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Lowe, S.; Salomon, M.; Pearce, S. 2016. Lower Peninsula Watershed Condition Assessment 2016. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond, CA. p 49.

In 2016 The Santa Clara Valley Water District and its consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the Lower Peninsula watershed wtihin Santa Clara County, CA based on available GIS data, and to assess the overall ecological condition of streams within the watershed based on a statistically based, random sample design and the California Rapid Assessment Method for streams (CRAM).

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Davis, J. A. 2004. The Long-Term Fate of PCBs in San Francisco Bay. Environmental Toxicology and Chemistry 23, 2396-2409.
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Gunther, A. J.; Blanchard, C.; Gardels, K. 1991. The Loading of Toxic Contaminants to the San Francisco Bay -Delta in Urban Runoff. SFEI Contribution No. 167. San Francisco Estuary Institue: Richmond, CA. p 82.
Hampton, L. M. Thornto; De Frond, H.; Hermabessiere, L.; Miller, E.; de Ruijter, V. N.; Faltynkova, A.; Kotar, S.; Monclús, L.; Siddiqui, S.; Völker, J.; et al. 2022. A living tool for the continued exploration of microplastic toxicity. Microplastics and Nanoplastics 2 (13).

Throughout the past decade, many studies have reported adverse effects in biota following microplastic exposure. Yet, the field is still emerging as the current understanding of microplastic toxicity is limited. At the same time, recent legislative mandates have required environmental regulators to devise strategies to mitigate microplastic pollution and develop health-based thresholds for the protection of human and ecosystem health. The current publication rate also presents a unique challenge as scientists, environmental managers, and other communities may find it difficult to keep up with microplastic research as it rapidly evolves. At present, there is no tool that compiles and synthesizes the data from these studies to allow for visualization, interpretation, or analysis. Here, we present the Toxicity of Microplastics Explorer (ToMEx), an open access database and open source accompanying R Shiny web application that enables users to upload, search, visualize, and analyze microplastic toxicity data. Though ToMEx was originally created to facilitate the development of health-based thresholds to support California legislations, maintaining the database by the greater scientific community will be invaluable to furthering research and informing policies globally. The database and web applications may be accessed at https://microplastics.sccwrp.org/.

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Vaughn, L. Smith; Panlasigui, S.; Spotswood, E. 2020. Livestock grazing and its effects on ecosystem structure, processes, and conservation. SFEI Contribution No. 1011. San Francisco Estuary Institute: Richmond, CA.
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Vaughn, L. Smith; Plane, E.; Harris, K.; Robinson, A.; Grenier, L. 2022. Leveraging Wetlands for a Better Climate Future: Incorporating Blue Carbon into California's Climate Planning. SFEI Contribution No. 1084. San Francisco Estuary Institute: Richmond, CA. p 31.

The 2022 update to California’s climate change Scoping Plan incorporates management actions in the state’s forests, shrublands/chaparral, grasslands, croplands, developed lands, deltaic wetlands, and sparsely vegetated lands. Missing from this list are the tidally-influenced coastal ecosystems outside the Sacramento-San Joaquin Delta. These blue carbon ecosystems support high rates of carbon storage and sequestration while providing many co-benefits that can enhance coastal climate change resilience. With sufficient data and robust modeling approaches, California has the opportunity to incorporate blue carbon in future Scoping Plan updates and set actionable targets for restoration, migration space conservation, and other management activities that promote long-term survival of the state’s coastal wetlands. To support this goal, this report offers a high-level overview of the state of the science for blue carbon quantification in California. This summary, which covers datasets and quantification approaches, key focus areas for additional science investment, and example scenarios for coastal wetland restoration, is intended to facilitate broader inclusion of blue carbon in future Scoping Plan updates and other state-level climate-planning documents.

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Flegal, A. R. 1997. Lead levels in the oceans. Encyclopedia of Environmental Analysis and Remediation(H. Ben-Zvi, editor)John Wiley & Sons, Inc. In press . SFEI Contribution No. 24.
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Grossinger, R. M.; Brewster, E. 2001. Land Use Timeline for Crow Canyon and the San Lorenzo Creek Watershed. SFEI Contribution No. 352. Alameda Countywide Clean Water Program. p 6 pp.
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SFEI. 2023. Landscape Scenario Planning Tool User Guide v2.2.0. San Francisco Estuary Institute: Richmond, Calif.
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Beller, E. E.; Robinson, A.; Grossinger, R. M.; Grenier, J. Letitia. 2015. Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
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Brewster, E. 2006. Land Grant Research and the Pictorial Collection. In Exploring the Bancroft Library. Exploring the Bancroft Library. The Bancroft Library/Signature Books. Vol. In Faulhab, p 196.
Lowe, S.; Huck, K.; Misico, A.; Scirbe, L.; Sussman, D. 2023. Lahontan Surface Water Ambient Monitoring Program’s 20-Year Water Quality Review and Program Recommendations. SFEI Contribution No. 1110. San Francisco Estuary Institute: Richmond. CA. p 137.

This 20-year water quality monitoring status and trends report for the Lahontan Water Board’s Surface Water Ambient Monitoring Program (Regional SWAMP) provides an overview of the environmental settings across the Region to give the reader a sense of the diverse ecological landscape, land uses, distribution and abundance of aquatic resources, and fire history. It includes a retrospective analysis of the Regional SWAMP’s ongoing, targeted water quality monitoring results (2000 - 2021), and concludes by presenting an adaptive monitoring and assessment framework (adapted from the California Wetlands Monitoring Workgroup's Wetland and Riparian Monitoring Plan, known as "WRAMP").  The framework was used to review the program and recommend future monitoring changes to improve efficiencies and address some of the recommendations listed in the Regional SWAMP's 2019 Core Program Review. 

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Davis, J. A. 1988. Inventory of Priority Datasets Relating to the San Francisco Estuary. SFEI Contribution No. 141. San Francisco Estuary Institute: Richmond, CA. p 51.
Kramer, K. S. 1989. Inventory of Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 156. AHI: Richmond, CA. p 48.
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Kramer, K. S. 1989. Inventory of Current Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 155. San Francisco Estuary Institute: Richmond, CA. p 39.
Cohen, A. N. 1999. Invasions status and policy on the U. S. west coast. First National Conference on Marine Bioinvasion, 40-45.
Cohen, A. N. 2000. Invasions status and policy on the U. S. west coast. in: Proc. First Nat'l Conf. on Marine Bioinvasions, Jan. 24-27, 1999, Cambridge MA, 40-45.
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Cohen, A. N. 2004. Invasions in the sea. Park Science 22, 37-41.
Cohen, A. N. 2004. Invasions in the sea. SFEI Contribution No. 312. Vol. 22, pp 37-41.
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Cohen, A. N. 2001. Invasions in the San Francisco Estuary. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N. 1998. The invasion of the Pacific Coast by the European green crab Carcinus maenas. Proc. Eighth Int'l Zebra Mussel and Aquatic Nuisance Species Conf., 173-177.
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Cohen, A. N. 1998. The invasion of the Pacific Coast by the European green crab. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, Page 44.
Cohen, A. N. 1997. The invasion of the estuaries. Proc. Second International Spartina Conference, Mar 20-21, 1997, 6-9.
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Cohen, A. N.; McGann, M.; Sloan, D. 2000. Invasion by a Japanese marine microorganism in western North America. Hydrobiologia 421, 25-30 . SFEI Contribution No. 343.
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Carlton, J. T. 1996. The Invaded estuary (abstract). In In: Third Biennial State of the Estuary Conf.. In: Third Biennial State of the Estuary Conf. San Francisco, CA.
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Cohen, A. N. 2001. An Introduction to the San Francisco Estuary Third Edition. San Francisco Estuary Project, Oakland CA, Save The Bay, Oakland CA and San Francisco Estuary Institute, Richmond CA: Oakland, Ca. Vol. Third Edit.
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Cohen, A. N. 2003. Introduction to the San Francisco Estuary. San Francisco Estuary Institute, Save the Bay and San Francisco Estuary Project: Oakland,CA.
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Hale, T.; Grosso, C. 2016. An Introduction to EcoAtlas: Applied Aquatic Science. San Francisco Estuary Institute: Richmond, CA. p 16 pages.

This memo was developed by SFEI to introduce the EcoAtlas tools, their intended (target) user community, and the short- and long-term intended applications. 

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Cohen, A. N.; Schaeffer, K.; McGourty, K.; Cosentino-Manning, N.; De La Cruz, S. E. Wainwri; Elliot, M.; Allen, S. 2007. Introduction for Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service. p 35.
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Cohen, A. N. 1995. Introduced Species. Prepared for: California's Ocean Resources: An Agenda for the Future, California Resources Agency: Sacramento, CA.
Cohen, A. N.; Carlton, J. T. 2007. Introduced Marine and Estuarine Invertebrates. In The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. Carlton, J. T., Ed.. The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. University of California Press: Berkeley, Ca.
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Hatje, V.; Bruland, K. W.; A. Flegal, R. 2016. Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record. Environ. Sci. Technol. 50 (8).

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg–1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.

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