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Environmental Health - Toxic Substances

Bibliography

Estuarine Contamination from Varied Human Influences — San Francisco Bay and Delta, California

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Jassby, A.D., and Cloern, J.E., 2000,
Organic matter sources and rehabilitation of the Scaramento-San Joaquin Delta (California, USA): Aquatic Conservation--Marine and Freshwater Ecosystems, v. 10, no. 5, p. 323-352, doi:10.1002/1099-0755(200009/10)10:5<323::AID-AQC417>3.0.CO;2-J.
Simpson, J.J., Dettinger, M.D., Gerhke, F., McIntyre, T.J., and Hufford, G.I., 2004,
Hydrologic scales, cloud variability, remote sensing and models--Implications for forecasting snowmelt and streamflow: Weather and Forecasting, v. 19, p. 251-276, doi:10.1175/1520-0434(2004)019<0251:HSCVRS>2.0.CO;2.
Cayan, D.R., Dettinger, M.D., Kammerdiener, S.A., Caprio, J.M., and Peterson, D.H., 2001,
Changes in the onset of spring in the Western United States: Bulletin of the American Meteorological Society, v. 82, no. 3, p. 399-416, doi:10.1175/1520-0477(2001)082<0399:CITOOS>2.3.CO;2.
Lundquist, J.D., Cayan, D.R., and Dettinger, M.D., 2004,
Spring onset in the Sierra Nevada--When is snowmelt independent of elevation?: Journal of Hydrometeorology, v. 5, no. 2, p. 327-342, doi:10.1175/1525-7541(2004)005<0327:SOITSN>2.0.CO;2.
Pereira, W.E., Domagalski, J.L., Hostettler, F.D., Brown, L.R., and Rapp, J.B., 1996,
Occurrence and accumulation of pesticides and organic contaminants in river sediment, water and clam tissues from the San Joaquin River and tributaries, California: Environmental Toxicology and Chemistry, v. 15, no. 2, p. 172-180, doi:10.1897/1551-5028(1996)015<0172:OAAOPA>2.3.CO;2.

A

Smalling, K.L., Morgan, S., and Kuivila, K.K., 2010,
Accumulation of current-use and organochlorine pesticides in crab embryos from northern California, USA: Environmental Toxicology and Chemistry, v. 29, no. 11, p. 2593-2599, doi:10.1002/etc.317.
Carter, J.L., and Resh, V.H., 2001,
After site selection and before data analysis--sampling, sorting, and laboratory procedures used in stream benthic macroinvertebrate monitoring programs by USA state agencies: Journal of the North American Benthological Society, v. 20, no. 4, p. 658-682.
Peterson, D., Smith, R., Hager, S., Cayan, D., and Dettinger, M., 2004,
Air temperature and snowmelt discharge characteristics, Merced River at Happy Isles, Central Sierra Nevada, in Dettinger, M., ed., Twentieth annual Pacific Climate (PACLIM) Workshop: Interagency Ecological Program for the Sacramento-San Joaquin Estuary Technical Report 72, 53-64 p.
Kuwabara, J.S., Davis, J.A., and Chang, C.C.Y., 1986,
Algal growth response to particle-bound orthophosphate and zinc: American Society of Limnology and Oceanography, v. 31, p. 503-511.
Peterson, D., Smith, R., Hager, S., Huber, K., Dettinger, M., and DiLeo, J., 2004,
Alpine hydroclimatology--Exploring the mystery of salinity change in portions of the Stanislaus and Merced Rivers: U.S. Geological Survey General Interest Publication, 18 p.
Winder, M., and Cloern, J.E., 2010,
The annual cycles of phytoplankton biomass: Philosophical Transactions of the Royal Society B--Biological Sciences, v. 365, no. 1555, p. 3215-3226, doi:10.1098/rstb.2010.0125.
Jassby, A.D., Cloern, J.E., and Cole, B.E., 2002,
Annual primary production--Patterns and mechanisms of change in a nutrient-rich tidal ecosystem: Limnology and Oceanography, v. 47, no. 3, p. 698-712.
Luoma, S.N., and Ho, K.T., 1993,
Appropriate uses of marine and estuarine sediment bioassays, in Calow, P., ed., Handbook of ecotoxicology: Oxford, U.K., Blackwell Scientific Publications, p. 193.
Kimmerer, W., Brown, L., Culberson, S., Moyle, P., Nobriga, M., and Thompson, J., 2008,
Aquatic ecosystems, in Healey, M.C., Dettinger, M.D., and Norgaard, R.B., eds., The State of Bay-Delta Science, 2008: Sacramento, Calif., CALFED Science Program, p. 73-102.
Johns, C., and Luoma, S.N., 1990,
Arsenic in benthic bivalves of San Francisco Bay and the Sacramento/San Joaquin River Delta: The Science of the Total Environment, v. 97/98, p. 673-684, doi:10.1016/0048-9697(90)90268-Y.
Hostettler, F.D., Kvenvolden, K.A., Rosenbauer, R.J., and Short, J.W., 1999,
Aspects of the Exxon Valdez oil spill--A forensic study and a toxics controversy, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2 of 3--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 135-144.
Luoma, S.N., Carter, J.L., and Brown, C.L., 1991,
Assessing adverse effects of contaminants in benthic species at the San Francisco Bay toxics site, in Mallard, G.E., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Monterey, California, March 11-15, 1991: U.S. Geological Survey Water-Resources Investigations Report 91-4034, p. 667-671.
Hladik, M.L., and Kuivila, K.M., 2009,
Assessing the occurrence and distribution of pyrethroids in water and suspended sediments: Journal of Agricultural and Food Chemistry, v. 57, no. 19, p. 9079-9085, doi:10.1021/jf9020448.
Pellerin, B.A., Downing, B.D., Kendall, C., Dahlgren, R.A., Kraus, T.E.C., Saraceno, J., Spencer, R.G.M., and Bergamaschi, B.A., 2009,
Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in situ optical nitrate sensor and dual nitrate isotopes: Freshwater Biology, v. 54, no. 2, p. 376-387, doi:10.1111/j.1365-2427.2008.02111.x.
Brown, C.L., Parchaso, F., Thompson, J.K., and Luoma, S.N., 2003,
Assessing toxicant effects in a complex estuary--A case study of effects of silver on reproduction in the bivalve, Potamocurbula amurensis, in San Francisco Bay: International Journal of Human and Ecological Risk Assessment, v. 9, no. 1, p. 95-119.
Stewart, A.R., Stern, G.A., Lockhart, W.L., Kidd, K.A., Salki, A.G., Stainton, M.P., Koczanski, K., Rosenberg, G.B., Savoie, D.A., Billeck, B.N., Wilkinson, P., and Muir, D.C.G., 2003,
Assessing trends in organochlorine concentrations in Lake Winnipeg fish following the 1997 Red River flood: Journal of Great Lakes Research, v. 29, no. 2, p. 332-354.
Janssen, E.M., Oen, A.M., Luoma, S.N., and Luthy, R.G., 2011,
Assessment of field-related influences on polychlorinated biphenyl exposures and sorbent amendment using polychaete bioassays and passive sampler measurements: Environmental Toxicology and Chemistry, v. 30, no. 1, p. 173-180, doi:10.1002/etc.367.
Reinfelder, J.A., Wang, W.-X., Luoma, S.N., and Fisher, N.S., 1997,
Assimilation efficiencies and turnover rates of trace elements in marine bivalves--A comparison of oysters, clams and mussels: Marine Biology, v. 129, no. 3, p. 443 - 452.
Wang, W.-X., Fisher, N.S., and Luoma, S.N., 1995,
Assimilation of trace elements ingested by the mussel Mytilus edulis--Effects of algal food abundance: Marine Ecology Progress Series, v. 129, no. 1-3, p. 165-176, doi:10.3354/meps129165.
Zheng, Y., Anderson, R.F., van Geen, A., and Kuwabara, J., 2000,
Authigenic molybdenum formation in marine sediments--A link to pore water sulfide in the Santa Barbara Basin: Geochimica et Cosmochimica Acta, v. 64, no. 24, p. 4165-4178, doi:10.1016/S0016-7037(00)00495-6.

B

Peterson, H.A., and Vayssieres, M., 2010,
Benthic assemblage variability in the upper San Francisco Estuary--A 27-year retrospective: San Francisco Estuary and Watershed Science, v. 8, no. 1.
Topping, B.R., Kuwabara, J.S., Parchaso, F., Hager, S.W., Arnsberg, A.J., and Murphy, F., 2001,
Benthic flux of dissolved nickel into the water column of South San Francisco Bay: U.S. Geological Survey Open-File Report 01-89, 50 p.
Kuwabara, J.S., Berelson, W.M., Balistrieri, L.S., Woods, P.F., Topping, B.R., Steding, D.J., and Krabbenhoft, D.P., 2000,
Benthic flux of metals and nutrients into the water column of Lake Coeur d'Alene, Idaho---Report of an August, 1999, pilot study: U.S. Geological Survey Water-Resources Investigations Report 00-4132, 74 p.
Kuwabara, J.S., Topping, B.R., Parchaso, F., Engelstad, A.C., and Greene, V.E., 2009,
Benthic flux of nutrients and trace metals in the northern component of San Francisco Bay, California: U.S. Geological Survey Open-File Report 2009-1286, 26 p.
Leland, H.V., and Fend, S.V., 1998,
Benthic invertebrate distributions in the San Joaquin River, California, in relation to physical and chemical factors: Canadian Journal of Fisheries and Aquatic Sciences, v. 55, p. 1051-1067.
Schemel, L.E., 1995,
Benthic macrofauna data for San Francisco Bay, California, September, 1989: U.S. Geological Survey Open-File Report 95-291, 33 p.
Kuwabara, J.S., Topping, B.R., Lynch, D.D., Carter, J.L., and Essaid, H.I., 2009,
Benthic nutrient sources to hypereutrophic Upper Klamath Lake, Oregon: Environmental Toxicology and Chemistry, v. 28, no. 3, p. 516-524, doi:10.1897/08-207.1.
Topping, B.R., Kuwabara, J.S., Athearn, N.D., Takekawa, J.Y., Parchaso, F., Henderson, K.D., and Piotter, S., 2009,
Benthic oxygen demand in three former salt ponds adjacent to South San Francisco Bay, California: U.S. Geological Survey Open-File Report 2009-1180, 21 p.
Caffrey, J.M., Hammond, D.E., Kuwabara, J.S., Miller, L.G., and Twilley, R.R., 1996,
Benthic processes in South San Francisco Bay--The role of organic inputs and bioturbation, in Hollibaugh, J.T., ed., San Francisco Bay--The ecosystem: San Francisco, American Association for the Advancement of Science, Pacific Division, p. 425-444.
Zehr, J.P., Harvey, R.W., Oremland, R.S., Cloern, J.E., George, L., and Lane, J.L., 1987,
Big Soda Lake (Nevada) - 1. Pelagic bacterial heterotrophy and biomass: Limnology and Oceanography, v. 32, p. 781-793.
Smith, R.L., and Oremland, R.S., 1987,
Big Soda Lake (Nevada) - 2. Pelagic sulfate reduction: Limnology and Oceanography, v. 32, p. 794-803.
Iversen, N., Oremland, R.S., and Klug, M.J., 1987,
Big Soda Lake (Nevada) - 3. Pelagic methanogenesis and anaerobic methane oxidation: Limnology and Oceanography, v. 32, p. 804-814.
Cloern, J.E., Cole, B.E., and Wienke, S.M., 1987,
Big Soda Lake (Nevada). 4. Vertical fluxes of particulate matter--Seasonality and variations across the chemocline: Limnology and Oceanography, v. 32, no. 4, p. 815-824.
Stewart, A.R., Grosell, M., Buchwalter, D.B., Fisher, N., Luoma, S.N., Mathews, T., Orr, P.L., and Wang, W.X., 2010,
Bioaccumulation and trophic transfer of selenium, in Chapman, P.M., and others, eds., Ecological Assessment of Selenium in the Aquatic Environment: Boca Raton, Fla., CRC Press, p. 93-139, ISBN:978-1-4398-2677-5 (SETAC Workshop on Ecological Assessment of Selenium in the Aquatic Environment Pensacola, Florida, February 22-28, 2009).
Casado-Martinez, M.C., Smith, B.D., Luoma, S.N., and Rainbow, P.S., 2010,
Bioaccumulation of arsenic from water and sediment by a deposit-feeding polychaete (Arenicola marina)--A biodynamic modelling approach: Aquatic Toxicology, v. 98, no. 1, p. 34-43, doi:10.1016/j.aquatox.2010.01.015.
Pereira, W.E., Hostettler, F.D., and Rapp, J.B., 1992,
Bioaccumulation of hydrocarbons derived from terrestrial and anthropogenic sources in the Asian Clam, Potamocorbula amurensis, in San Francisco Bay Estuary: Marine Pollution Bulletin, v. 24, no. 2, p. 103-109, doi:10.1016/0025-326X(92)90738-R.
Hornberger, M.I., Luoma, S.N., Cain, D.J., Parchaso, F., Brown, C.L., Bouse, R.M., Wellise, C., and Thomspon, J., 1999,
Bioaccumulation of metals by the bivalve Macoma balthica at a site in South San Francisco Bay between 1977 and 1997--Long-term trends and associated biological effects with changing pollutant loadings: U.S. Geological Survey Open-File Report 99-55, 42 p.
National Research Council, 2003,
Bioavailability of contaminants in soils and sediments--processes, tools, and applications: Washington, D.C., National Academy Press, 420 p.
Sobczak, W.V., Cloern, J.E., Jassby, A.D., and Mueller-Solger, A.B., 2002,
Bioavailability of organic matter in a highly disturbed estuary--The role of detrital and algal resources: Proceedings of the National Academy of Sciences of the United States of America, v. 99, no. 12, p. 8101-8105, doi:10.1073/pnas.122614399.
Schlekat, C.E., Dowdle, P.R., Lee, B.G., Luoma, S.N., and Oremland, R.S., 2000,
Bioavailability of particle-associated Se to the bivalve Potamocorbula amurensis: Environmental Science and Technology, v. 34, no. 21, p. 4504-4510, doi:10.1021/es001013f.
Luoma, S.N., 1983,
Bioavailability of trace metals to aquatic organisms--A review: The Science of the Total Environment, v. 28, p. 1-22, doi:10.1016/S0048-9697(83)80004-7.
Croteau, M.-N., and Luoma, S.N., 2008,
A biodynamic understanding of dietborne metal uptake by a freshwater invertebrate: Environmental Science and Technology, v. 42, no. 5, p. 1,801-1,806, doi:10.1021/es7022913.
Hostettler, F.D., Rapp, J.B., Kvenvolden, K.A., and Luoma, S.N., 1988,
Biogenic and anthropogenic organic markers as source discriminants and sediment transport indicators in South San Francisco Bay: U.S. Geological Survey Open-File Report 88-408, 28 p.
Miller, L.G., Baesman, S.M., Kirshtein, J., Voytek, M.A., and Oremland, R.S., 2013,
A biogeochemical and genetic survey of acetylene fermentation by environmental samples and bacterial isolates: Geomicrobiology Journal, v. 30, no. 6, p. 501-516, doi:10.1080/01490451.2012.732662.
Windham-Myers, L., Ward, K., Marvin-DiPasquale, M., Agee, J.L., Kieu, L.H., and Kakouros, E., 2013,
Biogeochemical implications of episodic impoundment in a restored tidal marsh of San Francisco Bay, California: Restoration Ecology, v. 21, no. 1, p. 124-132, doi:10.1111/j.1526-100X.2011.00849.x.
Windham-Myers, L., Marvin-DiPasquale, M.C., Agee, J.L., Kieu, L.H., Kakouros, E., Erikson, L., and Ward, K., 2010,
Biogeochemical processes in an urban, restored wetland of San Francisco Bay, California, 2007-2009--Methods and data for plant, sediment and water parameters: U.S. Geological Survey Open-File Report 2010-1299, 21 p.
Cloern, J.E., Hieb, K.A., Jacobson, T., SansÛ, B., Di Lorenzo, E., Stacey, M.T., Largier, J.L., Meiring, W., Peterson, W.T., Powell, T.M., Winder, M., and Jassby, A.D., 2010,
Biological communities in San Francisco Bay track large-scale climate forcing over the North Pacific: Geophys. Res. Lett., v. 37, no. 21, p. L21602, doi:10.1029/2010gl044774.
Thompson, B., Adelsbach, T., Brown, C., Hunt, J., Kuwabara, J., Neale, J., Ohlendorf, H., Schwarzbach, S., Spies, R., and Taberski, K., 2007,
Biological effects of anthropogenic contaminants in the San Francisco Estuary: Environmental Research, v. 105, no. 1, p. 156-174, doi:10.1016/j.envres.2006.10.005.
Luoma, S.N., and DiGiulio, 1999,
Biomarkers of cellular damage: Biomarkers, v. 4, p. 392-394.
Chapelle, F.H., 1999,
Bioremediation of petroleum hydrocarbon-contaminated ground water--The perspectives of history and hydrogeology: Ground Water, v. 37, no. 1, p. 122-132, doi:10.1111/j.1745-6584.1999.tb00965.x.
Ringwood, A.H., Hameedi, M.J., Lee, R.F., Brouwer, M., Peters, E.C., Scott, G.I., Luoma, S.N., and Digiulio, R.T., 1999,
Bivalve biomarker workshop--Overview and discussion group summaries: Biomarkers, v. 4, no. 6, p. 391-399, doi:10.1080/135475099230561.
Peterson, D.H., 1994,
Book review - Oxygen dynamics in the Chesapeake Bay by Smith, Leffler and Mackierman: Continental Shelf Research, v. 14, p. 321-323.
Cheng, R.T., Gartner, J.W., and Smith, R.E., 1997,
Bottom boundary layer in South San Francisco Bay, California, presented at the 7th International Biennial Conference on Physics of Estuaries and Coastal Seas, Woods Hole Oceanographic Institute, Woods Hole Mass., 28-30 November, 1994: Journal of Coastal Research, Special Issue No. 25, p. 49-62.
Pereira, W.E., Hostettler, F.D., and Wade, T.L., 1999,
Butyltin contamination in sediments and lipid tissues of the Asian clam, Potamocorbula amurensis, near Mare Island Naval Shipyard, San Francisco Bay, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2 of 3--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 41-49.

C

Jacobs, K.L., Luoma, S.N., and Taylor, K.A., 2003,
CALFED--An experiment in science and decisionmaking: Environment, v. 45, no. 1, p. 30-34.
van Geen, A., and Husby, D.M., 1996,
Cadmium in the California current system--Tracer of past and present upwelling: Journal of Geophysical Research, v. 101:C2, p. 3489-3507.
Luoma, S.N., Cain, D.J., and Rainbow, P.S., 2010,
Calibrating biomonitors to ecological disturbance--A new technique for deciphering metal effects in natural waters: Integrated Environmental Assessment and Management, v. 6, no. 2, p. 199-209, doi:0.1897/IEAM_2009-067.1.
Sommer, T., Harrell, B., Nobriga, M., Brown, R., Moyle, P., Kimmerer, W., and Schemel, L., 2001,
California's Yolo Bypass--Evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture: Fisheries, v. 26, no. 8, p. 6-16.
Luoma, S.N., 1989,
Can we determine the biological availability of sediment-bound trace elements?: Hydrobiologia, v. 176/177, p. 379-396.
Bergamaschi, B.A., Fram, M.S., Fujii, R., Aiken, G.R., Kendall, C., and Silva, S.R., 1999,
The carbon isotopic composition of trihalomethanes formed from chemically distinct dissolved organic carbon isolates from the Sacramento-San Joaquin River Delta, California, USA, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2 of 3--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 99-107.
Luoma, S.N., and Nichols, F.H., 1996,
Challenges in detecting contaminant effects on an estuarine ecosystem affected by many different disturbances--San Francisco Bay, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, v. 2, p. 689-694.
Kuwabara, J.S., Topping, B.R., Carter, J.L., Wood, T.M., Cameron, J.M., Asbill-Case, J.R., and Carlson, R.A., 2012,
Changes in benthic nutrient sources within a wetland after hydrologic reconnection: Environmental Toxicology and Chemistry, v. 31, no. 9, p. 1995-2013, doi:10.1002/etc.1914.
Caffrey, J.M., Cloern, J.E., and Grenz, C., 1998,
Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA--Implications for net ecosystem metabolism: Marine Ecology Progress Series, v. 172, p. 1-12, doi:10.3354/meps172001.
Stewart, I., Cayan, D.R., and Dettinger, M.D., 2004,
Changes in snowmelt runoff timing in western North America under a "Business as Usual" climate change scenario: Climate Change, v. 62, no. 1-3, p. 217-232, 5253277, doi:10.1023/B:CLIM.0000013702.22656.e8.
Dettinger, M.D., 2005,
Changes in streamflow timing in the western United States in recent decades: U.S. Geological Survey Fact Sheet 2005-3018, 4 p.
Stewart, I.T., Cayan, D.R., and Dettinger, M.D., 2005,
Changes toward earlier streamflow timing across western North America: Journal of Climate, v. 18, p. 1136-1155, doi:10.1175/JCLI3321.1.
Cloern, J.E., 2013,
Changing perspectives on how scientists should allocate our most precious resource--Time--AGU blogosphere--The plainspoken scientist--May 1, 2013: American Geophysical Union, access date September 12, 2013
Lucas, L.V., and Thompson, J.K., 2012,
Changing restoration rules--Exotic bivalves interact with residence time and depth to control phytoplankton productivity: Ecosphere, v. 3, no. 12, p. art117, doi:10.1890/es12-00251.1.
Croteau, M.-N., and Luoma, S.N., 2007,
Characterizing dissolved Cu and Cd uptake in terms of the biotic ligand and biodynamics using enriched stable isotopes: Environmental Science and Technology, v. 41, no. 9, p. 3140-3145, doi:10.1021/es0615122.
Venkatesan, M.I., de Leon, R.P., van Geen, A., and Luoma, S.N., 1999,
Chlorinated hydrocarbon pesticides and polychlorinated biphenyls in sediment cores from San Francisco Bay, in The impact of human activities on sediments of San Francisco Bay, California, van Geen, A., and Luoma, S.N., eds.,: Marine Chemistry, v. 64, no. 1-2, p. 85-97, doi:10.1016/S0304-4203(98)90086-X.
Jassby, A.D., Cloern, J.E., Cole, B.E., and Caffrey, J.M., 1995,
Choosing optimum station configurations for summarizing water quality characteristics, in 1994 annual report, San Francisco Estuary Regional Monitoring Program for Trace Substances: Richmond, Calif., San Francisco Estuary Institute, p. 157-169.
Chauvaud, L., Thompson, J.K., Cloern, J.E., and Thouzeau, G., 2003,
Clams as CO2 generators--The Potamocorbula amurensis example in San Francisco Bay: Limnology and Oceanography, v. 48, no. 6, p. 2086-2092.
Cloern, J.E., Schraga, T.S., Lopez, C.B., Knowles, N., Labiosa, R.G., and Dugdale, R., 2005,
Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay: Geophysical Research Letters, v. 32, L14608, doi:10.1029/2005GL023321.
Dettinger, M.D., Bennett, W.A., Cayan, D.R., Florsheim, J., Hughes, M., Ingram, B.L., Jassby, A., Knowles, N., Malamud, F., Peterson, D.H., Redmond, K., and Smith, L., 2003,
Climate science issues and needs of the CALFED Bay-Delta Program, in American Meteorological Society 83rd Annual Meeting, Impacts of Water Variability Symposium, Long Beach, California, February 9-13, 2003: American Meteorological Society, p. 7.11-1 to 7.11-4.
Cloern, J.E., Jassby, A.D., Thompson, J.K., and Hieb, K.A., 2007,
A cold phase of the east pacific triggers new phytoplankton blooms in San Francisco Bay: Proceedings of the National Academy of Sciences of the United States of America, v. 104, no. 47, p. 18561-18565, doi:10.1073/pnas.0706151104.
Monsen, N.E., Cloern, J.E., Lucas, L.V., and Monismith, S.G., 2002,
A comment on the use of flushing time, residence time, and age as transport time scales: Limnology and Oceanography, v. 47, no. 5, p. 1545-1553.
Thomson, E.A., Luoma, S.N., Johansson, C.E., and Cain, D.J., 1984,
Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination: Water Resources, v. 18, no. 6, p. 755-765.
Cloern, J.E., and Jassby, A.D., 2008,
Complex seasonal patterns of primary producers at the land-sea interface: Ecology Letters, v. 11, no. 12, p. 1,294-1,303, doi:10.1111/j.1461-0248.2008.01244.x.
Uncles, R.J., and Peterson, D.H., 1995,
A computer model of long-term salinity in San Francisco Bay--Sensitivity to mixing and inflows: Environmental International, v. 21, no. 5, p. 647-656.
Hladik, M.L., Domagalski, J.L., and Kuivila, K.M., 2009,
Concentrations and loads of suspended sediment-associated pesticides in the San Joaquin River, California and tributaries during storm events: Science of the Total Environment, v. 408, no. 2, p. 356-364, doi:10.1016/j.scitotenv.2009.09.040.
Crepeau, K.L., Kuivila, K.M., and Domagalski, J.L., 1996,
Concentrations of dissolved rice pesticides in the Colusa Basin Drain and Sacramento River, California, 1990-92, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, v. 2, p. 711-718.
Kuivila, K.M., and Foe, C.G., 1995,
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Schemel, L.E., 2002,
Supporting data for hydrologic studies in San Francisco Bay, California--Meteorological measurements at the port of Redwood City during 1998-2001: U.S. Geological Survey Open-File Report 02-231, data files plus 37 p.
Schemel, L.E., 1995,
Supporting data for hydrologic studies in San Francisco Bay, California--Meteorological measurements at the port of Redwood City, 1992-1994: U.S. Geological Survey Open-File Report 95-327, 30 p.
Hostettler, F.D., Rapp, J.B., Pereira, W.E., and Kvenvolden, K.A., 1996,
A survey of molecular marker compounds in sediments of San Francisco Bay, California, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, v. 2, p. 735-745.
Peterson, D.H., Noble, N., and Smith, R.E., 1993,
Suspended sediment in San Francisco Bay Estuary, California--Recent history and available data sets: U.S. Geological Survey Water-Resources Investigations Report 93-4128, 35 p.
Dybowska, A.D., Croteau, M.-N., Misra, S.K., Berhanu, D., Luoma, S.N., Christian, P., O'Brien, P., and Valsami-Jones, E., 2011,
Synthesis of isotopically modified ZnO nanoparticles and their potential as nanotoxicity tracers: Environmental Pollution, v. 159, no. 1, p. 266-273, doi:10.1016/j.envpol.2010.08.032.

T

Casulli, V., Bertolazzi, E., and Cheng, R.T., 1993,
TRIM_3D--A three-dimensional model for accurate simulation of shallow water flow, in 1993 National Conference on Hydraulic Engineering, Proceedings, San Francisco, California, July, 1993: American Society of Civil Engineers, p. 1988-1993.
Luoma, S.N., Cain, D.J., and Johansson, C.E., 1986,
Temporal fluctuation of silver, copper and zinc in the bivalve Macoma balthica in South San Francisco Bay: Hydrobiologia, v. 129, p. 109-120.
Thomson-Becker, E.A., and Luoma, S.N., 1985,
Temporal fluctuations in grain size, organic materials and iron concentrations in intertidal surface sediment of San Francisco Bay: Hydrobiologia, v. 129, p. 91-107.
Luoma, S.N., Dagovitz, R., and Axtmann, E., 1990,
Temporally intensive study of trace metals in sediments and bivalves from a large river-estuarine system--Suisun Bay/Delta in San Francisco Bay: The Science of the Total Environment, v. 97/98, p. 685-712, doi:10.1016/0048-9697(90)90269-Z.
MacWilliams, M.L., and Cheng, R.T., 2007,
Three-dimensional hydrodynamic modeling of San Pablo Bay on an unstructured grid, in Proceedings of the 7th International Conference on HydroScience and Engineering, Philadelphia, September 10-13, 2006: p. 16, ISBN:0977447405.
Cheng, R.T., Casulli, V., and Gartner, J.W., 1993,
Tidal, residual, intertidal mudflat (TRIM) model and its applications to San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 36, p. 235-280, doi:10.1006/ecss.1993.1016.
Kuwabara, J.S., Topping, B.R., Carter, J.L., Wood, T.M., Parchaso, F., Cameron, J.M., Asbill, J.R., Carlson, R.A., and Fend, S.V., 2012,
Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon: U.S. Geological Survey Open-File Report 2012-1057, 26 p.
Decho, A.W., and Luoma, S.N., 1991,
Time-courses in the retention of food material in the bivalves Potamocorbula amurensis and Macoma balthica--Significance to the absorption of carbon and chromium: Marine Ecology Progress Series, v. 78, p. 303-314.
Kuwabara, J.S., and Baker, J.E., 1993,
Trace contaminants and nutrients in estuaries--The importance of process interdependence: Estuaries, v. 16, no. 3A, p. 383-384.
Kuwabara, J.S., and Helliker, P., 1988,
Trace contaminants in streams (chap. 26), in Cheremisinoff, P.N., Cheremisinoff, N.P., and Cheng, S.L., eds., Water Resources/Environmental, v. 5 of Civil Engineering Practice: Lancaster, Pennsylvania, Technomic Press, p. 739-766.
Reinfelder, J.R., Fischer, N.S., Luoma, S.N., Nichols, J.W., and Wang, W.X., 1998,
Trace element trophic transfer in aquatic organisms--A critique of the kinetic model approach: The Science of the Total Environment, v. 219, no. 2-3, p. 117-135, doi:10.1016/S0048-9697(98)00225-3.
Kuwabara, J.S., Chang, C.C.Y., Cloern, J.E., Fries, T.L., Davis, J.A., and Luoma, S.N., 1989,
Trace metal associations in the water column of South San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 28, p. 307-325, doi:10.1016/0272-7714(89)90020-6.
van Geen, A., and Luoma, S.N., 1993,
Trace metals Cd, Cu, Ni, Zn, and nutrients in coastal waters adjacent to San Francisco Bay, California: Estuaries, v. 16, no. 3A, p. 559-566.
Luoma, S.N., Cain, D.J., Brown, C.L., and Hornberger, M., 1993,
Trace metals in clams (Macoma Balthica) and sediments at the Palo Alto mudflat in South San Francisco Bay--June 1992-May 1993: U.S. Geological Survey Open-File Report 93-500, 52 p.
Luoma, S.N., Cain, D.J., Brown, C., and Axtmann, E.V., 1991,
Trace metals in clams (Macoma balthica) and sediments at the Palo Alto Mudflat in south San Francisco Bay--April 1990-April 1991: U.S. Geological Survey Open-File Report 91-460, 47 p.
Luoma, S.N., Cain, D.J., and Brown, C., 1992,
Trace metals in clams (Macoma balthica) and sediments at the Palo Alto mudflat in South San Francisco Bay, California--May 1991 to May 1992: U.S. Geological Survey Open-File Report 92-456, 51 p.
Luoma, S.N., Cain, D.J., Brown, C., and Hornberger, M., 1993,
Trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnnyvale water quality control plants in South San Francisco Bay: U.S. Geological Survey Open-File Report 93-500, 49 p.
Giddings, E.M., Hornberger, M.I., and Hadley, H.K., 2001,
Trace-metal concentrations in sediment and water and health of aquatic macroinvertebrate communities of streams near Park City, Summit County, Utah: U.S. Geological Survey Water-Resources Investigations Report 01-4213, 22 p.
Kuwabara, J.S., Topping, B.R., Carter, J.L., Parchaso, F., Cameron, J.M., Asbill, J.R., Fend, S.V., Duff, J.H., and Engelstad, A.C., 2010,
The transition of benthic nutrient sources after planned levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon: U.S. Geological Survey Open-File Report 2010-1062, 18 p (includes additional tables and video file).
Domagalski, J.L., and Kuivila, K.M., 1991,
Transport and transformation of dissolved rice pesticides in the Sacramento River Delta, Calif., in Mallard, G.E., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Monterey, California, March 11-15, 1991: U.S. Geological Survey Water-Resources Investigations Report 91-4034, p. 664-666.
Stahle, D.W., Griffin, R.D., Cleaveland, M.K., Edmondson, J.R., Fye, F.K., Burnette, D.J., Abatzoglou, J.T., Redmond, K.T., Meko, D.M., Dettinger, M.D., Cayan, D.R., and Therrell, M.D., 2011,
A tree-ring reconstruction of the salinity gradient in the northern estuary of San Francisco Bay: San Francisco Estuary and Watershed Science, v. 9, no. 1.
Croteau, M.-N., Luoma, S.N., and Stewart, A.R., 2005,
Trophic transfer of metals along freshwater food webs--Evidence of cadmium biomagnification in nature: Limnology and Oceanography, v. 50, no. 5, p. 1511-1519, doi:10.4319/lo.2005.50.5.1511 (Abstract).
Rainbow, P.S., Poirier, L., Smith, B.D., Brix, K.V., and Luoma, S.N., 2006,
Trophic transfer of trace metals--Subcellular compartmentalization in a polychaete and assimilation by a decapod crustacean: Marine Ecology Progress Series, v. 308, p. 91-100, doi:10.3354/meps308091.

U

Williams, B.K., Wingard, G.L., Brewer, G., Cloern, J., Gelfenbaum, G., Jacobson, R.B., Kershner, J.L., McGuire, A.D., Nichols, J.D., Shapiro, C.D., van Riper, C., III, and White, R.P., 2012,
The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022--Advancing discovery and application through collaboration: U.S. Geological Survey Open-File Report 2012-1092, 25 p.
Williams, B.K., Wingard, G.L., Brewer, G., Cloern, J.E., Gelfenbaum, G., Jacobson, R.B., Kershner, J.L., McGuire, A.D., Nichols, J.D., Shapiro, C.D., van Riper, C., III, and White, R.P., 2013,
U.S. Geological Survey ecosystems science strategy--Advancing discovery and application through collaboration: U.S. Geological Survey Circular 1383-C, 43 p.
Luoma, S.N., and Fisher, N.S., 1997,
Uncertainties in assessing contaminant exposure from sediments (Chapter 14), in Ingersoll, C.G., Dillon, T., and Biddinger, G.R., eds., Ecological Risk Assessment of Contaminated Sediments: Pensacola, Florida, Setac Press, SETAC Special Publication Series, SP97-12, p. 211-237.
Kuwabara, J.S., Nichols, F.H., Kuivila, K.M., and DiLeo, J.S., 1999,
Understanding the human influence on the San Francisco Bay-Delta Estuary Ecosystem -- The Toxic Substances Hydrology Program and USGS Place-based Studies Program provide complimentary approaches and results, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2 of 3--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 109-113.
Kuivila, K.M., and Hladik, M.L., 2008,
Understanding the occurrence and transport of current-use pesticides in the San Francisco Estuary watershed: San Francisco Estuary and Watershed Science, v. 6, no. 3, Article 2.
Lee, B.G., Wallace, W.G., and Luoma, S.N., 1998,
Uptake and loss kinetics of Cd, Cr and Zn in the bivalves Potamocorbula amurensis and Macoma balthica--Effects of size and salinity: Marine Ecology Progress Series, v. 175, p. 177-189, doi:10.3354/meps175177.
Yoo, H., Lee, J.-S., Lee, B.-G., Lee, I.-T., Schlekat, C.E., Koh, D.-H., and Luoma, S.N., 2004,
Uptake pathway for Ag bioaccumulation in three benthic invertebrates exposed to contaminated sediments: Marine Ecology Progress Series, v. 270, p. 141-152, doi:10.3354/meps270141.
Hostettler, F.D., Rapp, J.B., and Kvenvolden, K.A., 1992,
Use of geochemical biomarkers in bottom sediment to track oil from a spill, San Francisco Bay, California: Marine Pollution Bulletin, v. 24, p. 15-20.
Brown, C.L., and Luoma, S.N., 1995,
Use of the euryhaline bivalve Potamocorbula amurensis as a biosentinel species to assess trace element contamination in San Francisco Bay: Marine Ecology Progress Series, v. 124, no. 1-3, p. 129-142, doi:10.3354/meps124129.
Buchwalter, D.B., Cain, D.J., Clements, W.H., and Luoma, S.N., 2007,
Using biodynamic models to reconcile differences between laboratory toxicity tests and field biomonitoring with aquatic insects: Environmental Science and Technology, v. 41, no. 13, p. 4,821-4,828, doi:10.1021/es070464y.
Buchwalter, D.B., Cain, D.J., Clements, W.H., and Luoma, S.N., 2008,
Using biodynamic models to reconcile differences between laboratory toxicity tests and field biomonitoring with aquatic insects: Environmental Science and Technology, v. 42, no. 8, p. 3,117-3,117, doi:10.1021/es703130e.

V

Johansson, C., Cain, D.J., and Luoma, S.N., 1986,
Variability in the fractionation of Cu, Ag, and Zn among cytosolic proteins in the bivalve Macoma balthica: Marine Ecology Progress Series, v. 28, p. 87-97.
Luoma, S.N., Cain, D.J., Ho, K., and Hutchinson, A., 1983,
Variable tolerance to Cu in two species from San Francisco Bay: Marine Environmental Research, v. 10, p. 209-222.

W

Peterson, D., Smith, R., and Hager, S., 2004,
A walk through the hydroclimate network in Yosemite National Park--River chemistry: Sierra Nature Notes, v. 4.
Luoma, S.N., and Cloern, J.E., 2004,
Water 2025--The CALFED Bay-Delta Program: People, Land and Water (News magazine of the U.S. Department of the Interior), v. 2, no. 4, p. 23.
Dodge, K.A., Hornberger, M.I., and Axtmann, E.V., 1996,
Water quality, bed sediment and biological data (October 1994-September 1995) and statistical summaries of data for streams in the upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 96-432, 109 p.
Dodge, K.A., Hornberger, M.I., and Bouse, R.M., 1999,
Water quality, bed sediment and biological data (October 1997 through September 1998) and statistical summaries of data for streams in the Upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 99-251, 102 p.
Luoma, S., Anderson, S., Bergamaschi, B., Holm, L., Ruhl, C., Schoellhamer, D., and Stewart, R., 2008,
Water quality, in Healey, M.C., Dettinger, M.D., and Norgaard, R.B., eds., The State of Bay-Delta Science, 2008: Sacramento, Calif., CALFED Science Program, p. 55-72.
Gartner, J.W., Prych, E.A., Tate, G.B., Cacchione, D.A., Cheng, R.T., Bidlake, W.R., and Ferreira, J.T., 1998,
Water velocity and the potential for the movement of bed sediments in Sinclair Inlet of Puget Sound, Washington: U.S. Geological Survey Open-File Report 98-572, 140 p.
Pagano, T., Pasteris, P., Dettinger, M., Cayan, D., and Redmond, K., 2004,
Water year 2004--Western water managers feel the heat: Eos, v. 85, p. 392-393.
Cloern, J.E., Cole, B.E., Edmunds, J.L., and Baylosis, J.I., 1999,
Water-quality variability in San Francisco Bay--General patterns of change during 1997, in 1997 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 67-81.
Dodge, K.A., Hornberger, M.I., and Lavigne, I.R., 2004,
Water-quality, bed-sediment and biological data (October 2002 through September 2003) and statistical summaries of data for streams in the upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 2004-1340, 107 p.
Dodge, K.A., Hornberger, M.I., and Lavigne, I.R., 2003,
Water-quality, bed-sediment, and biological data (October 2001 through September 2002) and statistical summaries of data for streams in the upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 03-356, 95 p.
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2005,
Water-quality, bed-sediment, and biological data (October 2003 through September 2004) and statistical summaries of data for streams in the Upper Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2005-1356, 124 p (includes map, 28 cm.).
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2006,
Water-quality, bed-sediment, and biological data (October 2004 through September 2005) and statistical summaries of data for streams in the Upper Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2006-1266, 109 p.
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2007,
Water-quality, bed-sediment, and biological data (October 2005 through September 2006) and statistical summaries of long-term data for streams in the Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2007-1301, 125 p.
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2008,
Water-quality, bed-sediment, and biological data (October 2006 through September 2007) and statistical summaries of long-term data for streams in the Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2008-1318, vi, 134 p.
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2009,
Water-quality, bed-sediment, and biological data (October 2007 through September 2008) and statistical summaries of long-term data for streams in the Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2009-1178, 140 p.
Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2010,
Water-quality, bed-sediment, and biological data (October 2008 through September 2009) and statistical summaries of long-term data for streams in the Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2010-1267, 17 p.
Bromirski, P.D., Cayan, D.R., and Flick, R.E., 2005,
Wave spectral energy variability in the northeast Pacific: Journal of Geophysical Research-Oceans, v. 110, C03005, doi:10.1029/2004JC002398.
Cloern, J.E., Jassby, A.D., Schraga, T.S., and Dallas, K.L., 2006,
What is causing the phytoplankton increase in San Francisco Bay?, in The Pulse of the Estuary -- Monitoring and managing water quality in the San Francisco Estuary: Oakland, California, San Francisco Estuary Institute Annual Report 2006, p. 62-70.
Lucas, L.V., Thompson, J.K., and Brown, L.R., 2009,
Why are diverse relationships observed between phytoplankton biomass and transport time?: Limnology and Oceanography, v. 54, no. 1, p. 381-390.
Luoma, S.N., and Rainbow, P.S., 2005,
Why is metal bioaccumulation so variable? Biodynamics as a unifying concept: Environmental Science and Technology, v. 39, no. 7, p. 1921-1931, doi:10.1021/es048947e.
Dettinger, M.D., Redmond, K.T., and Cayan, D.R., 2004,
Winter orographic precipitation ratios in the Sierra Nevada--Large-scale atmospheric circulations and hydrologic consequences: Journal of Hydrometeorology, v. 5, p. 1102-1116, doi:10.1175/JHM-390.1.
Cayan, D., VanScoy, M., Dettinger, M.D., and Helly, J., 2003,
The wireless watershed at the Santa Margarita Ecological Reserve: Southwest Hydrology, v. 2, no. 5, p. 18-19.

Y

Cloern, J.E., and Jassby, A.D., 1995,
Yearly fluctuation of the spring phytoplankton bloom in South San Francisco Bay--An example of ecological variability at the land-sea interface, in Steele, J.H., Powell, T.M., and Levin, S., eds., Ecological Time Series: New York, Chapman and Hall, p. 139-149.

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