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            <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/dataset/723568.rdf" xlink:actuate="onRequest">Acartia tonsa mortality collected from a plankton net with associated CTD data from 5 day-trips in mid-Chesapeake Bay from August to October 2013 (CopesPopDynHypoZone project)</gmx:Anchor>
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            <gco:CharacterString>Cite this dataset as: Roman, M. R., Pierson, J. J. (2018) Acartia tonsa mortality collected from a plankton net with associated CTD data from 5 day-trips in mid-Chesapeake Bay from August to October 2013 (CopesPopDynHypoZone project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2018-01-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/723568 [access date]</gco:CharacterString>
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        <gco:CharacterString>Acartia tonsa mortality from net tows and associated CTD data Dataset Description: &amp;lt;p&amp;gt;This dataset includes&amp;amp;nbsp;&amp;lt;em&amp;gt;Acartia tonsa&amp;lt;/em&amp;gt; mortality from plankton net samples and associated CTD information.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Related Datasets:&amp;lt;/strong&amp;gt;&amp;lt;br /&amp;gt;
&amp;lt;a href=&amp;quot;https://www.bco-dmo.org/dataset/723551&amp;quot; target=&amp;quot;_blank&amp;quot;&amp;gt;Acartia tonsa mortality with CTD data: RV Sharp&amp;lt;/a&amp;gt;&amp;lt;br /&amp;gt;
&amp;lt;a href=&amp;quot;https://www.bco-dmo.org/dataset/723801&amp;quot; target=&amp;quot;_blank&amp;quot;&amp;gt;Species composition with CTD data: 5 &amp;lt;/a&amp;gt;&amp;lt;a href=&amp;quot;https://www.bco-dmo.org/dataset/723801&amp;quot; target=&amp;quot;_blank&amp;quot;&amp;gt;daytrips&amp;lt;/a&amp;gt;&amp;lt;/p&amp;gt; Methods and Sampling: &amp;lt;p&amp;gt;This mortality data was obtained from several ~8 hour small-boat cruises done about every other week from August to October. Vertical tow samples were taken from the mid-bay of the Chesapeake from several stations in a transect, corresponding to the mid-line transect sampled by the two, week-long cruises (stations M1-M3, cruises 1301/1302). More stations along the same transect were included in the collection of this data set.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;The plankton net was 0.5m in diameter and made of 64µm mesh, equipped to close with a mechanical messenger trigger, and was deployed from the winch arm of the R/V Parker.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;A CTD cast was done at each station prior to sampling with the plankton net. Sampling depths were determined based on the location of the pycnocline; the aim was to capture zooplankton below and above the pycnocline. For sampling below the pycnocline, the net was deployed below the pycnocline, towed up to the pycnocline, triggered to close, and returned to the surface. Sampling above the pycnocline was done by standard vertical tow: deploy net to desired depth and winch to the surface.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Once brought on board, the nets were rinsed down with seawater to collect plankton in the codend. Codends were gently poured into 64µm sieves in a water bath of ambient seawater, then carefully poured into numbered glass jars for incubation; jar number, depth sampled, station, and cast number were entered into a log book.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Neutral red stain was added based on the volume in the jar- the desired concentration was 150μl per 100ml (for a stock solution of 0.1g Neutral Red powder per 10 ml DI water). The jars were returned to the water bath and incubated in the shade for 15-20 minutes (recorded in the log). After incubation, each sample was vacuum filtered onto a 64 μm mesh filter which was then transferred to a small petri dish. The dish was capped and labeled with the jar number of the sample, then wrapped in parafilm to seal. The samples were placed in a Ziploc bag labeled with the date and station and given a burst of Flash Freeze, then stored in a cooler with ice for the duration of the cruise.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;After returning from each cruise, samples were immediately transferred to -20°C freezers. Samples were individually processed within a week after collection using the protocol developed by David Elliott:&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;The petri dish containing the sample was thawed at room temperature, then the mesh was submerged in filtered seawater and gently shaken to resuspend the sample. The sample was then transferred to a counting wheel where it was checked for density and subsampled if necessary.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;The sample was then slightly acidified by adding 10% HCl drop-wise until the stained animals distinctly changed from pink to bright red. The sample was then tallied for live or dead status and general stage under dissecting microscope with darkfield illumination. Copepods which were bright red throughout their tissues were considered alive at the time of staining; copepods which had no stain, were cloudy white, or were only light pink were considered dead. Occasionally, photographs were taken of the acidified sample for secondary confirmation since the stain fades after 1 hour after acidification.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Data were entered into Excel spreadsheets and checked for transcription errors, then imported into MatLab for data analysis.&amp;lt;/p&amp;gt;</gco:CharacterString>
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        <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/award/555545.rdf" xlink:title="OCE-1259691" xlink:actuate="onRequest">Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1259691 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1259691</gmx:Anchor>
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The PIs will develop a mechanistic understanding of how circulation interacts with hypoxia-induced behavioral and physiological changes to affect the population dynamics of coastal zooplankton. They will do this by assessing two potentially contrasting mechanisms influencing the dynamics of the copepod &lt;em&gt;Acartia tonsa&lt;/em&gt; in the hypoxic zone of Chesapeake Bay. The first hypothesis is that maintenance of copepod populations in the hypoxic region requires replenishment by advection (immigration) of animals through wind-driven lateral transport processes. The second, counteractive, hypothesis is that bottom water hypoxia alters the vertical distribution of &lt;em&gt;A. tonsa&lt;/em&gt;, thereby making them more susceptible to advective losses from the region (emigration) via surface water transport in the estuarine circulation. They will take advantage of a current NSF-funded physical oceanography research program in Chesapeake Bay that will comprehensively measure and model axial and lateral water exchanges in the mid-Bay region.&lt;/p&gt;
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            http://lod.bco-dmo.org/id/dataset-parameter/723724.rdf
	Name: cruise
	Units: unitless
	Description: &lt;p&gt;Chronological cruise number used to refer to each day-long cruise&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723725.rdf
	Name: date
	Units: unitless
	Description: &lt;p&gt;Gergorian calendar date as recorded in the cruise log formatted as mm/dd/yyyy&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723726.rdf
	Name: time_EDT
	Units: unitless
	Description: &lt;p&gt;Time of sampling in EDT as recorded in the cruise log formatted as hhmm&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723727.rdf
	Name: EDT_DOY
	Units: decimal day
	Description: &lt;p&gt;Day of year calculation using cruise log EDT time&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723728.rdf
	Name: Station
	Units: unitless
	Description: &lt;p&gt;Station ID as recorded in the day-cruise log&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723729.rdf
	Name: Lateral_station
	Units: unitless
	Description: &lt;p&gt;Station ID as given in the Lateral Copepods week-long R/V Sharp cruises&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723730.rdf
	Name: Sample_num
	Units: unitless
	Description: &lt;p&gt;Numeric sample identifier; unique to each cruise; not across all cruises&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723731.rdf
	Name: Low_depth
	Units: meters
	Description: &lt;p&gt;The lowest depth of the range sampled&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723732.rdf
	Name: High_depth
	Units: meters
	Description: &lt;p&gt;The highest depth of the range sampled&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723733.rdf
	Name: Genus
	Units: unitless
	Description: &lt;p&gt;Genus or least specific identifier of organism in sample&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723734.rdf
	Name: Species
	Units: unitless
	Description: &lt;p&gt;Species or most specific identifier of organism in sample&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723735.rdf
	Name: Stage
	Units: unitless
	Description: &lt;p&gt;Life stage of organism in sample&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723736.rdf
	Name: Alive
	Units: specimens
	Description: &lt;p&gt;Number of organism stained in sample and therefore live&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723737.rdf
	Name: Dead
	Units: specimens
	Description: &lt;p&gt;Number of organism unstained in sample and therefore dead&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723738.rdf
	Name: Percent_live
	Units: unitless
	Description: &lt;p&gt;Percent of live organism out of total&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723739.rdf
	Name: Percent_dead
	Units: unitless
	Description: &lt;p&gt;Percent of dead organism out of total&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723740.rdf
	Name: Photo_files
	Units: unitless
	Description: &lt;p&gt;Filenames of photographs taken of acidified aliquot&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723741.rdf
	Name: Comments
	Units: unitless
	Description: &lt;p&gt;Notes from the technician made during sampling and sample processing&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723742.rdf
	Name: Latitude
	Units: decimal degrees
	Description: &lt;p&gt;Station latitude&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723743.rdf
	Name: Longitude
	Units: decimal degrees
	Description: &lt;p&gt;Station longitude&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723744.rdf
	Name: Year
	Units: unitless
	Description: &lt;p&gt;Year as recorded by CTD as yyyy&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723745.rdf
	Name: Month
	Units: unitless
	Description: &lt;p&gt;Month as recorded by CTD as mm&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723746.rdf
	Name: CTD_Day
	Units: unitless
	Description: &lt;p&gt;Day as recorded by CTD as dd&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723747.rdf
	Name: GMT_Hour
	Units: unitless
	Description: &lt;p&gt;Hour as recorded by CTD; GMT time as hh&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723748.rdf
	Name: Minute
	Units: unitless
	Description: &lt;p&gt;Minute as recorded by CTD as mm&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723749.rdf
	Name: Second
	Units: unitless
	Description: &lt;p&gt;Second as recorded by CTD as ss&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723750.rdf
	Name: GMT_DOY
	Units: decimal day
	Description: &lt;p&gt;Day of year calculation using CTD recorded GMT time for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723751.rdf
	Name: prSM
	Units: decibars
	Description: &lt;p&gt;Pressure as recorded by CTD sensor for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723752.rdf
	Name: t090C
	Units: degrees Celsius
	Description: &lt;p&gt;Temperature recorded by CTD sensor for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723753.rdf
	Name: c0S_m
	Units: microSiemens/meter (uS/m)
	Description: &lt;p&gt;Condictivity recorded by CTD sensor for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723754.rdf
	Name: sbeox0V
	Units: volts
	Description: &lt;p&gt;Raw oxygen measurements as recorded by CTD sensors for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723755.rdf
	Name: wetStar
	Units: volts?
	Description: &lt;p&gt;Fluorescence measure as recorded by WETStar fluorometer on CTD for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723756.rdf
	Name: obs
	Units: volts?
	Description: &lt;p&gt;Optical backscatter as recorded by CTD sensor for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723757.rdf
	Name: bat
	Units: per meter
	Description: &lt;p&gt;Beam attenuation as recorded by SBE software&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723758.rdf
	Name: xmiss
	Units: unitless
	Description: &lt;p&gt;Beam transmission as recorded by SBE software (percent)&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723759.rdf
	Name: sbeox0Mg_L
	Units: milligrams/liter (mg/L)
	Description: &lt;p&gt;Dissolved oxygen calculated in SEB post-processing from oxygen data recorded by CTD sensors  for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723760.rdf
	Name: sbeox0PS
	Units: unitless
	Description: &lt;p&gt;Dissolved oxygen pressure saturation calculated in SEB post-processing from oxygen data recorded by CTD sensors  for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723761.rdf
	Name: sigma_t00
	Units: ?
	Description: &lt;p&gt;Density recorded by CTD sensors  for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723762.rdf
	Name: depSM
	Units: meters
	Description: &lt;p&gt;Depth bins; one bin per half meter and then averaged over the depth range of each net cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723763.rdf
	Name: sal00
	Units: Practical Salinity Units (PSU)
	Description: &lt;p&gt;Salinity recorded by CTD sensor  for each cast&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723764.rdf
	Name: nbin
	Units: unitless
	Description: &lt;p&gt;Number of measures per depth bin; averaged per net depth range&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/723765.rdf
	Name: flag
	Units: unitless
	Description: &lt;p&gt;Flag for abberant data&lt;/p&gt; 
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&amp;lt;p&amp;gt;The plankton net was 0.5m in diameter and made of 64µm mesh, equipped to close with a mechanical messenger trigger, and was deployed from the winch arm of the R/V Parker.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;A CTD cast was done at each station prior to sampling with the plankton net. Sampling depths were determined based on the location of the pycnocline; the aim was to capture zooplankton below and above the pycnocline. For sampling below the pycnocline, the net was deployed below the pycnocline, towed up to the pycnocline, triggered to close, and returned to the surface. Sampling above the pycnocline was done by standard vertical tow: deploy net to desired depth and winch to the surface.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Once brought on board, the nets were rinsed down with seawater to collect plankton in the codend. Codends were gently poured into 64µm sieves in a water bath of ambient seawater, then carefully poured into numbered glass jars for incubation; jar number, depth sampled, station, and cast number were entered into a log book.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Neutral red stain was added based on the volume in the jar- the desired concentration was 150μl per 100ml (for a stock solution of 0.1g Neutral Red powder per 10 ml DI water). The jars were returned to the water bath and incubated in the shade for 15-20 minutes (recorded in the log). After incubation, each sample was vacuum filtered onto a 64 μm mesh filter which was then transferred to a small petri dish. The dish was capped and labeled with the jar number of the sample, then wrapped in parafilm to seal. The samples were placed in a Ziploc bag labeled with the date and station and given a burst of Flash Freeze, then stored in a cooler with ice for the duration of the cruise.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;After returning from each cruise, samples were immediately transferred to -20°C freezers. Samples were individually processed within a week after collection using the protocol developed by David Elliott:&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;The petri dish containing the sample was thawed at room temperature, then the mesh was submerged in filtered seawater and gently shaken to resuspend the sample. The sample was then transferred to a counting wheel where it was checked for density and subsampled if necessary.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;The sample was then slightly acidified by adding 10% HCl drop-wise until the stained animals distinctly changed from pink to bright red. The sample was then tallied for live or dead status and general stage under dissecting microscope with darkfield illumination. Copepods which were bright red throughout their tissues were considered alive at the time of staining; copepods which had no stain, were cloudy white, or were only light pink were considered dead. Occasionally, photographs were taken of the acidified sample for secondary confirmation since the stain fades after 1 hour after acidification.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Data were entered into Excel spreadsheets and checked for transcription errors, then imported into MatLab for data analysis.&amp;lt;/p&amp;gt;</gco:CharacterString>
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Niskin electronic data was post processed using a series of MATLAB scripts to read the raw and processed data, and SBE Data Processing software was used to calculate summary statistics for each bottle.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;Live zooplankton samples were stained immediately after capture with Neutral Red vital stain, incubated at ambient collection temperature and salinity for dye uptake, then flash-frozen for later analysis. Samples were sorted under a stereo dissecting microscope within 1 week of collection, and general &amp;lt;em&amp;gt;Acartia &amp;lt;/em&amp;gt;&amp;lt;em&amp;gt;tonsa&amp;lt;/em&amp;gt; stages were classed as live or dead according to staining.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;BCO-DMO Data Processing Notes:&amp;lt;/strong&amp;gt;&amp;lt;br /&amp;gt;
- added conventional header with dataset name, PI name, version date&amp;lt;br /&amp;gt;
- modified parameter names to conform with BCO-DMO naming conventions&amp;lt;br /&amp;gt;
- reduced decimal precision&amp;lt;br /&amp;gt;
- replaced commas with semicolons&amp;lt;br /&amp;gt;
- changed NaN to nd in Lateral_station column and in species column to sp. when associated with a genus name; changed to nd if no genus in record&amp;lt;br /&amp;gt;
- converted longitudes to negative degree (west)&amp;lt;/p&amp;gt;</gco:CharacterString>
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