AndreaBozzo/ceres-open-data-index huggingface dataset:
LCREP prey data - Lower Columbia River Ecosystem Monitoring Project

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU).

3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals.

5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists.

6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU.

7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis.

Prey composition in diet samples and water column tows at Lower Columbia River sites.

Tags: chemical contaminants, chinook salmon, chinook salmon growth rates, chum salmon, coho salmon, doc/noaa/nmfs/nwfsc, fish community composition, fish diet, gut content, habitat characteristics, lower columbia river, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, salmon lipid content, salmon prey availability
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Oceanographic Data - Bycatch Reduction Engineering Research

Through key regional collaborations with the Pacific States Marine Fisheries Commission, Oregon Department of Fish and Wildlife, Alaska Fisheries Science Center, and the fishing industry, the Marine Habitat Ecology Team at the  NWFSC has been able to pursue a wide-ranging array of conservation engineering projects relevant to reducing bycatch in the west coast groundfish and ocean shrimp trawl fisheries. Examples of types of research projects pursued during any given year include: 1) Reducing Chinook salmon, eulachon, rockfish, and Pacific halibut bycatch in midwater and bottom trawl fisheries using Bycatch Reduction Devices (BRDs), 2) Examining selectivity characteristics of codends that differ in mesh size and configuration in bottom trawl fisheries, and 3) Testing other novel bycatch engineering modifications to mobile and fixed gears. Much of our current work has been in response to the fishing industries concerns over catches of overfished and rebuilding rockfishes and Pacific halibut allocated in the Pacific coast Groundfish Trawl Rationalization Catch Share Program. The trawl rationalization program, starting in January 2011, established formal Annual Catch Limits (ACLs) and individual catch share quotas. In addition to ACLs, fishing opportunities may also be limited by hard caps or IBQs for non-groundfish species (e.g., Chinook salmon, and Pacific halibut). Bycatch of overfished and prohibited species in the west coast groundfish trawl fishery has the potential to constrain the fishery such that a substantial portion of available harvest may be left in the ocean.
Temperature and light radiance.

Tags: doc/noaa/nmfs/nwfsc, fram (fishery resource analysis and monitoring) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Geomorphic Analysis - Trinity River Restoration Potential

The goal of the Trinity River project is to identify the potential positive effects of large-scale restoration actions in a 63 kilometer reach of the Trinity River below Lewiston Dam, in the hope of guiding on the ground restoration actions. River restoration plans often propose numerous rehabilitation actions to address key habitat impairments for salmonids. However, restoration plans rarely propose alternative sets of actions or attempt to quantify the potential benefits to targeted biota. In this paper, we use geomorphic and biological analyses to estimate restoration potential for each of 37 reaches in a 64-km section of Trinity River, California, from the North Fork Trinity River to Lewiston Dam (the focus of habitat rehabilitation efforts under the Trinity River Restoration Program). We first predicted the channel pattern that might develop based in each reach on slope-discharge criteria, and then used these potential patterns along with floodplain width to estimate the maximum sinuosity that restoration actions could likely achieve, as well as a maximum side-channel length that might be created in each reach. For each scenario, we then used existing stream habitat and juvenile salmonid data from previous studies in the Trinity River and other watersheds to determine current and restored carrying capacity. Potential increases in Chinook and steelhead carrying capacity range from 39% for a relatively realistic estimate of increasing habitat quality (more low velocity areas with cover) to 67% for a more optimistic scenario that increases both sinuosity and habitat quality. Only the most optimistic scenario that increases habitat quality, increases sinuosity, and constructs tens of kilometers of side channels more than doubles potential juvenile salmonid production (140% increase). These quantitative predictions provide a frame of reference for evaluating alternative restoration options, and for setting measureable restoration goals.
Database of stream reach attributes.

Tags: chinook salmon, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, instrument not applicable, landscape ecology, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, restoration, steelhead, trinity river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
U.S. West Coast Groundfish Bottom Trawl Survey (extent)

This layer is intended to represent information collected during NOAA Fisheriesâ U.S. West Coast Groundfish Bottom Trawl Survey. The  U.S. West Coast Groundfish Bottom Trawl Survey started in 1998 and is led by NMFS Northwest Fisheries Science Center. This survey provides long-term time-series data for the management of West Coast groundfishes as well as coastwide environmental sampling for monitoring change within the California Current Ecosystem. The bottom trawl survey covers West Coast waters (55-1280 meters [30-700 fathoms]) twice annually using a trawl net and a random sampling design, stratified by depth and latitude. The survey collects fishery-independent data on abundance, distribution, and biology of most species included in the west coast groundfish management plan. Weight and measurements are collected from vertebrates and invertebrates alongside various biological samples. Samples collected include otoliths and other structures for aging, finclips for genetics, gonads for reproductive analysis, and stomach contents and tissue samples for diet/stable isotope analysis. Oceanographic sensors are affixed to the trawl net, collecting data such as temperature, salinity, and dissolved oxygen for each trawl at depth.

Tags: bottom sampler, california, ctd, demersal fish, doc/noaa/nmfs/nwfsc, fishery independent, groundfish survey, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
NWFSC OA facility water chemistry - Ocean acidification species exposure experimental facility

We have developed a unique facility for conducting high-quality experiments on marine organisms in seawater with controlled carbon chemistry conditions. The experimental system allows for the dynamic control of pCO2 and other environmental parameters, which enables us to mimic the natural patterns of variability in carbon chemistry that occur on diurnal and tidal cycles and with upwelling events and phytoplankton blooms. The system also provides control over temperature, dissolved oxygen, food delivery and photoperiod, allowing for experiments on multiple stressors. The relatively high water volumes in the system permit simultaneous experiments on multiple species. The laboratory requires constant uptake to maintain its function and will be modified as needed to support our research program.
Database of pH and other water chemistry measurements from the NWFSC OA experimental system.

Tags: carbon dioxide emissions, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, montlake ocean acidification lab, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, ocean acidification, unknown instrument, water quality
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Analysis Dataset - Observer Program Operations and Analysis

NWFSC Observer programs are the most comprehensive fishery dependent data collection system for total mortality estimation, protected species monitoring and discard data for stock assessments. Observer data is also used to track quotas in-season for the catch share IFQ fishery. The numerous observer program total mortality and bycatch reports are used by agency and council staff for management of federal and state fisheries on the west coast of the US. Observer program bycatch reports, data collection and research activities are also used to manage ESA listed species and fulfill Biological Opinion obligations.
Observer raw data is matched to fish tickets to produce haul specific catch totals.

Tags: by-catch, catch shares, crescent city office, data development methods, doc/noaa/nmfs/nwfsc, eureka office, fishery data preparation, fishery dependent, fishery observer, fishery-dependent, fram (fishery resource analysis and monitoring) division, groundfish biology, hammond office, hatfield - newport facility, instrument not applicable, morro bay offcie, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc-montlake, observer biological sample collections, observer deployments, sand point offices, tracked asset
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish and logger summaries - Physical and biological effects of fish-friendly tide gates

The purpose of this one-time stand-alone study is to evaluate how effective "fish-friendly" or self-regulating tide gates (SRTs) are at increasing connectivity for fish rearing in estuaries. The work was carried out in North Puget Sound, Washington Coast, and Columbia River estuaries by Correigh Greene, Jason Hall, and Eric Beamer (Skagit River System Cooperative), and compared SRTs with traditional flap gates and reference sites that were not blocked by any tide gate. Thus far, the study has produced a report for ESRP (Estuary Salmon Restoration Program), the organization that funded it. Up to two peer-reviewed papers are planned. The audience for this work includes federal and state managers, local planners, Watershed Councils, and applied ecologists.
Excel datasheets of fish and logger summaries.

Tags: animal and plant collection device, chehalis estuary, connectivity, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, habitat use, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, samish bay, skagit estuary, sonde and probe - sonde and probe (not specified), swinomish channel, tide gates, young's bay
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Otolith output - Project to study alternative life history types of fall Chinook based on otoliths

This project describes ongoing work by scientists in FE Ecosystem Analysis and EFS Environmental Chemistry programs to identify natal and rearing locations, reconstruct life history strategy, and evaluate juvenile performance of adult Snake River fall Chinook salmon. Due to dramatic declines in its abundance, Snake River fall Chinook salmon was listed as threatened under the Endangered Species Act. Management of Snake River fall Chinook salmon has been hindered by a great deal of uncertainty regarding key aspects of the population. In particular, the existence of an overwintering behavior in a portion of the population has complicated estimates of survival through the hydropower system. Further, differential detectability of redds has limited the ability to accurately develop run reconstructions. Effective management of Snake River fall Chinook salmon will require an understanding of the details of their early life-history, including where juveniles hatch and rear, the proportion of juveniles that exhibit the yearling strategy, when they initiate downstream migration, and estuarine residence time. In this project we investigate early life history movement and performance of Snake River fall Chinook salmon by using microchemistry and microstructure of otoliths sampled from juveniles and adults. Results from this study are intended to help inform recovery planning including future habitat restoration and conservation efforts in the Snake River Basin and Columbia River.
Images, increment measurements, and microchemistry trajectories.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) division, instrument not applicable, lyons ferry hatchery, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, otolith
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
POPs data for salmonids and macroinvertebrates from Glacier Bay, Alaska - Measuring persistent organic pollutants in resident salmonids and benthic macroinvertebrates in streams near Glacier National Park, Alaska

A 2007 pilot study was initiated by the University of Alaska â Southeast in which baseline levels of contaminants, including persistent organic pollutants (POPs) and total mercury, were determined in whole bodies of juvenile coho salmon collected in streams in and near national park units in the Southeast Alaska Inventory and Monitoring Network.  Although the concentrations of POPs determined in the juvenile coho were relatively low (< 10 ng/g, wet weight), the preliminary findings of this study indicate that, in the Glacier National Park region, salmon from streams with higher density of spawners had increased levels of certain banned chlorinated pesticides (i.e., alpha-chlordane, o,pâ-DDT, p,pâ-DDD) compared to salmon collected in other streams with lower salmon spawning density.  
A follow up study will be initiated in spring/summer 2015 to determine concentrations of POPs in resident salmonids, as well as benthic macroinvertebrates collected from five streams that have fish barriers near or adjacent to Glacier National Park.   Comparisons in contaminant concentrations and patterns will be made for fish collected below and above the barrier in each stream to help determine if certain classes of POPs are being transported by the spawners.  As part of this study, the NWFSC will analyze whole bodies/muscle of salmonids and benthic macroinvertebrate samples POPs using gas chromatography / mass spectrometry (GC/MS).  Percent lipid content of samples (with adequate sample mass) will also be determined.  These data will be included in a report to the NIH-sponsored  IDeA Network of Biomedical Research Excellence.
Determining levels of persistent organic pollutants in salmonids and macroinvertebrates.

Tags: ddts, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, instrument not applicable, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, salmonid recovery
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Acoustic data - RFP proposal - Distribution, abundance, and drivers of euphausiids in the California Current Ecosystem

In spite of their importance to fish habitat quality and broader ecosystem function, euphausiids have been understudied in the California Current Large Marine Ecosystem. The need for a time-series of euphausiid distribution data has been widely recognized by the IEA, MSE, and in the literature. This project captures the analytic work on euphausiid biomass and distribution that scientists in the FRAM Fisheries Engineering and Acoustic Technologies (FEAT) team will conduct in collaboration with NWFSC-CB, NWFSC-FE, SWFSC-ERD, and Department of Fisheries and Oceans Canada (DFO). A NRC Research Associate (i.e., postdoc) will support this work.

Data on large-scale patterns in euphausiid distribution and abundance are needed for top-down, bottom-up, and climate-related studies. This project will use a time series (2003-2019, n=10 surveys) of coast-wide (BC, WA, OR, CA) acoustic survey data to generate euphausiid distributions and point estimates of euphausiid biomass. Spatiotemporal statistical models will be applied to estimate euphausiid biomass as a function of environmental/habitat covariates. Models results and biomass estimates will then feed into a refinement of a Pacific Hake (Merluccius productus) habitat model to evaluate Hake-habitat linkages (identifier: âSeasonal forecasts of Pacific Hakeâ) and into growth potential models for Pacific Hake and Sablefish (Anoplopoma fimbria). Results from this work will be incorporated into the Pacific Hake Management Strategy Evaluation (MSE) base operating model. At the end of this project, euphausiid biomass data will be entered into the FRAM Data Warehouse (in conjunction with the FRAM Data Team) and made publically available to meet the requirements of the federal Public Access to Research Results (PARR) policy and facilitate collaborative research within the CCLME.
Raw acoustic backscatter (ER 60.raw) and Echolog 60 (Echoview.ek6) data files are logged.

Tags: acoustics, doc/noaa/nmfs/nwfsc, ecosystem-based management, fram (fishery resource analysis and monitoring) division, krill, marine ecosystems, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, sonar - echo sounding, u.s. and canadian waters off the pacific coast
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Temperature - Live Hauling of Fish

In certain markets, live fish can be sold for substantially higher prices than fresh dressed fish. A significant live-haul industry has developed in the U.S. and fish are commonly hauled 1,500-2,000 miles (25-30 hours) to market. The most common species hauled are tilapia, channel catfish, and rainbow trout; a smaller amount of marine rockfish, hybrid striped bass, and carp are also hauled. The most significant advancement in hauling technology in the last 20 years has been the use of bottled oxygen gas or liquid oxygen to maintain adequate dissolved oxygen levels. These types of systems can maintain significantly higher DO levels than systems using air. Some common stressors include harvest and loading procedures (pumping or out of water transfer), shaking as the transport vehicle is moving, low frequency sound from the vehicle and water treatment systems, crowding, and poor water quality (high ammonia and carbon dioxide levels, low dissolved oxygen), high light levels, or extreme water temperature. The physical shape and construction of the hauling unit may have an important impact on localized low DOs, physical damage to the fish, and survivability. Very little information has been published on the chemical and physical conditions in transport systems during long-distance transport and this limited data may not be representative of current commercial systems. 

This research will be conducted with NWFSC staff in cooperation with private fish farmers in the Pacific Northwest. Specific sub-objectives will include the following:

(1) Documentation of water quality during transport and impact on mortality and product quality

(2) Design of efficient aeration systems for oxygen transfer and carbon dioxide stripping

(3) Determination of the impact of transport tank design and aerator type on the thermal balance during hauling.

The impact of this project will be increased survival and product quality of transported fish as a result of adopting the recommended protocols and utilization of the models. Project outputs will include peer-reviewed publications, popular publications, and conference presentations.
Temperature will be measured using the thermistor sensors in the YSI ProODO or YSI 556 MPS units.

Tags: aquaculture, doc/noaa/nmfs/nwfsc, gas transfer, hagerman valley, heat transfer, idaho, migrated from resource enhancement and utilization technologies division, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, temperature sensor, water quality
Organization: National Oceanic and Atmospheric Administration, Department of Commerce