AndreaBozzo/ceres-open-data-index huggingface dataset:
Growth data - Development of methods to sterilize sablefish

Methods for reproductive sterilization are broadly needed in marine aquaculture due to biosafety concerns associated with escapement of farmed fish and potential genetic contamination of wild stocks. Current methods for sterilization have been primarily tested in freshwater fishes and are often ineffective, particularly in males. The proposed activity builds upon our recent success in producing the first-ever monosex female stocks of sablefish for aquaculture and seeks to develop eco-friendly, non-GMO methods for reproductive sterilization. We will use sablefish as our model marine species for sterilization and continue to collaborate with University of Maryland faculty with expertise in cutting-edge techniques for sterilization. Development of sustainable marine aquaculture is a high priority at the local (NWFSC), regional (WCR), and national levels (NOAA, DOC, Congress). Our sablefish sex control/sterilization project was also highlighted as a critical priority and outstanding area of research in the NOAA Aquaculture Science Review published 28 Feb 2019. We ultimately aim to transfer a sterilization technology to the US sablefish aquaculture industry and expand our methodology to other important species, with the goal of improving sustainability of marine aquaculture and mitigating impacts on the environment.
Fish in experiments are often PIT tagged and regularly checked for growth in fork length and body weight.

Tags: balance, doc/noaa/nmfs/nwfsc, gonadal sex differentiation, length board, 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, obsolete, reproductive biology, sablefish, sex control, sustainable aquaculture
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Sixgill Shark Data - Movement and habitat use patterns of top predators and keystone species in the benthic food web

We have been using and continue to use acoustic telemetry methods to monitor the movement behavior and define habitat use of groundfish species in and out of Puget Sound waters. Detections of individual fishes has been collected at small and large scales over short and long term periods. We have data on sixgill and sevengill sharks, spiny dogfish, lingcod, copper, quillback, yellowtail and black rockfish, and spotted ratfish. These data are being used to describe the spatio-temporal patterns of behaviors expressed by top predators and other important members of the groundfish community in Puget Sound and along the West Coast. We intend for this information to inform the strength of inter- and intra-specific interactions quantified by ecosystem-scale models as well as the development of models used to determine the efficacy of spatial management strategies such as Marine Protected Areas. This has been a research topic since 2003, and will continue with work on listed species such as yelloweye and canary rockfish.
Acoustic telemetry data for sixgill sharks.

Tags: acoustic tags, animal and plant collection device, animal movement, british columbia, cb legacy data sets, demersal fish, doc/noaa/nmfs/nwfsc, home range, instrument not applicable, lingcod, marine reserves, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound, strait of georgia and howe sound, strait of juan de fuca, west coast of united states
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Diet - Recolonization of the Cedar River, WA by Pacific salmon

The objective of this study is to quantify population, community, and ecosystem level changes as a result of salmon recolonization of the Cedar River, WA above Landsburg Dam. The dam was installed in 1901, blocking the upstream migration of adult salmon and steelhead from about 43 km of river habitat. A fish ladder was installed in 2003 to allow adult salmon passage. We collected baseline data on water chemistry, habitat, isotopes (periphyton, invertebrates, fish, riparian trees) and resident trout and sculpin populations in 2000-2002. These studies have been ongoing since 2000. A mark-recapture study in Rock Creek, the largest tributary available to salmon, was started in 2004 to quantify growth, movement, and survival of juvenile coho and resident trout.
Diet data from resident fish and juvenile coho.

Tags: abundance, balance, cedar river watershed, doc/noaa/nmfs/nwfsc, experiments, fe (fish ecology) division, fish passage, invertebrate processing, isotopes, juvenile salmonid, movement, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, pit tag, recolonization, rock creek pit tagging, survival, tributary to cedar r.
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Behavioral observations - Evaluating the impacts of pesticides on ESA-listed salmon and their habitats

Long-running science support for the agency (Office of Protected Resources, others) related to the use of modern pesticides throughout the United States as a limiting factor for endangered species conservation and recovery. This work is currently supporting several national ESA Biological Opinions, and is under review by the National Academy of Sciences. The NAS panel recommendations are expected in the summer of 2013, and these will guide additional research in FY14 and beyond.
Behavioral observations and video of salmonids following exposure to pesticides.

Tags: doc/noaa/nmfs/nwfsc, ecotoxicology, endangered species act, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, nwfsc mukilteo, salmon, stormwater, video camera
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Water Analyses - Neurobehavioral impacts of copper on juvenile salmon

Research support for various organizations in NOAA (Northwest Regional Office (NWR), HQ Office of Protected Resources, National Ocean Service (NOS) Coastal Services Center) for copper related to the harmful impacts of urban stormwater runoff, pesticide use, antifoulant use, and mining (e.g., proposed hardrock mining in Alaska). This has been a core focus of Ecotoxicology research for years, and may redirect to address key and high-profile data gaps specific to salmon habitat threats in Alaska.
Analyses of water samples for water chemistry (e.g., pH) and metals.

Tags: doc/noaa/nmfs/nwfsc, ecotoxicology, instrument not applicable, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, nwfsc montlake, nwfsc mukilteo, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
PNW cetacean muscle biochemistry - Muscle Myoglobin Content and Acid Buffering Capacity of Cetaceans from the Pacific Northwest to Assess Dive Capacity and the Development of Diving Capabilities

This project assesses the development of two important skeletal muscle adaptations for diving (enhanced myoglobin content and acid buffering capacities) in a range of cetaceans from the Pacific Northwest in order to understand constraints on diving capacities (primarily dive duration) with development. Myoglobin is an important oxygen store for supporting aerobic diving, while enhanced buffering capacity could support anaerobic metabolism during apnea. Yet little is known about the post-natal development of muscle biochemistry in cetaceans.

To assess the development of these important adaptations in cetaceans, muscle myoglobin content and buffering capacity due to non-bicarbonate buffers were measured in the longissimus dorsi of harbor porpoise (Phocoena phocoena), killer whale (Orcinus orca), and Dall's porpoise (Phocoenoides dalli).

Dawn Noren is the principal investigator from NWFSC. Projects on individual species within this larger project include different collaborators. For the project on harbor porpoise (completed), Shawn Noren (UCSC) and Joe Gaydos (SeaDoc Society) are external collaborators. Dawn Noren is responsible for project oversight, Shawn Noren trained Northwest Fisheries Science Center (NWFSC) staff on laboratory procedures for sample analysis and Joe Gaydos collected samples. The specific work includes experimental design, data collection, data analysis, and writing for submission to peer-reviewed journals. These projects are ongoing until sufficient samples are collected for sound statistical analysis. This research addresses some data gaps associated with dive capacities and potential limitations in habitat use by local cetaceans.
Muscle adaptation to diving.

Tags: 92372, 92606, acid buffering, cb legacy data sets, dall's porpoise, diving physiology, doc/noaa/nmfs/nwfsc, harbor porpoise, killer whale, myoglobin, 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
SRKW seasonal occurence - Population structure and viability of SRKW and other top marine predators

The Southern Resident killer whale (SRKW) population is threatened by a number of identified risk factors including prey availability, contaminants, vessel noise and disturbance, and small population size. However, the population may also be subject to internal factors that limit population growth.  Continued assessment of the discreetness of this population through morphological and genetic characteristics is important to maintaining ESA status.  In addition, an annual census provides important information that allows demographic analyses of this population to be conducted in order to assess population viability. The components of the project represent a significant level of investment of base funds over many years and these data and analyses provide the foundation of information on the population against which all research and management actions are measured that are attempting to address key risk factors of the SRKW population as protected under the ESA and MMPA.
Data taken seasonally.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, gps, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, population trends, southern resident killer whale
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
DWH damage assessment on marine species - Toxicity of petroleum hydrocarbons (PAHs) to fish early life stages

The Ecotox Program is at the forefront, nationally and internationally, of targeted research to characterize the impacts of petroleum hydrocarbons on NOAA trust resources, particularly fish early life stages. This work is extending lessons learned from the Exxon Valdez oil spill in Alaska, through the Cosco Busan spill in San Francisco Bay, to an array of current and intensive activities associated with the Deepwater Horizon natural resource damage assessment in the Gulf of Mexico. This research has been particularly influential in recent years (PNAS papers in 2011 and 2012), with major Deepwater papers forthcoming in 2012 and 2013. Funding has come from NOS/ORR, the Oiled Wildlife Care Network, the Prince William Sound Regional Citizen's Advisory Council, the San Francisco Estuary Institute, and other sources. Ecotox is currently developing new tools to assess PAH exposure and toxicity in fish and other animals, with national applicability - e.g., in advance of anticipated oil drilling in the Arctic, beginning in the summer of 2012.
Ongoing NRDA study of the effects of the 2011 Deepwater Horizon Oil Spill in the Gulf of Mexico. This work supports NOAAâs Damage Assessment, Remediation, and Restoration Program (DARRP).

Tags: 92372, ca, doc/noaa/nmfs/nwfsc, early development of fish, gulf of mexico, marine fishes, migrated from environmental conservation division legacy data sets, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, obsolete, oil spill-related contaminants, san francisco bay, sausalito, seattle, wa
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Salmon vulnerability maps - Effect of Climate Change on Salmon Population Vulnerability

1. Steelhead (Oncorhynchus mykiss) and other Pacific salmon are threatened by unsustainable
levels of harvest, genetic introgression from hatchery stocks and degradation or loss of freshwater
habitat. Projected climate change is expected to further stress salmon through increases
in stream temperatures and altered stream flows.
2. We demonstrate a spatially explicit method for assessing salmon vulnerability to projected
climatic changes (scenario for the years 20302059), applied here to steelhead salmon across
the entire Pacific Northwest (PNW). We considered steelhead exposure to increased temperatures
and more extreme high and low flows during four of their primary freshwater life stages:
adult migration, spawning, incubation and rearing. Steelhead sensitivity to climate change
was estimated on the basis of their regulatory status and the condition of their habitat. We
assessed combinations of exposure and sensitivity to suggest actions that may be most effective
for reducing steelhead vulnerability to climate change.
3. Our relative ranking of locations suggested that steelhead exposure to increases in temperature
will be most widespread in the southern Pacific Northwest, whereas exposure to substantial
flow changes will be most widespread in the interior and northern Pacific Northwest.
There were few locations where we projected that steelhead had both relatively low exposure
and sensitivity to climate change.
4. Synthesis and applications. There are few areas where habitat protection alone is likely to
be sufficient to conserve steelhead under the scenario of climate change considered here.
Instead, our results suggest the need for coordinated, landscape-scale actions that both
increase salmon resilience and ameliorate climate change impacts, such as restoring connectivity
of floodplains and high-elevation habitats.

Salmon gridded data for PNW.

Tags: climate change, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, habitat, habitat characteristics, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pacific nw, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Catcher Processor Cost Earnings Data - Economic Data Collection for Monitoring the Economic Effects of the West Coast Groundfish Trawl Rationalization Program

This project was initiated in response to regulation 50 CFR 660.114, which mandates that economic data be collected from every participant in the trawl rationalization program. The data are collected annually from catcher vessels, catcher processors, motherships, first receivers, and shorebased processors through paper-based forms. The four forms (specific to entity type) are mailed annually in May, and collect data about the fishing, buying, and processing information from the previous year. The entity must submit their data by September 1 in order to renew their limited entry trawl permits, reissue their quota share, vessel accounts, and receive their first receiver site licenses. The data, reports, tech memos, and academic papers are used by Northwest Region staff, Pacific Fishery Management Council (PFMC), and headquarters staff to inform management decisions, and to monitor the effects of the program.
Cost, earnings, and production data for catcher processors in the U.S. Pacific Hake Fishery.

Tags: costs, doc/noaa/nmfs/nwfsc, employment, fishery-dependent, fram (fishery resource analysis and monitoring) division, national marine fisheries service, net revenue, noaa. u.s. department of commerce, northwest fisheries science center, pacific coast of u.s., profit, revenue, surveys and questionnaires, tracked asset
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Transient killer whale range - Satellite tagging of West Coast transient killer whales to determine range and movement patterns

Transient killers whales inhabit the West Coast of the United States. Their range and movement patterns are difficult to ascertain, but are vital to understanding killer whale population dynamics and abundance trends. Satellite tagging of West Coast transient killer whales to determine range and movement patterns will provide data to assist in understanding transient killer whale populations.
Locational data.

Tags: animal mounted instrument, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, killer whale, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, population trends
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Broodyear data - Snake River sockeye salmon captive propagation

Gene rescue captive broodstock program was established for ESA-listed endangered Snake River sockeye salmon from Redfish Lake, Idaho.  The program has consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery.  Fish are being released to native habitats as part of recovery efforts.
Data is collected by broodyear on % survival to eye, % survival to spawning, % survival to smolt, % survival to adult, % maturity as two year olds, % maturity as three year olds, and % maturity as four year olds. Age of maturity data is available by sex.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Genetic data for groundfish - Genetics and genomics of northeastern Pacific groundfish

Conduct genetic analyses of groundfish in the northeastern Pacific, with a focus on population genetics and genomics of rockfishes and sablefish.
Genetic data for groundfish.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Observer Production (OBSPROD) - 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.
Fishery dependent data collected by observers. This data set includes the raw observer catch data.

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, sand point offices
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
LCREP genetic stock ID - 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.

Genetic stock information for chinook salmon from 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, genotype, 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