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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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Lowe, S.; Ross, J. R. M.; Thompson, B. 2003. CISNet San Pablo Bay Network of Environmental Stress Indicators; Benthic Microfauna. SFEI Contribution No. 299. 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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Livsey, D. N.; Downing-Kunz, M. A.; Schoellhamer, D. H.; Manning, A. J. 2020. Suspended Sediment Flux in the San Francisco Estuary: Part I—Changes in the Vertical Distribution of Suspended Sediment and Bias in Estuarine Sediment Flux Measurements. Estuaries and Coasts . SFEI Contribution No. 990.

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the San Francisco Estuary. Current methods for measuring continuous suspended sediment flux estimates relate continuous estimates of suspended-sediment concentration (SSC) measured at-a-point (SSCpt) to discrete cross-section measurements of depth-averaged, velocity-weighted SSC (SSCxs). Regressions that compute SSCxs from continuous estimates of SSCpt require that the slope between SSCpt and SSCxs, controlled by the vertical distribution of SSC, is fixed. However, in tidal systems with suspended cohesive sediment, factors that control the vertical SSC profile—vertical turbulent mixing and downward settling of suspended sediment mediated by flocculation of cohesive sediment—constantly vary through each tide and may exhibit systematic differences between flood and ebb tides (tidal asymmetries in water velocity or particle size). We account for changes in the vertical SSC profile on estimates of SSCxs using time series of the Rouse number of the Rouse-Vanoni-Ippen equation combined with optical turbidity measurements, a surrogate for SSCpt, to predict SSCxs from 2009 to 2011 and 2013. Time series of the Rouse number were estimated by fitting the Rouse-Vanoni-Ippen equation to SSC estimated from optical-turbidity measurements taken at two elevations in the water column. When accounting for changes in the vertical SSC profile, changes in not only the magnitude but also the direction of cumulative sediment-flux measurements were observed. For example, at a mid-depth sensor, sediment flux estimates changed from − 319 kt (± 65 kt, negative indicating net seaward transport) to 482 kt (± 140 kt, positive indicating net landward transport) for 2009–2011 and from − 388 kt (± 140 kt) to 1869 kt (± 406 kt) for 2013–2016. At the study location, estimation of SSCxs solely from SSCpt resulted in sediment flux values that were underestimates on flood tides and overestimates on ebb tides. This asymmetry is driven by covariance between water velocity and particle settling velocity (Ws) with larger Ws on flood compared to ebb tides. Results of this study indicate that suspended-sediment-flux measurements estimated from point estimates of SSC may be biased if systematic changes in the vertical distribution of SSC are unaccounted for.

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Lin, D.; Sun, J.; Yee, D.; Franz, A.; Trowbridge, P.; Salop, P. 2017. 2017 RMP Water Cruise Plan. SFEI Contribution No. 845. San Francisco Estuary Institute : Richmond, 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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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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Lin, D.; Sutton, R.; Sun, J.; Ross, J. 2018. Screening of Pharmaceuticals in San Francisco Bay Wastewater. SFEI Contribution No. 910. San Francisco Estuary Institute : Richmond, CA.
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Leatherbarrow, J. E.; Yee, D.; Davis, J. A. 2001. PCBs in effluent. SFEI Contribution No. 237.
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Kucera, T.; Breauz, A.; Zielinski, W. 2002. Data Collection Protocol Montioring River Otter (Lutra [=Lontra] canadensis). SFEI Contribution No. 241. CA State University Stanislaus, U.S Forest Service, San Francisco Bay Regional Water Quality Control Board: Oakland, CAStanislaus, CA. p 11.
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Kramer, K. S. 1989. Inventory of Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 156. AHI: Richmond, CA. p 48.
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Kramer, K. S. 1989. Inventory of Current Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 155. San Francisco Estuary Institute: Richmond, CA. p 39.
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King, A. 2019. Wind Over San Francisco Bay and the Sacramento-San Joaquin River Delta: Forcing for Hydrodynamic Models. SFEI Contribution No. 937. San Francisco Estuary Institute: Richmond, CA.
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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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Kauhanen, P.; Lowe, S. 2019. Prioritizing Candidate Green Infrastructure Sites within the City of Ukiah: A Demonstration of the Site Locator Tool of GreenPlan-IT. Report prepared for the City of Ukiah Department of Public Works under Supplemental Environmental Project # R1-018-0024. San Francisco Estuary Institute: Richmond. CA.

This report describes the application of GreenPlan-IT’s Site Locator Tool to identify and rank candidate GI installation sites within the City of Ukiah.  The Site Locator Tool is the first (foundational) tool of the GreenPlan-IT toolkit, meaning that the outputs are required inputs for both the Hydrologic Modeling and Optimization tools.   The Site Locator Tool addresses the question: where are the best locations for GI implementation based on local planning priorities? 

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Kauhanen, P.; Wu, J.; Hunt, J.; McKee, L. 2018. Green Plan-IT Application Report for the East Bay Corridors Initiative. SFEI Contribution No. 887. San Francisco Estuary Institute: Richmond, CA.
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Johnston, D. 2002. Data Collection Protocol Yuma Bat (Myotis yumanensis). SFEI Contribution No. 259. H.T Harvey & Associates: San Jose, CA. p 7.
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Jassby, A. D. 1996. Methods for Analysis of Spatial and Temporal Patterns. SFEI Contribution No. 18. San Francisco Estuary Institute: Richmond, CA.
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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.
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Jarman, W. M.; Davis, J. A. 1997. Observations on trace organic concentrations in RMP water samples. SFEI Contribution No. 210. San Francisco Estuary Institute. pp 67-77.
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Jahn, A. 2018. Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016. SFEI Contribution No. 900. San Francisco Estuary Institute: Richmond, CA.
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Jabusch, T. W. 2010. Selenium in the Grasslands Watershed. San Francisco Estuary Institute: Oakland, CA. pp 267-294.