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Marine Sciences Division

Recent Publications

138 publications found:

2009

  • Diefenderfer HL, KL Sobocinski, RM Thom, CW May, AB Borde, SL Southard, J Vavrinec, III, and NK Sather. 2009. "Multiscale Analysis of Restoration Priorities for Marine Shoreline Planning." Environmental Management 44(4 ):712-731.  doi:10.1007/s00267-009-9298-4
  • Yang Z, and TP Khangaonkar. 2009. "Modeling Tidal Circulation and Stratification in Skagit River Estuary Using an Unstructured Grid Ocean Model ." Ocean Modelling 28(1-3):34-49. (special issue). 
  • Richmond MC, Z Deng, CA McKinstry, RP Mueller, TJ Carlson, and DD Dauble. 2009. "Response Relationship Between Juvenile Salmon and an Autonomous Sensor in Turbulent Flows." Fisheries Research 97(1-2):134-139.  doi:10.1016/j.fishres.2009.01.011
  • Thom RM, MG Anderson, D Tyre, and CA Fleming. 2009. Adaptive Management for Decision Making at the Program and Project Levels of the Missouri River Recovery Program. PNNL-18261, Pacific Northwest National Laboratory, Richland, WA. 

2008

  • Roesijadi G, S Rezvankhah, A Perez-Matus, A Mitelberg, K Torruellas, and PA Van Veld. 2008. "Dietary cadmium and benzo(a)pyrene increased intestinal metallothionein expression in the fish Fundulus heteroclitus." Marine Environmental Research 67(1):25-30. 
  • Thom RM. 2008. "A.W.D., Larkum, R.J. Orth, C.M. Duarte (eds.), 2006, Seagrasses: Biology, Ecology and Conservation, Springer, ISBN: 978-1-4020-2942-4 (hardback), US$ 99.00, 691 pages." Journal of Experimental Marine Biology and Ecology 354(1):160. 
  • Yang Z, and TP Khangaonkar. 2008. "Modeling of Coastal Effluent Transport: an Approach to Linking of Far-field and Near-field Models." Acta Oceanologica Sinica 27:21-30. 
  • Yang Z, and TP Khangaonkar. 2008. "Modeling of Salt Intrusion, Intertidal Mixing, and Circulation in a Braided Estuary." In Surface Water Modeling, vol. 52, pp. 171-180.  Journal of Coastal Research, Boca Raton, FL. 
  • Bellgraph BJ, RS Brown, JR Stephenson, AE Welch, KA Deters, and TJ Carlson. 2008. "Healing Rate of Swim Bladders in Rainbow Trout." Transactions of the American Fisheries Society 137(6):1791-1794.  doi:10.1577/T07-167.1
  • Burkholder BK, GE Grant, R Haggerty, TP Khangaonkar, and PJ Wampler. 2008. "Influence of hyporheic flow and geomorphology on temperature of a large, gravel-bed river, Clackamas River, Oregon, USA." Hydrological Processes 22(7):941-953. 
  • Carlson TJ, JP Duncan, and Z Deng. 2008. Data Overview for Sensor Fish Samples Acquired at Ice Harbor, John Day, and Bonneville II Dams in 2005, 2006, and 2007 . PNNL-17398, Pacific Northwest National Laboratory, Richland, WA. 
  • Heilmayer O, JJ DiGialleonardo, L Qian, and G Roesijadi. 2008. "Stress tolerance of a subtropical Crassostrea virginica population to the combined effects of temperature and salinity." Estuarine, Coastal and Shelf Science 79(1):179-185. 
  • Hook SE, ME Cobb, JT Oris, and JW Anderson. 2008. "Gene Sequences for Cytochromes p450 1A1 and 1A2: The Need for Biomarker Development in Sea Otters (Enhydra lutris)." Comparative Biochemistry and Physiology Part B: Biochemistry & Molecular Biology 151(3):336-348.  doi:10.1016/j.cbpb.2008.08.003
  • Hook SE, AD Skillman, B Gopalan, JA Small, and IR Schultz. 2008. "Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture." Toxicological Sciences 102(1):42-60.  doi:10.1093/toxsci/kfm293
  • Johnson GE, HL Diefenderfer, AB Borde, EM Dawley, BD Ebberts, DA Putman, GC Roegner, M Russell, JR Skalski, RM Thom, and J Vavrinec, III. 2008. Evaluating Cumulative Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2007. PNNL-17437, Pacific Northwest National Laboratory, Richland, WA. 
  • Khangaonkar TP, Z Yang, J Paik, and F Sotiropoulos. 2008. "Simulation of Hydrodynamics at Stratified Reservoirs Using a Staged Modeling Approach." Journal of Coastal Research. JCR (Special Issue: 52):79-86. 
  • Khangaonkar TP, and Z Yang. 2008. "DYNAMIC RESPONSE OF STREAM TEMPERATURES TO BOUNDARY AND INFLOW PERTURBATION DUE TO RESERVOIR OPERATIONS." River Research and Applications 24(4):420-433.  doi:10.1002/rra.1088
  • Mueller RP, SS Southard, CW May, WH Pearson, and VI Cullinan. 2008. "Juvenile Coho Salmon Leaping Ability and Behavior in an Experimental Culvert Test Bed." Transactions of the American Fisheries Society 137(4):941-950.  doi:10.1577/T06-244.1
  • Roegner GC, HL Diefenderfer, AB Borde, RM Thom, EM Dawley, AH Whiting, SA Zimmerman, and GE Johnson. 2008. Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuary. PNNL-15793, Pacific Northwest National Laboratory, Richland, WA. 
  • Salice CJ, TJ Miller, and G Roesijadi. 2008. "Demographic responses to multi-generation cadmium exposure in two strains of the freshwater gastropod, Biomphalaria glabrata." Archives of Environmental Contamination and Toxicology.  doi:10.1007/s00244-008-9203-9
  • Tang H, J Paik, F Sotiropoulos, and TP Khangaonkar. 2008. "Three-Dimensional Numerical Modeling of Initial Mixing of Thermal Discharges at Real-Life Configurations." Journal of Hydraulic Engineering 134(9):1210-1224.  doi:10.1061/(ASCE)0733-9429(2008)134:9(1210)
  • Thom RM, SL Southard, AB Borde, and P Stoltz. 2008. "Light Requirements for Growth and Survival of Eelgrass (Zostera marina L.) in Pacific Northwest (USA) Estuaries." Estuaries and Coasts 31(5):969-980.  doi:10.1007/s12237-008-9082-3
  • Thom RM, SS Southard, AB Borde, and P Stoltz. 2008. "Light Requirements for Growth and Survival of Eelgrass (Zostera marina L.) in Pacific Northwest (USA) Estuaries." Estuaries and Coasts 31(5):969-980.  doi:10.1007/s12237-008-9082-3

2007

  • Blanton ML, and JL Specker. 2007. "The Hypothalamic-Pituitary-Thyroid (HPT) Axis in Fish and Its Role in Fish Development and Reproduction." Critical Reviews in Toxicology 37(1-2):97-115.  doi:10.1080/10408440601123529
  • Brown RS, TJ Carlson, AE Welch, JR Stephenson, CS Abernethy, CA McKinstry, and MH Theriault. 2007. Assessment of Barotrauma Resulting from Rapid Decompression of Depth Acclimated Juvenile Chinook Salmon Bearing Radio Telemetry Transmitters. PNNL-16790, Pacific Northwest National Laboratory, Richland, WA. 
  • Deng Z, TJ Carlson, JP Duncan, and MC Richmond. 2007. "Applications of the Sensor Fish Technology." Hydro Review 26(5):10-14. 
  • Deng Z, TJ Carlson, JP Duncan, and MC Richmond. 2007. "Six-degree-of-freedom Sensor Fish design and instrumentation." Sensors 7(12):3399-3415. 
  • Roesijadi G, S Rezvankhah, DM Binninger, and H Weissbach. 2007. "Ecdysone Induction of MsrA Protects Against Oxidative Stress in Drosophila." Biochemical and Biophysical Research Communications 354(2):511-516. 
  • Schultz IR, AD Skillman, and DL Woodruff. 2007. "Domoic Acid Excretion In Dungeness Crabs, Razor Clams and Mussels." Marine Environmental Research 66(1):21-23.  doi:Stenner, Robert D
  • Schultz IR, SM Reed, AV Pratt, and AD Skillman. 2007. "Quantitative oral dosing of water soluble and lipophilic contaminants in the Japanese medaka (Oryzias latipes)." Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology 145(1):86-95. 
  • Vavrinec J, III, WH Pearson, NP Kohn, JR Skalski, C Lee, KD Hall, BA Romano, MC Miller, and TP Khangaonkar. 2007. Laboratory Assessment of Potential Impacts to Dungeness Crabs from Disposal of Dredged Material from the Columbia River. PNNL-16482, Pacific Northwest National Laboratory, Richland, WA. 
  • Brandenberger JM, CW May, VI Cullinan, RK Johnston, DE Leisle, B Beckwith, G Sherrell, D Mettallo, and R Pingree. 2007. "Contaminant Concentrations in Storm Water Entering the Sinclair/Dyes Inlet Subasin of the Puget Sound, USA, During Storm Event and Baseflow Conditions." In 2007 Georgia Basin Puget Sound Research Conference, Vancouver, British Columbia, March 26–29, 2007, p. 9 pages.  Puget Sound Action Team, Olympia, WA. 
  • Cullinan VI, CW May, JM Brandenberger, C Judd, and RK Johnston. 2007. "Development of An Empirical Water Quality Model for Stormwater Based on Watershed Land Use in Puget Sound." In 2007 Georgia Basin Puget Sound Research Conference, Vancouver, British Columbia, March 26–29, 2007, p. 8 pages.  Puget Sound Action Team, Olympia, WA. 
  • Dauble DD, Z Deng, MC Richmond, RA Moursund, TJ Carlson, CL Rakowski, and JP Duncan. 2007. Biological Assessment of the Advanced Turbine Design at Wanapum Dam, 2005. PNNL-16682, Pacific Northwest National Laboratory, Richland, WA. 
  • Deng Z, GR Guensch, MC Richmond, MA Weiland, and TJ Carlson. 2007. "Prototype Measurements of Pressure Fluctuations in The Dalles Dam Stilling Basin." Journal of Hydraulic Research 45(5):674–678. 
  • Deng Z, JA Serkowski, T Fu, TJ Carlson, and MC Richmond. 2007. Synthesis of Sensor Fish Data for Assessment of Fish Passage Conditions at Turbines, Spillways, and Bypass Facilities – Phase 1: The Dalles Dam Spillway Case Study. PNNL-17148, Pacific Northwest National Laboratory, Richland, WA. 
  • Deng Z, TJ Carlson, GR Ploskey, MC Richmond, and DD Dauble. 2007. "Evaluation of Blade-Strike Models for Estimating the Biological Performance of Kaplan Turbines." Ecological Modelling 208(2-4):165-176.  doi:10.1016/j.ecolmodel.2007.05.019
  • Dresser TJ, CL Dotson, RK Fisher, MJ Graf, MC Richmond, CL Rakowski, TJ Carlson, D Mathur, and PG Heisey. 2007. "Wanapum Dam Advanced Hydro Turbine Upgrade Project: Part 2 - Evaluation of Fish Passage Test Results Using Computational Fluid Dynamics." In HydroVision 2006, July 31-August 4, 2006 Portland, Oregon, USA, p. 14 pages.  HCI Publications, Kansas City, MO. 
  • Frick WE, TP Khangaonkar, AC Sigleo, and Z Yang. 2007. "Estuarine-ocean exchange in a North Pacific estuary: comparison of steady state and dynamic model." Estuarine, Coastal and Shelf Science 74(1-2):1-11.  doi:10.1016/j.ecss.2007.02.019
  • Johnson GE, AB Borde, E Dawley, HL Diefenderfer, BD Ebberts, DA Putman, GC Roegner, RM Thom, J Vavrinec, III, and AH Whiting. 2007. Evaluating Cumulative Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2006. PNNL-16561, Pacific Northwest National Laboratory, Richland, WA. 
  • McKinstry CA, TJ Carlson, and RS Brown. 2007. Derivation of Mortal Injury Metric for Studies of Rapid Decompression of Depth-Acclimated Physostomous Fish. PNNL-17080, Pacific Northwest National Laboratory, Richland, WA. 
  • Moline MA, DL Woodruff, and NR Evans. 2007. "Optical Delineation of Benthic Habitat Using an Autonomous Underwater Vehicle." Journal of Field Robotics 24(6):461-471.  doi:10.1002/rob.20176
  • Rensel JE, DA Kiefer, JR Forster, DL Woodruff, and NR Evans. 2007. "Offshore finfish mariculture in the Strait of Juan de Fuca." Suisan Sogo Kenkyu Senta kenkyu hokoku. Bulletin of Fisheries Research Agency 19:113-129. 
  • Richmond MC, TJ Carlson, JA Serkowski, CB Cook, JP Duncan, and WA Perkins. 2007. Characterizing the Fish Passage Environment at The Dalles Dam Spillway: 2001-2004. PNNL-16521, Pacific Northwest National Laboratory, Richland, WA. 
  • Richmond MC, Z Deng, GR Guensch, H Tritico, and WH Pearson. 2007. "Mean Flow and Turbulence Characteristics of a Full-Scale Spiral Corrugated Culvert with Implications to Fish Passage." Ecological Engineering 30(4):333-340.  doi:10.1016/j.ecoleng.2007.04.011
  • Whelan G, WD Millard, GM Gelston, TP Khangaonkar, MA Pelton, DL Strenge, Z Yang, C Lee, C Sivaraman, AJ Stephan, BL Hoopes, and KJ Castleton. 2007. "Using FRAMES to Manage Environmental and Water Resources." In Proceedings of the World Environmental and Water Resources Congress 2007: Restoring our Natural Habitat, May 15–19, 2007, Tampa, Florida, USA, ed. Karen C. Kabbes.  American Society of Civil Engineers, Reston, VA.  doi:10.1061/40927(243)130
  • Woodruff DL, SS Southard, VI Cullinan, NP Kohn, MG Anderson, and J Vavrinec, III. 2007. Third Annual Report: 2006 Pre-Construction Eelgrass Monitoring and Propagation for King County Outfall Mitigation. PNNL-15678-3, Pacific Northwest National Laboratory, Richland, WA. 

2006

  • Anderson JW, and RF Lee. 2006. "Use of Biomarkers in Oil Spill Risk Assessment in the marine environment." Human and Ecological Risk Assessment 12(6):1192-1222. 
  • Deng Z, MC Richmond, and TJ Carlson. 2006. Characterization of The Dalles Dam Spillbay 6 Vortex Using Surface Entrained Sensor Fish Device: Preliminary Report . PNNL-15883, Pacific Northwest National Laboratory, Richland, WA. 
  • Diefenderfer HL, RM Thom, AB Borde, GC Roegner, AH Whiting, GE Johnson, E Dawley, JR Skalski, J Vavrinec, III, and BD Ebberts. 2006. Evaluating Cumulative Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2005. PNNL-15934, Pacific Northwest National Laboratory, Richland, WA. 
  • Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. "Gene expression patterns in Rainbow Trout, Oncorhynchus mykiss, exposed to a suite of model toxicants." Aquatic Toxicology 77(4):372-385.  doi:10.1016/j.aquatox.2006.01.007
  • Pearson WH, NP Kohn, and JR Skalski. 2006. Entrainment of Dungeness Crab in the Desdemona Shoals Reach of the Lower Columbia River Navigation Channel. PNNL-16139, Pacific Northwest National Laboratory, Richland, WA. 
  • Cook CB, B Dibrani, JA Serkowski, MC Richmond, PS Titzler, and GW Dennis. 2006. Acoustic Doppler Current Profiler Measurements in the Tailrace at John Day Dam. PNNL-15627, Pacific Northwest National Laboratory, Richland, WA. 
  • Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. "Dose-Response Relationships in Gene Expression Profiles in Rainbow Trout, Onorhyncus mykiss Exposed to Ethynylestradiol ." Marine Environmental Research 62(suppl.):S151-S155.  doi:10.1016/j.marenvres.2006.04.056
  • Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. "Temporal Changes in Gene Expression in Rainbow Trout Exposed to Ethynyl Estradiol ." Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology 145(1):73-85.  doi:doi:10.1016/j.cbpc.2006.10.011
  • Khangaonkar TP, SA Breithaupt, and FC Kristanovich. 2006. "Restoration of Hydrodynamic and Hydrologic Processes in the Chinook River Estuary, Washington – Feasibility Assessment ." In Estaurine and Coastal Modeling Proceedings of the 9th International Conference held in Charleston, SC, Oct. 31-Nov.2, 2005, ed. M.L. Spaulding, pp. 734-751.  American Society of Civil Engineers, Reston, VA. 
  • Khangaonkar TP, SA Breithaupt, and FC Kristanovich. 2006. "Restoration of Hydrodynamic and Hydrologic Processes in the Chinook River Estuary, Washington – Feasibility Assessment." In 9th International Conference on Estuarine Coastal Modeling Conference, ed. ML Spaulding.  American Society of Civil Engineering, New York, NY. 
  • Kohn NP, JM Brandenberger, LA Niewolny, and RK Johnston. 2006. Organics Verification Study for Sinclair and Dyes Inlets, Washington. PNNL-16070, Pacific Northwest National Laboratory, Richland, WA. 
  • Lee C, Z Yang, TP Khangaonkar, and AB Divers. 2006. "Application of a Hydrodynamic Model for Assessing the Hydraulic Capacity and Flow Field at Willamette Falls Dam, Oregon." In Estuarine and Coastal Modeling. Proceedings of 9th International Conference held in Charleston, SC, Oct.31-Nov. 2, 2005, ed. M.L. Spaulding, pp. 788-805.  American Society of Civil Engineers, Reston, VA. 
  • Muirhead EK, AD Skillman, SE Hook, and IR Schultz. 2006. "Oral Exposure of PBDE-47 in Fish: Toxicokinetics and Reproductive Effects in Japanese Medaka (Oryzias latipes) and Fathead Minnows (Pimephales promelas)." Environmental Science and Technology 40(2):523-528. 
  • Pearson WH, JR Skalski, KL Sobocinski, MC Miller, GE Johnson, GD Williams, JA Southard, and RA Buchanan. 2006. A Study of Stranding of Juvenile Salmon by Ship Wakes Along the Lower Columbia River Using a Before-and-After Design: Before-Phase Results. PNNL-15400, Pacific Northwest National Laboratory, Richland, WA. 
  • Pearson WH, MC Miller, GD Williams, NP Kohn, and JR Skalski. 2006. Preliminary Assessment of Potential Impacts to Dungeness Crabs from Disposal of Dredged Materials from the Columbia River. PNNL-15477, Pacific Northwest National Laboratory, Richland, WA. 
  • Whelan G, WD Millard, GM Gelston, MA Pelton, Z Yang, DL Strenge, C Lee, C Sivaraman, MJ Simpson, JK Young, TP Khangaonkar, TR Downing, BL Hoopes, and LE Hachmeister. 2006. Rapid Risk Assessment: FY05 Annual Summary Report. PNNL-15697, Pacific Northwest National Laboratory, Richland, WA. 
  • Yang Z, H Liu, and TP Khangaonkar. 2006. "Development of a Hydrodynamic Model for Skagit River Estuary for Estuarine Restoration Feasibility Assessment." In Estuarine and Coastal Modeling: Proceedings of the 9th International Conference held in Charleston, SC, Oct. 31-Nov.2, 2005, ed. M.L. Spaulding, pp. 752-767.  American Society of Civil Engineers, Reston, VA. 

2005

  • Anderson JW, SI Hartwell, and MJ Hameedi. 2005. "Regional Comparisons of Coastal Sediment Contamination Detected by a Biomarker (P450 HRGS; EPA Method 4425)." Environmental Science and Technology 39(1):17-23. 
  • Carlson TJ, and CS Abernethy. 2005. Pilot Study of the Effects of Simulated Turbine Passage Pressure on Juvenile Chinook Salmon Acclimated with Access to Air at Absolute Pressures Greater than Atmospheric . PNNL-15011, Pacific Northwest National Laboratory, Richland, WA. 
  • Carlson TJ, JP Duncan, and RL Johnson. 2005. Characterization of Pump Flow at the Grand Coulee Pumping Station for Fish Passage, 2004. PNNL-14998, Pacific Northwest National Laboratory, Richland, WA. 
  • Deng Z, MC Richmond, RP Mueller, JP Duncan, and TJ Carlson. 2005. "Laboratory study of biological response of juvenile salmon subjected to turbulent shear flows." In Proceedings of Waterpower XIV, Advancing Technology for Sustainable Energy, Austin, Texas, July 18-22, 2005, p. 15 pp.  HCI Publications, Kansas City, MO. 
  • Diefenderfer HL, C Roegner, RM Thom, EM Dawley, AH Whiting, GE Johnson, KL Sobocinski, MG Anderson, and B Ebberts. 2005. Evaluating Cumulative Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2004. PNNL-15102, Pacific Northwest National Laboratory, Richland, WA. 
  • Diefenderfer HL, RM Thom, and K Hofseth. 2005. "A Framework for Risk Analysis for Ecological Restoration Projects in the U.S. Army Corps of Engineers ." Chapter 4 in Economics and Ecological Risk Assessment: Applications to Watershed Management, Environmental and Ecological Risk Assessment Series, vol. 5, ed. Randall J. F. Bruins, Matthew T. Heberling, pp. 57-105.  CRC Press, Boca Raton, FL. 
  • Evans NR, DL Woodruff, and VL Trainer. 2005. "Development of coastal upwelling edge detection algorithms associated with harmful algal blooms off the Washington coast using sea surface temperature imagery." In Remote sensing of the coastal oceanic environment: 31 July-1 August, 2005, San Diego, California, USA ; Proceedings of SPIE--the International Society for Optical Engineering, vol. 5885, ed. R.J. Frouin, M. Babin, Shubha Sathyendranath, p. 58850L.  International Society for Optical Engineering, Bellingham, WA. 
  • May CW, and VI Cullinan. 2005. An Analysis of Microbial Pollution in the Sinclair-Dyes Inlet Watershed. PNNL-15373, Pacific Northwest National Laboratory, Richland, WA. 
  • Williams GD, NP Kohn, WH Pearson, and JR Skalski. 2005. Impacts to Dungeness Crab from the Southwest Washington Littoral Drift Restoration Project. PNNL-15385, Pacific Northwest National Laboratory, Richland, WA. 
  • Deng Z, TJ Carlson, GR Ploskey, and MC Richmond. 2005. Evaluation of Blade-Strike Models for Estimating the Biological Performance of Large Kaplan Hydro Turbines. PNNL-15370, Pacific Northwest National Laboratory, Richland, WA. 
  • Johnson GE, ME Hanks, F Khan, CB Cook, J Hedgepeth, RP Mueller, CL Rakowski, MC Richmond, SL Sargeant, JA Serkowski, and JR Skalski. 2005. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam in 2004. PNNL-15180, Pacific Northwest National Laboratory, Richland, WA. 
  • Khangaonkar TP, Z Yang, C DeGasperi, and K Marshall. 2005. "Modeling Hydrothermal Response of a Reservoir to Modifications at a High-Head Dam." Water International 30(3):378-388. 
  • Lee RF, and JW Anderson. 2005. "Significance of Cytochrome P450 System Responses and Levels of Bile Fluorescent Aromatic Compounds in Marine Wildlife Following Oil Spills." Marine Pollution Bulletin 50(7):705-723. 
  • Pearson WH, GD Williams, and JR Skalski. 2005. Dungeness Crab Dredging Entrainment Studies in the Lower Columbia River, 2002 – 2004: Loss Projections, Salinity Model, and Scenario Analysis . PNNL-15021, Pacific Northwest National Laboratory, Richland, WA. 
  • Rice CA, WG Hood, LM Tear, C Simenstad, GD Williams, LL Johnson, BE Feist, and P Roni. 2005. "Monitoring Rehabilitation in Temperate North American Estuaries." Chapter 7 in Monitoring Stream and Watershed Restoration, ed. Philip Roni, Ed Quimby, pp. 167-208.  American Fisheries Society, Bethesda, MD. 
  • Thom RM, GD Williams, AB Borde, JA Southard, SL Sargeant, DL Woodruff, JC Laufle, and S Glasoe. 2005. "Adaptively Addressing Uncertainty in Estuarine and Near Coastal Restoration Projects." Journal of Coastal Research. JCR 40(sp. iss.):94-108. 
  • Thom RM, GD Williams, and HL Diefenderfer. 2005. "Balancing the Need to Develop Coastal Areas with the Desire for an Ecologically Functioning Coastal Environment: Is Net Ecosystem Improvement Possible?" Restoration Ecology 13(1):193-203.  doi:10.1111/j.1526-100X.2005.00024.x
  • Weiland MA, RP Mueller, TJ Carlson, Z Deng, and CA McKinstry. 2005. Characterization of Bead Trajectories Through the Draft Tube of a Turbine Physical Model. . PNNL-14879, Pacific Northwest National Laboratory, Richland, WA. 
  • Wunschel DS, IR Schultz, AD Skillman, and KL Wahl. 2005. "Method for Detection and Quantitation of Fathead Minnow Vitellogenin (Vtg) by Liquid Chromatography and Matrix Assisted Laser Desorption/ Ionization Mass Spectrometry ." Aquatic Toxicology 73:256-267. 
  • Yang Z, H Liu, and TP Khangaonkar. 2005. "Development of a Hydrodynamic Model for Skagit River Estuary for Estuarine Restoration Feasibility Assessment." In The 9th International Conference on Estuarine and Coastal Modeling.  American Society of Civil Engineers, Reston, VA. 

2004

2003

  • Anderson JW, JM Jones, DL McCoy, A Fujita, T Yamamoto, and S Iijima. 2003. "Comparison Between a Rapid Biological Screening Method (EPA 4425) for TCDDs/TCDFs and Chemical Analytical Methods." Chapter Organohalogen Compounds in Proceedings to Dioxin 2003: The 23rd International Symposium on Halogenated Environmental Organic Pollutants and Persistent Organic Pollutants published in Organohalogen Compounds Vol. 60 , vol. 60, pp. 271-274.  Eco Informa Press, Bayreuth, Germany. 
  • Borde AB, RM Thom, S Rumrill, and LM Miller. 2003. "Geospatial Habitat Analysis in Pacific Northwest Coastal Estuaries." Estuaries 26(4B):1104-1116. 
  • Carlson TJ, and JP Duncan. 2003. Evolution of the Sensor Fish Device for Measuring Physical Conditions in Severe Hydraulic Environments. PNNL-15708, Pacific Northwest National Laboratory, Richland, WA. 
  • Carlson TJ, JP Duncan, and TL Gilbride. 2003. "The Sensor Fish: Measuring Fish Passage in Severe Hydraulic Conditions." Hydro Review 22(3):62-69. 
  • Diefenderfer HL, SL Sargeant, RM Thom, AB Borde, PF Gayaldo, CA Curtis, BL Court, DM Pierce, and DS Robison. 2003. "Dock Design to Facilitate the Restoration of Eelgrass in Port Townsend Bay, Washington." In Assembling the Pieces - Restoration, Design and Landscape Ecology: Proceedings of the Annual Conference of the Society for Ecological Restoration International, November 19-22, 2003, Austin, Texas.  Society for Ecological Restoration International, Tucson, AZ. 
  • Schultz IR, AD Skillman, JM Nicolas, DG Cyr, and JJ Nagler. 2003. "Short-term exposure to 17alpha-ethynylestradiol decreases the fertility of sexually maturing male rainbow trout (Oncorhynchus mykiss)." Environmental Toxicology and Chemistry 22(6):1272-1280. 
  • Johnson GE, RM Thom, AH Whiting, GB Sutherland, TJ Berquam, B Ebberts, NM Ricci, JA Southard, and JD Wilcox. 2003. An Ecosystem-Based Restoration Plan with Emphasis on Salmonid Habitats in the Lower Columbia River and Estuary. PNNL-14412, Pacific Northwest National Laboratory, Richland, WA. 
  • Moursund RA, TJ Carlson, and RD Peters. 2003. "A Fisheries Application of a Dual-Frequency Identification Sonar Acoustic Camera." ICES Journal of Marine Science 60(3):678-683. 
  • Pearson WH, GD Williams, and JR Skalski. 2003. Estimated Entrainment of Dungeness Crab During Maintenance Dredging of the Mouth of the Columbia River, Summer 2002. PNNL-14190, Pacific Northwest National Laboratory, Richland, WA. 
  • Powell DB, RC Palm, AD Skillman, and K Godtfredsen. 2003. "Immunocompetence of Juvenile Chinook Salmon Against Listonella anguillarum Following Dietary Exposure to Aroclor (R) 1254." Environmental Toxicology and Chemistry 22(2):285-295. 
  • Thom RM, AB Borde, S Rumrill, DL Woodruff, GD Williams, JA Southard, and SL Sargeant. 2003. "Factors Influencing Spatial and Annual Variability in Eelgrass (Zostera marina L.) Meadows in Willapa Bay, Washington, and Coos Bay, Oregon, Estuaries." Estuaries 26(4B):1117-1129. 
  • West JM, GD Williams, SP Madon, and JB Zedler. 2003. "Integrating spatial and temporal variability into the analysis of fish food web linkages in Tijuana Estuary." Environmental Biology of Fishes 67:297-309. 

2002

  • Pearson WH, MC Richmond, and J Schafer. 2002. "Culvert Testing Program for Juvenile Salmonid Passage." In Proceedings of the International Conference on Ecology and Transportation, Keystone, CO, September 24-28, 2001. , pp. 92-97.  NC State University, Center for Transportation and the Environment, Raleigh, NC. 
  • Blanton SL, RM Thom, AB Borde, HL Diefenderfer, and JA Southard. 2002. Evaluation of Methods to Increase Light Under Ferry Terminals. PNNL-13714, Pacific Northwest National Laboratory, Richland, WA. 
  • Huesemann MH, AD Skillman, and EA Crecelius. 2002. "The Inhibition of Marine Nitrification by Ocean Disposal of Carbon Dioxide." Marine Pollution Bulletin 44(2):142-148. 
  • Johnson RL, MA Simmons, CS Simmons, and SL Blanton. 2002. "A New Multibeam Sonar Technique for Evaluating Fine-Scale Fish Behavior Near Hydroelectric Dam Guidance Structures." In Behavioral Technologies for Fish Guidance, American Fisheries Society Symposium, 2001, vol. 26, no. 2001, ed. Coutant, C., pp. 161-170.  Amer. Fisheries Society, Bethesda, MD. 
  • Kohn NP, and NR Evans. 2002. Phase I Source Investigation, Heckathorn Superfund Site, Richmond, California. PNNL-14088, Pacific Northwest National Laboratory, Richland, WA. 
  • Miller MC, GD Williams, LK O'Rourke, JA Southard, and SL Blanton. 2002. Effects of Shoreline Hardening and Shoreline Protection Features on Fish Utilization and Behavior at Washaway Beach, Washington (Report 2). PNNL-13635-(2), Pacific Northwest National Laboratory, Richland, WA. 
  • Pearson WH, GD Williams, and JR Skalski. 2002. Estimated Entrainment of Dungeness Crab During Dredging For The Columbia River Channel Improvement Project. PNNL-14129, Pacific Northwest National Laboratory, Richland, WA. 
  • Thom RM, R Zeigler, and AB Borde. 2002. "Floristic Development Patterns in a Restored Elk River Estuarine Marsh, Grays Harbor, Washington." Restoration Ecology 10(3):487-496. 
  • Thom RM, SL Blanton, AB Borde, GD Williams, DL Woodruff, and MH Huesemann. 2002. "Investigations into Wetland Carbon Sequestration as Remediation for Global Warming ." In International Conference on Wetlands and Remediation; Wetlands and Remediation II, ed. KW Nehring and SE Brauning, pp. 311-320.  Battelle Press, Columbus, OH. 

2001

  • Carlson TJ, and MA Weiland. 2001. Light-Emitting Tag Testing in Conjunction with Testing of the Minimum Gap Runner Turbine Design at Bonneville Dam Powerhouse 1. PNNL-13415, Pacific Northwest National Laboratory, Richland, WA. 
  • Faber DM, MA Weiland, R Moursund, TJ Carlson, N Adams, and D Rhondorf. 2001. Evaluation of the Fish Passage Effectiveness of the Bonneville I Prototype Surface Collector using Three-Dimensional Ultrasonic Fish Tracking. PNNL-13526, Pacific Northwest National Laboratory, Richland, WA. 
  • Schultz IR, GA Orner, JL Merdink, and AD Skillman. 2001. "Dose-response relationships and pharmacokinetics of vitellogenin in rainbow trout after intravascular administration of 17 alpha-ethynylestradiol ." Aquatic Toxicology 51(3):305-318. 
  • Williams GD, NR Evans, WH Pearson, and JA Southard. 2001. Assessing Juvenile Salmonid Passage Through Culverts: Field Research in Support of Protocol Development. PNNL-13708, Pacific Northwest National Laboratory, Richland, WA. 
  • Carlson TJ, GR Ploskey, RL Johnson, RP Mueller, MA Weiland, and PN Johnson. 2001. Observations of the Behavior and Distribution of Fish in Relation to the Columbia River Navigation Channel and Channel Maintenance Activities. PNNL-13595, Pacific Northwest National Laboratory, Richland, WA. 
  • Clements W, SN Luoma, J Gerritsen, A Hatch, P Jepson, T Reynoldson, and RM Thom. 2001. "Stressor Interactions in Ecological Systems ." Chapter 7 in Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment, ed. Donald J. Baird and G. Allen Burton, Jr., pp. 215-233.  SETAC Press, Pensacola, FL. 
  • Johnson GE, and TJ Carlson. 2001. Monitoring and Evaluation of the Prototype Surface Collector at Bonneville First Powerhouse in 2000: Synthesis of Results. PNNL-13516, Pacific Northwest National Laboratory, Richland, WA. 
  • Long WL, and RM Thom. 2001. "Part III. Seagrass Habitat Conservation. Chapter 21. Improving seagrass habitat quality ." In Global Seagrass Research Methods , pp. 407-445.  Elsevier, Amsterdam, Netherlands. 
  • Luoma SN, W Clements, J Gerritsen, A Hatch, P Jepson, T Reynoldson, and RM Thom. 2001. "Separating stressor influences from environmental variability: eight case studies from aquatic and terrestrial ecosystems." Chapter 6 in Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment, ed. Donald J. Baird and G. Allen Burton, Jr., pp. 179-215.  SETAC Press, Pensacola, FL. 
  • Luoma SN, W Clements, T Dewitt, J Gerritsen, A Hatch, P Jepson, T Reynoldson, and RM Thom. 2001. "Role of Environmental Variability in Evaluating Stressor Effects." Chapter 5 in Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment, ed. Donald J. Baird and G. Allen Burton, Jr., pp. 141-179.  SETAC Press, Pensacola, FL. 
  • Madon SP, GD Williams, JM West, and JB Zedler. 2001. "The importance of marsh access to growth of the California killifish, Fundulus parvipinnis, evaluated through bioenergetics modeling." Ecological Modelling 136(2-3):149-165. 
  • Paluszkiewicz T, LF Hibler, MC Richmond, DJ Bradley, and SA Thomas. 2001. "Modeling the Potential Radionuclide Transport by the Ob and Yenisey Rivers to the Kara Sea." Marine Pollution Bulletin 43(1-6):111-121. 
  • Thom RM, AB Borde, KO Richter, and LF Hibler. 2001. "Influence of Urbanization on Ecological Processes in Wetlands ." In Land Use and Watersheds : Human Influence on Hydrology and Geomorphology in Urban and Forest Areas. Water Science and Application, vol. 2, ed. Mark Wigmosta and Stephen Burges, pp. 5-16.  American Geophysical Union, Washington, DC. 
  • Thom RM, AB Borde, GD Williams, JA Southard, SL Blanton, and DL Woodruff. 2001. "Effects of Multiple Stressors on Eelgrass Restoration Projects." In Proceedings of Puget Sound Research 2001, the fifth Puget Sound Research Conference, vol. 1, ed. Droscher, Toni.  Puget Sound Water Quality Action Team, Olympia, WA. 

2000

  • Geist DR, CS Abernethy, SL Blanton, and VI Cullinan. 2000. "The use of electromyogram telemetry to estimate energy expenditure of adult fall chinook salmon." Transactions of the American Fisheries Society 129(1):126-135. 
  • Thom RM. 2000. "Adaptive management of coastal ecosystem restoration projects." Ecological Engineering 15(3-4):365-372. 
  • Emmett R, R Llanso, J Newton, RM Thom, M Hornberger, C Morgan, C Levings, A Copping, and P Fishman. 2000. "Geographic Signatures of North American West Coast Estuaries." Estuaries 23(6):765-792. 
  • Woodruff DL, PJ Farley, AB Borde, JA Southard, and RM Thom. 2000. King County Nearshore Habitat Mapping Data Report: Picnic Point to Shilshole Bay Marina . PNNL-13396, Pacific Northwest National Laboratory, Richland, WA. 

1999

  • Pearson WH, RA Elston, RW Bienert, AS Drum, and LD Antrim. 1999. "Why did the Prince William Sound, Alaska, Pacific herring (Clupea pallasi) fisheries collapse in 1993 and 1994? Review of hypotheses." Canadian Journal of Fisheries and Aquatic Sciences 56(4):711-737. 
  • Nassar AF, SV Lucas, and SA Thomas. 1999. "Determination of O-isopropyl methylphosphonic acid in living microorganism-agar matrixes using ion chromatography conductivity detection." Analytical Letters 32(5):1023-1035. 

1998

  • Pearson WH, SM Al-Ghais, JM Neff, CJ Brandt, KF Wellman, and T Green. 1998. "Assessment of Damages to Commercial Fisheries and Marine Environment of Fujairah, United Arab Emirates, Resulting from the Seki Oil Spill of March 1994: A Case Study." In Transformations of Middle Eastern Natural Environments: Legacies and Lessons, Bulletin series, vol. 103, pp. 407-428.  Yale School of Forestry & Environmental Studies, New Haven, CT. 
  • Randolph RC, JT Hardy, SW Fowler, ARG Price, and WH Pearson. 1998. "Toxicity and Persistence of Nearshore Sediment Contamination Following the 1991 Gulf War." Environment International 24:33-42. 

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