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Open Access Publications from the University of California

Scholarly Works (30 results)

  • Thesis
  • Peer Reviewed
UC Santa Barbara Electronic Theses and Dissertations (2022)

Scholars of Spanish colonial Texas history have typically described the province as an impoverished economic backwater. With limited access to markets, according to this view, Hispanic residents barely scraped out a living. A close reading of a variety of archival documents and archaeological reports, however, reveals that a robust dual economy based on different systems of trade emerged in the province during the eighteenth century. A legal system of trade connected San Antonio with Mexico City, and with regional markets in Saltillo, Nueva Viscaya, and Coahuila. Extralegal trade among Hispanic and indigenous inhabitants in east Texas, and French traders and residents in Louisiana, tapped into the trans-Atlantic economy and the desire for European goods. This dissertation extends Daniel Usner, Jr.’s concept of a frontier exchange economy in the lower Mississippi Valley to the extralegal trade that took place in the Texas-Louisiana borderlands, and deepens understanding of the significance of extralegal trade in the broader Spanish American colonial world. By examining economic transactions within the mission system, trade conducted by governors, and exchanges carried out by people across the social spectrum, this study offers a new understanding of the ways in which institutions and individuals were able to support their livelihoods, while the Spanish Crown underfunded the military and ecclesiastical administration of Texas. The importance of the frontier exchange economy is further underscored by the fact that during the early nineteenth century, local insurrectionists and royalists alike viewed open, legal trade across the Texas-Louisiana border as strategic to their respective causes. The bloody aftermath of the rebellions in Texas, together with demographic change and Mexico’s nationalist policies following independence, disrupted the dual economies and eventually enmeshed the province in new tensions between market and state.

    Cover page: "Bartering Hunger for Nakedness": The Frontier Exchange Economy of Spanish Colonial Texas
    • Article
    • Peer Reviewed
    Proceedings of the Annual Meeting of the Cognitive Science Society, Volume 28 (2006)
      Cover page: Twenty-five Years After 'Metaphors we Live by': The Absence of the topic of metaphor in introductory psychology textbooks
      • Thesis
      • Peer Reviewed
      UC Irvine Electronic Theses and Dissertations (2024)

      This thesis presents an atomic-level investigation into chemical processes occurring on heterogeneous interfaces. Specifically, it delves into the catalytic surface reaction at the gas-solid interface and charge transfer at the liquid-solid interface, using ab initio simulations based on Density Functional Theory (DFT) calculations. The first topic addresses heterogeneous catalysis of ethane hydrogenolysis using Ru and Co catalysts with oxide supports (SiO2, TiO2, ZrO2), for chemical recycling of plastic waste. This study aims to investigate the role of oxide support on the reactivity of metal catalysts. We use DFT combined with Climbing Image Nudged Elastic Band (CI-NEB) and harmonic approximation (HA) methods to obtain the free energy profile of the molecular dissociation of adsorbed *CHCH* to 2CH* – the rate-limiting step of ethane hydrogenolysis – on metal surfaces. Comparing the two metals without the oxide support, we find that Ru(0001) has a lower free energy of the transition state (TS) compared to Co(0001), in agreement with Ru being the most reactive catalyst for ethane hydrogenolysis. However, we find that the free energy of the TS state in Co with SiO2, TiO2, ZrO2 is lower than either Co(0001) or Ru(0001). The results suggest that the reaction barrier using Co can be lowered using oxide supports, making the earth-abundant Co a competitive catalyst for rare-earth metal Ru. The second topic explores the charge stability of boron vacancy in hexagonal boron nitride (hBN) in contact with water with varying thicknesses of hBN for quantum sensing applications in an aqueous environment. Despite previous literature highlighting the existence of negatively charged boron vacancy in hBN as a promising spin qubit, little is known about its stability in water. To address this gap, we carry out ab initio molecular dynamics simulations based on DFT for hBN in contact with water to study the charge transfer to boron vacancy from two types of electron donors: an oxygen dopant in hBN serving as a “static electron donor”, and the hydronium radical in water serving as a “mobile electron donor”. We find that the spin triplet state of boron vacancy is stable in a monolayer hBN in contact with water using either electron donor, suggesting that the charge transfer efficiency from the donor to the vacancy is efficient for monolayer hBN. However, in bulk hBN, the charge transfer efficiency to the boron vacancy appears to be limited using a hydronium radical, and there is a significant fluctuation in the charge state of boron vacancy in bulk hBN. This finding contrasts sharply with spin defects in 3D semiconductors, e.g., nitrogen-vacancy centers in diamonds, where the charge stability decreases as the location of the defect is closer to the surface.

        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)

        Background

        Idiopathic inflammatory airway disease (IAD) in cats often is described as asthmatic (eosinophilic) or bronchitic (neutrophilic), but this designation requires collection of airway fluid and it fails to consider cats with mixed airway inflammation.

        Objective

        To identify clinical features that would differentiate inflammatory disease types.

        Animals

        Forty-nine cats with nonspecific airway inflammation identified by bronchoscopic bronchoalveolar lavage (BAL) between 2011 and 2018 were evaluated.

        Methods

        This is a retrospective study. Cats were categorized by BAL differential cytology as having eosinophilic (eosinophils >20% with neutrophils <14%, or eosinophils >50%), mixed (eosinophils 20%-50% and neutrophils >14% or discordant inflammation from 2 BAL sites), or neutrophilic (neutrophils >14% and eosinophils <20%) inflammation. Type and duration of presenting complaints, signalment, body condition score, respiratory rate, CBC results, bronchoscopy, BAL results (% recovery, total nucleated cell count, differential cell count), and radiographic findings were compared among groups.

        Results

        Idiopathic IAD was diagnosed in 49 cats, with BAL eosinophilic inflammation in 23, mixed inflammation in 14, and neutrophilic inflammation in 12. Cough was the predominant presenting complaint with no difference in duration of signs among groups (median, 5.5 months). Respiratory rate and effort also did not differ. Cats with eosinophilic inflammation were significantly younger (4.4 ± 3.3 years) than those with neutrophilic (8.0 ±5.6 years) or mixed inflammation (7.5 ± 4.0 years; P = .03). Results of CBC and interpretation of radiographic findings did not differ among groups.

        Conclusions and clinical importance

        Substantial overlap exists in clinical and radiographic findings in cats with various forms of idiopathic airway inflammation.
          Cover page: Clinical features and radiographic findings in cats with eosinophilic, neutrophilic, and mixed airway inflammation (2011‐2018)
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2020)
          Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6 We find that capsid hexamers and pentamers have differential binding modes for IP6 Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.
            Cover page: Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)Creative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Irvine Previously Published Works (2021)
            Spin defects in wide-bandgap semiconductors provide a promising platform to create qubits for quantum technologies. Their synthesis, however, presents considerable challenges, and the mechanisms responsible for their generation or annihilation are poorly understood. Here, we elucidate spin defect formation processes in a binary crystal for a key qubit candidate-the divacancy complex (VV) in silicon carbide (SiC). Using atomistic models, enhanced sampling simulations, and density functional theory calculations, we find that VV formation is a thermally activated process that competes with the conversion of silicon (VSi) to carbon monovacancies (VC), and that VV reorientation can occur without dissociation. We also find that increasing the concentration of VSi relative to VC favors the formation of divacancies. Moreover, we identify pathways to create spin defects consisting of antisite-double vacancy complexes and determine their electronic properties. The detailed view of the mechanisms that underpin the formation and dynamics of spin defects presented here may facilitate the realization of qubits in an industrially relevant material.
              Cover page: Stability and molecular pathways to the formation of spin defects in silicon carbide
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2022)
              SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.
                Cover page: Strain and rupture of HIV-1 capsids during uncoatingCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2020)

                Background

                A nonpedigreed male cat presented with epistaxis, severe bladder hemorrhage, and secondary urethral obstruction after cystocentesis.

                Objectives

                To characterize the phenotype of a cat with bleeding diathesis and use a precision medicine approach to identify the molecular genetic defect by whole genome sequencing.

                Methods

                Adenosine diphosphate (ADP) and arachidonic acid (AA)-induced whole blood platelet aggregometry was performed in the affected cat and a healthy cat. Platelet activation, measured by P-selectin expression, and surface integrin subunit β3 expression were evaluated by flow cytometry in the affected cat and healthy control. Total integrin subunit αIIb expression was assessed by western blot. Whole genome sequencing at 30× coverage was used to identify genetic variants that segregated in the affected cat compared to 194 cats from the 99 Lives Sequencing Consortium.

                Results

                Platelet aggregometry identified significant impairment in platelet aggregation in response to ADP and AA compared to the control cat. Targeted protein expression analyses by flow cytometry and immunoblot analysis determined that the surface expression and total expression of the integrin, αIIbβ3, was absent. Whole genome sequencing identified a homozygous c.1986delC frameshift variant in the integrin subunit αIIb (ITGA2B) gene that was not detected in the control population. The p.Pro662fs (ITGA2B P662X) variant terminates translation of the protein at the extracellular domain of the integrin prematurely, which is predicted to affect expression of the β3 unit.

                Conclusions and clinical importance

                This novel ITGA2B variant and the associated phenotype closely resemble Glanzmann's thrombasthenia, which has never been reported in cats.
                  Cover page: Precision medicine identifies a pathogenic variant of the ITGA2B gene responsible for Glanzmann's thrombasthenia in a cat
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  Introduction: The study objectives were to estimate plasma flunixin (FLU) pharmacokinetic parameters and milk depletion profiles for FLU and its metabolite (5-hydroxy flunixin; 5-OH) after subcutaneous (SC) and intravenous (IV) administration of single and multiple flunixin meglumine (FM) doses to non-lactating (nulliparous and pregnant does) and lactating dairy goats. Analytical methods (ELISA and UPLC-MS/MS) for quantifying plasma FLU concentrations were compared. The final objective was to use regulatory (FDA and EMA) methods to estimate milk withdrawal intervals following extra-label drug use in goats. Methods: FM was administered IV and SC to commercial dairy goats at 1.1 mg/kg for single and multiple doses. Plasma and milk samples were analyzed for FLU and 5-OH via UPLC-MS/MS. Plasma samples were also analyzed for FLU concentrations via ELISA. Using statistical approaches recommended by regulatory agencies, milk withdrawal intervals were estimated following FM extra-label use. Results: Following IV administration of a single FM dose, clearances were 127, 199, and 365 ml/kg/h for non-lactating (NL) pregnant does, NL nulliparous does, and lactating dairy does, respectively. Following multiple SC doses, clearance/F was 199 ml/kg/h for lactating does. After IV administration of a single FM dose, terminal elimination half-lives were 4.08, 2.87, and 3.77 h for NL pregnant does, NL nulliparous does, and lactating dairy does, respectively. After multiple SC doses, the terminal elimination half-life was 3.03 h for lactating dairy does. No significant differences were noted for samples analyzed by UPLC-MS/MS or ELISA. Milk withdrawal intervals ranged from 36 to 60 h depending on the regulatory statistical method and dosage regimen. Conclusions: Subcutaneous administration of FM to goats results in similar plasma pharmacokinetic parameters as IV administration. ELISA analysis is an alternative method to UPLC-MS/MS for quantifying FLU concentrations in caprine plasma samples. Following FM extra-label administration to dairy goats, clinicians could consider 36-60 h milk withdrawal intervals.
                    Cover page: Pharmacokinetic Parameters and Estimated Milk Withdrawal Intervals for Domestic Goats (Capra Aegagrus Hircus) After Administration of Single and Multiple Intravenous and Subcutaneous Doses of Flunixin Meglumine
                    • Article
                    • Peer Reviewed
                    Accelerator Tech-Applied Phys (2021)
                    A large bore 'High-Temperature Superconductor Cable Test Facility Magnet' for testing advanced cables and inserts in high transverse field is in its design phase. This magnet will be the core component of a facility for developing conductors and accelerator magnets operating above 15 T, an enabling technology for next-generation fusion devices using magnetic confinement of plasma and for future energy frontier colliders. The procurement of Nb3Sn conductor, fabrication of cables, winding of coils, and assembly of the dipole magnet will be done at Lawrence Berkeley National Laboratory (LBNL) and the test pit and cryostat will be constructed at Fermi National Accelerator Laboratory. This article will present the conductor element of the LBNL project, specifically cable design parameters (based on the Bruker OST RRP^{\bigcirc \!\!\!\! {\hbox{R}}} Nb3Sn superconducting wire) and the development phase cable fabrication experience. Challenges of the cable fabrication will be discussed. The wire and cable planned for this magnet are similar to those under study for the Future Circular Collider and other large facility magnets. The successful fabrication of the development cable has positive implications for these other projects.
                      Cover page: Cable Design and Development for the High-Temperature Superconductor Cable Test Facility Magnet
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