VictorJuiz/thesis huggingface dataset:
Fear, Fantasy, and Family: Israel's Significance to American Jews

This dissertation investigates the construction and maintenance of ethnic boundaries in the face of contestation over core values. The dynamics of American Jewish communal structures and American Jews' relationships to the state of Israel offer a case study for exploring questions of boundary-maintenance, diasporic nationalism, and the social power of emotion. Specifically, this dissertation asks how, given disagreement and struggle over the ways in which Jewish Americans relate to the state of Israel, Jewish organizations strategize to develop and maintain Jewish community. It argues that dominant American Jewish organizations act like a social movement in mobilizing American Jews to identify with a particular version of the Jewish collective, which contributes to nationalist and political goals. Contestation over the state of Israel is central to the organized Jewish community's efforts to produce and regulate Jewish identity./nDominant American Jewish organizations seek to shape collective identity in the face of growing challenge by reasserting three key emotional frames through which they promote American Jewish connection to the state of Israel. These frames, which draw from existing cultural understandings, beliefs, and practices, are: a sense of interconnectedness, interdependence, and love, which resembles and reflects the claim that the Jewish nation is family; a sense of the state of Israel as the potential culmination of the most noble of Jewish and liberal values, such that the state represents a collective fantasy of aspirations realized; and the dual sense of both vulnerability and power, as an historically persecuted people with access to substantial political and financial resources. These three main threads - familial love, collective fantasy, and vulnerability and empowerment - form the basis of the emotional disposition the dominant Jewish organizations seek to inculcate./nUsing qualitative data gathered through ethnography and content analysis, this dissertation argues that the performance of the prescribed emotional disposition towards the state of Israel facilitates and expresses a sense of belonging to the American Jewish collective. These emotions also operate as a boundary marker, disciplining Jewish identity and variations of belonging to the collective. American Jews who breach the boundaries of the collective through critique of Israeli state policies toward Palestinians face potential marginalization or exclusion. Finally, in looking at the ways in which American Jewish organizations make meaning out of, and regulate relationships with, the state of Israel, this dissertation argues that the collective identity making processes of American Jews have tangible implications in the lives of Jews and Palestinians in Israel and the Occupied Palestinian Territories.

Advisor: Ray, Raka
Regulation and function of antisense transcription in Saccharomyces yeast

Transcription of RNA antisense to protein-coding genes is widespread in genomes from bacteria to human. For most antisense transcription, the methods by which it is regulated and its potential function remain unknown. We sought to address these questions, using budding yeast as a model system, with two complementary approaches. First, we mapped antisense expression in four Saccharomyces species. Antisense transcripts conserved across yeasts were predominantly detected at open reading frames in a tail-to-head orientation with respect to the next gene 3' to the reference gene. For such tandem gene pairs, the region between the genes exhibited distinctive signatures of binding by transcription factors, suggesting that these factors could regulate transcription of both the mRNA from the 3' gene and the upstream antisense transcript. Transcription factor deletion experiments supported this hypothesis, conferring decreased expression of both antisense and downstream sense transcripts at such gene pairs; often in these mutants, as an antisense transcript dropped in expression, its host gene mRNA level increased, a hallmark of antisense-mediated repression. To test this model, we focused on the stress-response gene YKL151C and its downstream neighbor GPM1, which was strongly expressed in rich media. Cis-regulatory mutation experiments showed that YKL151C antisense expression was co-regulated with GPM1 and repressed mRNA levels of its overlapping sense transcript. In a second body of work, we used natural variation rather than engineered mutations to access the impact of variants that modulate antisense expression levels. We mapped naturally occurring polymorphisms between yeast strains that showed linkage to sense and antisense expression. We identified cases where such regulatory polymorphisms mediated their effects through transcription factors that bound at the promoters of linked antisense transcripts; in all such cases, expression of the downstream gene also showed linkage to the polymorphism, and, in several cases, sense transcription overlapping the antisense was linked as well. Our studies thus converged on a model in which antisense transcription at one yeast gene frequently originates from and is co-regulated with the promoter of a neighboring gene, mediated by the action of transcription factors; at a fraction of such loci, antisense transcription acts to repress expression of its overlapping mRNA, enabling the joint control of adjacent genes specialized to opposing conditions.

Advisor: Brem, Rachel B
The Metagenomic Epidemiology of Childhood Leukemia

The etiology of childhood acute lymphoblastic leukemia (ALL), the most common childhood cancer, is unknown. A role for infection is supported by considerable research over the last twenty years. Despite this evidence and many infection related hypotheses, no definitive infectious agent has been identified. Until recently broad surveys of the microbiome were not possible. Modern developments in next generation sequencing and bioinformatics however now allow unbiased investigation into the astounding diversity of organisms that inhabit the human body./nThis dissertation describes the first comprehensive analysis of tissue from children with childhood leukemia using metagenomic (the study of non-human nucleic acids) and epidemiologic methods. Metagenomes in pre treatment bone marrow from the Fallon, NV ALL cluster and other ALL non-clustered cases from California were interrogated for known and novel infections. A putative and potentially novel human virus was found in the Fallon cases. To investigate viruses involved more broadly in childhood ALL, viromes of pre-treatment bone marrow from children with acute myloid leukemia (AML) and from children with ALL (who we assumed to have similar background infections) were compared. In children with ALL, a greater intensity of viral infection as well as a significant difference in the expression of viral packets originating from double stranded DNA viruses was observed. Using 16s based bacterial metagenomics, no difference was observed in bacterial diversity between the groups showing the absence of differential contamination and suggesting that bacteria do not play a role in ALL. These results suggest a possible putative causal agent in the Fallon Nevada leukemia cluster and increased viral infection driven by double stranded DNA viruses in non-clustered children with ALL./nThese data contribute to an etiologic hypothesis of ALL where a combination of pre-natal and post-natal events lead to leukemia. First, an underlying genetic predisposition, combined with an in utero infectious exposure, cause chromosomal anomalies and immune dysregulation. This followed by postnatal events, including toxic and infectious exposures that further modify adaptive immunity lead to a greater intensity of infections. This feeds the loop of enhanced b-cell production that facilitates virally induced self- mutation caused by foreign nucleic acids invading pre b-cells. Resulting in an ABOBEC arbitrated hypermutation. Eventually the loop of enhanced yet less competent b-cell production, RAG mediated over mutation, increased infection leading to pre b-cell viral nucleic acid loading, and APOBEC caused self mutation remove the proliferative and apoptotic cellular checks. The result is childhood ALL.

Advisor: Buffler, Patricia A
Selvin, Steve
Undoing Architecture: Temporalities of Painted Space in Early Modern Amsterdam

This dissertation explores the entanglement of temporality, realism, and representation in the making and viewing of Dutch art. I explore these issues through paintings, prints, and drawings by Dutch artists of Amsterdam made in the second half of the seventeenth century. Printed maps, paintings, drawings, and engravings of the destruction and ruination, both historical and imagined, of well-known Amsterdam structures, and images that have been understood to be straight-forward portraits of Amsterdam buildings and spaces are the main subjects of this study. This is not, however, a dissertation about architecture, or even, directly, about the representation of real architecture. Instead, I consider what happens in the intervals between representation and represented, the spaces where imagination transforms the experienced into the imaged. That is, this study begins with the assumption that what is represented in the works of art under consideration is not something that resides in the physical world, but rather the artist's imagining of what could, or should, or might exist in its place. This dissertation therefore questions the very structure of Dutch realism, arguing that the realism effect was actually the location of the severing of world from image./nI argue that Amsterdam cityscapes subvert their own apparent status as realistic representations of contemporary Amsterdam. Though these images have always been treated as mimetic, they actively resist recording the present city, sometimes including structures that have yet to be built, in other instances destroying edifices that were already extant. These images, by Rembrandt, Ruisdael and Jan van der Heyden, among others, visually remake the city in a variety of ways: as it was meant to appear in the future; as a nostalgic and idealized version of its lost, past self; as a decayed ambivalent version that is neither clearly past nor clearly future. Denying the present, seventeenth-century images of Amsterdam convey unease about contemporary urban experience and probe the uncomfortable limits of representation itself. These creative reconstructions of Amsterdam were a form of resistance to the modernizing environment of the city, for they catered to both a false nostalgia for a fictive ancient past, and a deep ambivalence about the modernization and monumentalization of the urban fabric. I argue that Dutch art, which appears to insistently transcribe contemporary experience, is also paradoxically invested in the erasure of the present and the construction of alternate realities. The realist mode favored by many Dutch artists was far more concerned with the construction of new paradigms for society than with the representation of contemporary life.

Advisor: Honig, Elizabeth A
Divergent Metaphors: The Intertextuality between Guimarães Rosa and Mia Couto

Examining intersections and divergences between the often-compared Brazilian modernist João Guimarães Rosa and the Mozambican postmodernist Mia Couto, I propose an intertextual reading to broaden the perspective on their linguistic and thematic likenesses and subjective and cosmovisional differences. This study traces the trajectories of their orality and representation of the marginalized, especially children, from the point of view of race and identity. My research covers approximately two decades of work by each author, including Couto's Jesusalém (2009), Estórias abensonhadas (1994), Cronicando (1991), and Vozes anoitecidas (1987) alongside Rosa's Grande Sertão: Veredas (1956), Primeiras estórias (1962), Corpo de baile (1956), and Sagarana (1984)./nI find that contradictions in Rosean portrayals of mestiço-white versus Afro-Brazilian children reveal hierarchically racialized attitudes in Brazil's social foundations that are at odds with the postcolonial values of Couto's Mozambique. The legacy of Portuguese colonialism evident in the polarizing orality expressed by Rosean backlanders--whose narrations categorically render blacks as caricatured, dehumanized, and tragic in juxtaposition to the mestiços' embodiment of the full range of human experience and transformative individual potential--functions as a discursive strategy to challenge Gilberto Freyre's dominant racial discourses on Lusotropicalism, mestiçagem, and racial democracy. Conversely, Couto's narrations on the black experience are free of the racial stereotype, unindividuated uniformity, and tragedized foreclosure of patriarchal characterization, despite also exploring the violence and poverty left in the wake of imperialism. Like Rosa's more privileged mestiço-white children, capable of positive transformation no matter how marginalized their circumstances, Couto's children--rich or poor, orphaned or parented, black or mestiço--capitalize on the imaginative and sometimes magical "exercises of childhood," often while reconnecting to the indigenous and sacred practices of their ancestors. Unlike Rosa's most heroic children, Couto's do not usually dramatically improve in socio- economic conditions. Instead of the more linear worldview of scrappy self-determination or meritorious individualism that earn Rosean protagonists upward mobility, the Coutian protagonist follows a more circular pattern of self-discovery grounded in collective interdependence and a plurality of native traditions.

Advisor: Slater, Candace
Slow Photoelectron Imaging Spectroscopy of Cryogenically-Cooled Anions

Slow electron velocity-map imaging (SEVI) has been a powerful tool for acquiring high-resolution anion photoelectron spectra. However, extending the applications of this method have been limited by high internal temperatures of many ions, which lead to spectral congestion. In order to improve the performance, a cryogenic ion trap has been designed to cool all ions down to their ground vibronic state, increasing resolution and rendering assignments tractable for even complex systems./nSEVI has been used to understand the spectra and properties of aromatic molecules and main group clusters. The spectra of phenoxide (C6H5O-) and thiophenoxide (C6H5S-) were acquired without cryogenic cooling, but allowed for refined term energies and vibrational frequencies, requiring a reinterpretation of thiophenol photodissociation experiments. Spectra of indenyl (C9H7-) and fluorenyl (C13H9-) with ion trapping and cooling have resolved many closely-spaced peaks, allowing for confident assignments of non-Franck-Condon allowed transitions. The resolution and ion cooling allow us to assign lifetime broadening in the excited state, which are attributed to fast nonradiative decay processes through a conical intersection. Cooling experiments on S3- show that hydrogen is more effective as buffer-gas cooling, a crucial step in the optimization of cooling conditions in the ion trap./nThe cryogenic ion trap has been particularly helpful for transition metal oxide clusters, as the ions are often created at high temperatures from a laser ablation cluster source. The simplest group 4 metal dioxides (TiO2-, ZrO2-, and HfO2-) are used as a test system, and the spectra yield refined energies and geometries. The more complex system VO2 has multiple low-lying electronic states, which can be confidently disentangled as all vibrational structure is now resolved in the photoelectron spectra of VO2-. The dimer clusters Ti2O4- and Zr2O4- have congested spectra, but with the resolution now available, the anion clusters are shown to have different stable isomers. The trimer clusters Fe3O and Co3O and the corresponding anions exhibit high-spin ferromagnetic states. Finally, new information is obtained on even a small diatomic, FeO, as the flexibility, resolution, and temperature control have allowed for a more complete analysis of the photodetachment spectra of FeO-.

Advisor: Neumark, Daniel M
Weak Convergence and Rapidly Oscillating Pendula

The ordinary differential equation for the motion of an inverted pendulum whose support is subjected to a vertical harmonic excitation with high frequency and small amplitude is studied. A mathematical insight is provided as asymptotic methods are employed to derive the limiting equation when the excitation frequency tends to infinity. These show that as the frequency becomes high and certain parametric conditions are satisfied, the inverted pendulum theoretically can be stabilized. A new and rigorous proof using weak convergence methods is given, to confirm the conclusions of the formal asymptotics. Then the analysis is generalized to a single inverted pendulum on an oscillatory base driven at other angles, a single inverted pendulum on a flywheel and a double inverted pendulum on a vertically oscillatory base and, in each case, if the pendulum or pendula can be stabilized, parametric conditions for stability are given./nThen we also use this method to shed light on the `Paul Trap' which is a method of levitating charged particles via an oscillating electric field. Last, PDE analogues are studied in the same manner.

Advisor: Evans, Lawrence C.
A Framework for Composing High-Performance OpenCL from Python Descriptions

Parallel processors have become ubiquitous; most programmers today have access to parallel hardware such as multi-core processors and graphics processors. This has created an implementation gap, where efficiency programmers with knowledge of hardware details can attain high performance by exploiting parallel hardware, while productivity programmers with application-level knowledge may not understand low-level performance trade-offs. Ideally, we would like to be able to write programs in productivity languages such as Python or MATLAB, and achieve performance comparable to the best hand-tuned code./nOne approach toward achieving this ideal is to write libraries that get high efficiency on certain operations, and call these libraries from the productivity environment. We propose a framework that addresses two problems with this approach: that it fails to fuse operations for efficiency, and that it may not consider runtime information such as shapes and sizes of data structures. With our framework, efficiency programmers write and/or generate customized OpenCL snippets at runtime and the framework automatically fuses, compiles, and executes these operations based on a Python description./nWe evaluate the framework with case studies of two very different applications: space-time adaptive radar processing and optical flow. For a space-time adaptive radar processing application, our framework's implementation is competitive with a hand-coded implementation that uses a vendor-optimized library. For optical flow, a computer vision application, the framework achieves frame rates that are between 0.5x and 0.97x hand-coded OpenCL performance.

Advisor: Keutzer, Kurt
Regulation of Desnutrin and Function of Desnutrin-catalyzed Lipolysis

Lipolysis is the biochemical process during which triacylglycerol (TAG) stored in cellular lipid droplets undergoes stepwise hydrolysis to release fatty acids (FAs). FAs produced from lipolysis in adipose tissue are released into circulation, whereas, in other tissues, FAs are used intracellularly. There are 3 major lipases involved in intracellular/nTAG hydrolysis; Desnutrin/adipose triglyceride lipase (ATGL) catalyzes hydrolysis of TAG to form diacylglycerol (DAG). DAG is then hydrolyzed by hormone-sensitive lipase (HSL) to monoacylglycerol, which is further hydrolyzed by monoglyceride lipase (MGL)./nBy employing adipose-specific conditional desnutrin knockout strategy (desnutrin ASKO mice), we show that desnutrin ASKO mice not only manifests in obesity, but converts BAT to a WAT-like tissue. Desnutrin ASKO mice exhibit impaired thermogenesis with decreased expression of UCP-1, with lower PPAR alpha binding to its promoter, revealing the/nrequirement of desnutrin-catalyzed lipolysis in the maintenance of a BAT phenotype. We also found that ablation of desnutrin in islet beta cells by using RIP-Cre or RIP-CreER impairs glucose-stimulated insulin secretion (GSIS) and induces TAG accumulation in islets, leading to pronounced hyperglycemia. Furthermore, we show that desnutrin-catalyzed lipolysis activates PPAR delta, rather than PPAR alpha, which in turn is critical for expression of genes involved in mitochondrial function, and thus ATP production, required for GSIS./nWe next examined the mode of desnutrin regulation. We found that desnutrin is phosphorylated on Ser406 by AMP-activated protein kinase (AMPK) to increase its TAG hydrolase activity. To study the in vivo significance for AMPK phosphorylation, adipose-specific ablation of AMPK catalytic subunits alpha1 and alpha 2 (AMPK alpha 1/alpha 2 ASKO) were performed. We detected decreased phosphorylation of desnutrin on Ser406, accompanied with a lower TAG hydrolase activity. Furthermore, the inhibitory phosphorylation of hormone sensitive-lipase (HSL) on Ser565 by AMPK was reduced in AMPK alpha 1/alpha 2 ASKO WAT, resulting in an increased activating phosphorylation of HSL on Ser563 and Ser660 by PKA. Overall, AMPK alpha 1/alpha 2 ASKO mice manifest lean phenotype, with decreased fat mass, as well as reduced TAG and DAG content in WAT. We conclude that, when desnutrin activity is low, HSL dominates the lipolytic rate. These in vivo 2 transgenic mice studies reveal a novel function of lipolysis to provide specific ligands for the maintenance and function in adipose and non-adipose tissues. These studies may offer promising therapeutic approaches for obesity, diabetes, and related disorders.

Advisor: Sul, Hei Sook
The Ins & Outs of Nucleocytoplasmic Transport: Studies of the Nuclear Pore Complex

The nuclear pore complex (NPC) is one of the largest known protein structures in the cell. Evolutionarily conserved in eukaryotes ranging from fungi to plants and animals, the NPC is the main transporter of molecules between the cell cytoplasm and nucleus. Maintaining the proper compartment-specific localization of proteins and RNA is crucial for normal cell function, and the nuclear pore accomplishes this task both robustly and efficiently. Over the past several decades, insight into the composition, organization, structure, and mechanism of the NPC has been gradually teased out through careful experimentation. However, many questions about the pore's function remain unanswered./nIn this dissertation, I describe efforts aimed at elucidating several aspects of the NPC. First, I investigate the transport properties of the pore, specifically looking at how the nuclear transport receptor importin-β and the Ran GTPase interact not only with each other but also how they may affect the pore itself. The nucleoporin Nup153 is identified as an important player in the nuclear transport process which binds strongly to importin-β in a Ran-sensitive manner. Using multiple experimental techniques, the properties of importin-β, and Nup153's interactions are characterized and shown to be capable of modulating the selective permeability barrier of the NPC./nNext, I examine how members of a major class of nuclear pore proteins, the scaffold nucleoporins, are both structurally and functionally similar to the karyopherin family of soluble nuclear transport receptors. Structures of the proteins Nup188 and Nup192 are analyzed and shown to resemble those of karyopherins. Furthermore, in vitro assays indicate that at least a subset of the scaffold nucleoporins behave functionally as transport receptors, hinting at an evolutionary relationship between these two important classes of proteins./nFinally, a calcium-mediated phenomenon affecting the permeability of the NPC is explored. I show that certain cytosolic proteases are activated by millimolar concentrations of calcium ion which leads irreversibly to an increase in the nuclear pore's permeability to large molecules. A model for physiological pathways implicated in this effect is proposed.

Advisor: Liphardt, Jan