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Website
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Dusterhoff, S. D.; Doehring, C.; Shusterman, G. 2014. How Creeks Meet the Bay: Changing Interfaces (Interactive web map).

San Francisco Bay’s connections to local creeks are integral to its health. These fluvial-tidal (F-T) interfaces are the points of delivery for freshwater, sediment, contaminants, and nutrients. The ways in which the F-T interface has changed affect flooding dynamics, ecosystem functioning, and resilience to a changing climate. As the historical baylands have been altered, the majority of contemporary F-T interface types have changed leading to additional F-T interface types within the present-day landscape. Illustrations of each F-T interface type and methods for classification are available here

This project is part of Flood Control 2.0. For further information please visit this project page

Software
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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Report
Cohen, A. N.; Weinstein, A. 2001. Zebra Mussel's Calcium Threshold and Implications for its Potential Distribution in North America. SFEI Contribution No. 356. San Francisco Estuary Institute: Richmond CA.
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Cohen, A. N.; Nordby, J. C. 2005. Year-end Report to the National Science Foundation. SFEI Contribution No. 456. San Francisco Estuary Institute: Oakland, CA.
Williams, M.; Cayce, K. 2009. WRMP Factsheet — Wetland and Riparian Base Map. San Francisco Estuary Institute: Oakland, Ca.
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Stein, E. D.; Cayce, K.; Salomon, M. N.; Bram, D. L.; De Mello, D.; Grossinger, R. M.; Dark, S. 2014. Wetlands of the Southern California Coast: Historical Extent and Change Over Time. SFEI Contribution No. 720. Southern California Coastal watershed Research Project (SCCWRP), San Francisco Estuary Institute (SFEI), CSU Northridge Center for Geographical Studies: Costa Mesa, Richmond, Northridge.
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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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Cohen, A. N.; Gottleib, R. 1991. Water and GrowthL Restructuring the Relationship. Public Officials for Water and Environmental Reform: Sacramento, CA.
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Lowe, S.; Salomon, M.; Pearce, S.; Josh Collins; Titus, D. 2016. Upper Pajaro River Watershed Condition Assessment 2015. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 810. San Francisco Estuary Institute: Richmond, CA. p 60.

In 2015 The Santa Clara Valley Water District and it's consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the upper Pajaro River watershed wtihin Santa Clara County, CA based on available GIS datasets, 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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Jarman, W. M.; Bacon, C.; Owen, B. 1999. Trace Organic Sampler Intercalibration Results. SFEI Contribution No. 34. San Francisco Estuary Institute: Richmond, CA.
Phillips, D. J. H. 1987. Toxic Contaminants in the San Francisco Bay-Delta and their Possible Biological Effects. SFEI Contribution No. 145. Aquatic Habitat Institute: Richmond, CA. p 472.
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Smith, R.; Thompson, B. 1994. Towards an Optimal Sampling Design for the RMP. SFEI Contribution No. 6. San Francisco Estuary Institute: Richmond, CA.
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Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Crooks, J. A.; Grossinger, R. M.; Lorda, J.; Longcore, T. R.; Bram, D. L.; Dark, S. J.; Stein, E. D.; et al. 2017. Tijuana River Valley Historical Ecology Investigation. Prepared for the State Coastal Conservancy. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 760. San Francisco Estuary Institute - Aquatic Science Center : Richmond, CA. p 230.

The Tijuana River Valley Historical Ecology Investigation addresses a regional data gap by reconstructing the landscape and ecosystem characteristics of the river valley prior to the major modifications of the late 19th and 20th centuries. The research presented here, funded by the California State Coastal Conservancy, supplies foundational information at the regional and system scale about how the Tijuana Estuary, River, and valley looked and functioned in the recent past, as well as how they have changed over time. The ultimate goal of this study is to provide a new tool and framework that, in combination with contemporary research and future projections, can support and guide ongoing restoration design, planning, and management efforts in the valley.

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Greenfield, B. K.; Davis, J. A.; Collins, J. N.; Grenier, J. Letitia. 2002. The tidal marsh food web. SFEI Contribution No. 472. University of California: Berkeley, CA. p 12 pp.
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Cohen, A. N.; Woo, M.; Jabari, E. 2001. Testing Ballast Water Treatment at a Municipal Wastewater Treatment Plant. California Sea Grant/National Sea Grant College Program, La Jolla CA.
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Davis, J. A.; Gunther, A. J.; Abu-Saba, K. E. 2001. Technical Report of the Sources, Pathways, and Loadings Workgroup. SFEI Contribution No. 266. San Francisco Estuary Institute: Richmond, CA.
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Ruhl, C. A.; Schoellhamer, D. H. 1998. Technical Report of the San Francisco Estuary Regional Monitoring Program for Trace Substances. SFEI Contribution No. 375. San Francisco Estuary Institute: Richmond, CA.
Davis, J. A.; Yoon, J. 1999. Technical Report of the Chlorinated Hydrocarbon Workgroup. San Francisco Estuary Institute: Richmond, CA.
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May, M. D.; Kramer, K. S. 1993. Teaching About the San Francisco Bay and Delta - An Activities and Resource Guide, 2nd Ed. SFEI Contribution No. 174. San Francisco Estuary Institute: Richmond, Ca. p 500.
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Beagle, J.; Richey, A.; Hagerty, S.; Salomon, M.; Askevold, R. A.; Grossinger, R. M.; Reynolds, P.; McClain, C.; Spangler, W.; Quinn, M.; et al. 2017. Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study. SFEI Contribution No. 816.

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP).

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David, N. 2009. Sustainable Cotton Project. SFEI Contribution No. 592. San Francisco Estuary Institute: Oakland, Ca.
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Lin, D.; Davis, J. 2018. Support for Sediment Bioaccumulation Evaluation: Toxicity Reference Values for the San Francisco Bay. SFEI Contribution No. 916. San Francisco Estuary Institute : Richmond, CA.
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Buchanan, P. A.; Schoellhamer, D. H. 1996. Summary of Suspended-Solids Concentration Data, San Francisco Bay, California, Water Year 1995. SFEI Contribution No. 13. US Geological Survey Open-File Report. pp 96-591.
Buchanan, P. A.; Ganju, N. K. 2002. Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2000. SFEI Contribution No. 242. US Geological Survey Open-File Report. pp 96-591.
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Collins, J. N. 2002. Summary of Crissy Field Monitoring Elements. San Francisco Estuary Institute.
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Senn, D. B.; Novick, E. 2014. Suisun Bay Ammonium Synthesis. SFEI Contribution No. 706. San Francisco Estuary Institute: Richmond, CA. p 191.
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Cohen, A. N. 2001. Success factors in human-dispersed organisms. Page 8 in:. University of Reading, UK. British Ecological Society, London. p p. 8.
Cohen, A. N. 1988. Subsides in the Central Utah Project: Whose CUP is Running over?. Report for the Natural Resources Defense Council: San Francisco, CA.
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Trowbridge, P. 2018. Status & Trends Monitoring Design: 2018 Update. San Francisco Estuary Institute : Richmond, CA.
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