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Global dataset of nitrogen fixation rates across inland and coastal waters based on a coordinated synthesis effort
Biological nitrogen fixation converts inert di-nitrogen gas into bioavailable nitrogen and can be an important source of bioavailable nitrogen to organisms. This dataset synthesizes the aquatic nitrogen fixation rate measurements across inland and coastal waters. Data were derived from papers and datasets published by April 2022 and include rates measured using the acetylene reduction assay (ARA), 15N2 labeling, or the N2/Ar technique. The dataset is comprised of 4793 nitrogen fixation rates measurements from 267 studies, and is structured into four tables: 1) a reference table with sources from which data were extracted, 2) a rates table with nitrogen fixation rates that includes habitat, substrate, geographic coordinates, and method of measuring N2 fixation rates, 3) a table with supporting environmental and chemical data for a subset of the rate measurements when data were available, and 4) a data dictionary with definitions for each variable in each data table. This dataset was compiled and curated by the NSF-funded Aquatic Nitrogen Fixation Research Coordination Network (award number 2015825).
Biocomplexity at North Temperate Lakes LTER: Coordinated Field Studies: Riparian Littoral Sites 2001 - 2004
General descriptive data for sites sampled as part of the "cross-lake comparison" segment of the Biocomplexity Project (Landscape Context - Coordinated Field Studies). The goal of the study was to explore the links between terrestrial and aquatic systems across a gradient of residential development and lake landscape position. Specifically, this project attempted to relate the abundance of Coarse Wood in the littoral zone with abiotic, biotic and anthropogenic features of the adjacent shoreline. Sampling Frequency: each site sampled once Number of sites: 488 sites on 61 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year; eight sites per lake).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Littoral Plots 2001 - 2009
In 2001 - 2004 the abundance of coarse wood and other aspects of the physical structure of the littoral zone were surveyed along transects that followed the 0.5 m depth contour at 488 sites in Vilas County. These data were collected as part of the "cross-lake comparison" segment of the Biocomplexity Project (Landscape Context - Coordinated Field Studies). The study explored the links between terrestrial and aquatic systems across a gradient of residential development and lake landscape position. Specifically, this project attempted to relate the abundance of Coarse Wood in the littoral zone with abiotic, biotic and anthropogenic features of the adjacent shoreline. Each of the 488 sites was a 50 m stretch of shoreline. The transects started and ended at the beginning and end of the site; the length of each transect, therefore, varied. Logs which were at least 150 cm in length were counted; more detailed descriptions were taken of logs at least 10 cm in diameter and 150 cm long. Information on littoral and shoreline substrate was also collected. Sampling Frequency: each site sampled once Number of sites: 488 sites on 61 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year; eight sites per lake).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Riparian Plots 2001 - 2004
Living and dead trees and abiotic and anthropogenic characteristics of the shoreline were surveyed at 488 sites around lakes in Vilas County. These data were collected as part of the "cross-lake comparison" segment of the Biocomplexity Project (Landscape Context - Coordinated Field Studies). The study explored the links between terrestrial and aquatic systems across a gradient of residential development and lake landscape position. Specifically, this project attempted to relate the abundance of coarse wood in the littoral zone with abiotic, biotic and anthropogenic features of the adjacent shore. At each of the 488 sites, three 100 sq m plots, extending from the shoreline 10 m inland, were sampled. Additional plots farther inland were sampled at some sites. At each plot the survey team recorded the general appearance of the plot, measured all trees at least 5 cm dbh, measured and described downed wood and snags at least 10 cm in diameter, and recorded any overhanging trees. Saplings (at least 30 cm tall, but less than 5 cm dbh) were counted in two 5m x 5m plots per site. Sampling Frequency: each site sampled once Number of sites: 488 sites on 61 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year; eight sites per lake).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Littoral Macrophytes 2001 - 2004
The aquatic vegetation of 60 lakes selected for the "cross-lake comparison" segment of the Biocomplexity Project was surveyed during the month of August in years 2001 through 2004. The study lakes are located in Vilas County, Wisconsin and were chosen to represent a range of positions on gradients of both human development and landscape position. The purpose of the macrophyte portion of the "cross-lake comparison" study was to evaluate the roles of landscape position and human development in the presence and composition of macrophyte communities.
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Predation Study Data 2000 - 2004
These data were collected to track changes in dietary composition, changes in age and growth structure, and changes in species and size of prey of fish predators in Sparkling Lake, Vilas County, WI, USA. Sampling began in May of 2000 and ended in September of 2004. Fish were collected with a boat-mounted electrofishing system, usually by conducting a complete lap around Sparkling Lake shortly after dark. Commonly captured species were rock bass, smallmouth bass, and walleye. Less common species were pumpkinseed sunfish and yellow perch. Dietary Composition: Fish stomach contents were collected by gastric lavage, and fish were released after capture. Stomach contents were sorted and counted by major taxonomic groups, dried in polystyrene weighboats at 57 deg C for 48hrs, and then weighed to 0.001g. The count under a taxonomic group heading indicates how many individuals of that group were found in that diet sample. The mass of that group is given in the adjacent ''net wt'' column. Diets varied across sampling dates and years, with a trend towards decreased abundance of the exotics rusty crayfish and rainbow smelt and increased reliance on native minnows. Prey Data: Fish stomach contents were collected by gastric lavage, and fish were released after capture. Once collected, crayfish and fish prey were measured unless advanced digestion had occurred. If possible, the carapace, right chela and left chela of crayfish prey were measured . Due to digestion, it was usually not possible to get all three measurements. The total length of prey fish was recorded. Young-of-year smelt and crayfish were often too small or digested to measure; these were often just counted. Gut labels on each sampling date correspond with the same gut labels in other datasets. Prey fish and crayfish size and composition varied across sampling dates and years, with a trend towards decreased abundance of rusty crayfish and rainbow smelt and increased reliance on native minnows. Age Growth Data: Scale
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Zooplankton Presence/Absence 2001 - 2004
Zooplankton samples were taken at approximately the deepest part of 58 lakes included in the "cross-lake comparison" segment of the Biocomplexity Project. The samples were from years 2001 through 2004. The study lakes are located in Vilas County, Wisconsin and were chosen to represent a range of positions on gradients of both human development and landscape position. Zooplankton samples were analyzed for planktonic crustacean and insect species. Number of sites: 58 Sampling Frequency: each site sampled once
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Lakes 2001 - 2004
The study lakes selected for the "cross-lake comparison" segment of the Biocomplexity Project include 62 lakes located in Vilas County, Wisconsin. The lakes were chosen to represent a range of positions on gradients of both human development and landscape position.
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Coarse Woody Habitat Data 2001 - 2009
These data were collected to test for changes in the population dynamics and the food webs of the fish populations of Little Rock and Camp lakes, Vilas County, WI, USA. Little Rock Lake was the site of a whole-lake removal of coarse woody habitat in 2002 and Camp Lake was the site of a whole-lake coarse woody habitat addition in 2004. Sampling began in May of 2001 and ended in August of 2006. Some sampling was repeated from 2007 to 2009. Number of sites: 4. Two lakes with reference and treatment basin in each lake.
Biocomplexity at North Temperate Lakes LTER: Coordinated Field Studies: Large Mouth Bass Growth 2006
Lakeshore residential development is associated with changes in littoral habitat, riparian habitat, and ecosystem function with potential impacts ramifying through aquatic food webs. Effects of these changes on economically important game fishes may vary with fish size. We investigated largemouth bass (Micropterus salmoides) size-specific growth rates across 16 lakes spanning the range of lakeshore residential development in Wisconsin’s Northern Highland Lake District using a longitudinal multilevel model. Growth rates of small fish had a strong positive relationship with lakeshore residential development. The strength of the relationship decreased with length and became increasingly negative for fish longer than 210 mm. This pattern may be driven by a release from density-dependent growth, shifts in available prey sources, reduced macrophyte cover, or angling-induced selection pressures. Regardless of the mechanism, our results indicate, relative to undeveloped lakes, largemouth bass in highly developed lakes take 1.5 growing seasons longer to enter the fishery (356 mm).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Chemical Limnology 2001 - 2004
Chemical Limnology data collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies Replicate chemical samples were pumped from the surface water (0.5m depth) and secchi depth was recorded at each lake. Temperature/dissolved oxygen profiles were taken throughout the water column at one meter intervals on all lakes. For more detail see the Water Sampling Protocol. Sampling Frequency: During 2001, temperature/dissolved oxygen profiles and secchi depths were taken twice during the stratified summer period. Chemistry samples were only taken once during the 2001 stratified period. From 2002 through 2004, all chemical and physical water samples were taken once during June (or resampled during the stratified period if June samples were bad). All lakes in which color, DIC/DOC, and chlorophyll samples were taken in 2001 were resampled in 2002 due to error in collection and/or analysis. Number of sites: 62 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Color 2001 - 2004
Chemical Limnology data collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies Replicate chemical samples were pumped from the surface water (0.5m depth) and secchi depth was recorded at each lake. Temperature/dissolved oxygen profiles were taken throughout the water column at one meter intervals on all lakes. For more detail see the Water Sampling Protocol. Sampling Frequency: During 2001, temperature/dissolved oxygen profiles and secchi depths were taken twice during the stratified summer period. Chemistry samples were only taken once during the 2001 stratified period. From 2002 through 2004, all chemical and physical water samples were taken once during June (or resampled during the stratified period if June samples were bad). All lakes in which color, DIC/DOC, and chlorophyll samples were taken in 2001 were resampled in 2002 due to error in collection and/or analysis. Number of sites: 62 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Fish Individual 2001 - 2004
Fish Data collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies. The eight sportfishes of concern in this dataset; Bluegill, Pumpkinseed, Bluegill-Pumpkinseed hybrid, Largemouthbass, Smallmouthbass, Rockbass, Walleye, and Yellowperch, are the only species for which standard metrics (length (mm) and weight (g)) were taken. All other fish were identified to species and counted. Sampling Frequency: annually Number of sites: 58
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Secchi Disk Depth 2001 - 2004
Chemical Limnology data collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies Replicate chemical samples were pumped from the surface water (0.5m depth) and secchi depth was recorded at each lake. Temperature/dissolved oxygen profiles were taken throughout the water column at one meter intervals on all lakes. For more detail see the Water Sampling Protocol. Sampling Frequency: During 2001, temperature/dissolved oxygen profiles and secchi depths were taken twice during the stratified summer period. Chemistry samples were only taken once during the 2001 stratified period. From 2002 through 2004, all chemical and physical water samples were taken once during June (or resampled during the stratified period if June samples were bad). All lakes in which color, DIC/DOC, and chlorophyll samples were taken in 2001 were resampled in 2002 due to error in collection and/or analysis. Number of sites: 62 Vilas County lakes were sampled from 2001-2004 (approximately 15 different lakes each year).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Fish / Crayfish Abundance 2001 - 2004
Abundance data for fish and crayfish collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies http://infotrek.er.usgs.gov/doc/wdnr_biology/Public_Stocking/StateMapHotspotsAllYears.htm - Infomation on fish stocking by Wisconsin Department of Natural Resouces in Biocomplexity Lakes. Sampling Frequency: annually Number of sites: 58
Four lipidomics datasets (mouse liver, mouse pancreatic islets, mouse soleus muscle and mouse visceral adipose tissue), generated for the publication Mehl et al., "A multiorgan map of metabolic, signalling, and inflammatory pathways that coordinately control fasting glycemia in mice"
<p>Mehl, Thorens et al present a multiomics study aimiing to<span> identify the pathways that are coordinately regulated in pancreatic </span><span>b</span><span>-cells, muscle, liver, and fat to control fasting glycemia we fed C57Bl/6, DBA/2 and Balb/c mice a regular chow or a high fat diet for 3, 10 and 30 days. We measured fasted glycemia, insulinemia and whole-body insulin resistance. Transcriptomic and lipidomic analysis were used in a data fusion approach to identify organ-specific pathways related to the glycemic levels across all conditions investigated. In pancreatic islets, constant insulinemia despite higher glycemic levels were associated with reduced expression of mRNAs encoding hormone and neurotransmitter receptors as well as OXPHOS, cadherins, integrins and gap junction proteins. Higher glycemia and whole-body insulin resistance were associated, in muscle, with reduced expression of mRNAs encoding insulin signaling proteins and enzymes of the glycolysis, Krebs’ cycle and OXPHOS pathways, as well as endocytosis and exocytosis proteins; in hepatocytes, with lower expression of mRNAs of the insulin signaling pathway, of branched chain amino acid catabolism and of OXPHOS; in adipose tissue, with increased expression of mRNAs of innate immunity and lipid catabolism. These data provide a map of the pathways that are coordinately recruited in the investigated tissues to control fasting glycemia and a resource for further studies of interorgan communication in glucose homeostasis. </span></p>
Gaviota Fire Perimeter (Santa Barbara County, CA), June 9, 2004 - From Geospatial Multi-Agency Coordination Group (GeoMAC)
The Gaviota Fire burned from 2004-06-05 to 2004-06-12, 15 miles west of Santa Barbara, Santa Barbara County. Approximately 7440 acres were burned (information per http://cdfdata.fire.ca.gov). This dataset contains a KML polygon showing the extent of the fire on 2004-06-09, and was acquired by request from the Geospatial Multi-Agency Coordination Group (GeoMAC, http://www.geomac.gov). These data are based upon input from incident intelligence sources, Global Positioning System (GPS) data, and infrared (IR) imagery. See methods for more information.
Tea Fire Perimeter (Santa Barbara County, CA), November 15, 2008 - From Geospatial Multi-Agency Coordination Group (GeoMAC)
The Tea Fire burned from 2008-11-13 to 2008-11-17, Montecito, Cold Springs Creek and Hot Springs Road, Santa Barbara County. Approximately 1940 acres were burned (information per http://cdfdata.fire.ca.gov). This dataset contains a KML polygon showing the extent of the fire on 2008-11-15, and was acquired by request from the Geospatial Multi-Agency Coordination Group (GeoMAC, http://www.geomac.gov). These data are based upon input from incident intelligence sources, Global Positioning System (GPS) data, and infrared (IR) imagery. See methods for more information.
Jesusita Fire Perimeter (Santa Barbara County, CA), May 10, 2009 - From Geospatial Multi-Agency Coordination Group (GeoMAC)
The Jesusita Fire burned from 2008-05-05 to 2008-05-18, Northwest of Mission Canyon and Santa Barbara City, Santa Barbara County. Approximately 8733 acres were burned (information per http://cdfdata.fire.ca.gov). This dataset contains a KML polygon showing the extent of the fire on 2008-05-10, and was acquired by request from the Geospatial Multi-Agency Coordination Group (GeoMAC, http://www.geomac.gov). These data are based upon input from incident intelligence sources, Global Positioning System (GPS) data, and infrared (IR) imagery. See methods for more information.
Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold: Lifting atomic coordinates
<p>Here we provide the atomic coordinates and the topology file concerning the lifting process of a single stranded DNA molecule previously adsorbed on gold. In order to visualize it you will need a visualization software. Using VMD, you would only need to do in a terminal:</p> <p>vmd -e visualize.vmd </p> <p>and that is it. If you find this useful, please cite the corresponding paper:<br> Nature Communications 10, 685 (2019) [DOI: https://doi.org/10.1038/s41467-019-08531-4 ]</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.