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Cohen, A. N. 2008. Zebra & quagga mussel invasions in the western US. International Association of Great Lakes Research (IAGLR).
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.
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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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Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga, Sunnyvale East and West. Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds.. SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

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Cohen, A. N. 1992. Weeding the Garden. Atlantic Monthly 270, 76-86.
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Cohen, A. N. 2000. Weeding the garden. In Preserving Wildlife: An International Perspective. Michael, M. A., Ed.. Preserving Wildlife: An International Perspective. Prometheus Books: Amherst NY. pp 84-92.
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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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Hoenicke, R.; Bleier, C. 2007. Watershed Management and Land Use. CCMP Implementation Committee.
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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.
Sowers, J. M.; Salomon, M. N.; Ticci, M.; Beller, E. E.; Grossinger, R. M. 2012. Watching Our Watersheds: Santa Clara Valley Past, Google Earth KMZ files: Santa Clara Valley historical points of interest, stream courses and habitats.
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Hagerty, S.; Spotswood, E.; McKnight, K.; Grossinger, R. M. 2019. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. San Francisco Estuary Institute: Richmond, CA.

This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
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Bruland, K. W.; Phinney, J. T. 1994. Uptake of lipophilic organic Cu, Cd, and Pb complexes in the coastal diatom, Thalassiosira Weissflogii. Environmental Science and Technology 28, 1781-1790 . SFEI Contribution No. 179.
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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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Safran, S. M.; Hagerty, S.; Robinson, A.; Grenier, L. 2018. Translating Science-Based Restoration Strategies into Spatially-Explicit Restoration Opportunities in the Delta (2018 Bay-Delta Science Conference Presentation).

In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that emphasized restoring or emulating natural processes, anticipating future changes associated with climate change, establishing appropriate configurations of habitat types at the landscape scale, and utilizing a variety multi-benefit management strategies. In this talk, we present on our recent work to support regional restoration planning efforts by developing a repeatable process for using these guidelines to identify spatially-explicit restoration opportunities. The process is largely GIS-based and utilizes spatial data on existing land cover and conservation status, habitat configuration (including patch sizes and distances), surface elevations (including depth of subsidence), and future changes in tidal elevations associated with sea-level rise.  By distilling generalized guidelines into spatially-explicit opportunities, we hope to provide a practical tool for incorporating science into planning. To that end, these new methods are currently being piloted through planning efforts focused on the Central Delta Corridor and the McCormack Williamson Tract, and are also being used to assist with the quantification of ecological restoration potential in the Delta Plan Ecosystem Amendment.

Presentation recording: available here.

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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.