AndreaBozzo/ceres-open-data-index huggingface dataset:
Taurine Growth Effects - Determining Optimum Taurine Supplementation Levels for Plant Proteins Incorporated into Marine Finfish Feeds using Juvenile Sablefish Anoplopoma fimbria

Taurine, an amino sulfonic acid, has important roles in osmoregulation, bile acid conjugation, membrane stabilization and calcium homeostasis in vertebrates. Though many animals biosynthesize taurine, felines and some marine finfish have low cysteine sulfinate decarboxylase (CSD) activity, limiting their ability to produce taurine. In cats, a diet devoid of taurine will cause blindness and multiple birth defects. Thus, taurine is an essential nutrient for the cat. The capacity of aquaculture finfish to biosynthesize taurine depends on the species. Although the underlying physiological processes are not yet understood, recent studies have shown that taurine improves growth of fish such as yellowtail, Japanese flounder, sea bream, and cobia. Though a promising aquaculture species, it is unknown whether sablefish can synthesize taurine or whether they must obtain it through their diet to achieve optimal growth.

While ample amounts of taurine are found in many rendered animal proteins, including fishmeal, taurine is absent from plant proteins recently employed in fish feeds. Studies on yellowtail, red sea bream, and rainbow trout fed low (or zero) fishmeal diets saw improved growth with taurine supplementation. Taurine limited processes are a potential barrier to the optimum growth and successful transition of marine finfish species from currently available, fishmeal based feeds to alternative, more sustainable, plant-based feeds.
Fish weights and lengths for study.

Tags: aquaculture, doc/noaa/nmfs/nwfsc, instrument not applicable, 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
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Growth data - Development and optimization of grow out diets for sablefish (Anoplopoma fimbria)

Our experience with juvenile sablefish and long term rearing of broodstock indicate that salmon grower feeds currently used by commercial sablefish farmers for grow out are not optimally formulated to support maximum growth and efficient feed conversion. However, there are no published studies examining the effects of dietary nutrient balance on productive performance and growth at any post larval life-history stage for this species, and there are currently no commercial diets specifically formulated for sablefish in the marketplace. Because of the large impact of feed cost on the economic viability of farming sablefish, we are focusing on grow out diets intended for use during the post larval stages of development when the fish are being reared to harvest size. 
In this research, we use a novel statistical mixture model and response surface analysis method to determine the optimal level of dietary protein, lipid and digestible carbohydrate for testing. This approach permits simultaneous testing of diet formulations encompassing the full range of protein, lipid and digestible carbohydrate that can be produced commercially using todayâs most advanced extrusion feed manufacturing technology.
Fish in experiments may be PIT tagged and regularly checked for growth in length and weight.

Tags: aquaculture, aquafeeds, balance, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, length board, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester research station, nwfsc seattle, sablefish
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Habitat information in the region on the underwater San Andreas Fault - Topic: Exploring the Undersea San Andreas Fault: Revealing the Past, Present, and Future at the Centennial of the Great 1906 Earthquake

During this exploration, the first comprehensive high-resolution multi-beam sonar and seismic reflection survey of the Northern San Andreas Fault (NSAF) was completed. When combined, data from these two complementary geophysical surveys will provide an unprecedented high-resolution 3D visualization of the fault system. In addition, digital photographs and photomosaics obtained with a hovering autonomous underwater vehicle (AUV) will provide the collaborative team of geologists and biologists with direct observation of the seafloor and associated biological communities at selected sites. Mapping and imaging the NSAF at geo-referenced spatial scales from kilometers to meters will support ongoing studies and discoveries on the nature of the NSAF and contribute to the assessment of marine habitats in the California Current Ecosystem. Finally, the exploration provides a case study and outreach opportunity for conducting a green oceanographic research project.The AUV imagery data from this project is archived with the AUV group at the NWFSC. The seafloor mapping data from this project is archived at Oregon State University in the Active Tectonics and Seafloor Mapping Lab, http://activetectonics.coas.oregonstate.edu/.
Multiibeam information of  bottom.  Optical Information collected by the SeaBED Autonomous Underwater Vehicle (AUV).

Tags: doc/noaa/nmfs/nwfsc, habitat assessment, national marine fisheries service, noaa. u.s. department of commerce, northern california, northwest fisheries science center, sd (office of the science director), seafloor mapping, sonar - echo sounding, video camera
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Observer Logistics (OBSLOG) - 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.
Information on observers, such as deployment history, address, phone, email, emergency contacts, pictures and material that supports them meeting required standards (transcripts, statement of criminal history).

Tags: by-catch, catch shares, crescent city office, data development methods, doc/noaa/nmfs/nwfsc, eureka office, fishery data preparation, fishery dependent, fishery observer, 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, obsolete, sand point offices
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
West Coast fish, mammal, and bird species diets - Developing end-to-end models of the California Current Large Marine Ecosystem

The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web interactions, habitat, fisheries, economics, monitoring, and management into a common model framework. This framework allows for thought experiments, including evaluation of alternate management strategies, identifying robust indicators, and assessing relative importance of different ecosystem drivers in regulating important processes.  NMFS personnel are conducting this work in broad collaboration with other NOAA scientists, academics, and NGOs.  The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results.  Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders.  Management audiences include NMFS west coast regions and the PFMC.  The project is an on-going, stand-alone project with no firm deadline for completion.
West coast fish, mammal, bird diets. Available online as Dufault et al. 2009  NOAA Tech Memo NWFSC-103, with full xls format appendices.
https://www.nwfsc.noaa.gov/publications/scipubs/displayinclude.cfm?incfile=technicalmemorandum2009.inc.

Tags: atlantis, california current lme, cb (conservation biology) division, climate change, doc/noaa/nmfs/nwfsc, economics, ecosystem modeling, food web, global change, instrument not applicable, management strategy evaluation, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
KLA - 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.
The oxygen transfer coefficient (KLa) will be determined by deaeration with nitrogen gas followed by aeration (0.60 slpm) using a YSI ProODO dissolved oxygen meter. The KLa value will be computed from the ASCE Standard for the Measurement of Oxygen Transfer in Clean Water http://cedb.asce.org/cgi/WWWdisplay.cgi?156576 The measured KLa values will be reported at 20C using a theta = 1.047.

Tags: aquaculture, doc/noaa/nmfs/nwfsc, gas transfer, hagerman valley, heat transfer, idaho, in-situ instrument - automated dissolved oxygen sensor, 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, water quality
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
POPs and stable isotopes in bird and forage fish tissues - Persistent organic pollutant levels in juvenile salmonids, forage fish and their avian predators from Puget Sound and the outer WA coast

This project is examining contaminant loads of fish prey species of a resident marine bird (Rhinoceros Auklet) breeding in inland waters (Puget Sound) and in the northern California Current (outer Washington coast). It is being conducted by NMFS FTEs, in collaboration with scientists from the State of Washington and University of Puget Sound. Contaminant loads of fish prey as well as the marine bird predators are being assessed in the context of other upper trophic level predators in Puget Sound (Southern resident killer whales; harbor seals; adult salmonids). Scientific manuscripts and technical reports will be the main products. 

The target audience includes the Puget Sound Partnership, resource management agencies, stakeholders in the Puget Sound area, and marine scientists in general. This is an on-going, stand-alone project without a firm deadline.
POPs and stable isotopes in bird and forage fish tissues.

Tags: di rhinoceros auklet breeding colony, doc/noaa/nmfs/nwfsc, feeding ecology, marine ecosystems, mass spectrophotometer, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, persistent organic pollutants, pi rhinoceros auklet breeding colony, stable isotopes, ti rhinoceros auklet breeding colony, ylitalo lab
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Rockfish Recruitment and Ecosystem Assessment Survey (transect)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Rockfish Recruitment and Ecosystem Assessment Survey. The  Rockfish Recruitment and Ecosystem Assessment Survey  started in 1983 and is led by NMFS Southwest Fisheries Science Center. This survey is a long-term survey that estimates year-to-year variability in young-of-the-year (YOY) rockfish and other groundfish, as well as enumerates krill and many other forage fishes and invertebrates in the California Current. Key objectives include the development of recruitment indices of rockfish (and other groundfish) for use in stock assessments, informing oceanographic studies of groundfish recruitment processes, and supported a number of ecosystem studies, such as helping researchers understand how ecosystem shifts impact ocean biodiversity, seabird reproduction, unusual mortality events, and the rise of whale entanglements. The survey is conducted annually on a NOAA research vessel, in late Spring when most YOY groundfish are pelagic and vulnerable to the gear. Mid-water trawl sampling occurs at night, and samples not only rockfishes, but many additional species including gelatinous zooplankton, mesopelagic fishes, and forage species such as krill, market squid, anchovies, and sardines. The survey also includes conductivity, temperature, depth (CTD) casts to collect environmental data, quantitative marine mammal and seabird observations, fisheries acoustics data collection, and sample collection for collaborative research activities, including eDNA, stable isotopes, and age and growth studies.

Tags: abundance, california, ctd, doc/noaa/nmfs/nwfsc, ecosystem, juvenile rockfish, midwater trawl, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oceanography, recruitment, story map: noaa fisheries west coast offshore scientific surveys, united states
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Cedar River Chinook genotypes - Estimate relative reproductive success of hatchery and wild fall Chinook salmon in the Cedar River

We are using genetic pedigree information to estimate the reproductive success of hatchery and wild fall-run Chinook salmon spawning in the Cedar River, Washington.
Genotypes and associated phenotypes for Cedar River Chinook salmon.

Tags: artificial propagation, cb (conservation biology) division, cedar river, chinook salmon, dna sequencer, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, reproductive success
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Atlantis model outputs - Developing end-to-end models of the California Current Large Marine Ecosystem

The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web interactions, habitat, fisheries, economics, monitoring, and management into a common model framework. This framework allows for thought experiments, including evaluation of alternate management strategies, identifying robust indicators, and assessing relative importance of different ecosystem drivers in regulating important processes.  NMFS personnel are conducting this work in broad collaboration with other NOAA scientists, academics, and NGOs.  The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results.  Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders.  Management audiences include NMFS west coast regions and the PFMC.  The project is an on-going, stand-alone project with no firm deadline for completion.
Results of Atlantis ecosystem model simulations
Metadata and .nc datafile at https://www.nodc.noaa.gov/oceanacidification/data/0131198.xml
Generated from Atlantis ecosystem model, version AtlantisTrunk5425. 
Model code from CSIRO Australia, available via SVN after contacting CSIRO staff at http://atlantis.cmar.csiro.au/.

Tags: atlantis, california current lme, cb (conservation biology) division, climate change, doc/noaa/nmfs/nwfsc, economics, ecosystem modeling, food web, global change, instrument not applicable, management strategy evaluation, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Ichthyoplankton Data - Coastwide Cooperative Pre-recruit Survey

The Pre-recruit survey project is collaborative involving researchers from the FE Division based in 3 laboratories (Newport, Seattle and Hammond), scientists from the Southwest Fisheries Science Center (Santa Cruz), along with researchers from several universities (Oregon State University, University of Oregon, University of Washington, University of California, Santa Cruz).  In concert with a similar SWFSC survey effort through California, the purpose of this project is to conduct annual surveys within the coastal ecosystem off Oregon and Washington to quantify the environmental conditions and biota found along the California Current and to elucidate ecosystem-level processes affecting managed and protected marine resources.  

This project currently supports three main efforts:

1. An annual sampling regime of the hydrology, plankton, small fish, and predators along transects over the Continental Shelf from Oregon and Washington. This consistent survey has generated significant information on within- and between-year variability in the California Current Marine Ecosystem and has yielded valuable insights into the food web off our coast. 

2. Collection of specimens for diet analysis, growth, containment load, and other studies related to the ecology and production of commercially important taxa and their relationships within the food web.

3. Parameters and ecological processes quantified during this effort are used in forecasts involving species, assemblages, and ecosystems and also to parameterize ecosystem models used to evaluate cumulative risks and managerial strategies.
We towed a 71 cm diameter Bongo net at each trawl station from 100 m to the surface.

Tags: acoustic automated analysis, animal and plant collection device - plankton collection device - plankton net, bell m. shimada, climate indicators, doc/noaa/nmfs/nwfsc, ecosystem indicator, fe (fish ecology) division, fish eggs and larvae, food web, instrument not applicable, juvenile fishes, krill, national marine fisheries service, newport, noaa. u.s. department of commerce, northwest fisheries science center, northwest fisheries science center (nwfsc) in newport, oceanography, oregon, oregon coast located within marine layer area number 1, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Growth Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon.
The fork length to the nearest mm and weight to the nearest gram of a subsample of fish is recorded on an approximately quarterly basis.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, manchester research station, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Pacific Northwest Marine Mammal Survey (extent)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ  Pacific Northwest Marine Mammal Survey. The Pacific Northwest Marine Mammal Survey is part of the larger West Coast Marine Mammal Surveys started in 2021 and led by NMFS Alaska Fisheries Science Center. These surveys have a specific focus on small vessel surveys (Class II small vessel, 34-ft LOA) for marine mammals from the western Strait of Juan de Fuca south along the outer coast to Eureka, California. Although focal species vary from year-to-year, surveys have historically prioritized gray whales (Eschrichtius robustus), humpback whales (Megaptera novaeangliae), and Steller sea lions (Eumetopias jubatus) given the programâs long-term survey efforts for these species. Since 2021, surveys from June through September now represent a substantial increase in both spatial coverage and frequency relative to historical surveys, documenting all opportunistic sightings of marine mammals independent of program priorities. Data are used to derive estimates of species-specific occurrence, density, abundance, and resource utilization. As the length of the time series improves, data will be leveraged to better understand environmental drivers of occurrence, abundance and density, phenology of migration, and the health/condition of individuals and populations.The Pacific Northwest Marine Mammal Survey periodically samples marine mammals along coastal, shelf, and shelf edge ecosystems - out to approximately 20 nautical miles offshore - from northern Washington (including the western Strait of Juan de Fuca) to northern California. Periodic sampling efforts include collection of spatially explicit presence/absence data for all marine mammals, mark-resight observations of individually identifiable large whales (including gray whales, humpback whales, killer whales, blue whales, and fin whales) and Steller sea lions (from branded and tagged animals), boat-based tissue sampling of large whales, boat-based UAS surveys for enumerating pinnipeds at haulouts/rookeries along the PNW coast, and UAS-based photogrammetry for measuring body condition in large whales and pinnipeds.

Tags: boat-based tissue sampling, california, doc/noaa/nmfs/nwfsc, marine mammals, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, small vessel survey, story map: noaa fisheries west coast offshore scientific surveys, uas, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce