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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Article
  • Peer Reviewed
Research Theses and Dissertations (2009)

Although many shark species are currently fished past sustainable levels, we lack the data to fully assess their status under traditional frameworks. There is an increasing need to develop and validate new methods to assess shark populations. In chapter one, I tested how well the ad hoc methods that use linear models would reflect sustainability as seen from a more conventional fisheries point of view. I compared two examples of linear demographic models to a conventional approach, that directly measures a species' sustainability, by assessing 26 shark species' vulnerability to fishing pressure using each method. I found that the linear demographic models resulted in different rankings and numerical values than the conventional approach. Because these ranking are used to inform management decisions, it is important to use approaches similar to the conventional metric, which directly measure a species' vulnerability. In chapter two, I developed a method to use catch-per-unit-effort and size-structure data from the common thresher shark, Alopias vulpinus, in an age-structured model to determine the fishing mortality (0.76 y"1) and the resulting recruitment decline (0.20 recruits egg"1). I determined the status of the population based on the fraction of current biomass (22%) and lifetime reproduction (0.47) relative to unfished levels. These values indicated that thresher sharks were overfished in 1992. This method is useful for other new fisheries with similar kinds of available data. In chapter three, I developed a new method to estimate the population abundance of white sharks, Carcharodon carcharias, off central California, where no fishery data exist. Because a white shark's fin allows each individual to be uniquely identified and they showed predictable annual fidelity at coastal sites, I was able to compute a mark-recapture abundance estimate using a Bayesian algorithm. I collected 321 photographs identifying 131 unique individuals. The abundance off central California was estimated to be 251 individuals ([197,360] 2.5% and 97.5% quantiles). My methods can be readily expanded to include juvenile and young-of-the-year sharks and sharks from other locations, over extended time- series, and to monitor the status, population trends and protection needs for white sharks.

    Cover page: Methods for Assessment of Data-Poor Shark Species
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2019)

    The poems that follow explore the divinity that resides within the profane world, among other subjects. This is an excerpt from a longer, original work. The voice here fluctuates between higher and lower diction and offers a range of personas that seek to represent the multi-dimensional spheres of the self. Themes and subjects deal with interrogation of the self, gender, sexuality, transformation, family, spirituality, ethics, politics, and the contradictions that occur when one’s strivings towards idealism are met head-on with reality.

      • Article
      • Peer Reviewed
      UC Merced Previously Published Works (2008)
      Ice cores collected in 2000 (ITASE 00-1) and 2005 (WDC05A, WDC05Q) from the West Antarctic Ice Sheet Divide (WAIS Divide) project site were used to investigate the spatial and temporal variability in accumulation. The ice cores were dated based on annual layer counting of multiple glaciochemical measurements resulting in bottom depth ages for WDC05A, VVDC05Q, and ITASE 00-1 of 1775, 1521, and 1653 A.D., with mean annual accumulation rates of 0.200, 0.204, and 0.221 mweq a-1, respectively. Small-scale spatial variability (SSV) was determined using an analysis of variance of accumulation in the ice core array, thereby quantifying the uncertainty in individual accumulation records. Results indicate that the spatial variability was 0.030 mweq a-1, or approximately 15% of the average annual accumulation. An accumulation record representative of the WAIS Divide local area over recent centuries was developed using a principal component analysis to identify the coherent accumulation signal. The WAIS Divide local record exhibited 14% interannual variability (1 standard deviation of the mean) with the SSV reduced to 0.017 mweq a-1. Correlations of the WAIS Divide local accumulation record with atmospheric indices (e.g., Antarctic Oscillation) exhibited periods when the records oscillate in and out of phase. Thus, reconstructing local and global atmospheric indices from WAIS Divide accumulation records over recent centuries may prove problematic. Copyright 2008 by the American Geophysical Union.
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2019)
        Coordinated efforts between macrophages and epithelia are considered essential for wound healing, but the macrophage-derived molecules responsible for repair are poorly defined. This work demonstrates that lung macrophages rely upon Trefoil factor 2 to promote epithelial proliferation following damage caused by sterile wounding, Nippostrongylus brasiliensis or Bleomycin sulfate. Unexpectedly, the presence of T, B, or ILC populations was not essential for macrophage-driven repair. Instead, conditional deletion of TFF2 in myeloid-restricted CD11cCre TFF2 flox mice exacerbated lung pathology and reduced the proliferative expansion of CD45- EpCAM+ pro-SPC+ alveolar type 2 cells. TFF2 deficient macrophages had reduced expression of the Wnt genes Wnt4 and Wnt16 and reconstitution of hookworm-infected CD11cCre TFF2flox mice with rWnt4 and rWnt16 restored the proliferative defect in lung epithelia post-injury. These data reveal a previously unrecognized mechanism wherein lung myeloid phagocytes utilize a TFF2/Wnt axis as a mechanism that drives epithelial proliferation following lung injury.
          Cover page: Macrophages promote epithelial proliferation following infectious and non-infectious lung injury through a Trefoil factor 2-dependent mechanism.
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2006)
            Cover page: Feasibility of three-dimensional optical coherence tomography and optical Doppler tomography of malignancy in hamster cheek pouchesCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2020)
            BACKGROUND:Only 40-60% of patients with generalized anxiety disorder experience long-lasting improvement with gold standard psychosocial interventions. Identifying neurobehavioral factors that predict treatment success might provide specific targets for more individualized interventions, fostering more optimal outcomes and bringing us closer to the goal of "personalized medicine." Research suggests that reward and threat processing (approach/avoidance behavior) and cognitive control may be important for understanding anxiety and comorbid depressive disorders and may have relevance to treatment outcomes. This study was designed to determine whether approach-avoidance behaviors and associated neural responses moderate treatment response to exposure-based versus behavioral activation therapy for generalized anxiety disorder. METHODS/DESIGN:We are conducting a randomized controlled trial involving two 10-week group-based interventions: exposure-based therapy or behavioral activation therapy. These interventions focus on specific and unique aspects of threat and reward processing, respectively. Prior to and after treatment, participants are interviewed and undergo behavioral, biomarker, and neuroimaging assessments, with a focus on approach and avoidance processing and decision-making. Primary analyses will use mixed models to examine whether hypothesized approach, avoidance, and conflict arbitration behaviors and associated neural responses at baseline moderate symptom change with treatment, as assessed using the Generalized Anxiety Disorder-7 item scale. Exploratory analyses will examine additional potential treatment moderators and use data reduction and machine learning methods. DISCUSSION:This protocol provides a framework for how studies may be designed to move the field toward neuroscience-informed and personalized psychosocial treatments. The results of this trial will have implications for approach-avoidance processing in generalized anxiety disorder, relationships between levels of analysis (i.e., behavioral, neural), and predictors of behavioral therapy outcome. TRIAL REGISTRATION:The study was retrospectively registered within 21 days of first participant enrollment in accordance with FDAAA 801 with ClinicalTrials.gov, NCT02807480. Registered on June 21, 2016, before results.
              Cover page: Protocol for a randomized controlled trial examining multilevel prediction of response to behavioral activation and exposure-based therapy for generalized anxiety disorder.
              • Article
              • Peer Reviewed
              UC Merced Previously Published Works (2012)
              The white shark (Carcharodon carcharias) is a wide-ranging apex predator in the northeastern Pacific (NEP). Electronic tagging has demonstrated that white sharks exhibit a regular migratory pattern, occurring at coastal sites during the late summer, autumn and early winter and moving offshore to oceanic habitats during the remainder of the year, although the purpose of these migrations remains unclear. The purpose of this study was to use stable isotope analysis (SIA) to provide insight into the trophic ecology and migratory behaviors of white sharks in the NEP. Between 2006 and 2009, 53 white sharks were biopsied in central California to obtain dermal and muscle tissues, which were analyzed for stable isotope values of carbon (δ(13)C) and nitrogen (δ(15)N). We developed a mixing model that directly incorporates movement data and tissue incorporation (turnover) rates to better estimate the relative importance of different focal areas to white shark diet and elucidate their migratory behavior. Mixing model results for muscle showed a relatively equal dietary contribution from coastal and offshore regions, indicating that white sharks forage in both areas. However, model results indicated that sharks foraged at a higher relative rate in coastal habitats. There was a negative relationship between shark length and muscle δ(13)C and δ(15)N values, which may indicate ontogenetic changes in habitat use related to onset of maturity. The isotopic composition of dermal tissue was consistent with a more rapid incorporation rate than muscle and may represent more recent foraging. Low offshore consumption rates suggest that it is unlikely that foraging is the primary purpose of the offshore migrations. These results demonstrate how SIA can provide insight into the trophic ecology and migratory behavior of marine predators, especially when coupled with electronic tagging data.
                Cover page: Using stable isotope analysis to understand the migration and trophic ecology of northeastern Pacific white sharks (Carcharodon carcharias).
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2018)
                Increasingly, evidence suggests that exposure to maternal obesity creates an inflammatory environment in utero, exerting long-lasting postnatal signatures on the juvenile innate immune system and microbiome that may predispose offspring to development of fatty liver disease. We found that exposure to a maternal Western-style diet (WD) accelerated fibrogenesis in the liver of offspring and was associated with early recruitment of proinflammatory macrophages at 8-12 weeks and microbial dysbiosis as early as 3 weeks of age. We further demonstrated that bone marrow-derived macrophages (BMDMs) were polarized toward an inflammatory state at 8 weeks of age and that a potent antioxidant, pyrroloquinoline quinone (PQQ), reversed BMDM metabolic reprogramming from glycolytic toward oxidative metabolism by restoring trichloroacetic acid cycle function at isocitrate dehydrogenase. This resulted in reduced inflammation and inhibited collagen fibril formation in the liver at 20 weeks of age, even when PQQ was withdrawn at 3 weeks of age. Beginning at 3 weeks of age, WD-fed mice developed a decreased abundance of Parabacteroides and Lactobacillus, together with increased Ruminococcus and decreased tight junction gene expression by 20 weeks, whereas microbiota of mice exposed to PQQ retained compositional stability with age, which was associated with improved liver health. Conclusion: Exposure to a maternal WD induces early gut dysbiosis and disrupts intestinal tight junctions, resulting in BMDM polarization and induction of proinflammatory and profibrotic programs in the offspring that persist into adulthood. Disrupted macrophage and microbiota function can be attenuated by short-term maternal treatment with PQQ prior to weaning, suggesting that reshaping the early gut microbiota in combination with reprogramming macrophages during early weaning may alleviate the sustained proinflammatory environment, preventing the rapid progression of nonalcoholic fatty liver disease to nonalcoholic steatohepatitis in offspring of obese mothers. (Hepatology Communications 2018;2:313-328).
                  Cover page: Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice.Creative Commons 'BY' version 4.0 license
                  • Article
                  Lawrence Berkeley National Laboratory (2003)

                  The proposed SuperNova/Acceleration Probe (SNAP) mission will have a two-meter class telescope delivering diffraction-limited images to an instrumented 0.7 square degree field in the visible and near-infrared wavelength regime. The requirements for the instrument suite and the present configuration of the focal plane concept are presented. A two year R&D phase, largely supported by the Department of Energy, is just beginning. We describe the development activities that are taking place to advance our preparedness for mission proposal in the areas of detectors and electronics.

                    Cover page: SNAP Satellite Focal Plane Development
                    • Article
                    • Peer Reviewed
                    Recent Work (2017)
                    The Supernova / Acceleration Probe (SNAP) is a proposed space-based experiment designed to study the dark energy and alternative explanations of the acceleration of the Universe's expansion by performing a series of complementary systematics-controlled measurements. We describe a self-consistent reference mission design for building a Type Ia supernova Hubble diagram and for performing a wide-area weak gravitational lensing study. A 2-m wide-field telescope feeds a focal plane consisting of a 0.7 square-degree imager tiled with equal areas of optical CCDs and near infrared sensors, and a high-efficiency low-resolution integral field spectrograph. The SNAP mission will obtain high-signal-to-noise calibrated light-curves and spectra for several thousand supernovae at redshifts between z=0.1 and 1.7. A wide-field survey covering one thousand square degrees resolves ~100 galaxies per square arcminute. If we assume we live in a cosmological-constant-dominated Universe, the matter density, dark energy density, and flatness of space can all be measured with SNAP supernova and weak-lensing measurements to a systematics-limited accuracy of 1%. For a flat universe, the density-to-pressure ratio of dark energy can be similarly measured to 5% for the present value w0 and ~0.1 for the time variation w'. The large survey area, depth, spatial resolution, time-sampling, and nine-band optical to NIR photometry will support additional independent and/or complementary dark-energy measurement approaches as well as a broad range of auxiliary science programs. (Abridged)
                      Cover page: Supernova / Acceleration Probe: A Satellite Experiment to Study the Nature of the Dark Energy
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