VictorJuiz/thesis huggingface dataset:
Theory, Design, and Fabrication of Nanoplasmonic Architectures for Molecular Diagnostics

This dissertation presents new advancements in the theory, design, and fabrication of nanoplasmonic structures for molecular detection./nAfter introducing nanoplasmonics, I ask a deceivingly simple question: are the various commonly used measures of localized surface plasmon resonance (LSPR) really equivalent? I then develop a theoretical framework that proves that important differences occur among the measures of LSPR. Specifically, the optimum wavelength for maximizing the near field can be significantly redshifted compared to the optimum wavelength for far field scattering, which can in turn be significantly redshifted compared to the optimum wavelength for absorption. I show how these differences are dependent upon critical parameters, such as the material, the particle size, and particle shape. This theory, based on the quasi-static approximation, is also verified rigorously using using Mie theory and finite element analysis. The implications on design for molecular detection are discussed./nI then focus on fabrication techniques, developing new tools which can control the geometry and interparticle distance of nanoplasmonic antenna initially fabricated with nanosphere lithography. I introduce active polymer fabrication and electroless metal deposition as two methods that can significantly decrease the nanogaps in nanoplasmonic systems and create enhancements in spectroscopic signal for molecular detection./nNext, I investigate the issue of nanoplasmonic geometry in great detail for four structures, with a focus on new systems in which the close proximity of two or more nanoplasmonic components causes their resonances to be linked together (i.e. plasmon-coupling). I demonstrate the coupling in these structures can cause high electric fields ideal for molecular detection. Four such structures are discussed: the nanocrescent, the crescent-shaped nanohole, the plasmon enhanced particle-cavity (PEP-C) system, and the core-satellite system. The nanocrescent and its counterpart, the crescent-shaped nanohole, utilize both sharp tips and intra-particle coupling to achieve high local field enhancement. The PEP-C system combines particle and cavity geometries to create a high density of hot-spots. The core-satellite system is based on the interaction of a central nanoparticle with multiple smaller particles./nFinally, I introduce a special class of bioinspired nanoplasmonic structures called nanocorals, designed for molecular sensing within or on the surface of living cells. Nanocorals are unique in that they combine cellular specific targeting with biomolecular sensing, yet decouple the two functional modes. Analogous to natural sea corals that use rough surfaces to maximize surface area for efficient capture of light and food particles, nanocorals utilize a highly roughened surface at the nanoscale to increase analyte adsorption capacity, and create a high density of surface-enhanced Raman spectroscopy (SERS) hot-spots.

Advisor: Lee, Luke P
Exchange of fine sediments with gravel riverbeds

An excess of fine sediment is the leading cause of impairment of rivers in the United States. Fine sediment poses particular problems for salmon, which bury their eggs within gravel riverbeds. Sand infiltrates the salmon nest and creates a sand seal in the upper pore spaces near the surface. Silt and clay then deposit in the sand seal, reducing bed permeability and cutting o the supply of dissolved oxygen. Large stormflows can mobilize the riverbed and flush out the silt and clay, increasing permeability. Reservoir releases on dammed rivers can simulate this effect; it may also be possible to engineer releases to both increase reservoir flood storage and improve the quality of spawning habitat. Understanding the fraction of fines as a function of depth would allow estimation of bed permeability and ideal flushing depths, which would aid in the design of flushing flows. This dissertation improves/nunderstanding of the sand fraction as a function of depth in the sand seal by analyzing infiltration data, testing an existing model, and developing new models. It is found that a simple exponential model performs well at predicting the sand fraction as a function of depth but there is evidence of a more complex structure driven by a change in trapping efficiency as the bed clogs. This study allows for direct calculation of the effect of sand seals on bed permeability and can inform future studies of silt and clay deposition in the sand seal, but it is limited to uniform-flow, plane-bed conditions. The location and structure of salmon nests takes advantage of three-dimensional flowfields to enhance flow over the eggs. These/nforcing mechanisms should affect infiltration into nests. This relationship is explored in an experiment on sand infiltration into a gravel bed with alternate-bar topography. This study demonstrates that sand seals are created throughout the riverbed, even where sand transport is too small to measure. There is spatial variability in the thickness of a sand seal but not in the mean sand fraction in the sand seal. Local infiltration is increased by bed topography that promotes downwelling and is limited by very high sand transport and by thick sand deposits on the surface. The structure of a sand seal will affect flushing depth, but the/nduration of a flushing flow depends on the entrainment rate of silt and clay from within the sand seal. The entrainment rate of subsurface fines into suspension is not generally known. A case study on the Russian River in California is performed to estimated the entrainment rate during dam releases large enough to mobilize the riverbed. High-frequency turbidity and discharge data from two USGS gauging stations are used to create a timeseries of cumulative entrainment from the reach. Estimates of bed mobility are used to develop rough estimates of local entrainment. Entrainment decays exponentially at a timescale on the order of days,/nand this timescale decreases as the discharge event increases. Total estimated entrainment is similar to the supply of suspendable sediment calculated to be in the bed.

Advisor: Hunt, James R.
Dietrich, William E.
Examining NAEP: The Effect of Item Format on Struggling 4th Graders' Reading Comprehension

Mixed item formats are in extensive use in large-scale assessment today and widely accepted as a means to improve assessment validity. Many studies have investigated the differential effect of Item Format on gender and ethnic subgroups in mathematics, yet few of these studies have attended to their impact on students with limited language proficiency and linguistic abilities in the area of reading. As educational policy increasingly mandates the inclusion of minorities such as English Language Learners (ELL) and students diagnosed with Specific Learning Disability (SLD) in federal and state assessment, many question the validity of achievement test scores because the degree to which the test score is a function of language proficiency is not clearly understood (Mahoney, 2008). To fill that research void, this study investigated Item Format effect and its interaction with (a) group membership as an ELL and/or SLD student and (b) assessment format differences related to genre and reading content. The software program ConQuest (Wu et al., 2007) was used to conduct Item Response Modeling on the 2007 NAEP 4th grade reading achievement data. Analysis demonstrated an overall hierarchy of Item Format difficulty. Contrary to expectation, DIF analysis demonstrated that flagged CR items favored both ELL and SLD students, while flagged MC items generally favored the Non-SLD group. But, multidimensional regression analysis demonstrated that there is no interaction between Item Format and group membership because the effect was virtually equivalent across MC and CR formats for the reference and focal groups. In looking to the future of assessment design, more research is needed to fully understand how Item Format differences contribute to assessment difficulty, the limited application of various Item Formats, specifically how they are suited to particular content, and how to blend Item Formats in a manner that utilizes their unique benefits while also producing fair results (Hastedt & Sibberns, 2005).

Advisor: Pearson, David
The Cellular and Molecular Basis of Multicellular Development in the Choanoflagellate Salpingoeca rosetta

For more than a century and half choanoflagellates, the closest living relatives of animals, have fascinated evolutionary biologists. By characterizing the similarities and differences between choanoflagellates and animals, biologists have gained insight into their last common ancestor, the Urchoanimal. Understanding how choanoflagellates form multicelled colonies has important implications for understanding the cellular and evolutionary foundations of animal multicellularity. I determined that the colony forming choanoflagellate Salpingoeca rosetta forms colonies by cell division and not by cell aggregation. The observation that cytoplasmic bridges connect cells in S. rosetta colonies and other colonial choanoflagellates, as well as cells in sponges, suggests that this mechanism of colony formation may be ancestral within the choanoflagellate lineage and may have been present in the Urchoanimal as well. To understand the molecular mechanisms underlying S. rosetta colony formation and cellular differentiation, I analyzed the genome and transcriptome of S. rosetta. The comparison of choanoflagellate genomes with animal genomes has revealed that many of the genes involved in the basic mechanisms of cell adhesion, signaling, and differentiation that were previously thought to be unique to animals are present in choanoflagellates, indicating that these genes were present in the Urchoanimal. These insights also refine our understanding of genes that emerged on the stem lineage leading to the last common ancestor of all animals, the Urmetazoan. By characterizing patterns of gene expression in different cell types, in particular colonial cells, I determined that different cell types have unique patterns of gene expression suggesting there is transcriptional basis for the observed differentiation. By characterizing the set of genes that are expressed at higher levels in particular cell types, I discovered that septins, known regulators of cytokinesis, are over-expressed in colonial cells. I also found that subsets of the cadherin gene family, known for its role in intercellular adhesion and signaling, are over-expressed in colonial cells and attached cells. Taken together these data suggest that S. rosetta cells have a number of development trajectories, including multicellular colonies, whose biology involves homologs of animal genes operating in conserved and novel functions.

Advisor: King, Nicole
The Holarctic Hacklemesh Spider Genus Callobius (Araneae: Amaurobiidae): Morphology, Systematics, and Population Biology

Interest in the California Floristic Province as a study region for scientists interested in biodiversity, evolution, systematics, and phylogeography has been increasing over the last several years. The amaurobiid spider genus Callobius (Chamberlin) occurs throughout the Northern Hemisphere, but is particularly common in western North America and particularly diverse in the California Floristic Province. An understanding of the evolutionary history of Callobius would contribute a great deal to this growing body of work, but the genus has received little attention since being revised in 1972. Since that time, a great deal has changed in the way biodiversity is studied. The Hennigian revolution changed the fundamental framework of systematics, and molecular techniques based on DNA sequences have brought enormous inferential power to bear on questions of systematics and population genetics, as well as almost every other discipline in organismal biology./nIn my doctoral work I have approached Callobius in the context of phylogenetic systematics and the biogeography of the California Floristic Province. First, I have taken a broad approach to the morphology of Callobius, particularly the morphology of the copulatory organs, as it might apply to cladistic investigations both within Callobius and more broadly among spiders. Second, I have undertaken a phylogenetic analysis of the subfamily Amaurobiinae, to illuminate evolutionary pattern within Callobius as well as between Callobius and other amaurobiine genera. And thirdly, I have used geometric morphometrics and population genetics to look for divergence within the widespread species Callobius severus./nI have produced an atlas to the genitalic morphology of Callobius, and propose a morphological diagnosis that is more consistent with principles of homology than those previously in use. I have also found and described the male of Callobius pauculus, previously known only from females. Although my phylogenetic analysis did not resolve the relationships between the amaurobiine genera, it does offer some support for the monophyly of Callobius and identifies a clade of California Floristic Province neoendemic species. My study of Callobius severus supports infra-specific structure, and suggests that the geography of the California Floristic Province is influencing the evolution of Callobius in patterns similar to its influence on other taxa.

Advisor: Will, Kipling W.
Becoming Joaquin Murrieta: John Rollin Ridge and the Making of an Icon

Becoming Joaquin Murrieta: John Rollin Ridge and the Making of an Icon analyzes the transnational archive of Joaquin Murrieta narratives. An icon of Mexican resistance during the California Gold Rush era, Murrieta has been described by Luis Leal as "the only Californian hero on the level of art, history, and myth." This dissertation explores the incarnation of Murrieta's elusive subjectivity in the first novel written by a Native American: Cherokee writer John Rollin Ridge's 1854 publication, The Life and Adventures of Joaquin Murieta, the Celebrated California Bandit. By examining the multigenerational influence of Ridge's novel as the textual origin point of the Murrieta archive, Becoming Joaquin Murrieta proposes a new understanding of Ridge's global significance./nJoaquin Murrieta is unique among folk heroes in that performers often assume his persona and metaphorically become the mythical hero, a pattern evident in the traditional borderlands ballad, "El Corrido de Joaquin Murrieta," and Rodolfo "Corky" Gonzales's poem, I Am Joaquin. This pattern is rooted in Ridge's configuration of Murrieta as a persona with the capacity to be anywhere at any time. Becoming Joaquin Murrieta reads Ridge's novel in conjunction with several notable and influential versions of the story: the 1859 California Police Gazette plagiarism of Ridge; Ireneo Paz's 1904 plagiarism of the Police Gazette; Adolfo Carrillo's 1922 short story; Walter Noble Burns's 1932 novel, The Robin Hood of El Dorado, and the 1936 MGM film of the same name; Los Madrugadores's 1934 recording of the corrido; Gonzales's epic Chicano poem of 1967; Pablo Neruda's 1967 play, Fulgor y Muerte de Joaquin Murieta (Splendor and Death of Joaquin Murieta); and Isabel Allende's 1999 novel, Hija de la Fortuna (Daughter of Fortune). In tracing the transnational production of the Murrieta narrative, Becoming Joaquin Murrieta exposes nationalist constructions that shape the archive's patterns of racialized violence and culturally sanctioned retaliation.

Advisor: Sweet Wong, Hertha D
The Role of Intracellular Trafficking of Alzheimer's Disease Amyloid Precursor Protein in Beta-Amyloid Peptide Formation

Amyloid precursor protein (APP) is processed sequentially by β-site APP cleaving enzyme (BACE) and γ-secretase to generate amyloid β (Aβ) peptides, one of the hallmarks of Alzheimer's disease. Endosomes or the trans-Golgi network (TGN) are suggested as major subcellular compartments favorable for Aβ production; however, it is still controversial where this process actually occurs. In this study, we investigated the role of different post-endocytic trafficking events in Aβ production using an RNA interference (RNAi) approach. Depletion of Hrs and Tsg101 acting early in the multivesicular bodies (MVB) pathway retained APP in early endosomes and reduced Aβ production. Conversely, depletion of CHMP6 and VPS4 acting late in the pathway rerouted endosomal APP to the TGN for enhanced APP processing. We also showed that VPS35-mediated APP recycling to the TGN was required for efficient Aβ production. Interfering with the bidirectional trafficking of APP between the TGN and endosomes, particularly retromer-mediated retrieval of APP from early endosomes to the TGN, resulted in the accumulation of endocytosed APP in early endosomes with reduced APP processing. These data suggested that Aβ was generated predominantly in the TGN, from the endocytosed pool of APP that had recycled from early endosomes to the TGN.

Advisor: Schekman, Randy
A Hierarchical Approach to Characterizing the Fracture Behavior of Bone utilizing Synchrotron Radiation

Bone has a complex hierarchical microstructure that spans from the nanoscale of the collagen molecules to the macroscopic physiological scale. In order to assess bone's risk of fracture with issues such as aging, disease, or irradiation it is critical to have a clear mechanistic framework which analyzes bone's deformation and fracture behavior at each structurally significant length scale. In this context, this present study seeks to characterize the fracture properties of bone by applying a hierarchical approach. Accordingly, this study utilizes x-ray microtomography from synchrotron radiation in order to identify the crack-resistant extrinsic mechanisms in different types of cortical bone. It was found that bone, which is a highly anisotropic material, displays toughening through crack deflection, out of plane twist and crack bridging. Next this study utilizes in situ tensile tests with x-ray scattering to investigate the submicron deformation in bone; at this length scale bone toughens intrinsically through plasticity mechanisms such as fibrillar sliding. Lastly, this study uses this mechanistic framework to evaluate the effects of irradiation on the fracture properties of bone. Here it was found that bone exposed to high doses of irradiation, greater than 70 kGy (Gy=J/Kg), leads to a severe progressive dose dependent degradation in strength, ductility, and toughness which is attributed to a change in the crack path (extrinsic effect) and a degradation of the collagen integrity from altered collagen cross-link (intrinsic effect). Overall, the goal of this work is to outline a framework that can be applied to future studies investigating the effects of disease and aging on bone.

Advisor: Ritchie, Robert O
African American Parent Involvement: An examination of the characteristics that determine the most successful school and parent relationships between lower socioeconomic, African American parents, and highly effective schools

Abstract/nAfrican American Parent Involvement:/nAn examination of the characteristics that determine the most successful school and parent relationships between lower socioeconomic, African American parents and highly effective schools/nby/nMarcheta Ganther-Williams/nDoctor of Education/nUniversity of California, Berkeley/nProfessor Ingrid Seyer-Ochi, Chair/nThe literature contains extensive research that focuses on parent involvement and parent involvement programs. The past decade and a half has warranted some parent involvement programs that focused on the student populations of African American students and lower socioeconomic status students. In schools in which the African American student population is small, establishing an African American parent group can help to develop relationships between families and the school to support students. This is especially important in schools in which the African American student population represents a low percentage of the school. In this study of three elementary schools, African American families are identified and their relationships with schools within the African American parent group are examined. In a review of the literature it was determined that continued study of how social status and social capital may moderate the effects of different types of parent involvement. Teachers, principals, and parents were examined./nUsing a case study format, this study focuses on three schools that have established/nAfrican American parent groups. Through staff and parent interviews and observations, the study focuses on how the group develops and builds relationship between African American parents, the school, the principal and the school community./nThe findings of the study show that an effective group has structures in place that support the sustainability of the group over time. Principal and parent commitment is an important factor to ensure the stability and focus of the group. Other factors, such a unity among the group, are needed in order for the group to function in an optimal way. By being united in numbers, the group will prosper and be able to gain the support necessary to be successful. The influence of effective African American parent groups in schools in which the African American parent population is proportionally small can have important implications for district policies and practices.

Advisor: Seyer-Ochi, Ingrid
Cross-sectional Variation of Measurement Error and Predictability of Earnings and Stock Returns

In capital markets research, market expectation of future earnings plays a vital role. However, almost all proxies inevitably measure the market expectation of future earnings with error, which results in unsatisfactory empirical outcomes in prior research (e.g., small empirical values of earnings response coefficient and poor quality estimates of expected rates of return). Using analysts' consensus forecasts, this study investigates how noisy measurement of the market expectation of future earnings affects the predictability of future earnings and stock returns. Based on the errors-in-variables approach, this study first provides a framework to capture cross-sectional variation of the measurement error in analysts' consensus forecasts. With this framework in place, this study documents that analysts' consensus forecasts with more measurement error have less ability to predict future earnings and stock returns, and that incorporating information about cross-sectional variation of the measurement error can improve the predictability of future earnings and stock returns. These findings will be useful to accounting research that relies on the market expectation of future earnings and to practitioners seeking to forecast profitability and stock returns.

Advisor: Sloan, Richard G