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Jabusch, T. W.; Bernstein, B. 2010. Delta Regional Monitoring Program. Aquatic Science Center: Oakland, CA.
Jabusch, T. W. 2010. Selenium in the Grasslands Watershed. San Francisco Estuary Institute: Oakland, CA. pp 267-294.
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Aquatic Habitat Institute. 1990. Estuarine Index: A Guide to Bay-Delta Research and Monitoring Programs: Volume I. Association of Bay Area Governments Urban Runoff Studies, Association of Bay Area Governments Environmental Protection Agency. p 395.
Aquatic Habitat Institute. 1990. Estuarine Data Index: A Guide to Bay-Delta Research and Monitoring Programs, Volume I. SFEI Contribution No. 157. Aquatic Habitat Institute: RIchmond, CA. p 395.
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Hunt, J.; Trowbridge, P.; Yee, D.; Franz, A.; Davis, J. 2016. Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring. SFEI Contribution No. 827. San Francisco Estuary Institute: Richmond, CA. p 31 pp.
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Houtz, E. F.; Sutton, R.; Park, J. - S.; Sedlak, M. 2016. Poly- and perfluoroalkyl substances in wastewater: Significance of unknown precursors, manufacturing shifts, and likely AFFF impacts. Water Research . SFEI Contribution No. 780.

In late 2014, wastewater effluent samples were collected from eight treatment plants that discharge to San Francisco (SF) Bay in order to assess poly- and perfluoroalkyl substances (PFASs) currently released from municipal and industrial sources. In addition to direct measurement of twenty specific PFAS analytes, the total concentration of perfluoroalkyl acid (PFAA) precursors was also indirectly measured by adapting a previously developed oxidation assay. Effluent from six municipal treatment plants contained similar amounts of total PFASs, with highest median concentrations of PFHxA (24 ng/L), followed by PFOA (23 ng/L), PFBA (19 ng/L), and PFOS (15 ng/L). Compared to SF Bay municipal wastewater samples collected in 2009, the short chain perfluorinated carboxylates PFBA and PFHxA rose significantly in concentration. Effluent samples from two treatment plants contained much higher levels of PFASs: over two samplings, wastewater from one municipal plant contained an average of 420 ng/L PFOS and wastewater from an airport industrial treatment plant contained 560 ng/L PFOS, 390 ng/L 6:2 FtS, 570 ng/L PFPeA, and 500 ng/L PFHxA. The elevated levels observed in effluent samples from these two plants are likely related to aqueous film forming foam (AFFF) sources impacting their influent; PFASs attributable to both current use and discontinued AFFF formulations were observed. Indirectly measured PFAA precursor compounds accounted for 33%–63% of the total molar concentration of PFASs across all effluent samples and the PFAA precursors indicated by the oxidation assay were predominately short-chained. PFAS levels in SF Bay effluent samples reflect the manufacturing shifts towards shorter chained PFASs while also demonstrating significant impacts from localized usage of AFFF.

Holleman, R.; Nuss, E.; Senn, D. 2017. San Francisco Bay Interim Model Validation Report. SFEI Contribution No. 850. San Francisco Estuary Institute: Richmond, CA.
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Holleman, R.; MacVean, L.; Mckibben, M.; Sylvester, Z.; Wren, I.; Senn, D. 2017. Nutrient Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.
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Hoenicke, R.; Leatherbarrow, J. E. 2000. The Estuary Interface Pilot Study: 1998 Progress Report. SFEI Contribution No. 49. San Francisco Estuary Institute.
Hoenicke, R.; Tsai, P.; Bamford, H. A.; Baker, J.; Yee, D. 2002. Atmospheric Concentrations and Fluxes of Organic Compounds in the Northern San Francisco Estuary. Environmental Science and Technology 36 (22), 4741-4747 . SFEI Contribution No. 474.
Hoenicke, R.; Tucker, D.; Tsai, P.; Hansen, E.; Lee, K.; Yee, D. 2002. Atmospheric Deposition of Trace Metals in San Francisco Bay. SFEI Contribution No. 278. San Francisco Estuary Institute: Richmond, CA.
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Hoenicke, R.; Hayworth, J. 2005. A Watershed Monitoring Strategy for Napa County. SFEI Contribution No. 428. San Francisco Estuary Institute: Napa,. p 34.
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Hoenicke, R.; Bleier, C. 2007. Watershed Management and Land Use. CCMP Implementation Committee.
Hoenicke, R.; Tsai, P. 2001. San Francisco Bay Atmospheric Deposition Pilot Study Part 1: Mercury. SFEI Contribution No. 72. San Francisco Estuary Institute: Richmond, CA.
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Hoenicke, R.; Tsai, P.; Hansen, E.; Lee, K. 2001. San Francisco Bay Atmospheric Deposition Pilot Study Part 2: Trace Metals. SFEI Contribution No. 73. San Francisco Estuary Institute: Richmond, CA.
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Hoenicke, R. 1997. Creating data-quality objectives: A case study. Water Environment Laboratory Solutions 7-9 . SFEI Contribution No. 31.
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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.

Hale, T.; Sim, L.; McKee, L. J. 2018. GreenPlan-IT Tracker.

This technical memo describes the purpose, functions, and structure associated with the newest addition to the GreenPlan-IT Toolset, the GreenPlan-IT Tracker. It also shares the opportunities for further enhancement and how the tool can operate in concert with existing resources. Furthermore, this memo describes a licensing plan that would permit municipalities to use the tool in an ongoing way that scales to their needs. The memo concludes with a provisional roadmap for the development of future features and technical details describing the tool’s platform and data structures.

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Hale, T.; Grosso, C. 2017. Applied Aquatic Science: A Business Plan for EcoAtlas. San Francisco Estuary Institue: Richmond, CA.

The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions.

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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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Hale, T.; Azimi-Gaylon, S.; Fong, S.; Goodwin, P.; Isaac, G.; Osti, A.; Shilling, F.; Slawecki, T.; Steinberg, S.; Tompkins, M.; et al. 2015. Enhancing the Vision for Managing California's Environmental Information. SFEI Contribution No. 792. Delta Stewardship Council: Sacramento, CA.

The Environmental Data Summit, convened under the auspices of the Delta Stewardship Council’s Delta Science Program in June 2014, witnessed remarkable participation from experts across California, the nation, and even the world. Summit attendees from the public, private, federal, and non-profit sectors shared their views regarding the urgent needs and proposed solutions for California’s data-sharing and data-integration challenges, especially pertaining to the subject of environmental resource management in the era of “big data.” After all, this is a time when our data sources are growing in number, size, and complexity. Yet our ability to manage and analyze such data in service of effective decision-making lags far behind our demonstrated needs.

In its review of the sustainability of water and environmental management in the California Bay-Delta, the National Research Council (NRC) found that “only a synthetic, integrated, analytical approach to understanding the effects of suites of environmental factors (stressors) on the ecosystem and its components is likely to provide important insights that can lead to enhancement of the Delta and its species” (National Research Council 2012). The present “silos of data” have resulted in separate and compartmentalized science, impeding our ability to make informed decisions. While resolving data integration challenges will not, by itself, produce better science or better natural resource outcomes, progress in this area will provide a strong foundation for decision-making. Various mandates ranging from the California Water Action Plan to the President’s executive order demanding federal open data policies demonstrate the consensus on the merits of modern data sharing at the scale and function needed to meet today’s challenges.

This white paper emerges from the Summit as an instrument to help identify such opportunities to enhance California’s cross-jurisdictional data management. As a resource to policymakers, agency leadership, data managers, and others, this paper articulates some key challenges as well as proven solutions that, with careful and thoughtful coordination, can be implemented to overcome those obstacles. Primarily featured are tools that complement the State’s current investments in technology, recognizing that success depends upon broad and motivated participation from all levels of the public agency domain. Executive Summary

This document describes examples, practices, and recommendations that focus on California’s Delta as an opportune example likely to yield meaningful initial results in the face of pressing challenges. Once proven in the Delta, however, this paper’s recommended innovations would conceivably be applied statewide in subsequent phases.

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Hagerty, S.; Spotswood, E.; McKnight, K.; Grossinger, R. M. 2019. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. San Francisco Estuary Institute: Richmond, CA.

This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
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Gunther, A. J.; Ogle, S. R. 2000. San Francisco Bay Episodic Toxicity Report:1999 Progress Report. SFEI Contribution No. 346. San Francisco Estuary Institute: Richmond, CA.
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Gunther, A. J. 1988. The Bioavailability of Toxic Contaminants in the San Francisco Bay-Delta: Proceedings of a Two-Day Seminar Series. SFEI Contribution No. 142. San Francisco Bay - Delta Aquatic Habitat Institute, Richmond, CA: Berkeley, CA.
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Gunther, A. J. 1987. The Segmentation of the San Francisco Bay/Delta. SFEI Contribution No. 135. San Francisco Estuary Institute: Richmond, CA. p 18.
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Gunther, A.; Thompson, B. 2004. Development of Environmental Indicators of the Condition of San Francisco Estuary. SFEI Contribution No. 113. San Francisco Estuary Institute: Oakland.
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Gunther, A. J.; Phillips, D. J. H.; Davis, J. A. 1987. An Assesssment of the Loading of Toxic Contaminants to the San Francisco Bay-Delta. SFEI Contribution No. 137. San Francisco Estuary Institute: Richmond. p 330.
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.
Gunther, A. J.; O'Connor, J. M.; Davis, J. A. 1992. Priority pollutant loads from effluent discharges to the San Francisco Estuary. Water Environment Research 64, 134-140 . SFEI Contribution No. 171.
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Gunther, A. J.; Davis, J. A. 1998. An evaluation of bioaccumulation monitoring with transplanted bivalves in the RMP. SFEI Contribution No. 322. San Francisco Estuary Institute: Richmond, CA. pp 187-200.
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Grosso, C.; Hale, A.; Williams, M.; May, M. 2014. Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
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Grossinger, R. M.; Beller, E. E. 2011. Oak Landscapes in the Recent Past. In Oaks in the Urban Landscape: Selection, Care, and Preservation. Costello, L. R., Hagen, B. W., Jones, K. S., Eds.. Oaks in the Urban Landscape: Selection, Care, and Preservation. University of California Agriculture and Natural Resources: Richmond, CA.
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Grossinger, R. M. 2005. Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Egan, D., Howell, E. A., Trans.. The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Island Press.
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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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