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Open Access Publications from the University of California

Scholarly Works (11 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
        UCLA Previously Published Works (2015)
        © 2014. Neuronal pentraxin receptor (NPR) is a synaptic protein implicated in AMPA receptor trafficking at excitatory synapses. Since glutamate neurotransmission is disrupted in Alzheimer's disease (AD), NPR levels measured from plasma represent a potential biomarker for synaptic dysfunction associated with AD. We sought to determine the relationship between AD pathology and brain and plasma NPR levels by examining age-associated NPR levels in these compartments in a transgenic APP/PS1 rat model of AD. NPR levels in cortical homogenate were similar in wild-type (Wt) and APP/PS1 rats at 3. months of age (prior to Aβ plaque deposition), but significantly increased in APP/PS1 rats by 9 and 18-20. months of age (after the onset of plaque deposition). These age-dependent differences were driven by proportional increases in NPR in membrane-associated cortical fractions. Genotype-related differences in NPR expression were also seen in the hippocampus, which exhibits significant Aβ pathology, but not in the cerebellum, which does not. Plasma analyses revealed increased levels of a 26. kDa NPR fragment in APP/PS1 rats relative to Wt rats by 18-20. months of age, which correlated with the levels of full-length NPR in cortex. Our findings indicate that cerebral accumulation of NPR and Aβ occurs with similar temporal and regional patterns in the APP/PS1 model, and suggest that a 26. kDa plasma NPR fragment may represent a peripheral biomarker of this process.
          Cover page: Parallel age-associated changes in brain and plasma neuronal pentraxin receptor levels in a transgenic APP/PS1 rat model of Alzheimer's disease
          • 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 (2017)
            © 2017 Elsevier B.V. Background and aims With no established standard for assessing tobacco dependence (TD) across tobacco products in surveys, the Population Assessment of Tobacco and Health (PATH) Study provides a unique platform for examining the psychometric properties and validity of multiple indicators of tobacco dependence across a range of tobacco products. Participants A U.S. nationally representative sample from the 32,320 adult Wave 1 interviews with analyses focused on 14,287 respondents who were current established users of tobacco products. Findings This analysis confirms a single primary latent construct underlying responses to TD indicators for cigarettes, e-cigarettes, cigars, hookah, and smokeless tobacco products. Mutually exclusive past year tobacco-user groups included: cigarette only (n = 8689), e-cigarette only (n = 437), cigar only (traditional, cigarillo, or filtered) (n = 706), hookah only (n = 461), smokeless tobacco only (n = 971), cigarette plus e-cigarette (n = 709), and multiple tobacco product users (n = 2314). Differential Item Functioning (DIF) analyses supported use of 16 of the 24 examined TD indicators for comparisons across tobacco users. With cigarette users as a reference (mean = 0.0, SD = 1.0), we observed a range of TD with hookah (mean = −1.71) and cigar (mean = −1.92) only users being the lowest, and cigarette plus e-cigarette product users being the highest (mean = 0.35). Regression models including sociodemographic factors supported concurrent validity with increased product use frequency and TD among cigarette-only (p < 0.001), e-cigarette only (p < 0.002), cigar (p < 0.001), hookah only (p < 0.001), and smokeless tobacco users (p < 0.001). Conclusion The PATH Study Adult Wave 1 Questionnaire provided psychometrically valid measures of TD that enables future regulatory investigations of nicotine dependence across tobacco products.
              Cover page: Indicators of dependence for different types of tobacco product users: Descriptive findings from Wave 1 (2013–2014) of the Population Assessment of Tobacco and Health (PATH) study
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2017)
                Cover page: Design and methods of the Population Assessment of Tobacco and Health (PATH) Study
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2016)
                © 2016 AGA Institute Background & Aims Crohn's disease (CD) has the highest prevalence in Ashkenazi Jewish populations. We sought to identify rare, CD-associated frameshift variants of high functional and statistical effects. Methods We performed exome sequencing and array-based genotype analyses of 1477 Ashkenazi Jewish individuals with CD and 2614 Ashkenazi Jewish individuals without CD (controls). To validate our findings, we performed genotype analyses of an additional 1515 CD cases and 7052 controls for frameshift mutations in the colony-stimulating factor 2–receptor β common subunit gene (CSF2RB). Intestinal tissues and blood samples were collected from patients with CD; lamina propria leukocytes were isolated and expression of CSF2RB and granulocyte-macrophage colony–stimulating factor–responsive cells were defined by adenomatous polyposis coli (APC) time-of-flight mass cytometry (CyTOF analysis). Variants of CSF2RB were transfected into HEK293 cells and the expression and functions of gene products were compared. Results In the discovery cohort, we associated CD with a frameshift mutation in CSF2RB (P = 8.52 × 10-4); the finding was validated in the replication cohort (combined P = 3.42 × 10-6). Incubation of intestinal lamina propria leukocytes with granulocyte-macrophage colony–stimulating factor resulted in high levels of phosphorylation of signal transducer and activator of transcription (STAT5) and lesser increases in phosphorylation of extracellular signal–regulated kinase and AK straining transforming (AKT). Cells co-transfected with full-length and mutant forms of CSF2RB had reduced pSTAT5 after stimulation with granulocyte-macrophage colony–stimulating factor, compared with cells transfected with control CSF2RB, indicating a dominant-negative effect of the mutant gene. Monocytes from patients with CD who were heterozygous for the frameshift mutation (6% of CD cases analyzed) had reduced responses to granulocyte-macrophage colony–stimulating factor and markedly decreased activity of aldehyde dehydrogenase; activity of this enzyme has been associated with immune tolerance. Conclusions In a genetic analysis of Ashkenazi Jewish individuals, we associated CD with a frameshift mutation in CSF2RB. Intestinal monocytes from carriers of this mutation had reduced responses to granulocyte-macrophage colony–stimulating factor, providing an additional mechanism for alterations to the innate immune response in individuals with CD.
                  • 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
                    UCLA Previously Published Works (2016)
                    © 2016 Williams et al. Background: The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample. Results: A fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy. Conclusions: The identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased estimates of individual admixture with large error. This also occurs when estimating IGA using the Bayesian clustering method as implemented in the program STRUCTURE. Odds ratios for the associations of IGA with disease are consistent with what is known about the incidence and prevalence of diabetic nephropathy in these populations.
                      Cover page: Selecting SNPs informative for African, American Indian and European Ancestry: Application to the Family Investigation of Nephropathy and Diabetes (FIND)
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