performed in a proton-proton collision data sample collected during 2011 at sqrt(s) = 7 TeV by the ATLAS experiment at the Large Hadron Collider. The total data sample corresponds to an integrated luminosity of 4.7fb-1. Events are selected by requiring pairs of prompt and isolated like-sign muons with transverse momentum greater than 20 GeV. The observed dimuon invariant mass distribution is compared to the Standard Model expectation, searching for any deviation between the observed and predicted yields. No evidence for an excess beyond the Standard Model expectation is observed. The results are interpreted as inclusive cross-section limits on the production of like-sign muon pairs from non-Standard Model sources as function of the dimuon invariant mass. The cross-section limits range between 30 fb and 1.2 fb. The data are also searched for a new narrow resonance which decays to like-sign muon pairs. No evidence for such resonant production is observed and the results are interpreted as upper limits on the mass and production cross section of doubly charged Higgs bosons. Assuming pair-production and a 100% branching ratio to muons, masses below 398 GeV (306 GeV) are excluded assuming coupling to left-handed (right-handed) fermions.

Advisor: Heinemann, Beate H. E.
Partial-Transient-Liquid-Phase Bonding of Advanced Ceramics Using Surface-Modified Interlayers

Partial-transient-liquid-phase (PTLP) bonding of advanced ceramics employs an A/B/A sandwich-style interlayer that is designed such that the outer cladding, A, forms a transient-liquid phase that disappears at the bonding temperature due to diffusion of A into the core layer, B. The resultant bonds can have re-melt temperatures that are significantly higher than the bonding temperature. The success of PTLP bonding relies on the proper selection of the interlayer components: the transient liquid must be able to flow into and fill strength-limiting interfacial flaws, the adhesion between the interlayer and the bulk ceramic must be sufficiently high to prevent interfacial failure, the formation of strength-reducing brittle phases at the interface should be minimized, and the residual stresses due to coefficient of thermal expansion (CTE) mismatch should be minimized. The composition of the transient liquid predominately determines the interfacial characteristics of the bond, while the core composition determines the residual stresses in the assembly. In recent work, Al2O3 bonded using Ni/Nb/Ni interlayers produced joints that were of such high strength that all bonded samples failed exclusively in the ceramic and not at the joint during 4-point bend testing./nThe wetting characteristics of the Ni-Nb transient-liquid and the CTE of Nb are favorable for the fabrication of strong PTLP-bonded Al2O3. However, for other ceramic systems, using a binary interlayer system such as Ni-Nb may not be desirable. When using binary interlayers it is not possible to control the composition of the transient liquid and the core independently. In order to expand PTLP bonding to other advanced ceramics, this study examined a new interlayer design that employs a surface-modified core, such as Mo-surface-modified Nb, instead of a homogeneous core, such as pure Nb. A surface-modified core is a core layer with an intentionally inhomogeneous composition in order to better control the composition of the transient-liquid and the core layer independently. It was found that Al2O3 PTLP bonded using a Mo-surface-modified V core and a Ni cladding had fracture strengths of 302±29 MPa. This is comparable to those using Ni/Nb/Ni interlayers, 341±28 MPa. In both assemblies, all of the samples failed in the ceramic bulk. The insights gained from these experiments were used to develop interlayer design guidelines for the PTLP bonding of other advanced ceramics.

Advisor: Glaeser, Andreas M
Developmental genetics of Xenopus

Abstract/nDevelopmental genetics of Xenopus/nby/nJessica Burnham Lyons/nDoctor of Philosophy in Molecular and Cell Biology/nUniversity of California, Berkeley/nProfessor Richard Harland, Chair/nThe frog Xenopus laevis has been studied for over 200 years. Its advantages as a robust and easily manipulable model organism have been complemented more recently by genetic and genomic studies in Xenopus tropicalis. My thesis work utilized established and cutting-edge techniques to advance our knowledge of developmental genetics in both Xenopus systems./nI used an embryological approach to investigate the roles of the Fgf receptors (Fgfrs) during development. Knockdown and overexpression studies suggested that each Fgfr plays a different role in the specification of mesoderm, and my results are consistent with Fgfr4 playing a role in dampening the Fgf signal. I also showed that X. tropicalis Fgfrs 1-3 are alternatively spliced in D3, the extracellular immunoglobulin domain important for ligand specificity. These isoforms exhibit different temporal and spatial expression patterns, suggesting that control of this alternative splicing plays a role in regulating development./nMy thesis work has also harnessed the power of the X. tropicalis system to understand development using a forward genetic approach. Tadpoles homozygous for the recessive lethal mutation curly exhibit ventral edema and curled tails. I used classical genetics to map curly to a 1.9 Mb window on X. tropicalis chromosome 4. The pteg gene, which lies in this region, is misspliced in curly embryos. Isabelle Philipp and I used next-generation (nextgen) sequencing technology to identify differences between the curly mutant DNA and that of the reference genome. Focusing on the region around the pteg gene, we are currently evaluating these differences to find the lesion that causes the curly phenotype./nThe efficient application of genetic techniques requires a high-quality genetic map and reference genome, and those available for X. tropicalis were flawed (Wells et al., 2011) (Hellsten et al., 2010). Thus, I developed a genotyping by sequencing (GBS) technique using reduced-representation multiplex nextgen sequencing, and my collaborators in the Rokhsar lab have generated a high-quality SNP map for X. tropicalis based on my data from 192 F2 individuals. This map is being used to construct an improved X. tropicalis genome assembly. By finding regions of correlation for the pigmentation mutation gray, as well as the X. tropicalis sex locus, we demonstrated that this technique can be used for genetic mapping. I applied my GBS method to X. laevis as well, and the SNP map thus generated will facilitate the assembly of a reference genome for this allotetraploid species./nBy combining the classical advantages of the Xenopus system with modern techniques, my thesis work has contributed to our understanding of the development, genetics, and genomics of vertebrate biology.

Advisor: Harland, Richard M
Opera after Stunde Null

This dissertation discusses the musical, dramatic, and political implications of postwar German opera through the examination of four case studies: Boris Blacher's Abstrakte Oper Nr. 1 (1953), Hans Werner Henze's König Hirsch (1956), Carl Orff's Oedipus der Tyrann (1959), and Bernd Alois Zimmermann's Die Soldaten (1965). Both the composers' musical decisions and the finished works' critical and musicological reception demonstrate just how urgently the genre of opera was thought to be in crisis. Enabled by the myth of the "Stunde Null" or Zero Hour, many avant-garde composers shunned opera as artistically bankrupt and conservative, preferring instead genres that were less closely tied to the musical past./nOpera's coherence as a genre depended upon the maintenance and renewal of dramatic and musical conventions from eras both immediate and distant - a dependence that became politicized as the boundaries of "new music" were policed. Composers of new operas in this era were forced to attempt creative and productive solutions to the problem of how to write an opera in a milieu skeptical of opera's potential for innovation. The reception of these operas reflects these concerns, as critics and musicologists alike sought to make sense of the pieces within the context defined aesthetically by operatic tradition and politically by the Stunde Null./nIf opera was a problem in general for post-war composers in Germany, each of the four operas in this dissertation represents one set of solutions. By referring to a varied dramatic and musical heritage, these composers looked for artistic touchstones that would allow them to position themselves in meaningful artistic lineages, whether Italian bel canto, Wagnerian Gesamtkunstwerk, Greek tragedy, or abstract theater./nIn Boris Blacher's Abstrakte Oper Nr. 1, the authors' efforts to foil operaticism with nonsense opened the door for audiences to project their deepest fears onto the piece. The songs and arias in Henze's König Hirsch, which Henze revised and crafted to be as lyrical and transparent as possible, made the opera a target of harsh criticism because it was too "conventional." By contrast, Orff's Oedipus der Tyrann was met with both praise and confusion, for despite its striking effects, the piece's extreme asceticism proved incompatible with the expectations of an opera audience. Meanwhile, the ambition and message of Zimmermann's Die Soldaten earned it accolades, but the smaller, more intimate opera that lurks behind the noisy surface contradicts the received idea that Zimmermann conquered the tradition of operatic expressiveness./nThe relationship of these operas' musico-dramatic orientations to tradition is therefore indicative of their positions relative to the ideology of the post-war blank slate. Inasmuch as the aesthetics prized after Stunde Null were largely defined by a negation of tradition through the privileging of the radically new, the supposed conservatism of opera led many to declare it dead. But by approaching tradition more constructively, we can better understand the position of opera during this fraught era.

Advisor: Smart, Mary Ann
Applications of semiclassical analysis to partial differential equations

Semiclassical analysis and other types of asymptotic analysis are important tools in the study of partial differential equations. We demonstrate the versatility of these methods by proving two types of results./nFirst we study the dynamics of solitary waves for two different nonlinear Schr\"odinger equations. The first is the Hartree equation the second is a general nonlinear Schr\"odinger equation with an $L^2$-subcritical power nonlinearity. For both of these equations, we show that a solution found using initial conditions within $\eps \le \sqrt h$ of a soliton (in $H^1$) evolves according to the equations of motion given by the effective Hamitonian up to time $\sim |\log h|/h$, with errors up to size $\eps +h^2$. We achieve this result using the methods of Holmer-Zworski and the spectral results of Lenzmann and Weinstein./nNext we study the spectral properties of $n$-dimensional semiclassical radial Schr\"odinger operators. We prove that their spectrum determines the potential within a large class of potentials for which we assume no symmetry or analyticity. Our proof is analogous to the spectral determination of the sphere and uses the first two semiclassical trace invariants and the isoperimetric inequality.

Advisor: Zworski, Maciej
Workload-Driven Design and Evaluation of Large-Scale Data-Centric Systems

Large-scale data-centric systems help organizations store, manipulate, and derive value from large volumes of data. They consist of distributed components spread across a scalable number of connected machines and involve complex software/hardware stacks with multiple semantic layers. These systems help organizations solve established problems involving large amounts of data, while catalyzing new, data-driven businesses such as search engines, social networks, and cloud computing and data storage service providers. The complexity, diversity, scale, and rapid evolution of large-scale data-centric systems make it challenging to develop intuition about these systems, gain operational experience, and improve performance. It is an important research problem to develop a method to design and evaluate such systems based on the empirical behavior of the targeted workloads. Using an unprecedented collection of nine industrial workload traces of business-critical large-scale data-centric systems, we develop a workload-driven design and evaluation method for these systems and apply the method to address previously unsolved design problems. Specifically, the dissertation contributes the following:/n1. A conceptual framework of breaking down workloads for large-scale data-centric systems into data access patterns, computation patterns, and load arrival patterns./n2. A workload analysis and synthesis method that uses multi-dimensional, non-parametric statistics to extract insights and produce representative behavior./n3. Case studies of workload analysis for industrial deployments of MapReduce and enterprise network storage systems, two examples of large-scale data-centric systems./n4. Case studies of workload-driven design and evaluation of an energy-efficient MapReduce system and Internet datacenter network transport protocol pathologies, two research topics that require workload-specific insights to address./nOverall, the dissertation develops a more objective and systematic understanding of an emerging and important class of computer systems. The work in this dissertation helps further accelerate the adoption of large-scale data-centric systems to solve real life problems relevant to business, science, and day-to-day consumers.

Advisor: Katz, Randy H.
Archivization and Its Alternatives: Toward a Critique of Chicana/o Religions and Spiritualities

In this dissertation, I attempt to clarify a problem (i.e., how to think Chicana/o religion and spirituality in light of debates on the archive in South Asian and Latin American subaltern studies?) rather than propose a new approach to the question of the interpretation of Chicana/o religions (e.g., how to understand the relationship between Chicana/o cultural production and religious thought, practice, experience, expression, and so forth?)./n/nIn chapter 1, I consider the pros and cons of the history of religions and Chicana feminist thought as critical approaches to Chicana/o religion and spirituality. I conclude with the proposition that subaltern studies - and in particular, Spivak's notion of reading archivally - might add to the critical works of Davíd Carrasco and Laura E. Pérez. Chapter 2 examines Carrasco's attempt to link the history of religions to Chicana/o literary and cultural studies. I conclude with the assertion that such an approach may run the risk of reifying the religious/secular divide as hermeneutic foundation. In chapter 3, I turn to Pérez' distinction between secular religious studies and the politics of Chicana spirituality. I conclude with the suggestion that Chicana/o religion and spirituality might be read as a question of the archive. Chapter 4 argues that a critique of archival memory is central to debates on religion and spirituality in Chicana/o literary and cultural studies. I conclude with an exploration of archival silences within the Bancroft and Ethnic Studies libraries at the University of California, Berkeley.

Advisor: Saldívar, José D.
Rabasa, José
Multi-agent Cluster Scheduling for Scalability and Flexibility

This dissertation presents a taxonomy and evaluation of three cluster scheduling architectures for scalability and flexibility using a common high level taxonomy of cluster scheduling, a Monte Carlo simulator, and a real system implementation. We begin with the popular Monolithic State Scheduling (MSS), then consider two new architectures: Dynamically Partitioned State Scheduling (DPS) and Replicated State Scheduling (RSS). We describe and evaluate DPS, which uses pessimistic concurrency control for cluster resource sharing. We then present the design, implementation, and evaluation of Mesos, a real-world DPS cluster scheduler that allows diverse cluster computing frameworks to efficiently share resources. Our evaluation shows Mesos achieve high utilization, respond quickly to workload changes, and flexibly cater to diverse frameworks while scaling to 50,000 nodes in simulation and remaining robust. We also show existing and new frameworks sharing cluster resources. Finally, we describe and evaluate RSS, a cluster scheduling architecture being explored by Google in Omega, their next generation cluster management system. RSS uses optimistic concurrency control for sharing cluster resources. We show the tradeoffs between optimistic concurrency in RSS and pessimistic concurrency in DPS and quantify the costs of the added flexibility of RSS in terms of job wait time and scheduling utilization.

Advisor: Katz, Randy H
Evading/Invading History: Adolescent Preoccupations with Reality, the Historical Present and Popular Culture in Spanish GenX Narratives

The Spanish Generation X (GenX) refers to a group of writers, born in the 1960s and early 1970s, who published novels in the 1990s. Their work focused on a generation of Spanish adolescents who were raised during and the closing years of the Franco government and the Transition to democracy. Ray Loriga, José Ángel Mañas and Lucía Etxebarria are three writers who are consistently identified by critics as the figureheads of the generation. This dissertation explores the historical dimensions of their early texts./n/nGenX, a polemical group and categorical designation, is characterized by an emphasis on international popular culture, especially music, film and literature. The young characters in these novelists' works are alienated from society and their peers, immersed in the present, suspicious of the future, and indifferent to the past. They turn to gratuitous violence, sex and substance abuse in their search for meaning or in order to avoid the realities of their lives. While stylistically ranging from realism to postmodern skepticism about the real, the early novels of Loriga, Mañas and Etxebarria coincide in the representation of how Spain's young people grappled with the difficulties of a newly global, media-driven, consumerist society as Spain integrated into the European Union./nIn my dissertation, I analyze how these novelists, who have frequently been criticized for their seeming historical and political apathy in fact engage history in their representations of the their era. While debates rage on about the recuperation of historical memory and political corruption, these authors I study engage in very different projects. They capture in myriad ways the peculiar sense of time and history that characterizes a culture saturated in quick-hitting television news clips, sensationalist television shows and distorted newspaper headlines. GenX novels reflect this new historical consciousness. Everything and nothing is historical; Kurt Cobain's and Ian Curtis' suicides (lead singer of Joy Division) become historical markers, signaling the passage of time instead of the attempted coup in 1981 or the death of Franco in 1975. History is easily lost to the quickened pace of life, and these novelists show how the attempt to recover and narrate the past often results in fragmented and sometimes mythical texts.

Advisor: Iarocci, Michael
Translating Sweetness: Type 2 Diabetes, Race, Research, and Outreach

Through the lens of Type 2 diabetes this dissertation considers race and problems of difference and risk with developments in treatment, genomic science, and the conduct of research and research priorities. Based primarily on fieldwork in New York and California, I interrogate public health notions of outreach with biotechnology and clinical research concepts of biomedical translation as synonymous practices. Institutional relationships and marketing drivers, I argue, reflect relatedness back onto the Type 2 diabetes patient through causal narratives of risk and inevitability. In effect, kinship--genetic, familial, racial, ethnic, and environmental--becomes the driver of both risk and emergent forms of bioliterary discipline. I present a narrative of how diabetic risk became racialized over time and how African Americans became seen as a desirable research population. Arguing against biological race, I present an ethnographic example of how one such African American population, or community, emerged from particular social and political histories. Fieldwork uncovered lingering memories of the Tuskegee Experiment combined with cultural incompetency in both public health and biotechnology sectors. Further, I consider the bioethical challenges of African (American) participation in new genomic research aimed toward reducing health disparities. However, as a racial category, genetics researchers debate the precise genetic location and definition of "Africa" in the human genome. I suggest that the search for a pathological Africa in the human genome may deepen racial stigmatization as well as author new narratives of difference. I submit that social disparity, not biological disparity, presents the ultimate challenge to successful effective clinical translation and public health outreach.

Advisor: Hayden, Cori