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216 results for “water column”
Infectivity of the parasite Metschnikowia bicuspidata is decreased by time spent as a transmission spore, but exposure to phycotoxins in the water column has no effect
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Data from: A compendium of geochemical information from the Saanich Inlet water column
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Decades of water column temperature, lake level and meteorological data of Lake Lacawac, a pristine glacial lake at Lacawac Biological Field Station in the Pocono mountains, Pennsylvania USA (1992-2019)
Lake Lacawac weather and the lake water column were monitored to observe seasonal and interannual temperature and lake level patterns in response to solar heating, wind-driven water column mixing, precipitation, evaporation, watershed runoff and seepage, and outflow (L. Lacawac has an outflow stream but no inflow stream, and is surrounded on one side by peat bogs). Several studies have shown the lake to have a slow exchange by seepage (slightly more seeping in than out except during dry months). Over the years the raft data have been used to calibrate heat flux, mixing, and evaporation models for the lake, to study zooplankton and phytoplankton distribution and dissolved organic matter flux (photobleaching in the water column, influx from the watershed, and exchange with bottom sediments) and associated UV transparency. The data have also been used to accompany experimental manipulations of lake organisms (algae, zooplankton, fish) in relation to exposure to UV radiation. More recently these lake data have been useful in developing lake indices of climate change.
Hubbard Brook Experimental Forest: Chemistry of Mirror Lake water column 1967 - 2010
Numerous studies have been conducted on Mirror Lake since the mid-1960s, including extensive physical, chemical, biological, and paleoecological research (Likens 1985). This data set includes chemistry data for water samples collected approximately monthly at an anchored buoy station located at the deepest part (11 m at full pool) of Mirror Lake. Measurements include ANC, DIC, DO, base cations, pH, ammonium, anions, temperature and dissolved silica. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
McMurdo Dry Valleys LTER: Phytoplankton water column profiles in Lake Bonney, Antarctica from 2004 to 2015
Lake Bonney (McMurdo Dry Valleys, east Antarctica) represents a year-round refugia for life adapted to extreme conditions. Lake level has risen by more than 3 m since 2004, but impacts of rapid lake level rise on phytoplankton community structure is also poorly understood. From 2004 to 2015, in concert with the summer limnological samplings, an in situ submersible spectrofluorometer (bbe FluoroProbe) was used to profile phytoplankton throughout the water columns of east and west lobes Lake Bonney to quantify the vertical structure of four functional algal groups (green algae, brown/mixed algae, cryptophytes, cyanobacteria). Our findings showed that phytoplankton communities were differentially impacted by physical and chemical factors over long-term vs. seasonal time scales. Following a summer of rapid lake level rise (2010-11), an increase in depth integrated chlorophyll a (chl-a) occurred in Lake Bonney caused by stimulation of photoautotrophic green algae. Collectively our data reveal that phytoplankton groups possessing variable trophic abilities are differentially competitive during seasonal and long-term time scales owing to periods of higher nutrients (photoautotrophs) vs. light/energy limitation (mixotrophs).
Water column dissolved (DSi) and biogenic (BSi) concentrations and fluxes collected from Sweeney (Right), West (Left) and Clubhead along with temperature, salinity, and flow data from 7/2010
Found at the landesea interface, these systems are silica replete with large stocks in plant biomass, sediments, and porewater, and therefore, have the potential to play a substantial role in the transformation and export of silica to coastal waters. In an effort to better understand this role, we measured the fluxes of dissolved (DSi) and biogenic (BSi) silica into and out of two tidal creeks in the PIE LTER salt marsh system. One of the creeks (Sweeney) has been fertilized from May to September for six years allowing us to examine the impacts of nutrient addition on silica dynamics within the marsh.
Data collection for Tsuji et al., 2020, Microbial ecology of phototrophs in Boreal Shield lakes, Chapter 3: Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes (PhD thesis)
<p>This data collection includes supplementary or raw data files related to Chapter 3 of the PhD thesis of Jackson M. Tsuji, "Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes" (in "Microbial ecology of phototrophs in Boreal Shield lakes"). Specifically, the following files are included:</p> <ul> <li>ASV_table_non_rarefied_counts.tsv.gz -- non-rarefied ASV table containing 16S rRNA gene amplicon data presented in this study as raw counts. Beyond the index column and sample columns, two additional columns, "Consensus.Lineage" and "Sequence" are included in the table. These columns include the taxonomic classification of the ASV (according to Silva) and the ASV sequence, respectively.</li> <li>ASV_table_non_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>ASV_table_rarefied_counts.tsv.gz -- same as "ASV_table_non_rarefied_counts.tsv.gz", except that data is rarefied to 12,000 sequences per sample. Five samples were dropped due to having <12,000 sequences.</li> <li>ASV_table_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>MAG_abundances_to_unassembled_reads.tsv.gz -- table like an ASV table showing the relative abundances (expressed as percentages) of metagenome-assembled genomes within metagenomes. Aside from the index column and sample columns, additional columns are included to provide the taxonomic classification of the MAGs (based on the Genome Taxonomy Database) and the CheckM statistics of the MAGs. Relative abundances of MAGs in a metagenome are calculated as the number of mapped reads to the MAGs from the given metagenome divided by the total number of unassembled metagenome reads for that metagenome (times 100%).</li> <li>MAG_abundances_to_assembled_reads.tsv.gz -- same as above, except that relative abundances are divided by the total number of unassembled metagenome reads for that metagenome that mapped to that metagenome's assembled contigs.</li> <li>core_sample_metadata.tsv -- table of core physico-chemical and geographic metadata for the samples in this study (used to build biplots presented in the chapter). Note that "nd" means "no data available", and any measurements below detection limits have been set to 0. A limited number of values were inferred from other sampling time points -- these are noted in the table for TDFe measurements, and in addition, the light attenuation coefficient for Lake 373 in Sept. 2017 was inferred from the Sept. 2016 coefficient due to no light data being available for Sept. 2017 samples.</li> <li>metadata_descriptions.tsv -- descriptions of all metadata columns in the above file.</li> </ul> <p> </p>
Modelling plastic concentrations in sea ice and the water column
<p>Results for the last year of a 50-year simulation of the dispersion of plastics in the global ocean using the NEMO modelling framework in configuration ORCA1-LIM2. These are NetCDF. Variable names are largely self-explanatory. PLASTIC_1 to PLASTIC_3 refer to buoyant, neutrally boyant and non-buoyant plastic concentrations in water; plt1 to plt3 are the corresponding concentrations in sea ice. Data for years 1-to-49 will be made available by the authors upon request.</p>
Datasets for the publication "Heteroaggregation of PS microplastic with ferrihydrite leads to rapid removal of microplastic particles from the water column"
<p>This file contains datasets that were generated during laboratory-based experiments on sedimentation, zeta potential and z-average hyd. diameter.</p> <p>The article was published in <em>Environmental Science: Processes & Impacts</em> (accepted July 11, 2022).</p>
Supplementary Data for "Hydrate Formation on Marine Seep Bubbles and the Implications for Water Column Methane Dissolution"
<p>This data deposit contains the data necessary to reproduce results presented in the paper "Hydrate Formation on Marine Seep Bubbles and the Implications for Water Column Methane Dissolution", to appear in JGR Oceans. </p> <p>The files "Fu_AGUSupplementary_S11.xlsx" and "Fu_AGUSupplementary_S12.xlsx" are referenced in the supplement of the original paper. </p> <p>The file "Fu_AGUSupplementary_additionalDATA.xlsx" contains all the data and inputs used to create Figure 14, 15 and 16 of the original manuscript.</p>
Gravitational energy harvesting from hydrostatic water columns
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Mean annual Secchi depth measurements in the period starting in 1969 provide a measure of water column transparency in the CalCOFI inshore and offshore areas, 1969 - 2004.
The Secchi depth provides a measure of water turbidity. Measurements are made as part of the California Fisheries Cooperative Investigations (CalCOFI). Secchi depth is measured on each station on each cruise. The mean annual is obtained by averaging stations over time and at stations defined as either inshore or offshore.
Total Thorium-234 (Th-234) taken from discrete water column samples collected during CCE Process Cruises (2006 - 2017).
Thorium-234 (Th-234) is the first long-lived (half-life = 24.1 days) daughter particle of Uranium-238 (U-238). While U-238 is conserved in the ocean (it covaries with salinity and has a half-life of 4.5 billion years), Th-234 is scavenged onto particles and hence removed from the surface ocean when those particles sink to depth. By measuring vertical profiles of total Th-234 activity in the euphotic zone and assuming steady-state between production of Th-234 from U-238 decay and removal of Th-234 on sinking particles, we can thus estimate the export of Th-234 from sampled water parcels. These measurements of Th-234 export can be converted to estimates of carbon export by multiplying by the C:Th-234 ratio of sinking particles measured at the same time and location.
Particulate organic carbon and nitrogen measurements from Go-Flo bottles sampling the water column from a zodiac during Palmer LTER station seasons at Palmer Station Antarctica, 1991 - 2012.
All organisms are composed of organic matter. Organic matter is synthesized from dissolved inorganic carbon (dissolved CO2) and inorganic nutrients by phytoplankton photosynthesis, and consumed (oxidized) by respiration by heterotrophs (zooplankton and bacteria). The organic matter in seawater is a variable mixture of dissolved and particulate organic matter (DOM and POM). Typically DOM predominates over POM by an order of magnitude, but the relative amount of POM can be highly enhanced during large phytoplankton blooms. The principal elemental components of POM include organic carbon (POC), organic nitrogen (PN), there is no particulate inorganic N) and phosphorus (POP). These elements exist in a relatively stable, characteristic ratio of 106:6:1 (C:N:P) in seawater, known as the Redfield Ratio. Marine particulate matter is a complex mixture of live and dead plankton and detritus, and of carbohydrates, proteins, lipids and nucleic acids. POC and PN are enhanced in the euphoric zone, reflecting their origin by photosynthesis. The particulate pool is also a complex assemblage of particles of different sizes, shapes and densities. A simplified scheme divides the particles into large, rapidly sinking particles (10s - 100s of meters per day) and smaller, suspended particles. The transition between small particles and dissolved organic matter is typically specified by filtration through GF/F filters. POC and PN are analyzed for all samples in the upper 50 meters at Palmer Station B (75 m depth) and the upper 65 m at Station E (200 m depth). There is a gradient of POM from higher values inshore to much lower values in deep ocean water beyond the continental shelf break (sampled on the annual cruise).
Bacterial properties in discrete water column samples collected during Palmer LTER station seasons at Palmer Station Antarctica, 2002 - 2019.
The microbial biogeochemistry component of PAL focuses on marine bacterioplankton, and is thus a counterpart to the phytoplankton and zooplankton components, which together provide a detailed and comprehensive description of plankton ecology in PAL-LTER. Bacteria and Archaea (hereafter called "bacteria") are taxonomically and metabolically diverse. In coastal and offshore surface waters Bacteria generally predominate over Archaea, but Archaea are equal or greater in abundance in the mesopelagic layer below the euphoric zone. We focus on aerobic, heterotrophic bacteria in the upper 65 m at Palmer Station which oxidize recently-produced low molecular weight dissolved organic compounds released by phytoplankton and zooplankton, decomposing them back into CO2 and inorganic nutrients. Globally, marine bacteria respire an amount of carbon roughly equal to about half the daily photosynthetic production. In cold polar waters, relative bacterial activity is lower, with bacterial biomass production being equal to <5% of the daily photosynthesis. The ratio at lower latitudes is 10-20%. The factors responsible for this contrast are not entirely clear. Resolving this pattern is a key aim of the PAL microbial component. At Palmer Station, bacterial production is low (< 10 mgC/m2/d) in the winter (polar night) when there is little if any photosynthesis. There is a climatological (2003-14 average) summer peak of 50-60 mgC/m2/d in January-February but with considerable seasonal and annual variability. The 2016/2017 season data contains bacteria abundances for preserved samples for comparison to abundances from live samples. See the documentation for this in the accompanying file, 2016_live_vs_preserved.pdf.
Bacterial properties in discrete water column samples at selected depths, collected aboard Palmer LTER annual cruises off the coast of the Western Antarctica Peninsula, 2003 - 2019.
The microbial biogeochemistry component of PAL focuses on marine bacterioplankton, and is thus a counterpart to the phytoplankton and zooplankton components, which together provide a detailed and comprehensive description of plankton ecology in PAL-LTER. Bacteria and Archaea (hereafter called "bacteria") are taxonomically and metabolically diverse. In coastal and offshore surface waters Bacteria generally predominate over Archaea, but Archaea are equal or greater in abundance in the mesopelagic layer below the euphoric zone. We focus on aerobic, heterotrophic bacteria in the upper 100 m on the annual summer cruise. These bacteria oxidize recently-produced low molecular weight dissolved organic compounds released by phytoplankton and zooplankton, decomposing them back into CO2 and inorganic nutrients. Globally, marine bacteria respire an amount of carbon roughly equal to about half the daily photosynthetic production. In cold polar waters, relative bacterial activity is lower, with bacterial biomass production being equal to <5% of the daily photosynthesis. The ratio at lower latitudes is 10-20%. The factors responsible for this contrast are not entirely clear. Resolving this pattern is a key aim of the PAL microbial component. Bacterial production is generally low across the grid, relative to primary production, but with considerable spatial and annual variability. Discrete BP can reach >200mgC/m2/d following bloom-fueled high organic matter events. Across the grid and over years, BP is highly correlated with chlorophyll, highlighting the close relationship with phytoplanktonic organic matter production.
Dissolved oxygen of discrete water column samples at selected depths collected aboard Palmer LTER annual cruises off the coast of the Western Antarctic Peninsula, 1993 - 2012.
Oxygen is produced by phytoplankton photosynthesis and consumed by respiration of phytoplankton, zooplankton and bacteria. Oxygen also enters and exits the ocean via physical exchange with the atmosphere. Oxygen concentrations in the surface ocean may be supersaturated by photosynthesis and turbulence enhancing air-sea exchange via bubble injection; or undersaturated due to excess respiration. In cases where exchange with the atmosphere is limited, and/or respiration exceeds photosynthesis, oxygen concentration can be reduced to very low levels (hypoxia) or entirely depleted (anoxia). This is uncommon in cold Antarctic Seas where respiration is depressed and oxygen solubility is enhanced by low temperature. Different water masses have characteristic oxygen concentrations which serve as tracers for diagnosing physical mixing and advection. Dissolved oxygen was analyzed by Winkler Titration (see Methods) in CTD-Rosette bottle samples at all depths sampled until 2012. This measurement was discontinued in 2013. The CTD has duplicate oxygen electrodes that provide continuous vertical profiles of oxygen concentration at all depths on all casts. The vessel also has continuous underway, Optode determination of dissolved oxygen in the surface (ship's intake at 6 meters depth) on all cruises. Finally we now routinely measure net community production by Equilibrator Inlet Mass Spectroscopy (EIMS) on LTER cruises
Dissolved organic carbon (DOC) taken from discrete water column samples collected during annual cruise along western Antarctic Peninsula, 2003-2012.
Dissolved organic carbon (DOC) is a poorly-characterized but large and dynamic pool of actively-cycling carbon in the oceans, and one of the largest organic carbon pools on the planet. The total DOC pool consists of three major fractions: refractory DOC resistant to microbial oxidation with a turnover time of millennia; semi-labile DOC, produced and decomposed on seasonal timescales, and labile DOC, consisting of simple, recently-produced compounds with nanomolar concentrations, and turnover times of minutes-days. The background concentration of refractory DOC in the deep ocean is 35-45 micromolar. DOC concentration in the upper 100-200 meters is enhanced by 10-50 micromolar with the addition of semilabile DOC. In subtropical and temperate oceans, semilabile DOC can form an important part of the carbon export by deep vertical mixing into the oceanic mid-depths. Concentrations of semilabile DOC are lower in the polar Southern Ocean than in most other regions.
Dissolved organic carbon (DOC) taken from discrete water column samples collected between October and April at Palmer Station, 2002-2012.
Dissolved organic carbon (DOC) is a poorly-characterized but large and dynamic pool of actively-cycling carbon in the oceans, and one of the largest organic carbon pools on the planet. The total DOC pool consists of three major fractions: refractory DOC resistant to microbial oxidation with a turnover time of millennia; semi-labile DOC, produced and decomposed on seasonal timescales, and labile DOC, consisting of simple, recently-produced compounds with nanomolar concentrations, and turnover times of minutes-days. The background concentration of refractory DOC in the deep ocean is 35-45 micromolar. DOC concentration in the upper 100-200 meters is enhanced by 10-50 micromolar with the addition of semilabile DOC. In subtropical and temperate oceans, semilabile DOC can form an important part of the carbon export by deep vertical mixing into the oceanic mid-depths. Concentrations of semilabile DOC are lower in the polar Southern Ocean than in most other regions.
Data from: The Palaeozoic colonization of the water column and the rise of global nekton
The colonization of the water column is among the most important transformations in the evolution of animal life and global ecosystems. The Devonian Nekton Revolution (DNR) has been identified as a major macroevolutionary event signifying the sudden occupation of the water column by independent radiations of swimming animals. Using new data, an expanded taxonomic coverage, sample standardization, and increased ecological resolution, we reanalysed the timing, duration, and magnitude of this event. We find that nekton and eunekton were well established prior to the Devonian and did not diversify dramatically during any Palaeozoic interval. Relative nektic diversity and occurrences decreased rather than increased during the Devonian. Eunektic diversity and occurrences increased throughout the Palaeozoic, but this rise was protracted and cannot be attributed to any single interval. Our new data indicate that the metazoan colonization of the water column was considerably more complex and gradual than previously understood.
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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.