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Salop, P.; Shimabuku, I.; Davis, J.; Franz, A. 2018. 2018 Bivalve Retrieval Cruise Report. SFEI Contribution No. 920. San Francisco Estuary Institute : Richmond, CA.
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Davis, J. 2018. 2018 Regional Monitoring Program Update. SFEI Contribution No. 906. San Francisco Estuary Institute : Richmond, CA.
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Trowbridge, P.; Wong, A.; Davis, J.; Ackerman, J. 2018. 2018 RMP Bird Egg Monitoring Sampling and Analysis Plan. SFEI Contribution No. 891. San Francisco Estuary Institute: Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Plan. SFEI Contribution No. 892. San Francisco Estuary Institute: Richmond, CA.
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Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Report. SFEI Contribution No. 903. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P.; Franz, A. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute: Richmond, CA.
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Trowbridge, P. 2017. 2018 RMP Detailed Workplan and Budget. San Francisco Estuary Institute : Richmond, CA.
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Salop, P.; Franz, A. 2018. 2018 RMP Sediment Cruise Report. SFEI Contribution No. 907. San Francisco Estuary Institute : Richmond, CA.
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Franz, A.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Sediment Sampling and Analysis Plan. SFEI Contribution No. 904. San Francisco Estuary Institute: Richmond, CA.
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Foley, M. 2019. 2019 Bay RMP Multi-Year Plan. SFEI Contribution No. 940. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N.; Carlton, J. T. 1998. Accelerating invasion rate in a highly invaded estuary. Science 279, 555-558 . SFEI Contribution No. 226.
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Nordby, C. 2001. Adult song sparrows do not alter their song repertoires. Ethology . SFEI Contribution No. 482.
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Pearce, S.; McKee, L. J. . 2009. Alameda Creek Bulk Sediment Study Technical Memorandum. San Francisco Estuary Institute: Oakland,Ca.
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Lin, D.; Sutton, R. 2018. Alternative Flame Retardants in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 885. San Francisco Estuary Institute : Richmond, CA.
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Collins, J. N.; Pearce, S. 2004. Analysis of Reference Tidal Channel Plan Form for the Montezuma Wetlands Restoration Project. SFEI Contribution No. 80. San Francisco Estuary Institute: Oakland, CA.
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Associates, H. T. Harvey and; San Francisco Estuary Institute (SFEI). 2017. Annotated Bibliography for Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project.

One component of the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project is this annotated bibliography of existing scientific literature pertaining to California sycamore ecology. This annotated bibliography is a product of an extensive review into documents, mapping efforts, and personal communications, and presents sources that have been determined to be relevant to understanding the factors that influence California sycamore health and regeneration in central California. The annotated bibliography is divided into the following sections by topic: General Ecology; Historical and Present Distribution; Restoration Ecology and Management; Wildlife Ecology; Geomorphology; Hydrology and Soils; and Health and Regeneration. Each item is briefly summarized and its relevance to the project is described. References that fall under multiple categories are cross-referenced within the document. Similarly, key words are indicated or each reference to highlight various subtopics affecting California sycamore ecology.

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Greenfield, B. K. 2004. APMP Alternatives Program Executive Summary. SFEI Contribution No. 118. San Francisco Estuary Institute: Oakland, CA.
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2005. APMP Phase 3 Bioassesment Report. SFEI Contribution No. 462.
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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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Willis-Norton, E.; Ranasinghe, J. A.; Greenstein, D.; Bay, S. 2013. Applying Sediment Quality Objective Assessments to San Francisco Bay Samples from 2008-2012. San Francisco Estuary Institute and Southern California Coastal Water Research Project: Richmond, CA.
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Cohen, A. N. 2005. Approaches to presenting the science of the San Francisco Bay/Delta estuary. SFEI Contribution No. 514. San Francisco Estuary Institute: Oakland, CA.
Cohen, A. N.; Weinstein, A.; Carlton, J. T. 1999. Aquatic bioinvasions in the San Francisco Estuary. Berkeley Society for Conservation Biology Annual Meeting.
Siemering, G.; David, N.; Franz, A.; Malamud-Roam, F.; Hayworth, J. 2003. Aquatic Pesticide Monitoring Program Literature Review. SFEI Contribution No. 71. San Francisco Estuary Institute: Oakland, CA.
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Siemering, G. 2005. Aquatic Pesticides Monitoring Program Monitoring Project Final Report. SFEI Contribution No. 392. San Francisco Estuary Institute: Oakland, CA.
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Siemering, G. 2004. Aquatic Pesticides Monitoring Program Phase 2 (2003) Monitoring Project Report. SFEI Contribution No. 108. San Francisco Estuary Institute: Oakland, CA.
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Lowe, S.; Thompson, B. 2004. Assessment of macrobenthos resonse to sediment contamination in the San Francisco Estuary, USA. Environmental Toxicology and Chemistry 23 . SFEI Contribution No. 60.
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Jabusch, T.; Trowbridge, P.; Wong, A.; Heberger, M. 2018. Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends. SFEI Contribution No. 865. Aquatic Science Center: Richmond, CA.

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

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Greenfield, B. K.; Siemering, G.; Hayworth, J. D. 2008. Assessment of Potential Aquatic Herbicide Impacts to California Aquatic Ecosystems. Archives of Environmental Contamination and Toxicology . SFEI Contribution No. 539.
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Beller, E. E.; Salomon, M.; Grossinger, R. M. 2013. An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone. SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.
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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.
Thompson, B.; Daum, T. 1999. Atlas of Sediment Contamination, Toxicity, and Benthic Assemblages in San Francisco Bay. SFEI Contribution No. 38. San Francisco Estuary Institute: Richmond, CA.
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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Shimabuku, I.; Trowbridge, P.; Sun, J. 2018. Bay 2017 Bay RMP Field Sampling Report. SFEI Contribution No. 849. San Francisco Estuary Institute : Richmond, CA.
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Gilbreath, A.; Pearce, S.; Shimabuku, I.; McKee, L. 2018. Bay Area Green Infrastructure Water Quality Synthesis. SFEI Contribution No. 922. San Francisco Estuary Institute : Richmond, CA.
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Collins, J. N. 1998. Bay Area Wetlands Ecosystem Goals Project: Key Baylands Habitats. SFEI Contribution No. 122. San Francisco Estuary Institute.
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Collins, J. N. 1998. Bay Area Wetlands Ecosystem Goals Project: Key Baylands Species. SFEI Contribution No. 121. San Francisco Estuary Institute.
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