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Open Access Publications from the University of California

Scholarly Works (69 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2020)

Understanding how shoreline positions change in response to the variability of multitemporal climate and weather phenomena is essential for predicting the impact of future climate extremes. This dissertation aims to provide the first quantitative assessment on the relative influence of climate phenomena operating in the southwest Pacific region, i.e. El Niño-Southern Oscillation, on coastal morphodynamics along the southeast Queensland coast on a yearly to decadal timescale. Morphodynamic changes occurring at the timescale of days are also assessed in response to Tropical Cyclone Oma striking the region in February 2019. Previous attempts at directly correlating climate to natural shoreline evolution elsewhere were limited in their ability to observe the geomorphic changes as they relied on infrequent aerial photography, isolated beach profile data, or morphodynamic modeling results with no ground trothing. In an effort to capture intra-annual shoreline variability across large spatial scales (100’s km), shorelines are mapped using historical Landsat imagery. The accuracy of shorelines mapped automatically using spectral water indices was assessed by comparison to two contemporaneous GPS-surveyed intertidal zones, which represents the true position of the shoreline interface, which were conducted in Brazil and Massachusetts. The Modified Normalized Difference Water Index was determined to be the best index for automated shoreline mapping based on its superior accuracy and repeatable threshold value. MNDWI was used to automatically map over 9,000 km of historical shoreline positions along Queensland using Google Earth Engine. Shoreline change curves were generated using the USGS Digital Shoreline Analysis System and corrected for tidal variations using in situ gauge data and seasonal intertidal widths estimated from equilibrium beach profiles. Cross correlations between the shoreline dataset and the various climate indices were calculated using a 20 month maximum lag. Correlations suggest a bimodal climate control on shoreline change whereby El Niño-Southern Oscillation has the largest influence during negative Interdecadal Pacific Oscillation with the Subtropical Ridge becoming dominant during positive IPO. As observed using revolutionary PlanetScope satellite imagery, longshore transport along SE Queensland turned northwards in response to a significant anti-clockwise rotation of incident wave direction during Oma with erosion peaking at 41 m along the Sunshine Coast.

    Cover page: Climate-Driven Coastal Morphodynamics along Southeast Queensland, Australia
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2016)

    Background

    In 2012, the United States Preventative Services Task Force issued new guidelines recommending that male U.S. residents, irrespective of race, no longer be screened for prostate cancer. In African American men, the incidence of prostate cancer is almost 60 % higher and the mortality rate is two to three times greater than in Caucasians. The purpose of this study is to reduce African American men's prostate cancer burden by demonstrating they need separate screening guidelines.

    Methods

    We performed a PubMed search using the keywords: African American, Prostate cancer, Outcomes, Molecular markers, Prostate-specific Antigen velocity, PSA density, and to derive data relevant to our hypothesis.

    Results

    In our literature review, we identified several aspects of prostate cancer that are different in Caucasian and African American men. These included prostate cancer incidence and outcome, the clinical course of the disease, serum PSA levels, genetic differences, and social barriers. It's also important to note that the USPSTF guidelines were based on two studies, one of which reported that only 4 % of its participants were African American. The other did not report demographic information, but used participants from seven European countries with small African American populations.

    Conclusion

    Given the above, we conclude that separate prostate cancer screening guidelines are greatly necessary to help save the lives of African Americans.
      Cover page: Do African-American men need separate prostate cancer screening guidelines?
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2005)

      Functional-structural plant models simulate the development of plant structure, taking into account plant physiology and environmental factors. The L-PEACH model is based on the development of peach trees. It demonstrates the usefulness of L-systems in constructing functional-structural models. L-PEACH uses L-systems both to simulate the development of tree structure and to solve differential equations for carbohydrate flow and allocation. New L-system-based algorithms are devised for simulating the behavior of dynamically changing structures made of hundreds of interacting, time-varying, nonlinear components. L-PEACH incorporates a carbon-allocation model driven by source-sink interactions between tree components. Storage and mobilization of carbohydrates during the annual life cycle of a tree are taken into account. Carbohydrate production in the leaves is simulated based on the availability of water and light. Apices, internodes, leaves and fruit grow according to the resulting local carbohydrate supply. L-PEACH outputs an animated three-dimensional visual representation of the growing tree and user-specified statistics that characterize selected stages of plant development. The model is applied to simulate a tree's response to fruit thinning and changes in water stress. L-PEACH may be used to assist in horticultural decision-making processes after being calibrated to specific trees.

        Cover page: Using L-systems for modeling source-sink interactions, architecture and physiology of growing trees: the L-PEACH model
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2018)
          Cover page: Irradiation of HPV-associated oropharyngeal cancer: Is less really more?Creative Commons 'BY' version 4.0 license
          • Article
          LBL Publications (2006)
            Cover page: Biocompatible Ag-doped Carbon Coatings with Biocidal Effect
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2006)

            In contrast to the body of work in more mesic habitats, few studies have examined boundary processes between natural and anthropogenic desert landscapes. Our research examined processes occurring at boundaries between a desert sand dune community and an encroaching suburban habitat. We measured responses to an anthropogenic boundary by species from multiple trophic levels, and incorporated measures of habitat suitability, and temporal variation, at multiple spatial scales. At an edge versus core habitat scale the only aeolian sand species that demonstrated an unambiguous negative response to the anthropogenic habitat edges was the flat-tailed homed lizard (Phrynosoma mcallii). Conversely loggerhead shrikes (Lanius ludovicianus) demonstrated a positive response to that edge. At a finer scale, species that exhibited a response to a habitat edge within the first 250 m included the horned lizards along with desert kangaroo rats (Dipodomys deserti). The latter species' response was confined to 25 In from the edge. For the flat-tailed horned lizard, edge effects were measured up to 150 m from the habitat boundary. Three potential causal hypotheses were explored to explain the edge effect on horned lizards: (1) invasions of exotic ant species reducing potential prey for the lizards; (2) road avoidance and road associated mortalities; and (3) predation from a suite of avian predators whose occurrence and abundance may be augmented by resources available in the suburban habitat. We rejected the exotic ant hypothesis due to the absence of exotic ants within the boundary region, and because native ant species (prey for horned lizards) did not show an edge effect. Our data supported the predation and road mortality hypotheses. Mechanisms for regulating population dynamics of desert species are often "bottom-up," stochastic processes driven by precipitation. The juxtaposition of an anthropogenic edge appears to have created a shift to a "top-down," predator-mediated dynamic for these lizards. (c) 2006 Elsevier Ltd. All rights reserved.

              Cover page: Boundary processes between a desert sand dune community and an encroaching suburban landscape
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2014)

              Purpose

              Uncertainty exists regarding the optimal surveillance imaging strategy following stereotactic body radiation therapy (SBRT) for early-stage non-small cell lung cancer (NSCLC), particularly with respect to timing. We sought to determine how routine use of early (<6 months) posttreatment imaging affects subsequent management.

              Methods and materials

              The records of all patients treated with SBRT between January 2007 and January 2013 for early-stage NSCLC were reviewed. Eligible patients underwent ≥ 1 early (defined as within 6 months following SBRT) surveillance imaging study. Radiographic findings and subsequent diagnostic or therapeutic interventions were identified. Proportions and exact 95% confidence intervals (CI) with early posttreatment surveillance findings and altered treatment were calculated, and cases were examined descriptively.

              Results

              Sixty-two patients with 67 lung tumors underwent 92 early surveillance imaging studies (86 computed tomographic [CT] and 6 positron emission/CT) at a median of 2.1 months (range, 0.1-5.9 months). New lung nodules were identified in 8 patients (13%), leading to a diagnosis of metastatic disease treated with systemic therapy in 2 patients and biopsy proven solitary lung recurrence in 2 patients, both treated successfully with local therapy. Tumor growth meeting Response Evaluation Criteria in Solid Tumors (RECIST) criteria was identified in 1 patient, who was followed with subsequent radiographic regression. In aggregate, the treatment of 4 patients (6.5%, 95% CI 1.7%-15.2%) was altered by early imaging; 2 (3.2%, 95% CI 0.4%-10.8%) with a potentially curative intervention. No predictors for utility of early surveillance were identified.

              Conclusions

              Imaging within 6 months following SBRT for early-stage NSCLC resulted in a definitive intervention in approximately 3% of patients. In the era of cost-effective health care, a first scan at 6 months posttreatment may be adequate for most patients. Larger scale prospective studies are needed to address the optimal surveillance regimen following SBRT and to identify patients who may benefit from more aggressive surveillance regimens.
                Cover page: Does early posttreatment surveillance imaging affect subsequent management following stereotactic body radiation therapy for early-stage non-small cell lung cancer?
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2016)

                Objective

                Prior studies have relied on CT to assess alterations in anatomy among patients undergoing radiation for head and neck cancer. We sought to determine the feasibility of using MRI-based image-guided radiotherapy to quantify these changes and to ascertain their potential dosimetric implications.

                Methods

                6 patients with head and neck cancer were treated with intensity-modulated radiotherapy (IMRT) on a novel tri-60Co teletherapy system equipped with a 0.35-T MRI (VR, ViewRay Incorporated, Oakwood Village, OH) to 66-70 Gy in 33 fractions (fx). Pre-treatment MRIs on Fx 1, 5, 10, 15, 20, 25, 30 and 33 were imported into a contouring interface, where the primary gross tumour volume (GTV) and parotid glands were delineated. The centre of mass (COM) shifts for these structures were assessed relative to Day 1. Dosimetric data were co-registered with the MRIs, and doses to the GTV and parotid glands were assessed.

                Results

                Primary GTVs decreased significantly over the course of IMRT (median % volume loss, 38.7%; range, 29.5-72.0%; p < 0.05) at a median rate of 1.2%/fx (range, 0.92-2.2%/fx). Both the ipsilateral and contralateral parotid glands experienced significant volume loss (p < 0.05, for all) and shifted medially during IMRT. Weight loss correlated significantly with parotid gland volume loss and medial COM shift (p < 0.05).

                Conclusion

                Integrated on-board MRI can be used to accurately contour and analyze primary GTVs and parotid glands over the course of IMRT. COM shifts and significant volume reductions were observed, confirming the results of prior CT-based exercises. Advances in knowledge: The superior resolution of on-board MRI may facilitate online adaptive replanning in the future.
                  Cover page: Anatomic and dosimetric changes in patients with head and neck cancer treated with an integrated MRI-tri-60Co teletherapy device
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2018)

                  Purpose

                  The treatment of apical lung tumors with stereotactic body radiation therapy (SBRT) is challenging due to the proximity of the brachial plexus and the concern for nerve damage.

                  Methods and materials

                  Between June 2009 and February 2017, a total of 75 consecutive patients underwent SBRT for T1-T3N0 non-small cell lung cancer involving the upper lobe of the lung. All patients were treated with 4-dimensional computed tomography (CT)-based image guided SBRT to a dose of 40 to 60 Gy in 3 to 5 fractions. For dosimetric analysis, only apical tumors as defined by the location of the tumor epicenter superior to the aortic arch were included. The anatomical brachial plexus was delineated using the Radiation Therapy Oncology Group atlas.

                  Results

                  Thirty-one patients with 31 apical lung tumors satisfied the anatomical criteria for inclusion. The median age was 73 years (range, 58-89). The median planning target volume was 26.5 cc (range, 8.2-81.4 cc). The median brachial plexus, brachial plexus maximum dose (Dmax), Dmax per fraction, V22 (cc, 3-4 fractions), V30 (cc, 5 fractions), and biologically effective dose 3 Gy were 15.8 Gy (range, 1.7-66.5 Gy), 3.4 Gy (range, 0.6-14.7 Gy), 0.0 cc (range, 0-0.9 cc), 0.06 cc (range, 0-2.5 cc), and 31.5 Gy (range, 3.3-133.1 Gy), respectively. At a median follow-up of 17 months, the observed incidence of brachial plexopathy was 0%.

                  Conclusions

                  There is significant variation in dose to the brachial plexus for patients treated with SBRT for apical lung tumors. Although the incidence of neuropathic symptoms in this series was zero, further attention should be focused on the clinical implications of these findings.
                    Cover page: Brachial plexopathy after stereotactic body radiation therapy for apical lung cancer: Dosimetric analysis and preliminary clinical outcomes
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2019)
                    This paper has been retracted at the request of the authors.
                      Cover page: Retraction Note: Endocrine disruptors induce perturbations in endoplasmic reticulum and mitochondria of human pluripotent stem cell derivatives
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