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Open Access Publications from the University of California

Scholarly Works (24 results)

  • Article
  • Peer Reviewed
The Indigenous Peoples’ Journal of Law, Culture & Resistance, Volume 5, Issue 1 (2019)
    Cover page: The Doctrine of Discovery: The International Law of Colonialism
    • Article
    American Indian Culture and Research Journal , Volume 32, Issue 3 (2008)
      Cover page: Pagans in the Promised Land: Decoding the Doctrine of Christian Discovery. By Steven T. Newcomb.Creative Commons 'BY-NC' version 4.0 license
      • Thesis
      • Peer Reviewed
      UC Santa Barbara Electronic Theses and Dissertations (2023)

      Rocky intertidal ecosystems in California have been significantly degraded. Of particular concern is the precipitous population decline of rockweeds attributed to increased urbanization and accompanying impacts. As foundation species, rockweeds modify the physical environment of rocky intertidal habitats and increase biodiversity by decreasing environmental stress under their canopy. No substitute macrophyte species in southern California provides a comparable function to rockweeds in the intertidal zone. Recovery of impacted rockweed populations is typically slow and unpredictable, due to their poor dispersal capacity. To determine the status of the dominant rockweed species in southern California, Silvetia compressa, I analyzed canopy cover data from 30 sites spanning 18 years. I found that the rockweed had declined markedly at sites south of the major biogeographic break, Point Conception (PC), including the California Channel Islands and southern California mainland. Analyses using climatological data revealed that substantial declines in Silvetia cover in southern California were associated with strong, hot offshore Santa Ana wind events. To assess the recovery of disturbed rocky intertidal ecosystems, I analyzed 28 years of data from a controlled disturbance experiment at a remote site with limited human visitation. I found the recolonization rates for species cleared to be highly variable ranging from years to decades, and that even relatively mild disturbances from pedestrian traffic can have long-lasting effects on rockweeds. Long-lived species such as rockweeds and mussels took more time to recover from extreme disturbances than species with shorter lifespans such as barnacles and turfweed. Since rockweeds foundational to ecosystem functioning have sustained extensive degeneration and range contractions worldwide, and recovery of impacted rockweed populations is typically slow and unpredictable due to their limited dispersal capacity, I propose that rockweeds are optimal candidates for restoration. In my third chapter, I summarize the current knowledge of rockweed ecology, highlighting studies that could inform restoration practices, and recommend ways to improve our ability to implement scalable restoration of rockweeds and accompanying ecosystem-wide benefits.

        Cover page: Assessing Decline and Recovery of Rocky Intertidal Foundation Species Using Long-Term Data
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2020)
        Artificial surfaces in coastal waters and offshore oceans, including boat hulls, docks, and offshore structures, are invariably colonized, or fouled, by a host of sessile species known collectively as fouling communities. Fouling has great economic impacts on shipping and other marine industries and plays an important role in the spread of marine invasive species across the globe. The main strategy to prevent fouling of artificial surfaces is application of antifouling coatings containing varying concentrations and mixtures of biocides. Presently, copper and zinc are popular antifouling biocides, and the latter is gaining in usage due to the known toxic characteristics of copper in the marine environment and consequent regulation and consumer opinion. Nanomaterials, including Cu and ZnO nanoparticles, have been explored as a way to efficiently deliver biocides from coating matrices. Here, we examine the efficacy and biocide release characteristics of several copper- and zinc-based antifouling coatings, including formulations containing traditional micron-sized Cu and ZnO particles and two containing copper and ZnO nanoparticles, respectively. Most of the antifouling coatings tested significantly reduced the abundance and biodiversity of the fouling community in the three study locations across California. Invasive species were suppressed by most coatings at similar levels to natives, suggesting that in general, antifouling coatings do not favor invasive species. We found that zinc-based antifouling coatings were similar and in some cases better performing than copper, despite the generally lower toxicity of zinc to aquatic organisms compared with copper. The performance of zinc-based coatings, moreover, was not directly related to the amount of zinc released into the water or their zinc content. Nano-based coatings did not offer any clear advantages over non-nano coatings, either in the degree of Zn leaching or fouling suppression. Coating matrix properties clearly are an important factor affecting the efficacy and biocide leaching rate of antifouling coatings.
          Cover page: Nano and traditional copper and zinc antifouling coatings: metal release and impact on marine sessile invertebrate communities
          • Article
          • Peer Reviewed
          UC Santa Barbara Previously Published Works (2017)
          Logistical and financial limitations of underwater operations are inherent in marine science, including biodiversity observation. Imagery is a promising way to address these challenges, but the diversity of organisms thwarts simple automated analysis. Recent developments in computer vision methods, such as convolutional neural networks (CNN), are promising for automated classification, detection and segmentation tasks but are typically computationally expensive and require extensive training on large datasets. Therefore, harnessing distributed computation, large storage and human annotations of diverse marine datasets is crucial for effective application of these methods. BisQue is a cloud-based system for management, annotation, visualization, analysis and data mining of complex multi-dimensional underwater and remote sensing imagery and associated data. It is designed to hide the complexity of distributed storage, large computational clusters, diversity of data formats and heterogeneous computational environments behind a user friendly web-based interface. BisQue is built around an idea of flexible and hierarchical annotations defined by the user. Such textual and graphical annotations can describe captured attributes and the relationships between data elements. Annotations are powerful enough to describe cells in fluorescent 4D images, fish species in underwater videos and kelp beds in aerial imagery. We are developing a deep learning service for automated image classification. The service allows training various models with a single click, validating their performance and providing several modes of classification: point classification for percent cover, image partitioning for substrate description and object detection for counting organisms. Semantic segmentation can be used to classify all pixels in an image, allowing estimation of organism size and species interactions. Our experiments on identification of 11 benthic marine organisms within a dataset of 2K images with 200K annotations demonstrate good performance with the overall accuracy of 86% and 4% error. We are now constructing a hierarchical model of more than 300 species on 6K images with 1M annotations.
            Cover page: Deep learning for all:  managing and analyzing underwater and remote sensing imagery on the web using BisQue
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2019)
              Cover page: Spatial Planning of Marine Aquaculture Under Climate Decadal Variability: A Case Study for Mussel Farms in Southern California
              • Article
              • Peer Reviewed
              UC Santa Barbara Previously Published Works (2013)
              Estuarine and marine sediments are a probable end point for many engineered nanoparticles (ENPs) due to enhanced aggregation and sedimentation in marine waters, as well as uptake and deposition by suspension-feeding organisms on the seafloor. Benthic infaunal organisms living in sediments encounter relatively high concentrations of pollutants and may also suffer toxic effects of ENPs. We tested whether three heavily used metal oxide ENPs, zinc oxide (ZnO), copper oxide (CuO), and nickel oxide (NiO) were toxic to an estuarine amphipod, Leptocheirus plumulosus. We used results from 10-day laboratory bioassays to estimate potential demographic impacts of ENP exposure. We also evaluated fate and transport pathways of the ENPs in the experiments to elucidate routes of uptake and exposure. Dissolved Zn was found in sediment pore water and overlying water samples at 10 fold the concentrations of Cu or Ni, a pattern indicative of the relatively high dissolution rate of ZnO ENPs compared with CuO and NiO ENPs. Accumulation of metals in amphipod tissues increased with exposure concentrations for all three ENPs, suggesting possible exposure pathways to higher taxa. Amphipods accumulated ≤600 μg Zn and Cu g(-1) and 1000 μg Ni g(-1). Amphipod mortality increased with ZnO and CuO concentrations, but showed no significant increase with NiO to concentrations as high as 2000 μg g(-1). The median lethal concentration in sediment (LC50) of ZnO was 763 μg g(-1) and 868 μg g(-1) for CuO ENPs. Our results indicate that ZnO and CuO ENPs, but not NiO ENPs, are toxic to L. plumulosus and that ZnO toxicity primarily results from Zn ion exposure while CuO toxicity is due to nanoparticle exposure.
                Cover page: Accumulation and toxicity of metal oxide nanoparticles in a soft-sediment estuarine amphipod
                • Peer Reviewed
                UC Santa Barbara Previously Published Works (2016)
                Logistical and financial limitations of underwater operations are inherent in marine science, including biodiversity observation. Imagery is a promising way to address these challenges, but the diversity of organisms thwarts simple automated analysis. Recent developments in computer vision methods, such as convolutional neural networks (CNN), are promising for automated classification and detection tasks but are typically very computationally expensive and require extensive training on large datasets. Therefore, managing and connecting distributed computation, large storage and human annotations of diverse marine datasets is crucial for effective application of these methods. BisQue is a cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery and associated data. Designed to hide the complexity of distributed storage, large computational clusters, diversity of data formats and inhomogeneous computational environments behind a user friendly web-based interface, BisQue is built around an idea of flexible and hierarchical annotations defined by the user. Such textual and graphical annotations can describe captured attributes and the relationships between data elements. Annotations are powerful enough to describe cells in fluorescent 4D images, fish species in underwater videos and kelp beds in aerial imagery. Presently we are developing BisQue-based analysis modules for automated identification of benthic marine organisms. Recent experiments with drop-out and CNN based classification of several thousand annotated underwater images demonstrated an overall accuracy above 70% for the 15 best performing species and above 85% for the top 5 species. Based on these promising results, we have extended bisque with a CNN-based classification system allowing continuous training on user-provided data.
                  Cover page: Bisque: cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2023)
                  Foundation species, such as trees, corals, grasses, oysters, and rockweeds, must be common and abundant to effectively modify the physical environment and increase biodiversity by buffering environmental stress. Yet many of these important species have been declining due to disease, climate change, and other factors. A prime example is the precipitous population decline of marine rockweeds, which is attributed to increased urbanization and its accompanying impacts. Rockweeds provide three-dimensional habitat in harsh rocky intertidal environments and regulate ecosystem functioning, essential roles that no substitute species are capable of filling. Recovery of impacted rockweed populations is typically slow and unpredictable due to their limited dispersal capacity. These issues have motivated efforts to conserve remaining populations of rockweeds and reestablish or enhance depleted ones. Successfully doing so requires a robust understanding of factors that affect survival of the species and the processes that influence ecosystem structure, along with rigorous scientific testing of restoration methods and the factors that affect restoration success. In this comprehensive review, we summarize the current knowledge of rockweed ecology, highlight studies that could inform restoration practices, and recommend ways to improve our ability to implement scalable restoration of rockweeds and accompanying ecosystem-wide benefits.
                    Cover page: Ecological restoration using intertidal foundation species: Considerations and potential for rockweed restorationCreative Commons 'BY-ND' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC Santa Barbara Previously Published Works (2015)
                    Potential effects of metal nanoparticles on aquatic organisms and food webs are hard to predict from the results of single-species tests under controlled laboratory conditions, and more realistic exposure experiments are rarely conducted. We tested whether silver nanoparticles (Ag NPs) had an impact on zooplankton grazing on their prey, specifically phytoplankton and bacterioplankton populations. If Ag NPs directly reduced the abundance of prey, thereby causing the overall rate of grazing by their predators to decrease, a cascading effect on a planktonic estuarine food web would be seen. Our results show that the growth rates of both phytoplankton and bacterioplankton populations were significantly reduced by Ag NPs at concentrations of ≥500 μg L(-1). At the same time, grazing rates on these populations tended to decline with exposure to Ag NPs. Therefore, Ag NPs did not cause a cascade of effects through the food web but impacted a specific trophic level. Photosynthetic efficiency of the phytoplankton was significantly reduced at Ag NPs concentrations of ≥500 μg L(-1). These effects did not occur at relatively low concentrations of Ag that are often toxic to single species of bacteria and other organisms, suggesting that the impacts of Ag NP exposure may not be apparent at environmentally relevant concentrations due to compensatory processes at the community level.
                      Cover page: Impacts of Silver Nanoparticles on a Natural Estuarine Plankton Community
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