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Dataset Title:  Bulk and cell-specific CO2 fixation and PO4 uptake from Atlantic Explorer
cruise AE1524 (BATS validation cruise BV50), September 2015
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_771701)
Range: longitude = -65.37 to -64.14°E, latitude = 22.16 to 33.25°N
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  cruise {
    String bcodmo_name "cruise_id";
    String description "cruise identifier";
    String long_name "Cruise";
    String units "unitless";
  }
  station {
    Byte _FillValue 127;
    Byte actual_range 3, 14;
    String bcodmo_name "station";
    String description "station identifier";
    String long_name "Station";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 22.16, 33.25;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "station latitude; north is positive";
    String ioos_category "Location";
    String long_name "Latitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float64 _FillValue NaN;
    Float64 actual_range -65.37, -64.14;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "station longitude; east is positive";
    String ioos_category "Location";
    String long_name "Longitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
    String standard_name "longitude";
    String units "degrees_east";
  }
  PO4 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.6, 2.3;
    String bcodmo_name "PO4";
    String description "Phosphate concentration estimate";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "nanomol Phosphate/liter (nmol P L-1)";
  }
  PO4_33P {
    Float32 _FillValue NaN;
    Float32 actual_range 0.1, 0.33;
    String bcodmo_name "P33_PO4_uptake";
    String description "Bulk phosphate uptake rate �(>0.2 microns)";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "nanomol Phosphate/liter/hour (nmol P L-1 h-1)";
  }
  Vmax {
    Float32 _FillValue NaN;
    Float32 actual_range 0.54, 0.94;
    String bcodmo_name "unknown";
    String description "Phosphate uptake kinetic parameter Vmax";
    String long_name "Vmax";
    String units "nanomol Phosphate/liter/hour (nmol P L-1 h-1)";
  }
  Km {
    Float32 _FillValue NaN;
    Float32 actual_range 2.4, 5.2;
    String bcodmo_name "unknown";
    String description "Phosphate uptake kinetic parameter Km";
    String long_name "KM";
    String units "nanomol Phosphate/liter (nmol P L-1)";
  }
  CO2_14C {
    Float32 _FillValue NaN;
    Float32 actual_range 1.9, 3.6;
    String bcodmo_name "unknown";
    String description "Bulk CO2 fixation rate (>0.2 microns)";
    String long_name "CO2 14 C";
    String units "milligrams Carbon/meter^3/day (mg C m-3 d-1)";
  }
  PO4_Pro_33P {
    Float32 _FillValue NaN;
    Float32 actual_range 0.1, 0.6;
    String bcodmo_name "P33_PO4_uptake";
    String description "Phosphate uptake rate by Prochlorococcus";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "attomole/cell/hour (amol cell-1 h-1)";
  }
  PO4_Syn_33P {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 1.2;
    String bcodmo_name "P33_PO4_uptake";
    String description "Phosphate uptake rate by Synechococcus";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "attomole/cell/hour (amol cell-1 h-1)";
  }
  PO4_P_Euk_33P {
    Float32 _FillValue NaN;
    Float32 actual_range 0.4, 2.6;
    String bcodmo_name "P33_PO4_uptake";
    String description "Phosphate uptake rate by pigmented eukaryotes";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "attomole/cell/hour (amol cell-1 h-1)";
  }
  PO4_NP_Euk_33P {
    Float32 _FillValue NaN;
    Float32 actual_range 0.4, 1.6;
    String bcodmo_name "P33_PO4_uptake";
    String description "Phosphate uptake rate by non-pigmented eukaryotes";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "attomole/cell/hour (amol cell-1 h-1)";
  }
  CO2_Pro_14C {
    Float32 _FillValue NaN;
    Float32 actual_range 0.9, 1.4;
    String bcodmo_name "unknown";
    String description "CO2 fixation rate by Prochlorococcus";
    String long_name "CO2 Pro 14 C";
    String units "femtogram Carbon/cell/hour (fg C cell-1 h-1)";
  }
  CO2_Syn_14C {
    Float32 _FillValue NaN;
    Float32 actual_range 2.6, 7.9;
    String bcodmo_name "unknown";
    String description "CO2 fixation rate by Synechococcus";
    String long_name "CO2 Syn 14 C";
    String units "femtogram Carbon/cell/hour (fg C cell-1 h-1)";
  }
  CO2_P_Euk_14C {
    Float32 _FillValue NaN;
    Float32 actual_range 68.8, 88.0;
    String bcodmo_name "unknown";
    String description "CO2 fixation rate by pigmented eukaryotes";
    String long_name "CO2 P Euk 14 C";
    String units "femtogram Carbon/cell/hour (fg C cell-1 h-1)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Seawater was collected into acid washed, ultra-pure water and sample rinsed,
clear polycarbonate incubation bottles. PO4 assimilation rates were measured
in triplicate 70-mL samples with ~259 kBq of added 33P-PO4 (Perkin-Elmer
#NEZ08000; carrier free), incubated for 30 min to 1h. CO2 fixation rates were
measured in duplicate 70-mL samples with ~17 MBq of added 14C-sodium
bicarbonate (Perkin Elmer #NEC086H000, 1.6 GBq/mmol), incubated from dawn to
dusk. Samples were incubated under simulated light and temperature conditions
measured at the sampling site. A killed control sample was also prepared by
adding paraformaldehyde (PFA, 2 % final concentration prepared with electron
microscopy grade 16 % aqueous solution, Electron Microscopy Sciences) at least
15 minutes before introducing the radioisotope, in order to account for
unincorporated radioactivity. At the end of incubation, samples were fixed
with PFA (2% final, for 15-min in the dark), and triplicate 20-microliters
aliquots were sampled to measure the total radioactivity added (with beta-
phenylethylamine for 14C samples). The total microbial activity was determined
by filtering a 3-mL aliquot through a 0.2-micron, pore-size polycarbonate
membrane filter (Nuclepore). To reduce unincorporated 33P-PO4, the membrane
filter was placed onto a filter type HA soaked in 100 mM KH2PO4, then rinsed
three times with ~1 mL of 0.2-micron filtered seawater. To remove
unincorporated 14C-sodium bicarbonate, the filter was acidified with 0.5 mL of
1N HCl for 24 h. To determine plankton groups specific uptake rates, a 20-mL
aliquot was passed through a 0.2-micron polycarbonate membrane filter under
gentle vacuum filtration, and the remaining volume from the 70-mL incubation
bottle was passed through a 0.8-micron polycarbonate membrane filter. The
0.2-micron and 0.8-micron filters were stored in separate cryovials with 2 mL
and 4 mL of the corresponding radiolabeled sample, respectively, vortexed to
detach the cells from the filter, then flash frozen for later flow cytometric
sorting (see below). The added radioactivity and total microbial activity were
assayed by liquid scintillation counting in 7-mL plastic scintillation vials
(Simport) with 4 mL of scintillation cocktail (Ultima Gold LLT, Perkin Elmer)
added.
 
Turnover times (TPO4, h) were calculated by dividing the total radioactivity
added (Bq L\\u20131) by the rate of radiolabel uptake into the particulate
fraction (Bq L\\u20131 h\\u20131). PO4 assimilation rates (nmol P L\\u20131
h\\u20131) were calculated by dividing PO4 concentration by TPO4. We used PO4
concentration estimated from a concentration series bioassays following the
method of Wright and Hobbie (1966). Briefly, seawater samples were amended
with non-radioactive PO4 to target additions of 0, 5, 10, 25, 50, 75, and 150
nmol PO4 L\\u20131, spiked with 33P-PO4, incubated and sampled as described
above. The resulting TPO4 values were plotted against a corresponding
concentration of PO4, and extrapolated using linear regression (TPO4 = a x PO4
+ b) to estimate the ambient concentration (Sn = b/a), which represents an
upper estimate of ambient concentrations as detailed in Zubkov and Tarran
(2005). Results from these bioassays were also used to calculate the
Michaelis-Menten kinetic parameters for PO4 assimilation rates (Vmax, the
maximum rate at saturating substrate concentration and Km, the half-saturation
constant).
 
For cell sorting of Prochlorococcus, Synechococcus, pigmented and non-
pigmented protists, the Influx flow cytometer was set at the highest sorting
purity (1.0 drop single mode) and potential attached cells were discarded
using a pulse width vs. forward scatter plot. The drop delay was calibrated
using Accudrop Beads (BD Biosciences, USA) and verified manually by sorting a
specified number of reference beads onto a glass slide and counting the beads
under an epifluorescence microscope. Performance was validated as described in
Duhamel et al. (2018). Three to four proportional numbers of cells from the
same incubation sample were sorted for each target population. Sorted cells
were assessed by liquid scintillation analysis following previously published
protocols (Talarmin et al. 2011; Duhamel et al. 2012; Rii et al. 2016). The
14C-labeled samples were acidified with 1 mL of 2 mol L-1 HCl for 24 h to
remove any unincorporated 14C-sodium bicarbonate.
 
For each group, at least three samples were sorted and regression analysis
between the number of cells sorted and the radioactivity taken up by the
sorted cells was used to calculate the per cell activity (dpm cell\\u22121).
Radioactivity in sorted cells from the PFA-killed control samples (dpm
cell\\u22121) was deduced from radioactivity in the sorted cells from the
respective samples (dpm cell\\u22121). The cell-specific assimilation rate
(nmol cell-1 h-1) was calculated by dividing the radioactivity per cell (dpm
cell\\u22121) by the total microbial activity (dpm L\\u22121) measured in the
same sample, and then multiplied by the total microbial assimilation rate at
ambient substrate concentration (nmol L\\u22121 h\\u22121).
 
Michaelis\\u2013 Menten kinetic parameters were determined using the
Michaelis\\u2013Menten model in Prism 6.";
    String awards_0_award_nid "553098";
    String awards_0_award_number "OCE-1458070";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458070";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"BV50_C&P: Bulk and cell-specific CO2 fixation and PO4 uptake 
   Atlantic Explorer cruise AE1524 (BATS validation cruise BV50), September 2015 
   PI: S. Duhamel, O.R. Anderson (LDEO), E. Kim (Amer. Museum Natl. History) 
   version date: 2019-06-24 
  
   Published in Duhamel et al. 2019, doi: 10.1002/lno.11193, Table 3";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-06-24T19:17:57Z";
    String date_modified "2019-08-19T13:36:44Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.771701.1";
    Float64 Easternmost_Easting -64.14;
    Float64 geospatial_lat_max 33.25;
    Float64 geospatial_lat_min 22.16;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -64.14;
    Float64 geospatial_lon_min -65.37;
    String geospatial_lon_units "degrees_east";
    String history 
"2020-07-05T13:58:50Z (local files)
2020-07-05T13:58:50Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_771701.das";
    String infoUrl "https://www.bco-dmo.org/dataset/771701";
    String institution "BCO-DMO";
    String instruments_0_acronym "Fluorometer";
    String instruments_0_dataset_instrument_description "Used to measure fluorescence";
    String instruments_0_dataset_instrument_nid "771712";
    String instruments_0_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
    String instruments_0_instrument_name "Fluorometer";
    String instruments_0_instrument_nid "484";
    String instruments_0_supplied_name "Horiba FluoroMax-4 spectrofluorometer";
    String instruments_1_acronym "LSC";
    String instruments_1_dataset_instrument_description "Used to assay sample radioactivity.";
    String instruments_1_dataset_instrument_nid "771714";
    String instruments_1_description "Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (� and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
    String instruments_1_instrument_name "Liquid Scintillation Counter";
    String instruments_1_instrument_nid "624";
    String instruments_1_supplied_name "Packard Tri-Carb 3110 TR liquid scintillation counter with ultra-low-level option kit";
    String instruments_2_acronym "Flow Cytometer";
    String instruments_2_dataset_instrument_description "Used for flow cytometry analyses";
    String instruments_2_dataset_instrument_nid "771710";
    String instruments_2_description 
"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
    String instruments_2_instrument_name "Flow Cytometer";
    String instruments_2_instrument_nid "660";
    String instruments_2_supplied_name "BD Influx flow cytometer";
    String instruments_3_dataset_instrument_description "Used to count calibration beads.";
    String instruments_3_dataset_instrument_nid "771715";
    String instruments_3_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
    String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_3_instrument_name "Microscope-Fluorescence";
    String instruments_3_instrument_nid "695";
    String instruments_3_supplied_name "Epifluorescence microscope";
    String keywords "bco, bco-dmo, biological, carbon, carbon dioxide, chemical, chemistry, co2, CO2_14C, CO2_P_Euk_14C, CO2_Pro_14C, CO2_Syn_14C, concentration, cruise, data, dataset, dioxide, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Phosphate, erddap, euk, latitude, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, ocean, oceanography, oceans, office, phosphate, po4, PO4_33P, PO4_NP_Euk_33P, PO4_P_Euk_33P, PO4_Pro_33P, PO4_Syn_33P, preliminary, pro, science, sea, seawater, station, syn, vmax, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/771701/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/771701";
    Float64 Northernmost_Northing 33.25;
    String param_mapping "{'771701': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/771701/parameters";
    String people_0_affiliation "Lamont-Doherty Earth Observatory";
    String people_0_affiliation_acronym "LDEO";
    String people_0_person_name "Dr Solange Duhamel";
    String people_0_person_nid "542287";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Lamont-Doherty Earth Observatory";
    String people_1_affiliation_acronym "LDEO";
    String people_1_person_name "Dr O. Roger Anderson";
    String people_1_person_nid "542313";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "American Museum of Natural History";
    String people_2_affiliation_acronym "AMNH";
    String people_2_person_name "Dr Eunsoo Kim";
    String people_2_person_nid "542321";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Small protists in microbial loop";
    String projects_0_acronym "Small protists in microbial loop";
    String projects_0_description 
"This project is an NSF Collaborative Research Project.
Description from NSF award abstract:
Protists are mostly single-celled, eukaryotic microorganisms, including algae and protozoans. They are ubiquitous, diverse, and major contributors in oceanic food webs. Determining their taxonomic identity and the extent to which they contribute to carbon and nutrient cycles (whereby carbon and minerals are continuously changed chemically in the environment and reincorporated in living organisms) are among the major goals of this study. Moreover, the investigators will study how they respond to environmental change, one of the most important and challenging current problems in oceanography. Answering these questions is fundamental to understanding how living organisms in the ocean environment interact with one another and contribute to the health and productivity of the ocean. The main goal of the project is to investigate biotic interactions of small-sized protists with very tiny cyanobacteria also known as picocyanobacteria, which represent the most abundant photosynthetic organisms in the ocean. These studies will be done both in ocean environments and in laboratory experimental settings. Considering the limited knowledge on this topic, the work planned in this project promises important and exciting discoveries. Two early career female scientists will lead this project. In addition, one postdoctoral scholar, one graduate student, and at least three undergraduate summer interns will participate in the proposed research activities. The principal investigators will create a strong public outreach program that will engage middle school students in hands-on activities related to ocean sciences, and will produce a video in collaboration with the Education Department at the American Museum of Natural History. The video will summarize the major findings of the proposed research. It can be used in schools and in informal learning settings, including access by the public on the Internet through the Museum's Science Bulletins web page.
Single-celled eukaryotic microorganisms or protists, though largely outnumbered by picocyanobacteria (Prochlorococcus and Synechococcus), contribute significantly to ocean carbon biomass and primary productivity, partially by virtue of their larger cell size. In addition, small planktonic protists can regulate picocyanobacteria abundance through grazing. The main goal of this project is to investigate biotic interactions of planktonic pico- and nano-sized eukaryotes with picocyanobacteria, both in the field and in laboratory settings. A set of field- and culture-based experiments will be conducted, using state-of-the-art methodologies, including fluorescence-activated cell sorting, isotope and fluorescent stain labeling, and next-generation molecular sequencing to address the research objectives.
Operationally, this project is structured around two objectives:
Objective 1 is to assess the contribution of small protists to carbon and nutrient cycling through measurement of primary production, bacterivory, mixotrophy and phosphorus uptake in major microbial groups, and evaluate the role of nutrient availability in controlling mixotrophy.
Objective 2 will focus on assessing the distribution and diversity of small-sized protists that feed on picocyanobacteria and further evaluate the role of nutrient availability among the protists that are mixotrophic.
To reach these objectives field-based experiments will be conducted in contrasted environments: the North Pacific subtropical gyre (phosphorus replete, dominated by Prochlorococcus at Sta. ALOHA) and the North West Mediterranean sea (phosphorus deplete, dominated by Synechococcus at Sta. DYFAMED). Complementary experiments using model protists and picocyanobacteria will be conducted using controlled cultures in the lab. The work will provide critical new information on the phylogenetic diversity and function of marine microbial eukaryotes, with emphasis on their ecological role as predators (phagotrophy, mixotrophy) on, and competitors with, the picoyanobacteria Prochlorococcus and Synechococcus.";
    String projects_0_end_date "2018-05";
    String projects_0_geolocation "North Pacific subtropical gyre (Station ALOHA) and Northwestern Mediterranean Sea (Station DYFAMED)";
    String projects_0_name "Collaborative Research: Role of small-sized protists in the microbial loop with emphasis on interactions between mixotrophic protists and picocyanobacteria";
    String projects_0_project_nid "542308";
    String projects_0_start_date "2015-06";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 22.16;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "cruise";
    String summary "Bulk and cell-specific CO2 fixation and PO4 uptake from Atlantic Explorer cruise AE1524 (BATS validation cruise BV50), September 2015. Phosphate uptake rates were measured in Prochlorococcus, Synechococcus, pigmented eukaryotes, and unpigmented eukaryotes. Also reported are CO2 fixation rate by Prochlorococcus, Synechococcus, and pigmented eukaryotes.";
    String title "Bulk and cell-specific CO2 fixation and PO4 uptake from Atlantic Explorer cruise AE1524 (BATS validation cruise BV50), September 2015";
    String version "1";
    Float64 Westernmost_Easting -65.37;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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