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Cohen, A. N. 1995. Place Invaders. Energy and Resources News 4, 1-3.
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Cohen, A. N. 1993. Place Invaders. Pacific Discovery (Calif. Acad. Sci.) 46, 22-26.
Oros, D. R. 2002. Polar aromatic biomarkers in the miocene Maritza-East Lignite, Bulgaria. Organic Geo-chemistry . SFEI Contribution No. 476.
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Gilbreath, A.; Hunt, J.; Mckee, L. 2019. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
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Gilbreath, A.; Wu, J.; Hunt, J.; McKee, L. 2018. Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
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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.

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Sutton, R.; Sedlak, M.; Davis, J. A. 2014. Polybrominated Diphenyl Ethers (PBDEs) in San Francisco Bay: A Summary of Occurrence and Trends. SFEI Contribution No. 713. San Francisco Estuary Institute: Richmond, CA. p 62.
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Oram, J. J.; McKee, L. J. .; Davis, J. A.; Hetzel, F. 2007. Polychlorinated biphenyls (PCBs) in San Francisco Bay. Environmental Research 105, 67-86 . SFEI Contribution No. 526.
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Ross, J. R. M.; Oros, D. R. 2004. Polycyclic aromatic hydrocarbons in San Francisco Estuary sediments. Marine Chemistry 86, 169-184 . SFEI Contribution No. 82.
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Cohen, A. N.; Weinstein, A. 1998. The potential distribution and abundance of the zebra mussel in California. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, 65.
Weinstein, A.; Cohen, A. N. 1998. The potential distribution and abundance of zebra mussels in California. Dreissena! (New York Sea Grant) 9, 1-3 . SFEI Contribution No. 323.
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Cohen, A. N.; Weinstein, A. 1998. The Potential Distribution and Abundance of Zebra Mussels in California. SFEI Contribution No. 225. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N.; Weinstein, A. 2001. The Potential Distribution of Chinese Mitten Crabs (Eriocheir sinensis) in selected waters of the Western United States with U.S. Bureau of Reclamation Facilities. SFEI Contribution No. 353. United States Department of the Interior, Bureau of Reclamation, Mid-Pacific Region and the Technical Service Center. Vol. 21.
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Greenfield, B. K.; Hrabik, T. R.; Harvey, C. J.; Carpenter, S. R. 2000. Predicting mercury levels in fish: use of water chemistry, trophic ecology, and spatial traits. Canadian Journal of Fisheries and Aquatic Sciences 58, 1419 -1429 . SFEI Contribution No. 306.
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Cohen, A. N. 1999. Prevention vs. control of biological invasions. First National Conference on Marine Bioinvasions.
Cloern, J. E.; Robinson, A.; Richey, A.; Grenier, J. Letitia; Grossinger, R. M.; Boyer, K. E.; Burau, J.; Canuel, E.; DeGeorge, J. F.; Drexler, J. Z.; et al. 2016. Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

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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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Cohen, A. N. 2005. Project Report: 2004 Rapid Assessment Survey for Exotic Species in San Francisco Bay. SFEI Contribution No. 451. San Francisco Estuary Institute: Oakland, Ca.
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SFEI. 2019. The Pulse of the Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2017. The Pulse of the Bay: The 25th Anniversary of the RMP. SFEI Contribution No. 841. San Francisco Estuary Institute: Richmond, CA.
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May, M. 2000. The Pulse of the Estuary: Tracking Contamination with the Regional Monitoring Program 1993-1998. SFEI Contribution No. 100. San Francisco Estuary Institute.
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Kerrigan, J. F.; Engstrom, D. R.; Yee, D.; Sueper, C.; Erickson, P. R.; Grandbois, M.; McNeill, K.; Arnold, W. A. 2015. Quantification of Hydroxylated Polybrominated Diphenyl Ethers (OH-BDEs), Triclosan, and Related Compounds in Freshwater and Coastal Systems. PLOS ONE . SFEI Contribution No. 765.

Hydroxylated polybrominated diphenyl ethers (OH-BDEs) are a new class of contaminants of emerging concern, but the relative roles of natural and anthropogenic sources remain uncertain. Polybrominated diphenyl ethers (PBDEs) are used as brominated flame retardants, and they are a potential source of OH-BDEs via oxidative transformations. OH-BDEs are also natural products in marine systems. In this study, OH-BDEs were measured in water and sediment of freshwater and coastal systems along with the anthropogenic wastewater-marker compound triclosan and its photoproduct dioxin, 2,8-dichlorodibenzo-p-dioxin. The 6-OH-BDE 47 congener and its brominated dioxin (1,3,7-tribromodibenzo-p-dioxin) photoproduct were the only OH-BDE and brominated dioxin detected in surface sediments from San Francisco Bay, the anthropogenically impacted coastal site, where levels increased along a north-south gradient. Triclosan, 6-OH-BDE 47, 6-OH-BDE 90, 6-OH-BDE 99, and (only once) 6’-OH-BDE 100 were detected in two sediment cores from San Francisco Bay. The occurrence of 6-OH-BDE 47 and 1,3,7-tribromodibenzo-p-dioxin sediments in Point Reyes National Seashore, a marine system with limited anthropogenic impact, was generally lower than in San Francisco Bay surface sediments. OH-BDEs were not detected in freshwater lakes. The spatial and temporal trends of triclosan, 2,8-dichlorodibenzo-p-dioxin, OH-BDEs, and brominated dioxins observed in this study suggest that the dominant source of OH-BDEs in these systems is likely natural production, but their occurrence may be enhanced in San Francisco Bay by anthropogenic activities.

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Cohen, A. N.; Chapman, J. W. 2005. Rapid Assessment Channel Survey for Exotic Species in San Francisco Bay - November 2005. SFEI Contribution No. 454. San Francisco Estuary Institute: Oakland, CA. p 7.
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Cohen, A. N.; Tyler, S.; Mathieson, A.; Dyrynda, P.; Dean, H.; Calder, D.; Bullock, R.; Lambert, C.; Chapman, J.; Pederson, J.; et al. 2001. Rapid Assessment Survey of nonindigenous species in coastal Massachusetts. In: Abstracts, Second International Conf. on Marine Bioinvasions, April 9-11, 2001, New Orleans LA..
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Cohen, A. N. 1988. Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
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