                                             If symbols do not display correctly 
                                                    set your browser's character 
                                                             encoding to unicode




CRUISE REPORT: A095
(Updated JUL 2011)

 


1.  HIGHLIGHTS

                           Cruise Summary Information

          WOCE Section Designation  A095
Expedition designation (ExpoCodes)  740H20090307
                  Chief Scientists  Brian A. King / NOCS 
                             Dates  2009 MAR 07 - 2009 APR 21
                              Ship  RSS JAMES COOK
                     Ports of call  Montevideo, Uruguay - Walvis Bay, Namibia

                                               22° 12' S
             Geographic Boundaries  53° 29' W             13° 42' E
                                               37° 24' S

                          Stations  118
      Floats and drifters deployed  16 Argo Floats Deployed
    Moorings deployed or recovered  0

                      Chief Scientist Contact Information
                                 Brian A. King
                    National Oceanography Centre Southampton
             Empress Dock • Southampton • SO14 3ZH • United Kingdom
                 tel (44) 23 8059 6438 • fax (44) 23 8059 6204
                         email b.king @ noc.soton.ac.uk



 








                   National Oceanography Centre, Southampton



                              Cruise Report No. 48


                          RRS James Cook Cruise JC032
                               07 MAR-21 APR 2009

                Hydrographic sections across the Brazil Current
                          and at 24°S in the Atlantic

                              Principal Scientist
                                    B A King

                                    Editors
                           D R C Hamersley & B A King





                                      2010














                    National Oceanography Centre, Southampton
                   University of Southampton Waterfront Campus
                                  European Way
                                  Southampton
                                Hants S014 3ZH
                                       UK

                            Tel: +44 (0)23 8059 6438
                           Email: bak@noc.soton.ac.uk



DOCUMENT DATA SHEET

AUTHOR                                                          PUBLICATION DATE 
King, B A et al                                                             2010

TITLE
    RSS James Cook Cruise JC032, 07Mar -21 Apr 2009. Hydrographic sections 
    across the Brazil Current and at 24°S in the Atlantic.

REFERENCE
    Southampton, UK: National Oceanography Centre, Southampton, 173pp.
    (National Oceanography Centre Southampton Cruise Report, No. 48)

ABSTRACT

Hydrographic sections were occupied in the South Atlantic Ocean and during 
March - April 2009 aboard the RRS James Cook (JC032). Three of these sections 
intersected the Brazil current at three separate latitudes during the steam 
northwards from Montevideo. The main trans-Atlantic section was occupied at 
24°S. The primary objective of this cruise was to measure ocean physical, 
chemical and biological parameters in order to establish regional budgets of 
heat freshwater and carbon. The main section completed an overall aim, 
devised under the Oceans 2025 project, to create a box around the South 
Atlantic and Southern Ocean region to expose the regional circulation scheme 
and basin-scale budgets of physical and biogeochemical properties by 
performing a box-inverse analysis of the new observations.

A total of 118 CTD/LADCP stations were sampled across the South Atlantic. In 
addition to temperature, salinity and oxygen profiles from the sensors on the 
CTD package, water samples from a 24-bottle rosette were analysed for 
salinity, dissolved oxygen and inorganic nutrients at each station. Water 
samples were collected from strategically selected stations and analysed 
onboard ship for SF6, CFC's, pCO2, TIC, alkalinity, and nutrient 
biogeochemistry. In addition, samples were collected from the ship's underway 
system to calibrate and compliment the data continually collected by the TSG 
(thermosalinograph). Full depth velocity measurements were made at every 
station by an LADCP (Lowered Acoustic Doppler Current Profiler) mounted on 
the frame of the rosette. Throughout the cruise, velocity data in the upper 
few hundred metres of the water column were collected by the ship's VMADCP 
(vessel mounted acoustic Doppler current profiler) transducers (75Hz and 
150Hz) mounted on the hull. Meteorological variables were monitored using the 
onboard surface water and meteorological sampling system (SURFMET). 
Bathymetric data was collected using the EA600 echo sounder and EM 120 swath 
system, which is attached to the hull.

This report describes the methods used to acquire and process the data aboard 
the ship during cruise JC032.

KEYWORDS

ADCP, Atlantic Ocean, biogeochemical budgets, Brazil Current, carbon budgets, 
Carbon Tetrachloride, Carbon, CFC, James Cook, climatic changes, cruise JC032 
2009, CTD, hydrographic section, Lowered ADCP, Meridional Overturning 
Circulation, nutrients, oxygen, phytoplankton, potential temperature, 
salinity, Sulphur Hexafluoride, temperature, Vessel Mounted ADCP

ISSUING ORGANISATION    National Oceanography Centre, Southampton
                        University of Southampton, Waterfront Campus
                        European Way
                        Southampton S014 3ZH      UK
                        Tel: +44(0)23 8059611 6   Email: nol@noc.soton.ac.uk

A pdf of this report is available for download at: http://eprints.soton.ac.uk
List of Tables

Table 1:  Differences and adjustments calculated for standardisations for each 
          run...
Table 2:  Set of calibration standards used for dissolved inorganic nutrient 
          analysis.
Table 3:  Compounds used to prepare stock standard solutions, weight dissolved 
          in lL of Milli-Q water and Molarity of the solution 
Table 4:  Mean and variation of all standards measured, and precision of the 
          analysis at each concentration (µmol L-1) 
Table 5:  JC032 O2 determinations 
Table 6:  Underway SST and salinity instrument details 
Table 7:  SURFMET instrument details 
Table 8:  Configurations of individual control files used on JC032 
Table 9:  Best estimates of OS75 calibration for the section from Montevideo to 
          Arraial  do Cabo for water tracking and bottom tracking 
Table 10: Best estimates of OS150 calibration for the section from Montevideo 
          to Arraial do Cabo for water tracking and bottom tracking 
Table 11: Best estimates of OS75 calibration for the section from Arraial do 
          Cabo to Walvis Bay for water tracking and bottom tracking 
Table 12: Best estimates of OS150 calibration for the section from Arraial do 
          Cabo to Walvis Bay for water tracking and bottom tracking
Table 13: Simple overview of sampling giving listings of stations sampled for 
          each parameter 
Table 14: Key Argo 
Float Information 
Appendix: Details of Stations sampled 




List of Figures

Figure 1:   Bathymetric map of the JC032 study area and the positions of the 
            stations sampled  
Figure 2:   Bathymetric map of the Brazil current sections and the positions 
            of the stations sampled  
Figure 3:   Raw data from the original primary and secondary conductivity 
            (salinity) sensors 
Figure 4:   Salinity residuals for the original conductivity sensor after 
            adjustment for a pressure effect  
Figure 5:   Oxygen residuals plotted on a regular grid revealing hysterysis 
Figure 6:   Oxygen residuals calculated from bottle oxygen minus pressure 
            corrected downcast CTD data  
Figure 7:   Oxygen outliers found from Niskin 3 
Figure 8:   CTD oxygen and fluorescence parameters across the first Brazil 
            current transect 
Figure 9:   CTD oxygen and fluorescence parameters across the second Brazil 
            current transect 
Figure 10:  CTD oxygen and fluorescence parameters across the third Brazil 
            current transect  
Figure 11:  Contour plot of the oxygen parameter along the Atlantic 24°S 
            hydrographic section  
Figure 12:  Potential temperature and salinity parameters across the first 
            Brazil current transect  
Figure 13:  Potential temperature and salinity parameters across the second 
            Brazil current transect  
Figure 14:  Potential temperature and salinity parameters across the third 
            Brazil current transect  
Figure 15:  Contour plot of potential temperature along the Atlantic 24°S 
            hydrographic section  
Figure 16:  Comparison of salintiy standardisation adjustments and 
            differences  
Figure 17:  Details of the dilution loop for the silicate line  
Figure 18:  Silicate standard measurements 
Figure 19:  Complete set of 'measured' standards plotted against the 
            'prepared or intended' concentration and 'measured' standards 
            plotted against respective analysis number  
Figure 20:  Chemical baseline time series  
Figure 21:  Chemical calibration slopes time series  
Figure 22:  Chemical calibration correlation coefficients  
Figure 23:  Low Nutrient Seawater (LNSW) time series  
Figure 24:  Time series of bulk nutrient seawater concentrations  
Figure 25:  The ratio of nitrate to nitrite for all analyses 
Figure 26:  Bottle oxygen and Silicate parameters for the first Brazil 
            Current transect  
Figure 27:  Bottle oxygen and Silicate parameters for the second Brazil 
            Current transect 
Figure 28:  Bottle oxygen and Silicate parameters for the third Brazil 
            Current transect  
Figure 29:  Bottle oxygen and Silicate parameters for the main transect 
Figure 30:  Total nitrate and phosphate parameters for the first Brazil 
            current transect  
Figure 31:  Total nitrate and phosphate parameters for the second Brazil 
            current transect 
Figure 32:  Total nitrate and phosphate parameters for the third Brazil 
            current transect  
Figure 33:  Total nitrate and phosphate parameters for the main transect  
Figure 34:  Dissolved oxygen analysis calibrations 
Figure 35:  The absolute replicate difference for the oxygen bottles in each 
            CTD cast .  
Figure 36:  Depth-longitude grid of samples analysed for DIC and TA  
Figure 37:  Alkalinity and dissolved inorganic carbon parameters for
            the first Brazil current transect  
Figure 38:  Alkalinity and dissolved inorganic carbon parameters for 
            the second Brazil current transect 
Figure 39:  Alkalinity and dissolved inorganic carbon parameters for 
            the third Brazil current transect 
Figure 40:  Alkalinity and dissolved inorganic carbon parameters for 
            the main transect 
Figure 41:  Calibrated CRM values for (a) for the refurbished SOMMA 
            instrument and (b) for the VINDTA #007 
Figure 42:  Differences between replicates of all samples analysed for 
            DIC, (a) for the refurbished SOMMA instrument and (b) for 
            the VINDTA #007 
Figure 43:  Alkalinity CRM values recorded by (a) VINDTA #004 and (b) 
            VINDTA #007  
Figure 44:  The differences between replicates of all samples analysed 
            for alkalinity (a) for the VINDTA #004 and (b) for the 
            VINDTA #007  
Figure 45:  CFC calibration data from JC032  
Figure 46:  Combined surface seawater data from the 24°S JC032 transect  
Figure 47:  CFC11 and CFC12 parameters for the first Brazil current 
            transect  
Figure 48:  CFC11 and CFC12 parameters for the second Brazil current 
            transect  
Figure 49:  CFC11 and CFC12 parameters for the third Brazil current 
            transect  
Figure 50:  CFC11 and CFC12 parameters for the main transect  
Figure 51:  F113 and CCL4 parameters for the first Brazil current 
            transect  
Figure 52:  F113 and CCL4 parameters for the second Brazil current 
            transect  
Figure 53:  F113 and CCL4 parameters for the third Brazil current 
            transect  
Figure 54:  F113 and CCL4 parameters for the main transect  
Figure 55:  SF6 parameter for the first Brazil current transect  
Figure 56:  SF6 parameter for the second Brazil current transect  
Figure 57:  SF6 parameter for the third Brazil current transect  
Figure 58:  SF6 parameter for the main transect  
Figure 59:  Comparison of CTD surface temperature measurements with the 
            FSI remote temperature  
Figure 60:  A comparison of the 5BE45 housing temperature with the FSI 
            housing temperature and the SST  
Figure 61:  5BE45 and FSI underway salinity compared to bottle and CTD 
            measurements 
Figure 62:  Calculated salinity difference between 5BE45 and bottle and 
            CTD data. 
Figure 63:  Schematic diagram showing the instruments on the foremast 
            platform.  
Figure 64:  Meteorological data for days 65 to 70  
Figure 65:  Meteorological data for days 70 to 75  
Figure 66:  Meteorological data for days 75 to 80  
Figure 67:  Meteorological data for days 80 to 85  
Figure 68:  Meteorological data for days 85 to 90  
Figure 69:  Meteorological data for days 90 to 95  
Figure 70:  Meteorological data for days 95 to 100  
Figure 71:  Meteorological data for days 100 to 105  
Figure 72:  Meteorological data for days 105 to 109  
Figure 73:  Differences in latitude and longitude measured from 
            different GPS systems  
Figure 74:  Comparison of GPS headings during dayofyear 80  
Figure 75:  Five minute averaged bathymetry data for the duration of 
            the cruise  
Figure 76:  Example plot of echo amplitude with depth from Station 40  
Figure 77:  A plot of the u component of the flow on Station 44 
            measured in the downcast, upcast, and mean  
Figure 78:  Plots from Station 51 displaying the number of pings with 
            depth  
Figure 79:  An example of the ADCP comparison plots  
Figure 80:  An example of the plots produced for ADCP shear velocities  
Figure 81:  Representation of the cumulative number of turns on the CTD  
Figure 82:  The gautoedit editing window within the CODAS suite 
Figure 83:  Amplitude scale and phase calibrations for OS75 instrument 
            for the period of bottom tracking on the continental shelf 
            of Namibia  
Figure 84:  Amplitude return for the OS75 for file sequence 025  
Figure 85:  Bias parameter for the same period 
Figure 86:  Anomalous region of low percentage good below bins 15-20 on 
            decimal day 93  
Figure 87:  Abrupt cut-off in percentage good around bin 16 for 
            profiles collected between decimal day 93.3 and 93.4 using 
            the OS75  
Figure 88:  Amplitude return for beam 1 for decimal day 93.3 to 93.4 
Figure 89:  Median on-station VMADCP velocities from the OS75 at 98m 
            for the first Brazil Current Crossing 
Figure 90:  Median on-station VMADCP velocities from OS75 at 98m for 
            the second Brazil Current crossing 
Figure 91:  Median on-station VMADCP velocities from OS75 at 98m for 
            the third Brazil Current crossing 
Figure 92:  Median on-station VMADCP velocities from OS75 at 98m for 
            the 24°S section  
Figure 93:  Off-station VMADCP v velocity at the eastern boundary of 
            the 24°S section  
Figure 94:  Preliminary contoured section of chlorophyll a measured on 
            discrete samples collected across the 24°S section  
Figure 95:  Optode O2 concentration and temperature over time 
Figure 96:  Optode Dphase raw against Dphase solved for the discrete 
            U5W samples collected for O2 continuous calibration  
Figure 97:  Map of the South Atlantic Ocean with locations of old 
            floats and the launch positions of floats on JC032 




Scientific Personnel

Name                   Role                 Affiliation
---------------------  -------------------  -------------------------
Brian King             Principle Scientist  NOCS
Ben Moat               Physics              NOCS
Lorna McLean           Physics              NOCS
Alex Brearley          Physics              NOCS
Carolina Gramcianinov  Physics              Sao Paulo University
David Hamersley        Physics              NOCS
Gerard McCarthy        Physics              NOCS
Sinhue Tones Valdes    Nutrients            NOCS
Lily Chambers          Nutrients            NOCS
Louise Darroch         Nutrients            NOCS
Alba Posada-Gonzalez   O2/Ar                UEA
Mark Moore             Phytoplankton        NOCS
Ute Schuster           Carbon               UEA
Agatha De Boer         Carbon               UEA
Shaun Scally           Carbon               UEA
David Cooper           CFCs and SF6         UEA
Steve Woodward         CFCs and SF6         UEA
Andrew Brousseau       CFCs and SF6         UEA
Niki Silvera           Observer             Uruguay National Observer
Phellipe De Araujo     Observer             Brazilian Navy Observer

NOCS = National Oceanography Centre Southampton
UEA = University of East Anglia
NMF = National Marine Facilities


Technical Personnel

Name          Position                          Affiliation
------------  --------------------------------  -----------
Paul Duncan   Computer/Ship systems Technician  NMF
Paul Provost  CTD Technician                    NMF
Peter Keen    CTD Technician                    NMF
Neil Sloan    Mech. Technician                  NMF


Ship's Personnel

     Name              Position/Rank
     ----------------  -----------------
     Peter Sarjeant    Master     
     Richard Warner    Chief Officer
     Malcolm Graves    2nd Officer
     Vanessa Laidlow   3rd Officer
     George Parkinson  Chief Engineer
     John Hagan        2nd Engineer
     Ian Collin        3rd Engineer
     Ian Wight         ETO     
     Paul Lucas        Purser     
     Kevin Luckhurst   CPOD     
     Steve Smith       CPOS     
     lain Thompson     POD     
     Gerald Cooper     SG1A     
     John Dale         SG1A     
     Ian Cantlie       SG1A     
     Charles Cooney    SG1A     
     Leslie Hillier    ERPO     
     Danen Caines      Head Chef     
     Dean Hope         Assistant Chef
     Graham Mingay     Steward     
     Brian Conteh      Assistant Steward



Background, Objectives and Overview


JC032 occupied a section across the Atlantic at 24°S. It immediately followed 
two other hydrographic cruises: JC030 was intended as a section across the 
entrance to the Weddell Sea, but was interrupted by a medical emergency. 
JC031 completed sections in the western and eastern Drake Passage, on the 
WOCE A2l and SRlb lines. Combining JC031 and JC032 with a US section from 
Africa to Antarctica at 30°E completed in February 2008, the Atlantic sector 
of the Southern Ocean is enclosed in a box. Inverse methods will be used to 
construct a basin-scale budget, with horizontal fluxes through the 
boundaries, of heat, salt, nutrients carbon and CFCs. Decadal variability 
will be investigated by comparison with previous occupations of the sections. 
The standard measurements on a CLIVAR hydrographic cruise were supplemented 
with some biological measurements. The cruise was funded under the Oceans2O2S 
program at NOCS and a SOFT award at the University of East Anglia.

In total 118 CTDO (conductivity-temperature-depth-oxygen) stations were 
occupied with a 24-bottle rosette. After the loss of a set of 20-litre 
bottles during the previous cruise, JC032 was equipped with four 20-litre 
bottles deployed near the surface with the remaining depths sampled using 
10-litre bottles. Other instruments on the package included a single WH300 
LADCP (Lowered Acoustic Doppler Current Profiler), fluorometer and 
transmissometer. Two major incidents occurred with the CTD winch. On station 
048, the gearbox on the storage drum failed with 3000 metres wire out. The 
station was abandoned and a delay of nearly 48 hours occurred while the 
package was recovered and the spare CTD wire commissioned. On station 061, a 
glitch in the winch system during deployment meant that the package was 
hauled up into the block and fell back to the deck from a height of about 2 
metres, resulting in further significant delay while the fault was 
investigated and new operating procedures adopted. Several Niskin bottles 
were replaced due to cracks and damaged valves. All of the instruments 
mounted on the package were tested and found to be in working order although 
there were small calibration offsets.

Continuous underway sampling included: two vessel mounted ADCPs (VMADCP): 
OS75 and OS150; thermosalinograph (TSG); surface meteorology; bathymetry.

The embarkation of observers from Uruguay and Brazil meant that observations 
of the Brazil Current could be made within the 200-mile zones of those 
countries. The cooperation of the observers and the efforts that led to 
diplomatic clearance being granted were greatly appreciated by the Principal 
Scientist and all members of the scientific party.

The highly professional and friendly support provided by the ship's personnel 
was fundamental to the success of the expedition. There were many outstanding 
individual contributions, but it is a particular pleasure to acknowledge 
those of the Chief Engineer and ETO, who seemed to spend as much time working 
on ship's scientific equipment as they did in the engine room (their duties 
there no doubt covered in part by the other Engineer Officers), and the 
Master, whose considered leadership ensured that neither of the major winch 
incidents prevented the cruise from meeting all its objectives.


Itinerary and Cruise Track

Depart from Montevideo, Uruguay, 7th March 2009 - arrive in Walvis Bay, 
Namibia, 21st April 2009.

 
Figure 1:  Bathymetric map of the JC032 study area and the positions of the 
           stations sampled (*).

Figure 2:  Bathymetric map of the Brazil current sections and the positions 
           of the stations sampled (*).


1.  CTD Systems Operation
    (Gerard McCarthy, Carolina Gramcianinov, David Hamersley, Lorna McLean, 
    and Paul Provost)

One hundred and eighteen, 24-bottle rosette CTD-O (Conductivity-Temperature-
Depth-Oxygen) stations were occupied during JC032 (Figure 1). Stations 1-9 
intersected the Brazil Current, near Uruguay. A second transect of the Brazil 
Current was completed between Stations 10-22. Stations 23-118 made up the 
main section. This work was accomplished in two parts. Stations 23-35 were 
those within the Brazilian 200 mile zone. After Station 35, the ship sailed 
into Anaial do Cabo to put the Brazilian observer ashore. A termination of 
the CTD wire was carried out whilst alongside. This resulted in a two-day 
hiatus in work. The section recommenced with Station 36, which was a repeat 
of Station 35.

Stations 1-47 were completed routinely. On the downcast on Station 48 a 
problem occurred with the gears on the CTD002 and the gearbox on the storage 
drum failed with 3000m of wire out on the downcast. The CTD was recovered 
using the traction system to haul the wire with the CTD storage drum turned 
by hand. The CTD was re-terminated with the wire from the CTD001 drum and 
work recommenced with Station 49. On deployment at Station 61 a problem 
occurred where the remote winch operation failed, as did the emergency stop 
on the belly box. The emergency stop on deck was not activated. This led to 
the CTD being hauled up to the block and then dropped from a height of about 
2 metres when the wire snapped. One Niskin bottle was broken, and the primary 
conductivity and temperature sensors were knocked loose from the CTD frame. 
This resulted in a constant offset in both the primary conductivity and the 
oxygen. The decision was made not to change the sensors at this stage. The 
CTD was re-terminated and work commenced again. On cast 89, near the bottom 
of the downcast, the deck unit went down and had to be restarted. Shortly 
after this, the primary conductivity sensor received another offset. This 
lasted until Station 93 when the primary conductivity sensor failed 
completely near the end of the downcast and had to be replaced.



2.  CTD DATA PROCESSING AND CALIBRATION
    (Gerard McCarthy)


2.1  Initial Processing Using SeaBird Programs

The files output by Seasave (version 7.18) have the appendices: hex, HDR, bl, 
.CON. The .CON files for each cast contain the calibration coefficients for 
the instrument. The HDR files contain the information in the header of each 
cast file. The hex files are the data files for each cast and are in hex 
format. The bl files contain information on bottle firings of the rosette.

Initial data processing was performed on a PC using the Seabird processing 
software SBE Data Processing, Version 7.18. We used the following options in 
the given order:

Data Conversion - turns the raw data into physical units. It takes the .CON 
files and .hex files. The input files were named ctdnnn.hex where nnn refers 
to the three-digit station number. The output files were specified as 
ctd_jc032_nnn_ctm.cnv, where nnn is the station number.

Align CTD - takes the cnv file and applies a temporal shift to align the 
sensor readings. The offsets applied were zero for the primary and secondary 
temperature and conductivity sensors as the CTD deck unit automatically 
applies the conductivity lag to the conductivity sensors. An offset of 5 was 
applied to the oxygen sensor.

Cell Thermal Mass - takes the cnv files output from Align CTD and makes 
corrections for the thermal mass of the cell, in an attempt to minimize 
salinity spiking in steep vertical gradients due to a temperature/conductivity 
mismatch. The constants applied were; thermal anomaly amplitude α = 0.03; 
thermal anomaly time constant 1/β = 7.


2.2  Mstar CTD Processing

The entire Mstar software suite is written in Matlab and uses NetCDF file 
format to store all the data. There are four principal types of files:

• SAM files: store all information about rosette bottles samples, including 
  upcast CTD data from when the bottles were fired. Data from chemistry 
  samples corresponding with each bottle are uploaded into this file as well. 
  Other information about the station is stored too.
• CTD files: store all data from CTD sensors. There are five CTD files: raw, 
  24Hz, 1Hz, psal and 2db. The program averages and interpolates the raw data 
  until it has 2db resolution.
• DCS files: store information necessary to know CTD downcast (for e.g. start, 
  bottom and end points of the cast). It is also used to merge in latitude 
  and longitude.
• FIR files: keep information about CTD data in points when each rosette 
  bottle was fired. Also stores information about winch work.


2.3  Processing Procedure Used on JC032

After having converted CTD with the SBE processes, there were two files to 
work on; ctd_jc032nnn_ctm.cnv and ctd_jc032_nnn.bl. The first one contains 
all raw CTD data including cast information. The other one contains 
information about the firing of each bottle on the cast.

To start the CTD data processing, run m_setup in Matlab to add Mstar tools 
and information needed for the processing.

msam_01: creates an empty sam file to store all information about rosette 
         bottle samples. The set of variables are available on M_TEMPLATES 
         directory and can be changed according to what it needs to store. 
         This file, named as sam_jc032_nnn.nc, contains space to store data 
         for each sample bottle, their flags, and some CTD data at firing 
         time.

mctd_0l: reads the raw data (ctd_jc032_nnn_ctm.cnv) and stores it in a NetCDF 
         file named ctd_jc032_nnn_raw.nc, which becomes write protected.

mctd_02: copies ctd_jc032_nnn_raw.nc into ctd_jc032_nnn_24hz.nc renaming the 
         variables for the SBE sensor.

mctd_03: using 24Hz data (ctd_jc032_nnn_24hz) it averages to 1Hz data. Then, 
         using the 1Hz file (ctd_jc032_nnn_lhz) it calculates potential 
         salinity and potential temperature (ctd_jc032_nnn_psal).

mdcs_01: creates empty file named as dcs_jc032_nnn to store information about 
         the start, bottom and end of the cast.

mdcs_02: populates dcs_jc032_nnn with information from the bottom cast. It 
         takes the highest pressure point as bottom.

mdcs_03: selects and shows surface data < 20db (ctd_jc032_nnn_surj) then 
         the analyst chooses the positions of the start and end scan numbers.

The start is selected by scrolling from the top of data printed out by 
mdcs_03. The operator identifies where the CTD went from being on deck 
(zero/negative pressure) to roughly 10 db and then the point where is it was 
brought back to the surface for start the downcast. The scan number at which 
the pressure begins to increase is selected as the start point of the 
downcast.

To find the end of upcast, scroll the data up from the bottom and identify 
where the CTD came back onboard. The operator chooses the point before an 
abrupt change in conductivity due to the CTD coming out of the water.

mctd_04:  using information on dcs_jc032_nnn it selects the CTD downcast data 
from ctd_jc032_nnn_psal file and averages it into 2db resolution 
(ctd_jc032_nnn_2db).

mdcs_04:  loads position from navigation file and merges it on the cast's 
          points previously defined on mdcs_03 and store it on 
          dcs_jc032_nnn_pos.nc.

mfir_0l:  extracts information about fired bottles from ctd_jc032_nnn.bi and 
          copies them into a new file named fir_jc032_nnn_bl.nc.

mfir_02:  using firjc032_nnn_bl and ctd_jc032_nnn_lhz it merges the time from 
          the CTD using scan numbers and puts it into a new file 
           (fIr_jc032_nnn_time.nc).

mfir_03:  stores the CTD data at each bottle firing time in fir_jc032_nnn_ctd. 
          The CTD data are taken from ctd_jc032_nnn_psal and selected 
          according to the firing time information stored in 
          fir_jc032_nnn_time.

mfir_04:  copies information of each bottle from fir_jc032_nnn_winch onto 
          sam_jc032_nnn.

mwin_01:  creates a new file named win_jc032_nnn.nc to store information 
          about winch working (for e.g. angles, rate and tension).

mwin_03:  using time stored in fir_jc032_nnn_time, it selects wire-out from 
          win_jc032_nnn at each bottle firing location to fir_jc032_nnn_winch.

mwin_04:  pastes wire-out information from fir_jc032_nnn winch into 
          sam_jc032_nnn.nc.

mbot_01:  creates a bottle file (bot_jc032_nnn) to store information 
          regarding the state of each Niskin bottle. It uses a text file 
          named as bot_jc032_01.csv (on BOTTLE_FILE/ directory) that must be 
          always updated after each station with the number of the bottle, 
          position on rosette, and a flag number.

mbot_02:  copies information from bot_jc032_nnn to sam_jc032_nnn.nc.

mdep_01:  applies full water depth into all files. The depth is taken from 
          the LDEO processing of the LADCP.

mdcs_05:  applies positions from dcs_jc032_nnn_pos.nc to all files. If a file 
          on the set doesn't exist yet it won't be uploaded.


2.4 Sample Files

Chemistry and tracer data from the various groups were merged with CTD data 
to create master sample files. The sample files (sam_jc032_nnn.nc) were 
created whilst processing each CTD station. These were, at this stage, filled 
with upcast conductivity, temperature, oxygen and pressure from both primary 
and secondary sensors coincident with bottle firings. Winch data were merged 
on, as were Niskin bottle flags.

Merging of these data took two steps for each tracer: the first step 
generated an Mstar file, which contained all the tracer data for a given 
section - these were the programs named moxy_01, mnut_01, mcfc_01 and 
mco2_01. This step contains code specific to the format of the data received 
from the various groups. The files were named oxy_jc032_nnn.nc, for example 
in the case of oxygen. The second step was to merge these individual Mstar 
files onto the master sam file for the station. This was performed by the 
programs moxy_02 etc.

This method of processing provided an efficient and consistent method of 
assimilating data from the many different components of an interdisciplinary 
cruise like JC032. It also facilitated the production of contour plots of the 
various station data as we progressed through the section.


2.5 Calibration of the Primary Conductivity Sensor

The conductivity sensor was calibrated against conductivities derived from 
bottle samples. The CTD used on JC032 was equipped with two conductivity and 
temperature sensors. The primary conductivity-temperature sensor was attached 
near the bottom of the main frame. The secondary sensor was attached to the 
fin of the CTD. The secondary conductivity sensor was noted to have 
hysteresis and hence the primary sensor was chosen for calibration as the 
final conductivity. The differences between the two sensors and their 
uncorrected offsets are shown in Figure 3.

Upcast conductivity - present in the sam file at bottle depths as 'ucond' - 
was calibrated against conductivity derived from bottle samples. A 
multiplicative correction factor applied to conductivity is associated with a 
deformation of the conductivity cell. The shape of this correction is 
comparable to an additional correction to salinity. As the calibration was 
applied at the transition between the raw files and the 24Hz files, it was 
necessary to do a conductivity correction.

The ratio between conductivity derived from bottle samples and upcast 
conductivity was investigated. While the ratio was close to unity, there was 
an offset roughly equivalent to 0.002 in salinity. The ratio also showed a 
trend against pressure. From 1000m to 4500m, the CTD conductivity had a 
linearly decreasing trend with depth and from 4500m to the maximum depths 
encountered (around 5700m) the conductivity trend tended towards higher 
conductivities. No trends were noted in salinity residuals against 
temperature or conductivity.

The calibration was applied by correcting conductivities with a 
multiplicative factor decided by a pressure lookup table. This reduced the 
interquartile range of salinity residual to 0.001 (equivalent to an 
interquartile range of 0.00003 in conductivity ratio). This calibration 
removed the trend with pressure deeper than 1000m. Above 1000m there were 
large gradients in both temperature and salinity. In this region the bottle 
conductivities often read lower than those of the CTD. This was interpreted 
as a Niskin bottle flushing issue. The water in the Niskin was from a few 
metres deeper than the CTD was reading. Hence no extra correction was applied 
to the CTD in this region.

The calibration had to be reviewed after the CTD was dropped at Station 61. 
The primary conductivity did receive a conductivity offset of 1.0001 
(equivalent to 0.004 in salinity). This was traced to the primary 
conductivity by comparison with both the secondary sensors and previous 
casts. Close investigation of the temperature sensors revealed no similar 
offset. The same procedure as mentioned previously was applied to calibrate 
these data. The result was similar. The spread of the data was restricted to 
0.002 in salinity and the trends with pressure were removed.

The primary conductivity sensor began to fail on Station 89. Near the bottom 
of the downcast, at scan 155720, the conductivity ratio jumped by a factor of 
1.000076 (equivalent to 0.003 in salinity). This adjustment was made to the 
24Hz files before the pressure correction was applied. This remained a 
constant offset until the sensor had failed completely on Station 93 and 
began wandering in comparison to the secondary sensor. It failed near the 
bottom of the downcast at scan 143986. For the remainder of the downcast the 
conductivity data from the secondary sensor were pasted in so as to have the 
most accurate data available in the 2db file. The upcast data were not 
corrected for this cast.

The new conductivity sensor was fitted from Station 94. This sensor was seen 
to be stable and well calibrated. A small pressure effect of a similar shape 
to that seen in the original sensor was noted, although the effect was less 
obvious with this sensor. This was corrected for in the same manner as 
before. The similarity of the shape of the pressure offset, which needed to 
be applied to both of the primary sensors, may indicate that there was some 
issue with the pressure sensor.


2.6 Calibration of the Oxygen Sensor

The oxygen sensor was attached to the primary conductivity-temperature sensor 
on the CTD frame. Early on in the cruise, the sensor was noted to suffer from 
large hysteresis between the down and up casts. This is shown in Figure 4. No 
correction for this hysteresis was applied, but the downcast oxygen (rather 
than the upcast) was calibrated against bottle samples. The downcast data 
were matched with the bottle samples (taken on the upcast) on density. 
Density was chosen as a parameter more representative of the water mass than 
pressure/depth, which may change between downcasts and upcasts. The residuals 
calculated were shown to have a dependence on pressure. This pressure effect 
was corrected for by applying an additive correction with respect to 
pressure. The results reduced the residuals to below 1µmo1/kg.

After the drop on Station 61, the oxygen sensor received an offset of roughly 
2.5µmo1/kg. Due to the sensors' excellent stability before the drop, the 
decision was taken not to replace the sensor. The sensor remained stable 
after this and did not change after the primary conductivity sensor was 
replaced after Station 93. The correction to this jump involved the same 
procedure as beforehand. The final residuals are shown in Figure 5.


2.7 Calibration of the Transmittance Sensor

The transmittance sensor was noted to be producing values of the order of 104 
-105% in clear water. This was adjusted in post-processing by capturing the 
maximum voltage recorded in clear water and setting this to a transmittance 
of 99.9%. The other values in the station were adjusted accordingly.


2.8 Addition of Metadata to the Mstar Files

Position, time and full water depth were added to the header of all Mstar 
files including the sam and ctd_2db files.

Time: Time exists in Mstar files in seconds from the Mstar time origin. The 
Mstar time origin is parsed out from a UTC timestamp in the header of the 
SeaBird CTD files.

Position: Latitude and longitude in both decimal degrees, and degrees and 
minutes, were pasted into the files. The time according to the bottom of the 
cast was found from the DCS files with the posmvpos position merged on.

Water Depth: Water depth was added after processing of the LADCP was 
complete. The LDEO with CTD processing provides an estimate of full water 
depth by combining CTD depth with a height above the bottom estimate provided 
by the LADCP. A backup water depth was provided by a combination of the 
altimeter and depth of the package from the CTD data. This was not used in 
the final file.

2.9 Niskin Bottles

Four 20L bottles were used for the surface measurements (positions 21 to 24) 
and the remaining twenty positions held 10L bottles. During sampling the 
bottles were checked for problems such as leaking and dribbling and any 
issues were noted on the deck log. During the processing of the data, quality 
control flags were assigned and are as follows (refer to the WOCE operations 
manual):

  2 = No problems noted (data assumed to be good)
  3 = Leaking (these bottles are therefore not sampled)
  9 = Samples not drawn from this bottle (e.g. a duplicate depth but no 
      issues with bottle)
 10 = Tap dribbling before the top valve was opened

Flag number 10 was introduced on this cruise after a number of incidences 
where the tap of a bottle was dribbling before the valve was opened. It was 
thought unlikely that the water in these bottles would have been contaminated 
(often it was the surface bottle affected) but it was flagged as anomalous 
and data was recorded from these bottles. Flags 2, 3 and 9 are taken from the 
WOCE operations manual.

During Station 61 the CTD was dropped on deck during deployment. As a result 
the 20L Niskin bottle in position 21 was broken and was replaced by a spare 
20L bottle, which was subsequently named number 25 for processing purposes.

On a number of casts, the chemistry team reported anomalous results in oxygen 
and nutrient samples from bottle 3 suggesting that water had been picked up 
in another part of the water column. Anomalous salinity samples furthered the 
suspicion that the bottle contains water from higher in water the column. 
This was reported in four stations (81, 85, 91 and 93) and the bottle was 
given a quality control flag of 3. A new 10L bottle was installed in position 
3 (this was named number 26 for processing) before the deployment of cast 95. 
However, after analysing data from cast 96 the nutrient team once again 
reported anomalous data. For two additional casts the bottle was not fired in 
order to determine if bottle 3 was closing by itself somewhere else in the 
water column. On both occasions when the CTD was recovered this bottle 
remained open. Again on cast number 107 anomalous results in oxygen and 
nutrients and salinity were found. On following casts, where possible, this 
bottle was used as a duplicate of the 'bottom-50' depth and was not sampled.

 
Figure 3:  Raw data from the original primary and secondary conductivity 
           (salinity) sensors.

Figure 4:  Salinity Residuals for the original conductivity sensor after 
           adjustment for a pressure effect.
 
Figure 5:  A selection of stations were taken in this graph and are 
           represented by different colours. Data is taken from the 1Hz files. 
           Both the upcast and the downcast were put on a regular grid and the 
           upcast subtracted from the downcast. These data points are 
           represented by the dots. The lines show the dots after smoothing 
           with a running average. Hysteresis was seen to be present in the 
           oxygen sensor. The downcast oxygen was reading higher than the 
           upcast up to a maximum of 10 µmol/kg on the deepest casts.
 
Figure 6:  Oxygen residuals calculated from bottle oxygen minus pressure 
           corrected downcast CTD data

Figure 7:  Oxygen outliers found from Niskin 3
 
Figure 8:  CTD oxygen and fluorescence parameters across the first Brazil 
           current transect

Figure 9:  CTD oxygen and fluorescence parameters across the second Brazil 
           current transect
 
Figure 10: CTD oxygen and fluorescence parameters across the third Brazil 
           current transect

Figure 11: Contour plot of the oxygen parameter along the Atlantic 24°S 
           hydrographic section
 
Figure 12: Potential temperature and salinity parameters across the first 
           Brazil current transect

Figure 13: Potential temperature and salinity parameters across the second 
           Brazil current transect
 
Figure 14: Potential temperature and salinity parameters across the third 
           Brazil current transect

Figure 15: Contour plot of potential temperature along the Atlantic 24°S 
           hydrographic section



3.  WATER SAMPLE SALINITY ANALYSIS
    (David Hamersley, Gerard McCarthy and Lorna McLean)


3.1  Sampling

For the purpose of measuring salinity, samples were collected in 200ml glass 
bottles from each bottle fired at each station. In addition to this, TSG 
samples were collected every 4 hours. Two crates were set aside for TSG 
samples. The TSG crates did not have complete sets of sample bottles because 
some were substituted and re-labelled to make up complete crates for sampling 
the CTD. Standard procedure for sampling from both the CTD and the TSG was to 
rinse the sample bottles using sample water from the Niskin bottles on the 
rosette, and then fill the bottle completely to collect the sample. It was 
considered good practise to run the samples for the TSG through the hose for 
approximately 1 minute in order to flush through any water that may have been 
sitting in the system since the previous sample was taken. The rim and the 
inside of the lid of each bottle were wiped dry using disposable paper towels 
to prevent salt crystals forming. Each sample bottle was then sealed with a 
disposable plastic stopper and its respective screw cap. When a crate was 
completed it was taken into the constant temperature (CT) laboratory and left 
for a minimum of 24 hours to equilibrate with the temperature of the 
laboratory. It was necessary to record the identity of the crate and the time 
it was placed in the CT lab so that it could be easily identified when a 
crate was ready to be analysed.


3.2  Laboratory Setup

The CT lab space was shared between the salinity and noble gas analysis (Alba 
Gonzalez Posada). For the purpose of salinity analysis, a Guildline 8400B 
laboratory salinometer, serial number 68426, was used. The temperature of the 
laboratory should be between 22-23°C, lower than temperature of the water 
bath in the Autosal, which in this case was set to 24°C. Over the duration of 
this cruise the room temperature was recorded in the watchkeeping logs, and 
was found to fluctuate between 21.5-23.5°C. It is possible that these 
temperatures are slightly erroneous because the thermometer is situated 
against the casing of the Autosal. When measuring different areas of the 
room, it was found that near air conditioning outlets the temperature could 
be as low as 16°C. The same components and setup for the Autosal are used on 
this cruise as on JC031. The only adjustment that has been made is the 
addition of an on/off switch on the peristaltic pump. The object of this was 
simply to improve the functionality of the pump for the analyst.


3.3  Analysis

Salinity analysis duties were shared between the members of the physics 
watch; Brian King, Gerard McCarthy, Lorna McLean, David Hamersley, Alex 
Brearley, and Carolina Gramcianinov. In the beginning there were inevitably a 
few teething problems in terms of getting new analysts familiarised with the 
Autosal, either because they had never performed any salinity measurements 
before, or because they had done so on a different type of salinometer. One 
of the problems that commonly occurred was failure to alter the suppression 
settings of the salinometer when necessary. However, this was not a major 
problem as the values were easily corrected by hand after the analysis was 
complete. Various changes, which will be discussed in this report, were made 
to the analysis procedures from the previous cruise (JC031) after discussion 
between Brian King and the rest of the physics watch. The number of remaining 
seawater standards was found to be approximately 170. This meant that the 
number of standards was limited for the number of stations on this cruise. It 
was therefore determined that salinity analysis should only be performed when 
3 or more crates had equilibrated to room temperature. This way the number of 
standards used for analyses could be minimised.

Additional methods for ensuring efficient use of standards included flushing 
the cell in the Autosal with old standard before the usual prescribed three 
flushes with new standard. The reason behind this was to bring the salinity 
of the sample in the cell closer to the value of the new standard to increase 
the likelihood of any previous sample being completely flushed out. When 
entering bottle numbers into the data logging software, standards were 
designated 9nnn, where 'nnn' relates to the sequential number of the standard 
e.g. the first standard used was 9001. This number, along with the times and 
crates associated with the respective standard were recorded in a 
standardisation log sheet.

The same standard seawater samples, produced by Ocean Scientific Instruments 
Ltd. (OSIL), were used throughout the cruise. Batch number: P150, K15 ratio: 
0.99978, K15 ratio x2: 1.99956. Instead of running standardisations and 
altering the standardization setting on the Autosal (which was set at 490), 
it was agreed that standards would be run as samples and then adjusted for 
the difference between the measured value and labelled value. Several Matlab 
scripts were written by Gerard McCarthy to perform the adjustments to the 
salinities of the bottle samples and the TSG samples.

There were several adjustments to the standardisation setting of the Autosal 
at the beginning of the cruise. At Station 1 the standardisation setting was 
changed from 490 to 583, this was changed again to 570 at Station 4. The 
standardisation setting was finally changed to 490 when analysing Station 10, 
because it was found that the values were too close to the 2.00000 
suppression setting to allow a coherent standardisation to be achieved. After 
this station it was agreed that the standardisation setting should be kept 
the same and only to run standards as samples. Doing this meant that the 
salinity adjustments had to be performed manually using the scripts generated 
by Gerard McCarthy, which would otherwise have been performed by the data 
logging software from standardisations.

 
Figure 16: Comparison of standardisation adjustments and differences.


Figure 16 plots the differences that were calculated between the label value 
on the standard bottles and the measured value of the standard. Adjustments 
were made to the calculated differences in order to try and smooth out the 
readings that were thought to be attributed to noise. It can be seen that 
there has been considerable drift in the values of the standards measured by 
the salinometer. These adjustments were made manually to the salinity data, 
using scripts written in Matlab. (See table 1 for salinity standard 
adjustments).

It has been frequently noted by the members of the physics team, that the 
readings from the salinometer show much less variation (noise) on the 2.00000 
suppression, as opposed to the 1.90000 suppression. It is thought that this 
could potentially be an electronic fault that occurs when the suppression 
switch is put on this setting. The degree of the variability on this 
suppression has been found to increase at certain times throughout this 
cruise, but has always returned to periods of relative stability. However, 
due to the uncertainty that the noise is having on the final average 
calculated by the software, it was decided by Brian King that the analysts 
should record the readings visually, so that efforts could be made to observe 
how much of an effect the noise was having on the computer calculated 
average. Findings showed that there was generally a difference between the 
computer-calculated and manually calculated average of approximately 1 or 2 
counts (0.00001-0.00002). Despite the noise observed on the salinometer 
display, this does not appear to hugely affect the calculated average. 
However, continued visual observation was suggested in order to maintain a 
record that could be consulted if results produced by the data-logging 
software continued to appear anomalous.


3.4  Specific Observations

This section merely draws attention to specific incidents that are considered 
to be relevant to the reliability and quality of the salinity samples. This 
should not only serve as an account of the salinity analysis that has taken 
place on JC032, but also as an indication of potential problems that may be 
encountered on future cruises.

Whilst analysing Station 10, it was realised by the analyst that the drainage 
can was overflowing with the drainage pipe dangling in the can. It is 
believed that this could have caused an electrical circuit that possibly 
altered the electrical conductivity in the cell, hence leading to 
comparatively large variation in the data. The issue was explained to the 
physics team and the situation has thus been rectified by emptying the 
drainage can at the end of every set of analyses.

For the crate sampled at Station 25, Brian King checked both temperature 
sensors separately on different temperature settings. The temperature sensors 
are wired in series allowing each of the sensors to operate independently. 
The two temperature sensors are separated in their calibration by 
approximately 10-20 m°C (millidegrees Celsius). When temperature sensor 1 is 
selected the heater lamps should stay on temporarily to bring the temperature 
of the bath up, whereas when sensor 2 is selected the lamps should remain off 
until the temperature of the bath has fallen sufficiently. When changing 
between these temperature sensors the lamps should be observed to see how 
long it takes for them to begin cycling again.

The analysis of Station 31 was suspended after the first sample bottle was 
run and it was decided that the readings being produced by the Autosal were 
far too variable. The machine was left to settle and was re-run the following 
day when the readings being produced appeared to be stable. It should be 
noted the sample, that was originally run before analysis was suspended, was 
re-run despite the bottle being half empty for several hours, so it is likely 
that the salinity of this sample may have altered from its original value.
On several occasions, the plastic insert was found to be very loose in the 
sample bottle. This could have potentially led to some evaporation from the 
sample, which would have altered the salinity. In addition to this, samples 
were intermittently found to have no plastic inserts. These samples were not 
analysed on the basis of them being contaminated.

The third sample collected at Station 60 was analysed but the last reading 
taken from the bottle yielded a very high value 8 counts higher than the 
previous readings. Due to the large variability an additional reading was 
taken which was found to be within one count of the first two readings, this 
value was replaced manually in the spreadsheet.

Sample bottle 8 was discarded from the analysis of Station 70 due to pieces 
of blue paper towel found in the sample.

At Station 76 a second crate of samples from the bottom -50m bottle (Niskin 
bottle 2) were collected with the view to assess the stability of the 
Autosal, however these samples were not actually analysed in the end as the 
Autosal appeared to have become stable again by this point.

The problem of large variability and instability in the readings from the 
Autosal continued, consequently, from Station 80 onwards it was decided to 
allow the software to log the data as usual, but to also perform readings 
using the visual display. The reason for this was so that we could manually 
filter out the noisy readings from the Autosal, and have a basis for 
comparison in the variability of the results. It was found that there was 
generally very little difference in the final averages calculated by the 
software and the averages calculated from the visual readings taking by the 
analyst. The averages taken for processing were those calculated by the 
software, but if the averages had a difference of more than two counts then a 
note was made in order to flag the result as potentially noisy.


3.5  Processing

Various additions were made to the Excel spreadsheet files created by the 
data logging software. However, the files were edited differently according 
to whether the files contained CTD or TSG data. For TSG samples, the files 
were amended by adding the collection times of each TSG sample in the 
following format; 'dddhhmmss'. For CTD samples unique sample numbers were 
assigned according to the station number and the position the sample was 
taken from on the CTD rosette. For example, for the first bottle of Station 
67 would be recorded as 6701. It was necessary to consult the CTD log sheets 
to check whether any bottles were missing due to leaks or misfires. 
Similarly, special identification numbers were given to standards that were 
run. This basically consisted of adding another two nines onto the sequential 
numbers of the standards, e.g. '999nnn'. After all the files had been edited 
accordingly, they were saved as comma delimited csv files.

It was necessary to determine the adjustments to give to the values from each 
crate due to the choice not to standardise at the beginning of the cruise. 
From the differences that were determined an adjustment value was chosen 
according to the variability in adjacent difference values. After these 
amendments to the files had been made, the files could be processed using 
Matlab scripts prepared by Gerard McCarthy. Separate scripts existed for CTD 
and TSG samples. The difference between these scripts is that the TSG script 
parses out the data in terms of time whereas the script for the bottle 
samples sorts the data according to sample number. Both scripts perform the 
task of applying the adjustments from the standards to the respective 
datasets.


3.6  Assessment

The Guildline 8400B laboratory salinometer has been used heavily on 
consecutive cruises, and thus in this regard it has been deemed to provide 
reliable results. However, it is recommended that certain aspects of this 
piece of equipment be investigated further, such as the high degree of 
variability in the readings when the machine is set to the 1.90000 
suppression.


Table 1: Differences and adjustments calculated for standardisations for each 
         run

Station  Crate  Difference  Adjustment  Run Position  Comments
-------  -----  ----------  ----------  ------------  --------------
1        7       -0.00009    -0.00009                    
2        7       -0.00009    -0.00009                    
3        7       -0.00009    -0.00009                 (bottles 41-48)
3        4       -0.00003    -0.00003                 (bottles 73-77)
4        4       -0.00003    -0.00003                 
5        6       -0.00003    -0.00003                 
6        28      -0.00004    -0.00004                 
7        28&20   -0.00007    -0.00007                 
8        20&25   -0.00011    -0.00011                 
9        39      -0.00012    -0.00012                 
TSG 001  3       -0.00012    -0.00012                 
10       7        0.00006     0.00006                 (bottles 25-38)
10       7        0.00022     0.00022                 (bottles 39-44)
11       28       0.00021     0.00021                 
12       6        0.00019     0.00019                 
13       38       0.00018     0.00018                 
14       4        0.00019     0.00019                 
15       11       0.0002      0.0002                  
16       20       0.0002      0.0002                  
17       39       0.0002      0.0002                  
18       23       0.0002      0.0002                  
                  0.00021                  END        
19       1        0.00019     0.00018      START       
20       1        0.00018     0.00018      END/START       
                  0.0002                   END        
21       25       0.00018     0.00018      START       
22       25       0.00018     0.00018      END/START       
TSG 002  5        0.00018     0.00018      END/START       
23       11       0.00017     0.00017      END/START       
24       11       0.00017     0.00017      END        
                  0.00011                  START       
25       4        0.00013     0.00016      MID        
26       25       0.00018     0.00018      MID        
27       6        0.00016     0.00016      END        
28       20      -0.00003    -0.00005      START      Standard left in?
                 -0.00006                  END          
29       38      -0.00006     0            START          
                  0.00004                  END          
30       7        0.00004     0.00003      START          
                  0.00001                  END          
31       23       0.00005     0.00004      START          
32       39       0.00003     0.00003      START          
                  0.00003                  END          
33       6        0.00003     0.00005      START          
                  0.00006                  END          
34       25       0.00006     0.00006      START          
                  0.00007                  END          
35       4        0.00006     0.00006      START          
                  0.00006                  END          
TSG 003  3        0.00006     0.00006                    
36       39       0.00012     0.00012      START          
37       11       0.00012     0.00011      END/START          
38       25       0.0001      0.00008      END/START          
39       28       0.00005     0.00009      END/START          
                  0.00012                  END          
40       23       0.00013     0.00012      START          
TSG 004  5        0.00012     0.00012      END/START          
41       6        0.00012     0.00012      END/START          
42       20       0.00003     0.00007      END/START  Standard left in?
                  0.00011                  END          
43       11       0.00024     0.00009      START          
44       39       0.00008     0.00009      END/START          
45       7        0.0001      0.00009      END/START          
46       4        0.00008     0.00009      END/START          
                  0.00011                  END          
47       1        0.00023     0.00011      START      MilliQ left in?
TSG 005  3        0.0001      0.00011      END/START          
49       23       0.00011     0.00011      END/START          
50       11       0.00011     0.00011      END/START          
51       28       0.00013     0.00011      END/START          
                  0.00011                  END      
52       20       0.00015     0.00011      START          
53       6        0.00012     0.00012      END/START  Warm standard
54       39       0.00004     0.00012      END/START  Warm standard
55       7        0.00005     0.00012      END/START  Warm standard
                  0.00003                  END        Warm standard
TSG 006  5        0.00006     0.00012      START      Warm standard
56       25       0.00011     0.00012      END/START          
57       28       0.00012     0.00012      END/START          
58       11       0.00012     0.00009      END/START          
59       20       0.00004     0.00009      END/START          
                  0.00009                  END      
60       38       0.00014     0.00013      START          
61       11       0.00013     0.00013      END/START          
62       6        0.00013     0.00013      END/START          
63       23       0.00013     0.00013      END/START          
                  0.00012                  END      
TSG 007  3        0.00017     0.00013      START          
64       25       0.00011     0.00012      END/START          
65       1        0.00012     0.00012      END          
66       28       0.00015     0.00013      START          
67       7        0.00012     0.00013      END/START          
68       11       0.00014     0.00013      END/START          
69       6        0.00012     0.00012      END/START          
                  0.00009                  END      
70       1        0.00014     0.00007      START          
71       38       0.00006     0.00007      END/START          
TSG 008  5        0.00008     0.00007      END/START          
                  0.00008                  END      
72       4        0.00008     0.00007      START          
73       25       0.00007     0.00006      END/START          
74       11       0.00006     0.00005      END/START          
75       39       0.00004     0.00006      END/START          
                  0.00007                  END      
76       20       0.00005     0.00006      START          
77       6        0.00008     0.00006      END/START          
78       38       0.00008     0.00005      END/START          
                  0.00003                  END      
79       1        0.00013     0.00013      START          
80       11       0.00014     0.00013      END/START          
81       23       0.00012     0.00012      END/START          
                  0.00011                  END      
82       28       0.00015     0.00013      START          
TSGO09   3        0.00012     0.00013      END/START          
83       4        0.00013     0.00013      END/START          
                  0.00013                  END      
84       39       0.00009     0.00011      START          
85       6        0.00011     0.00011      END/START          
86       25       0.00005     0.00011      END/START          
                  0.00011                  END      
87       1        0.00011     0.00009      START          
88       23       0.00009     0.00009      END/START          
TSGO1O   5        0.00007     0.00009      END/START          
89       7        0.00004     0.00009      END/START          
90       6        0.00012     0.00009      END/START          
                  0.00008                  END      
91       11       0.00014     0.00013      START          
92       28       0.00014     0.00013      END/START          
93       20       0.00013     0.00013      END/START          
94       7        0.00013     0.00011      END/START          
                  0.00009                  END      
95       6        0.00008     0.00007      START          
96       4        0.00007     0.00007      END/START          
97       38       0.00008     0.00007      END/START          
98       25       0.00006     0.00007      END          
                  0.00007                         
99       1       -0.00001     0            START          
100      39       0.00001     0            END/START          
101      11      -0.00002     0            END/START          
TSG11    3        0           0            END/START          
                  0           0            END          
102      23      -0.00009    -0.00005      START          
103      6       -0.00006    -0.00005      END/START          
104      20      -0.00005    -0.00003      END/START          
                 -0.00001     0            END          
105      4        0.00002     0.00001      START          
106      11       0.00001     0.00001      END/START          
107      1       -0.00001     0            END/START          
                  0.00001     0            END          
108      25       0.00002     0.00001      START          
109      7        0           0            END/START          
110      6        0           0            END/START          
                  0           0            END          
111      1       -0.00003    -0.00002      START          
TSG 12   5       -0.00002    -0.00001      END/START          
                  0           0            END          
112      11       0.00001     0.00001      START          
113      20      -0.00006    -0.00004      END/START          
114      38      -0.00002    -0.00003      END/START          
115      39      -0.00002    -0.00001      END/START          
116      23       0           0            END          
117      23       0.00001     0.00001      START          
TSG 13   3        0.00001     0.00001      END/START          
118      28      -0.00001     0            END/START          
                  0.00001     0.00001      END          



4.  INORGANIC NUTRIENT ANALYSIS
    (Sinhue Torres, Lily Chambers, Louise Darroch and Mark Moore)


4.1  Method

Seawater was collected for the analysis of micro-molar concentrations of 
dissolved inorganic nutrients; nitrate and nitrite (hereafter nitrate), 
phosphate and silicate. Samples were collected directly into 30m1 plastic 
pots after these had been rinsed with sample water at least three times. When 
required, samples were stored in a fridge at approximately 4°C until 
analysis. Samples were usually analysed within 4 hours of collection.

In general, analyses were started within 30 minutes of sample collection 
using a segmented continuous-flow Skalar San Autoanalyser set up for analysis 
and data logging with the Flow Access Software version 1.3.11. This system 
follows the method described by Kirkwood (1996), with the exception that the 
pump rates through the phosphate line were increased by a factor of 1.5, 
which improves reproducibility and peak shape. In addition, a dilution loop 
(2.9x, Figure 17) was set up by Dr. Paul Morris for cruises JC030-32 in 
anticipation of high silicate concentrations within the study regions.

For JC032 the analysis was calibrated using the set of standards shown in 
Table 2. Top nitrate and silicate standards were based on the highest values 
reported by Siedler et al., (1996). The phosphate calibration range of 
standards was left as used during JC030 and JC031.

Table 2 shows target and actual standard concentrations. Target 
concentrations are values aimed at when preparing working standards (i.e., 
every day used standards). Actual concentrations are values corrected by 
taking into account i) the weight of the dry chemical used to prepare a given 
standard (Table 3) and, ii) the calibrated volume of the pipettes used for 
diluting stock standards (i.e., high concentration standards).

Stock standard solutions of ~5µmol L-1 prepared in Milli-Q water were used to 
produce working standards. Working standards were prepared in a saline 
solution (40g NaC1 in 1L of Milli-Q water, here after artificial seawater), 
which was also used as a diluent for the analysis.

 
Figure 17: Details of the dilution loop for the silicate line


Table 2: Set of calibration standards (Std) used for dissolved inorganic 
         nutrient analysis. Bold numbers are target concentrations, otherwise 
         actual concentrations. Concentration units are µmol L-1

                           Nitrate    Phosphate    Silicate
                  -----   ---------   ---------   -----------
                  Std l   40  39.89   4.0  4.0    120  120.05
                  Std 2   25  24.93   3.0  3.0     80   80.03
                  Std 3   15  14.96   2.0  2.0     40   40.02
                  Std 4    5   4.99   1.0  1.0     10   10.00
                  Std 5    1   1.00   0.5  0.5      1    1.00
                  Std 6   ---------   ---------   140  140.05


Table 3: Compounds used to prepare stock standard solutions, weight dissolved 
         in IL of Milli-Q water and Molarity of the solution

                Compound  Weight (g)  Molarity 1L stock solution
                --------  ----------  --------------------------
                KH2PO4      0.6820             5.0115
                Na2SiF6     0.9445             5.0224
                NaN03       0.4255             5.0061
                NaNO2       0.3465             5.0221


The autoanalyser was washed through with 10% Deacon 90 and with Milli-Q water 
for at least 30 minutes each after each run, except when the time between 
stations wasnot enough to do so, in which case the autoanalyser was left with 
the reagent tubing connected ready for the next run. New pump tubing was 
installed at the start of the cruise and turned around to use the other half 
of the tubing just before starting the main crossing of the Atlantic section. 
Tubing was replaced again on the 7th April, just before Station 79. The bulbs 
in the two detectors were also replaced at the start of the cruise. During 
JC030 it was observed this produced a smoother baseline and cleaner peaks.

At the start of the cruise all labware used was washed with 10% HC1 and 
rinsed with Milli-Q water, and was similarly treated prior to any further 
use.

Time series of baseline, instrument sensitivity, calibration curve 
correlation coefficient, and nitrate reduction efficiency were compiled to 
check the performance of the autoanalyser over the course of the cruise.


4.2  Observations

1. Most of the stations from the three transects made across the Brazilian 
   boundary current and close to the Namibian coast were analysed in pairs or 
   in sets of three stations over shallow waters. However, stations along the 
   main trans-Atlantic section were individually analysed. Station 22 was an 
   ADCP cast without any water sampled. Station 48 was renamed Station 49 due 
   to an issue with the winch which required two casts to be made at the same 
   station. CTD 48 was not sampled.

2. New batches of artificial seawater were prepared almost once a week and 3 
   sets of calibration standards were produced and used from Stations 1, 50 
   and 89, respectively. Both artificial seawater and standards were analysed 
   prior to being used in order to check for contamination and consistency.

3. During the run for Stations 14 and 15 the baseline of the nitrate and 
   silicate analysis changed suddenly and affected almost half of the 
   calibration standards. Peak heights (in digital units) from the three 
   nutrient signals were checked for consistency with previous and following 
   runs. It was determined that the phosphate line was not affected, but the 
   silicate and nitrate signals needed to be edited in the Flow Access 
   software individually. This was done by comparing peak heights and 
   cancelling the signals that were evidently wrong, and by correcting the 
   peaks that were not properly picked by the software. After correcting these 
   errors, results seemed consistent with previous and further analyses, 
   although bulk nutrient results were higher relative to other runs. This may 
   suggest that results from this run may have been slightly overestimated by 
   about 0.05, 1 and 2µmol L-1 at concentrations over 1.5, 25 and 80µmol L-1 for 
   phosphate, nitrate and silicate respectively (with the effect decreasing at 
   lower concentrations). Attention should be paid to these two stations when 
   producing contour sections or depth profiles in order to verify whether 
   they are consistent with adjacent stations.

4. The auto-sampler we started the cruise with broke on the April 2009. The 
   sample tray would start spinning all of a sudden in the middle of a run, 
   which thus needed to be re-started. Initially, the sampler would work after 
   shutting it off and turning it on again, but after three further runs it 
   stopped working. One of the technicians looked into the problem, but could 
   not fix it. This did not present a problem for the analysis since spare 
   auto-samplers were brought onboard.

5. Bottom samples (in general Niskin bottles 1 to 3 or 4) at Station 9 and 
   Stations 35 to 57 exhibited silicate concentrations higher than the top 
   silicate standard (i.e., 120µmol L-1). Since concentrations higher than this 
   were only expected within the deepest section of the western South Atlantic 
   Basin, the calibration set of standards (i.e., Table 3) was kept unchanged. 
   However, the following steps were taken. Samples drawn from Niskin bottles 
   1 to 4 were taken in duplicate. One of these were analysed unmodified and 
   another was analysed whilst 50% diluted. In addition, a 140µmol-Si L-1 
   standard was prepared and analysed unmodified and also 50% diluted in every 
   run from Station 42 to 59. This standard was measured in order to test 
   whether the calibration equation held up to this concentration and also to 
   test whether diluting the samples produced reliable results. The mean 
   concentration of this silicate standard was 140.3±l.7µmol L-1 and the mean 
   concentration of the 50% diluted standard times 2 was 139.9±1.7µmol L-1 
   (Figure 18). This suggests i) that the calibration equation holds at least 
   up to this concentration and ii) that diluting samples also produced 
   reliable results. Having processed these measurements, it was decided to 
   keep the original high concentration sample values unmodified since these 
   were never higher than 140µmol-Si L-1. In case these values require further 
   revision, it is possible to include the extra silicate standard as part of 
   the calibration set in the Flow Access software and results can be 
   recalculated. However, given that the results above were satisfactory, this 
   process was deemed unnecessary while on the cruise.


Figure 18: 140 µmol L-1 silicate standard measured unmodified (red dots) and 
           50% diluted (dark green dots). Light green is the 50% diluted 
           standard times 2. The red line represents the mean concentration of 
           the measurements and the black lines are ± 1 standard deviation.


6. Niskin bottle number 3 produced anomalous results at Stations 81, 85, 91, 
   93, 96, 105 and 107. These were characterised by higher levels of phosphate 
   and nitrate, low levels of silicate and low levels of dissolved oxygen 
   relative to adjacent Niskin bottles. These notes were given to the physics 
   group in order to compare results with salinity determinations.


4.3  Performance of the Analyser

The performance of the autoanalyser was monitored by producing time series 
plots of the following parameters: standards concentration, baseline, 
calibration slope (instrument sensitivity), calibration correlation 
coefficient, nitrate reduction efficiency, low nutrient seawater and bulk 
nutrient seawater. These are plotted against run/analysis number rather than 
date or station number given that runs sometimes included 2 or 3 stations, 
with an average of 3 runs per day. A total of 97 plus 3 test runs were done.

The precision of the method was determined by monitoring the variations of the 
complete set of standards measured throughout the cruise. Results of the 
standard measurements are summarised in Table 4 and shown in Figure 19. 
Triplicate analyses were performed on the first and last sample of every 
station and sometimes a third sample was also analysed as a replicate. These 
showed that the sample variability of replicates from a given mean 
concentration was in general <0.8% (n=459). The limits of detection of this 
method were determined from the concentrations of lowest standard of each 
nutrient. The limits of detection of this method during JC032 were 0.03µmol L-1 
for PO43-, 0.15µmol L-1 for NO3- and 0.2µmol L-1 for Si(OH)4.


Table 4: Mean and variation of all standards measured, and precision of the 
         analysis at each concentration (µmol L-1)

            NO3-      Prec.    PO(4)3-   Prec.      Si(OH)4    Prec.
-----   -------------------  -----------------   -------------------
Std 1   39.85 ± 0.39  1%     3.99 ± 0.02  0.4%   120.03 ± 0.6   0.5%
Std 2   24.95 ± 0.22  0.9%   3.01 ± 0.01  0.5%    79.99 ± 0.34  0.4%
Std 3   14.79 ± 0.18  1.2%   2.01 ± 0.01  0.6%    39.92 ± 0.19  0.5%
Std 4    4.87 ± 0.1   2.0%   1.00 ± 0.01  0.9%     9.94 ± 0.07  0.7%
Std 5    1.05 ± 0.05  4.6%   0.50 ± 0.01  1.7%        1 ± 0.07  6.9%


Figure 19: Complete set of 'measured' standards plotted against the 
           'prepared or intended' concentration (left side panels). 'Measured' 
           standards plotted against respective analysis number (right side 
           panels)

Figure 20: Baselines time series. The baseline for nitrate has a trend of 
           decreasing digital units with time

Figure 21: Calibration slopes time series. These show the sensitivity of the 
           three different autoanalyser channels (i.e., nitrate, silicate and 
           phosphate), with increasing values (in digital units) indicating 
           better sensitivity. The calibration slopes for nitrate and silicate 
           decrease with time, though the slope for phosphate shows the 
           opposite trend. This shift however, does not affect analysis results 
           as suggested by the reproducibility of bulk nutrients (Figure 24)

Figure 22: Calibration correlation coefficients. All r2 values were better 
           than 0.999.


4.4  Low Nutrient Seawater

Certified Ocean Scientific Instruments Ltd. (OSIL), Low Nutrient Seawater 
(LNSW) was measured in duplicate in every run in order to test artificial 
seawater for contamination. LNSW has been also used as a quality control in 
order to check for the reproducibility of low nutrient concentrations. 
However, during the ANDREX cruise (JC030) measurements of LNSW showed 
increasing nitrate concentrations with time. This was also observed during 
JC032 (Figure 23, black dots). A simple experiment was carried out in order 
to test Nitrile gloves as a potential source of nitrate, since this was the 
only cause of contamination thought of in the lab. Two nutrient pots were 
filled with Milli-Q water. A small piece of a Nitrile glove was placed inside 
one of the pots, and the other pot was left as a control. Both were left for 
24 hours and the contents were then measured. The pot with the piece of glove 
inside produced nitrate concentrations higher than 40µmol L-1, while the 
control produced undetectable levels. The original container of LNSW has a 
screw cap and a plastic insert (similar to those used for salinity bottles). 
This insert has to be removed every time LNSW is used, thus if gloves are 
worn this would contaminate the contents gradually. We opened a new bottle of 
LNSW and decided to remove the insert from it, leaving only the screw cap. 
This seemed to have stopped the LNSW from being contaminated (see Figure 23). 
However, following the replacement of the tubing, one of the duplicates is 
affected by the carry-over from a previous high concentration standard, 
resulting in higher concentrations being calculated. This same effect can be 
seen for silicate measurements (Figure 23, green dots). Phosphate was always 
undetectable, suggesting there are no major sources of phosphate carry-over 
or contamination during the analysis or while handling the samples.

 
Figure 23: Low Nutrient Seawater (LNSW) time series. Green dots represent 
           silicate, black dots represent nitrate and grey dots represent 
           phosphate concentrations. Dotted lines show when a new LNSW batch 
           was used. Dashed line shows when the autoanalyser tubing was 
           replaced, after which the carry-over effect in the first replicate 
           of the nitrate line increased. LNSW was analysed in duplicate.
           
Figure 24: Time series of bulk nutrient seawater concentrations. The average 
           concentration was 26.4±0.4µmol L-1, 87.9±0.8µmol L-1, 1.83±0.01µmol 
           L-1 (x±σ, n=100) for nitrate, silicate and phosphate respectively.
            
Figure 25: The efficiency of the cadmium column in reducing nitrate to 
           nitrite is tested by measuring a nitrite standard of similar 
           concentration to the top nitrate standard (40µmol L-1 for JC032). 
           This figure shows the ratio of nitrate to nitrite for all analysis 
           carried out. A new cadmium column was installed at the beginning of 
           the cruise and this was further replaced on the 25/03/2009 just 
           before CTD 49 (run 34). The average cadmium reduction efficiency was 
           101±1%.
           
Figure 26: Bottle oxygen (left) and Silicate (right) parameters for the first 
           Brazil Current transect

Figure 27: Bottle oxygen (left) and Silicate (right) parameters for the second 
           Brazil Current transect

Figure 28: Bottle oxygen (left) and Silicate (right) parameters for the third 
           Brazil Current transect
 
Figure 29: Bottle oxygen (left) and Silicate (right) parameters for the main 
           transect

Figure 30: Total nitrate (left) and phosphate (right) parameters for the first 
           Brazil current transect
 
Figure 31: Total nitrate (left) and phosphate (right) parameters for the 
           second Brazil current transect

Figure 32: Total nitrate (left) and phosphate (right) parameters for the third 
           Brazil current transect
 
Figure 33: Total nitrate (left) and phosphate (right) parameters for the main 
           transect



5.  DISSOLVED OXYGEN
    (Sinhue Torres, Louise Darroch and Lily Chambers)


All stations occupied during JC032 were sampled for dissolved oxygen (DO). 
Sampling for DO was done just after CFCs were sampled. Seawater was collected 
directly into pre-calibrated glass wide neck bottles using a Tygon® tube. 
Before the sample was drawn, bottles were flushed with seawater for several 
seconds (approximately 3 times the volume of the bottle) and the temperature 
of the water was recorded simultaneously using a handheld thermometer. The 
fixing reagents (i.e., manganese chloride and sodium hydroxide/sodium iodide 
solutions) were then added. Care was taken to avoid bubbles inside the 
sampling tube and sampling bottle. Samples were thoroughly mixed following 
the addition of the fixing reagents and were then kept in a dark plastic 
crate for 30-40 mm to allow the precipitate to settle to <50% the volume of 
the bottle. Once the precipitate had settled all samples were thoroughly 
mixed for a second time in order to maximize the efficiency of the reaction. 
Analyses were carried out within two hours of sample collection.


5.1  Methods

DO determinations were made using a Winkler Ω-Metrohm titration unit (794 DMS 
Titrino) with an amperometric system to determine the end point of the 
titration (Culberson and Huang, 1987). Chemical reagents were prepared in 
advance at NOCS following the procedures described by Dickson (1994). 
Recommendations given by Dickson (1994) and by Holley and Hydes (1994) were 
adopted. In general, thiosulphate calibrations were carried out every 4-5 
days using a l.667µmol L-1 certified OSIL iodate standard. Calibration values 
are summarised in Table 5 and shown in Figure 33. Calculations of oxygen 
concentrations were facilitated by the use of an Excel spreadsheet provided 
by Dr. Richard Sanders (NOCS). This spreadsheet has been modified/corrected 
to include the calibrated dispensing volumes of the pipettes used (i.e., 
reagents and iodate standard additions have been calibrated).


5.2  Observations

1. Generally, replicate measurements of randomly selected samples are carried 
   out in order to test for reproducibility. At least 1 Niskin bottle is 
   always sampled in duplicate and any misfires are used to either duplicate 
   other Niskin bottles or to sample in triplicates. In recent cruises (e.g., 
   ASBO I and ASBO II) the mean difference between replicates was to be better 
   than 0.3µmol-O2 L-1. However, we have encountered problems with a batch of 
   oxygen bottles recently bought (July 2007). Bottle lids started falling 
   apart due to manufacturing defects. This situation prompted us to use 
   bottles of different makes and lid designs. As a consequence, the mean 
   difference of replicate samples during JC030 (ANDREX) was ≤0.8µmol-O2 L-1.

2. During JC030 it was also noticed that in many cases the first oxygen 
   measurement was producing lower concentrations than expected (e.g., 
   relative adjacent samples). It was thought one reason for this might be 
   that after the first titration, the thiosulphate within the dispenser may 
   have been slightly diluted by the sample being titrated since after the 
   endpoint is detected the system waits for a few seconds until the reading 
   is stable. This would actually indicate that in the following titrations 
   required by the thiosulphate would be higher if diluted. Another potential 
   reason was that the calibrated glass bottle designated to sample the first 
   Niskin bottle was responsible for these results. Unfortunately, due to a 
   medical emergency resulting in the early termination of JC030, these ideas 
   were not tested then.
   
3. During JC032 it was confirmed that using old bottles of different design 
   and with worn out lids produced variable results. It was thus decided to 
   form a single set with the best bottles available and this set was used for 
   most of the cruise. Reproducibility improved this way.

4. During JC032 it was also found that placing the electrode in artificial 
   seawater for at least 5 minutes before starting a set of titrations 
   produced better reproducibility of the first replicates. In addition, a 
   small amount of thiosulphate was dispensed prior to the first replicate 
   analysis. The problem of having relatively low concentrations in the first 
   oxygen bottle titrated was solved in this way.
   
5. It was decided that the first bottle would always be replicated and any 
   misfires would be used to replicate any other sample. In total, 218 
   replicates (2 or 3) were performed and the results of these showed that the 
   mean difference of replicate measurements was ≤0.6µmol-O2 L-1 (Figure 34).

6. In addition to showing calibration results, Table 5 indicates the station 
   numbers where a given calibration was used to calculate oxygen 
   concentrations. A new solution of thiosulphate was prepared on the 26th 
   March 2009, and a calibration was done right after. Later calibrations 
   however, suggested the first one was rather odd. Even when blank and 
   standard volume titres change between calibrations, the difference between 
   them is constant (Table 5, STD-BLK). Consequently, oxygen concentrations 
   from stations where the odd calibration was originally used were 
   recalculated with a calibration performed on the 31st March 2009 instead. 
   At a later date, 19 April 2009, analysis of the residuals of the 
   measurements versus the CTD oxygen sensor suggests that the stations 
   corrected for the above issue, were actually offset and these were then 
   re-calculated again with the original calibration. This issue will be 
   reviewed further.

7. Niskin bottle number 3 produced anomalous results at various stations. 
   Usually lower relative to adjacent Niskin bottles. See point 6 in the 
   nutrients section.
   
8. A calibration was done on the 17th April 2009, but produced odd values and 
   thus was not used. A final calibration done on the April 2009, confirms 
   this was the case and suggests the thiosulphate solution remained stable 
   throughout its use (Table 5).


Table 5: JC032 O2 determinations; number of thiosulphate calibrations, dates on 
         which calibrations were carried out, mean blank titre volume (BLK), 
         standard titre volume (STD), STD minus BLK, molarity of thiosulphate 
         solution and stations affected by each calibration (*new thiosulphate 
         solution prepared).

      Calib-                                            Thio-
      ration                                          sulphate  Used from
       no.       Date     BLK (mL) STD (mL)  STD-BLK  Molarity    CTD No.
      ------  ----------  -------- --------  -------  --------  ----------
        1     07/03/2009   0.0026   0.4969   0.4943    0.1998       1
        2     12/03/2009   0.0029   0.2522   0.2493    0.1981       10
        3     21/03/2009   0.0030   0.2519   0.2489    0.1984       36
        4*    26/03/2009   0.0022   0.2499   0.2477    0.1994       49
        5     31/03/2009   0.0006   0.2474   0.2468    0.2001       60
        6     02/04/2009   0.0015   0.2482   0.2467    0.2002       63
        7     06/04/2009   0.0019   0.2481   0.2462    0.2006       76
        8     10/04/2009   0.0017   0.2485   0.2468    0.2001       85
        9     14/04/2009   0.0015   0.2479   0.2464    0.2004       94
        10    17/04/2009   0.0021   0.2515   0.2494    0.1980       --
        11    19/04/2009   0.0019   0.2486   0.2467    0.2001       --


Figure 34: Dissolved oxygen analysis calibrations. Blank volume titre, 
           standard volume titre, standard minus blank (STD, STD-BLK), and 
           thiosulphate molarity. Dotted line indicates when a new thiosulphate 
           solution was prepared. Values plotted here are shown in Table 5.

Figure 35: The absolute replicate difference (µmol/L) for the oxygen bottles 
           in each CTD cast. The mean (0.61µmol L-1) and the standard deviation 
           (± 1) are specified with a red dash and black lines respectively. 
           Overlaid are the calibration numbers. Niskin 1 was always sampled 
           in duplicate. From CTD 28 onwards only one set of bottles was used 
           to sample due to deficiencies noted in the other sampling bottle 
           sets.


5.3  References

Culberson, C.H. and Huang, S. (1987), Automated amperometric oxygen 
    titration, Deep Sea Research, 34, 875-880.

Dickson, A.G. (1994), Determination of dissolved oxygen in seawater by 
    Winkler titration. Technical report, WOCE operations manual, WOCE report 
    68/91 Revision 1 November 1994.

Holley, S.E. and Hydes, D.J. (1994), Procedures for the determination of 
    dissolved oxygen in seawater. Technical report, James Rennell Centre for 
    Ocean Circulation.

Kirkwood, D. (1996), Nutrients: Practical notes on their determinations in 
    seawater. ICES Techniques in marine environmental sciences. 17, 1-25.

Siedler, G., Muller T. S., Onken R., Arhan M., Mercier H., King B. A. and 
    Saunders P. M (1996), The zonal WOCE sections in the South Atlantic. In: 
    Wefer, G., Berger W. H., Siedler G. and Webb D. J. (Eds). The South 
    Atlantic: Present and Past Circulation. Springer-Verlag, Germany, pp 
    83-104.



6.  INORGANIC CARBON PARAMETERS
    (Ute Schuster, Agatha De Boer and Shaun Scally)

The analytical equipment for the carbon parameters was set up in the seagoing 
laboratory container of the Laboratory for Global Marine and Atmospheric 
Chemistry (LGMAC), University of East Anglia (UEA), Norwich, UK. Discrete CTD 
samples were analysed for total inorganic carbon (DIC) and total alkalinity 
(TA). Additionally, a continuous, automated instrument for the analysis of 
sea surface pCO2 and atmospheric pCO2 was run throughout the cruise.


6.1  Methods

6.1.1  CTD Sampling Strategy for Inorganic Carbon

Water samples for the determination of DIC and TA were drawn from the 20L and 
10L Niskin bottles on the CTD rosette and collected in 500m1 glass bottles 
according to the Standard Operating Procedure (SOP) # 01 (Dickson et al., 
2007), to avoid gas exchange with the air. All samples were poisoned with 
mercuric chloride (100 µl per 500m1 sample) to kill all organisms that may 
alter the chemistry of the sample. Samples were kept cold and stored in the 
dark until they were put into a 25°C water bath to bring to this temperature 
prior to analysis. A total of 1666 samples were drawn from 116 CTD stations 
(last Station number 118, with Station 22 only sampled for physics, and 
Station 48 failed). Samples for DIC and alkalinity were not taken from all 
depths of each station: generally, the top two (5m and 25m or 50m) and the 
bottom two (bottom and bottom - 50) were always sampled, and in between, 
alternative depths with neighbouring stations were sampled. This way it is 
possible to sample all stations (instead of every second station) and attempt 
to analyse all samples during the cruise, yet give best resolution of data 
for optimum interpolation across the section. All stations were analysed 
during the cruise. This was comprised of all depths from a total 112 
stations, and the top two and the bottom two depths of Stations 68, 79, 104, 
and 107. Figure 36 shows the depth-longitude grid of samples analysed for DIC 
and TA during the cruise.

 
Figure 36: Depth-longitude grid of samples analysed for DIC and TA
 
Figure 37: Alkalinity (left) and dissolved inorganic carbon (right) parameters 
           for the first Brazil current transect

Figure 38: Alkalinity (left) and dissolved inorganic carbon (right) parameters 
           for the second Brazil current transect

Figure 39: Alkalinity (left) and dissolved inorganic carbon (right) parameters 
           for the third Brazil current transect

Figure 40: Alkalinity (left) and dissolved inorganic carbon (right) parameters 
           for the main transect


6.1.2  Dissolved Inorganic Carbon Analyses

Water samples were first analysed for Dissolved Inorganic Carbon (DIC, also 
denoted as Total CO2 [TCO2]). Total inorganic carbon was analysed by 
coulometry (Dickson et al. (2007) SOP #02). All inorganic dissolved carbon is 
converted to CO2 by addition of excess phosphoric acid (IM, 8.5%) to a 
calibrated volume of seawater sample. Oxygen-free-Nitrogen (OfN) gas, passed 
through soda lime to remove any traces of CO2 is used to carry the evolving 
CO2 to the coulometer cell, where all CO2 is quantitatively absorbed, forming 
an acid that is coulometrically titrated.

Two different instruments were used during JC032 for this analysis. Firstly a 
stand-alone DIC analyser consisting of a coulometer and a CO2 extraction unit 
based on the Single Operator Multiparameter Metabolic Analyzer (SOMMA), 
developed by Kenneth Johnson (Johnson et al., 1993; Johnson et al., 1985; 
Johnson et al., 1987, Johnson and Wallace, 1992), and modified at UEA (called 
hereafter refurbished SOMMA); and secondly a coulometer with a Versatile 
Instrument for the Detection of Titration Alkalinity (VINDTA), combined 
DIC/alkalinity instrument (version 3C, serial number #007, (Mintrop, 2004)). 
For both, samples were brought to 25°C prior to analysis. Two replicate 
analyses were made on each sample bottle; the coulometer counts were 
calibrated against Certified Reference Material (CRM, batch 90).

First DIC calibration has been done during the cruise for each instrument, by 
setting the mean of all DIC coulometer readings to the certified reference 
value of batch 90 (1985.61 ± 0.89µmol kg-1). Figure 40 shows these 
"calibrated" CRM values for (a) for the refurbished SOMMA instrument and (b) 
for the VINDTA #007, together with the mean, control limits and warning 
limits (Dickson et al., 2007); whole-cruise CRM values varied by ± 3.3µmol kg-1 
for the refurbished SOMMA and by ± 3.4µmol kg-1 for the VINDTA #007.

Post-cruise data quality control will include calibration of DIC readings for 
each coulometer cell used during JC032, identification and removal of further 
outliers, and accounting for the instruments' drift during the cruise.

6.1.3  Titration Alkalinity Analyses

The alkalinity measurements were made by potentiometric titration (Dickson et 
al., 2007) with two VINDTA instruments (#004 and #007, version 3C, Mintrop, 
2004). The systems use a highly precise Metrohm Titrino for adding acid, an 
ORION-Ross pH electrode and a Metrohm reference electrode. The pipette 
(volume approximately l00m1), and the analysis cell have a water jacket 
around them. The titrant (0.lM hydrochloric acid, HC1) was made in the home 
laboratory; Batch A was used throughout the cruise. Samples on Vindta #004 
were run after DIC analysis on the refurbished SOMMA (see above). Samples on 
the VINDTA #007 were run for both DIC and alkalinity at 25°C. Replicate 
analyses were run for all samples. Alkalinity values were calibrated using 
CRM batch 90 (certified at 2216.00 ± 0.52µmol kg-1).

Figure 43 shows alkalinity CRM values recorded by (a) VINDTA #004 and (b) 
VINDTA #007, showing a whole-cruise variation of ± 9.3µmol kg-1 on VINDTA #004 
and ± 5.2µmol kg-1 on VINDAT #007 after preliminary data quality control 
during the cruise.
 

Figure 41: Calibrated CRM values for (a) for the refurbished SOMMA instrument 
           and (b) for the VINDTA #007.
 
Figure 42: Differences between replicates of all samples analysed for DIC, (a) 
           for the refurbished SOMMA instrument and (b) for the VINDTA #007; 
           differences were 0 ± 2.4µmol kg-1 for the refurbished SOMMA and -0.7 
           ± 1.9µmol kg-1 for the VINDTA #007.
 
Figure 43: Alkalinity CRM values recorded by (a) VINDTA #004 and (b) VINDTA 
           #007.
 
Figure 44: The differences between replicates of all samples analysed for 
           alkalinity (a) for the VINDTA #004 and (b) for the VINDTA #007


The alkalinity cell stirrer of VINDTA #004 stopped working on 9 March 2009, 
resulting in a few hours of downtime. The quality of alkalinity measurements 
made immediately before and after this will be investigated during 
post-cruise quality control. A major technical/electrical breakdown occurred 
on VINDTA #004 at approximately 01:00 on 4 April 2009, when the peristaltic 
pumps and temperature sensors stopped working; this resulted in almost 12 
hours of downtime for repairs. Following the repairs, calibration by CRM 
revealed alkalinity readings approximately 30µmol kg-1 below expected values, 
which recovered during the following 48 hours. A low CRM outlier occurred on 
25 March 2009, the reason for this is going to be investigated during 
post-cruise quality control.

Post-cruise data treatment will include recalculation of alkalinities with 
CTD temperature, salinity, and nutrients, after recalibration of alkalinity 
pipettes' volume and temperature sensors. Post-cruise data quality control 
will then include identifying and removing further outliers, and accounting 
for drift in the instruments' alkalinity, especially for VINDTA #007.

The differences between replicates of all samples analysed for alkalinity are 
shown in Figure 44 (a) for the VINDTA #004 and (b) for the VINDTA #007; 
differences were 0 ± 2.4µmol kg-1 for the VINDTA #004 and 0.4 ± 2.5µmol kg-1 
for the VINDTA #007.

6.1.4  Continuous Seawater Supply for Underway pCO2

The ship's seawater supply provided a high volume of water for underway 
sampling. A screw pump transported the water from 5m depth at the bow to the 
UEA laboratory container on the aft deck. Temperature and salinity of the 
intake water were determined by the ship's remote sensor (temperature) and 
the thermosalinograph (TSG) (salinity) in the CTD bottle annex. In the 
laboratory container the seawater passed an oxygen sensor, a strainer with a 
bypass, and finally the equilibrator for pCO2 analysis. The seawater flow 
across the equilibrator was kept fairly low in order to avoid bubbles leaving 
the equilibrator. Flow across the bypass was kept high.

6.1.5  Partial Pressure of CO2 in Surface Water and Marine Air

Continuous measurements of pCO2 (read as xCO2 in ppm or µmol mol-1) in surface 
water and marine air were made throughout the cruise with the UEA underway 
pCO2 system. Marine air was pumped through tubing from the deck, to a height 
of about 16m above the bridge (Monkey Island). Seawater from the ship's 
surface water supply was introduced at a rate of 2-3L min-1 into the 
equilibrator. Two Pt-100 probes accurately determined the water temperature 
in the equilibrator. A long vent kept the headspace of the equilibrator close 
to atmospheric pressure. The CO2 content and the moisture content of the 
headspace were determined by an infrared LI-COR 7000 analyser. The analysis 
of the CO2 content in the headspace was interrupted for that of the CO2 
content in marine air (20 minutes per 6 hours) and in three CO2 standards (30 
minutes per six hours each). Samples from the equilibrator headspace and 
marine air were only dried sufficiently to avoid condensation in the 
detector. Gas standards bought from BOC amounting to mixing ratios of 248.44 
± 0.03 (25-B18), 350 (35-B04) and 455.59 ± 0.08µmol CO2 mol-1 (45-B18) had been 
calibrated against certified NOAA standards. The analyses were carried out at 
a flow speed of 100m1 min-1 through the LI-COR at a slight overpressure. A 
final analysis for each parameter was made at atmospheric pressure with no 
flow. The flow and overpressure did not have a discernable effect on the CO2 
and moisture measurements, once corrections for the pressure had been 
performed. The correction by Takahashi et al. (1993) will be used to correct 
for warming of the seawater between the ship's water intake and the 
equilibrator. The pCO2 measurements will be time stamped by our own GPS 
positions. The precision and accuracy of the pCO2 data are likely to be 
approximately 1µatm, as determined during previous cruises (e.g., Bakker et 
al., 2001).


6.2  References

Dickson, A.G., Sabine, C.L., and Christian, J.R. (Eds.) (2007) Guide to best 
    practices for ocean CO2 measurements, PICES Special Publication 3, pp. 
    191

Johnson, K.M., King, A.E., and Sieburth, J.M. (1985) Coulometric TCO2 analyses 
    for marine studies; an introduction, Marine Chemistry, 16, pp. 61-82.

Johnson, K.M., Sieburth, J.M., Williams, P.J.1., and Braendstroem, L. (1987) 
    Coulometric total carbon dioxide analysis for marine studies: automation 
    and calibration, Marine Chemistry, 21, pp. 117-133.

Johnson, K.M., and Wallace, D. W.R. (1992) The Single-Operator Multiparameter 
    Metabolic Analyzer for total carbon dioxide with coulometric detection, 
    DOE Res. Summary, 19, pp. 1-4.

Johnson, K.M., Wills, K.D., Butler, D.B., Johnson, W.K., and Wong, C.S. 
    (1993) Coulometric Total Carbon-Dioxide Analysis for Marine Studies - 
    Maximizing the Performance of an Automated Gas Extraction System and 
    Coulometric Detector, Marine Chemistry, 44, pp. 167-187.



7.  CHLOROFLUOROCARBONS (CFCs) AND SULPHUR HEXAFLUORIDE (SF6)
    (David Cooper, Steve Woodward and Andrew Brousseau)


7.1  Sample Collection and Analysis Technique

Water samples for CFCs (F11, F12, F113 and CCL4) and SF6 were collected from 
20L or 10L Niskin bottles attached to the CTD sampling rosette. The samples 
were analysed onboard as soon as possible after collection using a coupled SF6 
and CFC system. The method combines the LDEO CFC method (W. Smethie, E. 
Gorman) and the Plymouth Marine Laboratory (PML) SF6 method (Law et al.) with 
a common valve for the introduction of gas and water samples. This system has 
the advantage of simultaneous analysis of SF6 and CFCs from the same water 
sample, but takes longer than the individual systems. The throughput time 
averaged just less than 30 minutes per sample. Representative samples were 
collected from CTD bottles to ensure the optimum depth coverage, since not 
all bottles could be analysed in the time available. Samples were collected 
in 500m1 ground glass stopper sealed bottles. The bottles were rinsed with 
sample water, and then filled from the bottom using Tygon tubing. The bottles 
were overflowed at least one full time before being sealed. Full bottles were 
then stored in the sampling hanger in cool boxes containing deep cold 
seawater. Ice packs were added to maintain a temperature below 5°C. As per 
WOCE protocol, CFC/SF6 samples were the first samples drawn from the Niskin 
bottles.

The samples were introduced to the system by applying nitrogen (N2) pressure 
to the top of the sample bottles, forcing the water to flow through and fill 
a 25cm3 calibrated volume for CFCs and a 300cm3 calibrated volume for SF6. The 
measured volumes of seawater were then transferred to separate purge and trap 
systems. Each purge and trap system was interfaced to an Agilent 6890 gas 
chromatograph with electron capture detector (GC-ECD). The samples were 
stripped with N2 and the CFCs and SF6 were respectively trapped at -80°C on a 
Unibeads trap and at -100°C Porapak Q trap immersed on the headspace of 
liquid nitrogen. Then the traps were heated to 100°C for CFCs and 60°C for SF6 
and injected into the respective gas chromatograph. The SF6 separation was 
achieved using a molecular sieve packed 2m main column and 2m buffer column. 
The CFC's separation was achieved using a 1m Porasil B packed pre-column and 
a 1.5m carbograph AC main column. The carrier gas was pure oxygen-free 
nitrogen, which was cleaned by a series of chemical scrubbers.

Air samples were periodically collected via a tube running from the bow of 
the ship, pumped into the laboratory. The tube was flushed for approximately 
a half hour before beginning analysis. Air samples were trapped in an 
identical manner to standards, using either a 1ml or 2m1 sample.


7.2  Calibration

The CFC/ SF6 concentrations in air and water were calculated using an external 
gaseous standard. The standard supplied by NOAA corresponds to clean dry air 
slightly enriched in SF6, F11 and CCL4. The calibration curves were made by 
multiple injections of different volumes of standard that span the range of 
tracers measured in the water. Examples of fitting calibration data are given 
in Figure 45. Complete calibration curves were made at the beginning, middle 
and end of the cruise. The changes in the sensitivity of the systems were 
checked by measuring a fixed volume of standard gas every 8-10 runs. The 
preliminary data presented in this report have not been adjusted for any such 
variation, which should be minimal for all gases with the exception of CCL4.

A blank correction may be used to compensate for any trace CFC or SF6 
originating from the sampling bottles, handling and/or measurement 
procedures. This correction is normally estimated from analysis of either 
samples collected in waters that are free of CFCs or water collected after 
sparging all the CFCs out of a sample. Zero CFC water was not observed in the 
South Atlantic Ocean, so blanks were run by resparging a sample from the deep 
water. In a preliminary analysis of the data, there does not appear to be any 
systematic contamination, and no blank corrections have been applied to the 
preliminary data presented in this report.


7.3  Precision and Accuracy

The precision of the measurements can be determined from duplicate samples 
drawn on the same Niskin bottles. During this cruise, duplicate samples were 
routinely drawn from the surface seawater (nominal 5m) Niskin bottle, time 
permitting. During JC032, 27 duplicate samples were analysed, from which we 
calculate the following precision, expressed as the ratio of standard 
deviation to mean concentration:


                        SF6   CFC12  CFC11  F113   CCL4
                       -----  -----  -----  -----  -----
                       2.42%  1.36%  0.92%  3.72%  4.51%


Additional factors affecting accuracy include sparging and trapping 
efficiency (functions of temperature and flow rate), final determination of 
calibrated volumes, and chromatographic considerations, such as interferences 
and baseline variation. These effects will all be assessed and accounted for 
in the final dataset, but have not been addressed for the purpose of this 
preliminary report. Particular difficulty was noted for CCL4, where 
significant variation in standards was noted.

Any potential effects from sample deterioration or contamination in storage 
were minimised by storing them at low temperature and analysing the samples 
as soon as possible after collection. Most samples were analysed within a day 
of collection.


7.4  Data

This data set comprises the third part of three consecutive South Atlantic 
cruises on the RRS James Cook by the UEA CFC/SF6 team. A total of 1706 samples 
were analysed during JC032 along the four transects, with 283 samples on the 
two initial coastal transects and 1423 samples along the 24°S transect of the 
South Atlantic. A brief summary of some aspects of the data is presented 
here. Final interpretation and validation will be carried out at UEA by Drs. 
A. Watson and M.-J. Messias.


Figure 45: Calibration data from JC032. Units are shown as mol/L equivalent 
           in seawater.

Figure 46: Combined surface seawater data from the 24°S JC032 transect. Units 
           are mols/L.
 
Figure 48: CFC 11 (left) and CFC 12 (right) parameters for the second 
           Brazil current transect
 
Figure 50: CFC11 (left) and CFC12 (right) parameters for the main transect
 

Figure 51: F113 (left) and CCL4 (right) parameters for the first Brazil 
           current transect

Figure 52: F113 (left) and CCL4 (right) parameters for the second Brazil 
           current transect
 
Figure 53: F113 (left) and CCL4 (right) parameters for the third Brazil 
           current transect

Figure 54: F113 (left) and CCL4 (right) parameters for the main transect
 
Figure 55: SF6 parameter for the first Brazil current transect

Figure 56: SF6 parameter for the second Brazil current transect
 
Figure 57: SF6 parameter for the third Brazil current transect

Figure 58: SF6 parameter for the main transect




8.  INSTRUMENTATION
    (Paul Duncan)


8.1  EM-120 Multibeam Echo Sounder

This system has been run off and on for the majority of the duration of the 
cruise, with the expectation that the raw data will be taken back to NOCS and 
processed there by other scientific personal that specialise in multi-beam 
processing. The Uruguayan Observer has also been given a subset of the data, 
as they have the necessary processing software to clean up the data.

For the majority of the cruise, the weather conditions have been very good, 
and so the data quality has also been good. The system is, however, still 
suffering from the "banding problem" which has been reported on previous 
cruises. In addition it may have picked up an additional fault, which appears 
as one or two deep trenches, on either side of the centre of the ship's 
track. Kongsberg hydrographic personnel are due to sail on JC034T, and 
hopefully they will be able to diagnose the problems.

There are two Valeport Midas sound velocity profilers on board, one of which 
is in calibration, and has (at the time of writing) been used on two CTD 
casts. More batteries have been ordered for this unit, as it will be needed 
on JC034T. The other profiler will be sent for calibration when the vessel 
reaches Southampton.


8.2  EA-600

Hard copy output from this system was finally set up with some shore-side 
support from Chris Barnard. Only one previous cruise has used the hard copy 
facility of the EA-600, but I suspect this will now become the norm.

There is a problem with the EA-600. The computer often looses contact with 
the transceiver (which it talks to via a dedicated network link). The only 
solution at the moment seems to be power-cycling the transducer and then 
restarting the EA-600 software.


8.3  Vessel-Mounted ADCP

The two RDI Ocean Surveyor ADCP systems (75 and 150KHz) were used during the 
cruise with the port drop keel lowered, to help give better data. The plan 
was to copy the data across to the data32 area every so often, just using the 
Windows Explorer utility. Unfortunately, this would not work, as the system 
would claim that we did not have permission to read the files that were to be 
transferred. Eventually it was found that the data could be transferred using 
PSFTP (A Windows secure FTP client). Unfortunately, that was not the end of 
the matter, as after a few days, one or other of the machines' network stacks 
would crash, necessitating a reboot in order to transfer the data.

Network access to the Main Lab LaserJet was set up during this cruise (it had 
already been set up, but the IP address was incorrect). Again, this worked 
for a while, but once the networking had crashed, there was no printing until 
the next reboot. We may have to consider trying alternative network cards in 
these systems. Currently, the systems are using networking hardware 
integrated into their motherboards.


8.4  Chernikeeff EM Log

During the last 24 hours at sea, an attempt is being made to obtain a better 
EM Log calibration, although this is being hampered by adverse wind 
conditions, which will probably preclude accurate low-speed data points.


8.5  TECHSAS

Due to worries over the accuracy (and possible imminent failure) of the FSI 
seasurface temperature sensor, the principal scientist asked about the 
possibility of getting access to the sea-surface sound velocity data (from 
the AML SmartSV) used by the multibeam echo sounders.

A small cable was made to split the RS-232 signal from the probe, so that it 
could also be sent to the TECHSAS system (via the ship's FieldBus wiring) as 
well as to the EM-120 computer. Once there, the raw message was observed on 
the TECHSAS system, and initially just displayed on the screen.

After a day or so, a TECHSAS module had been written to log the data. The 
module suffered from two problems. Firstly the displayed sound velocity data 
has a few extra characters added to it, which appear to come from the maximum 
and minimum data limits. This does not affect the logged data. The second 
problem was that the probe was putting out data at quite a high frequency - 
one that was just not necessary. After a while a modification to the module 
was made so that it logged just one in every ten data values. This works, but 
now, when TECHSAS logging is stopped, the module does not seem to want to 
stop logging with all the other modules.

The scientific party identified TECHSAS time-keeping problems, and it seems 
that they only affect modules that are used by the SSDS (Scientific Ship 
Display System-AKA little green boxes). TECHSAS imparts data to the SDSS in 
two parts, firstly, the modules that log the necessary data (e.g. GPS, Winch, 
Gyro) re-write a small file with the latest message. Secondly, a small shell 
script reads these files and transmits the data over an RS-232 line to the 
SSDS distribution box. The only thing I can think of that can be causing 
these timing problems, is that the overhead of writing to these additional 
files somehow adversely affects the time keeping of the modules. If this is 
the case, a new program, monitoring the UDP data broadcasts from TECHSAS 
could write data to the RS-232 line without the need for any disc access, or 
any need for the TECHSAS modules to write to the disc.


8.6  Seapath 200 logging

The Seapath 200 positioning system was purchased by Platform Systems after it 
was noted that the Applanix PosMV was the only system providing attitude data 
to the vessel's dynamic positioning system. In addition, at the time, the 
Seapath DPS-116 was the only system providing position information.

The Seapath 200 was purchased and set up as GPS 2 on the bridge DP system. Up 
until this cruise, its data has never been used scientifically. After 
problems with the system (and it not getting adequate differential 
corrections from the Seastar receiver) it was noted in the manual that the 
system had an Ethernet port and could output NMEA data over UDP.

The system was connected to the ship's network and configured to output both 
position and attitude data on two different UDP ports. The TECHSAS system was 
then configured to listen for the information on those ports. Unfortunately, 
it seems that when the Seapath system sends multiple NMEA sentences (e.g. a 
GGA and VTG) at the same time, it does not split them into separate packets, 
and the current TECHSAS modules ignore all but the first NMEA sentence in a 
packet. The way to get around this is to add some code to check for line 
breaks within a packet, and then parse the individual messages within a 
packet. At present this has not been done, but may be done by the end of the 
JC034T trials.

It should be made clear that the Seapath 200 has not been a total disaster. 
Basic position information has been successfully logged for a large part of 
JC032, and Ben Moat has done some work indicating that the Seapath 200 may 
give significantly better position data than the Applanix PosMV. Consequently, 
in future cruises we should consider making the Seapath 200 position the primary 
fix file in Level C bestnav processing.


8.7  Level C

With the additional data being logged via TECHSAS, changes were made to the 
fromtechsas.ini file to enable the data to be logged on the Level C streams.

Normal relmov and bestnav navigational processing was performed with the 
PosMV position as primary fix file and the Seapath DPS-116 as secondary fix 
file.

Since the EA-600 was setup to use 1500m/s as its sound velocity, prodep was 
used to correct the depth for Carter Area.

Windcalc was also run to provide a stream with absolute wind speed.


8.8  SSDS

A wiring problem was corrected on the SSDS so that displays were available at 
both the forward and aft ends of the Deck Lab.


8.9  Mk II Splitter

A Prototype Mk II splitter system was installed at the start of the cruise, 
and a splitter cable installed so that it received the same messages that the 
Mk I splitter received. Further development of the software was undertaken 
during the cruise to change it from being a "hard coded" system to using a 
configuration file (currently identical to the setup of the original Mk I 
splitter). This will allow the relatively easy addition of a user interface 
(web or terminal-based) later on. It is intended to give the system a major 
test during the passage back to the UK and during JC034T. One minor barrier 
to the full acceptance of this system is minor problems with the performance 
of the Edgeport 416 under Linux. We are in contact with Digi, (the 
manufacturers) and they are working on a solution. This problem affects not 
only us, but also Deep Platforms at NOCS, and also many users outside of NOCS.


8.10  Dartcom HRPT/CHRPT System

The system was primarily used to have a quick look at what the weather was 
like in the immediate area around the vessel. Both visible light and JR 
(night-time) images were collected from the NOAA and Chinese satellites. 
There were problems with the acquisition computer setup towards the beginning 
of the cruise, but these were quickly solved. There is also an intermittent 
problem with the Orbit dish controller failing to respond to commands from 
the acquisition computer. Normally a restart of the controller would remedy 
this.


8.11  Network Storage

Data32, a 300GB external RAID I array on the Cook3 workstation, was used for 
shared storage of various data. CTD and LADCP data were immediately copied 
over after each cast. Access to the area was available to all scientists on 
their laptop computers, as well as both of the Sun workstations installed in 
the Main Lab. The area was backed up to LTO-2 tape every evening using tar.


8.12  End of Cruise Media

At the end of the cruise LTO-2 tapes of Level C data, TECHSAS data and the 
data32 area will be given to the principal scientist.




9.  UNDERWAY TEMPERATURE AND SALINITY
    (Lorna McLean and Ben Moat)


9.1  Introduction

Near surface oceanographic parameters were measured by sensors located in the 
nontoxic supply. These included fluorescence, light visibility 
(transmittance) of the surface waters, and an FSI thermosalinograph measuring 
conductivity, housing temperature and sea surface temperature. Salinity was 
not measured directly. The FSI salinity was calculated from the conductivity 
variable using the script mcalc_sal.m. The conductivity ratio was calculated 
by sw_condr.m, which divides the measured conductivity by the conductivity at 
S=35psu, T=15°C, p=0db. Salinity was calculated from the conductivity ratio 
using sw_salt.m, which uses the UNESCO algorithm from Fofonoff and Millard, 
(1983). Pressure was set to zero. The housing temperature was used for 
temperature, since this is the temperature at which the conductivity is 
measured by the instrument. A new TSG system (SBE45 microTSG) provides 
another source of underway salinity data. In contrast to the FSI, the 
salinity was calculated in real time using the SBE45 housing temperature and 
conductivity. The sea surface temperature (SST) was measured at a depth of 
5.5m below the sea surface. This section describes the calibration of the 
underway temperature (Section 9.2) and salinity (Section 9.3) measurements.


Table 6:  Underway SST and salinity instrument details

                              Calibration 
                  Serial     Y=C0+C 1*x+C2       Sensor           Parameter 
  Instrument      number      *X^2+C3*X^3       position          (Accuracy)
---------------  ---------  ----------------  --------------  ------------------
FSI OTM          1374       C0 = -1.4333E-2   Water sampling  Thermosalinograph
                            C1 =  l.00118E0   room            -housing 
                            C2 = -1.0617E-4                   temperature
                            C3 =  2.16844E-6 
---------------  ---------  ----------------  --------------  ------------------
FSI OCM          1333       C0 =  0           Water sampling  Thermosalinograph
Conductivity                C1 =  1           room            -conductivity
---------------  ---------  ----------------  --------------  ------------------
FSI OTM Remote   1370       C0 =  3.91747E-2  Near intake     Sea surface 
temperature                 C1 =  1.00087E0                   temperature
                            C2 = -7.20672E-5
                            C3 =  1.40575E-6
---------------  ---------  ----------------  --------------  ------------------
Wetlabs          WS3S-351P  C0 = -0.8721      Water sampling  Fluorescence
Fluorometer                 C1 =  15.3        room
---------------  ---------  ----------------  --------------  ------------------
Seatech          CST1132PR  C0 = -0.01337     Water sampling
Transmissometer             C1 =  0.2157      room
---------------  ---------  ----------------  --------------  ------------------
Nudam 6017,                                                   Voltage converters 
      6018                                                    +/- 5V
---------------  ---------  ----------------  --------------  ------------------
SBE45 Micro TSG  0231                         Water sampling  Conductivity,
                                              room            temperature


9.2  Calibration of Underway Sea Surface Temperature

The sea surface temperature (SST) was measured by an FSI remote temperature 
module located close to the non-toxic supply intake on the hull. The SST 
measurements were compared to the surface temperature measurements from the 
primary (temp) and secondary (temp 1) sensors on the CTD frame. Measurements 
were selected at 5db and 7db, which are the approximate depths of the remote 
temperature intake. Figure 59 shows that the remote temperature sensor 
overestimates the CTD measurements by 0.132°C (s.d. 0.07). The offset was 
near constant over the temperature range encountered during the cruise. The 
scatter in the data above temperature differences 0.2°C is believed to be 
from days when the top of the mixed layer was slightly stratified due to 
periods of low winds and strong solar heating of the surface waters.


Figure 59: Comparison of CTD surface temperature measurements with the FSI 
           remote temperature


The FSI and SBE45 systems in the water sampling room record their housing 
temperatures, which are used in the calculation of underway salinity. Figure 
60 shows that the housing temperatures from both systems agreed with each 
other to within 0.018°C (s.d. 0.01) and indicates no drift between systems 
during the cruise.

Figure 60 shows that the SBE45 temperature agrees to within 0.007°C (s.d. 
0.04) of the SST. With such a good agreement the SBE45 housing temperature 
may be used as a measure of the sea surface temperature. However, caution 
must be used if the SBE45 housing temperature was to be used as an 
approximation of the remote temperature outside the temperature range of this 
cruise. It is currently unknown how the two instruments correlate at lower 
sea surface temperatures.
 

Figure 60: A comparison of the SBE45 housing temperature with the FSI 
           housing temperature and the SST



9.3  Calibration of Underway Salinity Data

9.3.1  Introduction

Two approaches were taken towards the calibration of the underway salinity 
data. The salinities measured by the FSI and SBE45 were compared with; 1) 
salinity samples collected from the non-toxic water supply outflow, and 2) 
the surface salinities measured from near surface CTD.

Water samples from the TSG outflow pipe were collected in 200m1 flat glass 
bottles every 4 hours. Before each collection, the hose connected to the 
outflow pipe was flushed with the sample water for several seconds (on 
occasions when the supply was not already running), and the sample bottles 
were rinsed twice with the sample water. Bottles were filled to halfway up 
the shoulder and the necks were wiped dry to prevent salt crystallisation at 
the bottle opening. The bottles were closed using airtight single-use plastic 
inserts and secured with the original bottle caps. The samples were stored in 
open crates and left beside the salinometer in the controlled temperature 
laboratory for a minimum of 24 hours before analysis. This allowed their 
temperature to adjust to the ambient temperature of the laboratory. A total 
of 242 TSG samples were taken over the duration of the cruise.

The conductivity ratio of each sample was measured using the salinometer, and 
the corresponding salinity value was calculated using the OSIL salinometer 
data logger software, and stored in a Microsoft Excel spreadsheet. The 
measured salinities of the samples were transferred to a text file, along 
with the date and time of collection. This file was converted to Mstar 
format, and the dates and times were converted into seconds since midnight on 
1st January 2009.

Another method for calibrating the underway salinity is to use the surface 
salinity values from the near surface CTD casts. On JC032, 118 CTD casts were 
taken between days 66 to 109.

9.3.2  Underway Salinity Compared to Surface CTD Measurements and Bottle 
       Samples

Figure 61 shows that the FSI salinity measurements had a strong dependence on 
SST, e.g. a difference of 3psu at 28°C.

FSI offset = (12.84-0.551)*SST         R2 = 0.99                            (1)

The large differences in the FSI measurements with CTD and bottle samples 
below an SST of 23°C are produced by the FSI over-reading the salinity during 
the second day of the cruise. It is unknown why the FSI overestimated the 
SBE45 shortly after it was switched on. These data points were excluded from 
the FSI data to generate Eq. 1.

 
Figure 61: SBE45 and FSI underway salinity compared to bottle and CTD 
           measurements. The SST was corrected by comparison to the CTD 
           (Section 2).


Figure 62 shows that the SBE45 overestimated the salinity from the combined 
bottle and near surface CTD measurements by 0.034psu (s.d. 0.042) and was 
corrected accordingly. The FSI data were not corrected as the SBE45 performed 
well throughout the cruise.


9.4  References

Fofonoff N.P. and Millard R.C., (1983), Algorithms for Computation of 
    Fundamental Properties of Seawater, UNESCO Technical Papers in Marine 
    Science, 44.
 

Figure 62: Calculated salinity difference between SBE45 and bottle and CTD 
           data respectively




10.  SURFACE METEOROLOGICAL SAMPLING SYSTEM (SURFMET)
     (Ben Moat, Lorna McLean and Peter Keen)


10.1  Introduction

The surface meteorological conditions were measured throughout the cruise. A 
brief discussion of the performance of the meteorological sensors is given in 
this section. Appendix A lists significant events such as periods when data 
logging was stopped, and Appendix B contains figures showing a time series of 
the meteorological data. All times refer to UTC.


10.2  Instrumentation

The RRS James Cook was instrumented with a variety of meteorological sensors 
to measure; air temperature and humidity, atmospheric pressure, short wave 
radiation, and wind speed and direction. These are logged as part of the 
SURFMET system.

The meteorological instruments were mounted on the ship's foremast (Figure 
63) in order to obtain the best exposure. The height of the instruments above 
the foremast platform is approximately 2.81m.


10.3  Routine Processing

Files were transferred from the onboard logging system (TECHSAS) to the UNIX 
system on a daily basis, using the script mday_00_get_all.m. The raw SURFMET 
data files have names of the form met_jc03l_d***_raw.nc, where *** represents 
the day number. These were copied to met_jc03l_d***_edit.nc for editing.

The 1Hz SURFMET data were adjusted according to the calibration equations 
specific to the serial number of each instrument. This was carried out by the 
mcalib_surfmet_jc032.m script. Spikes in the data were assigned an absent 
data value using mplxyed.

True wind speed and direction were calculated using the script 
'truewindl_surfmet_jc032' as follows. Bestnav navigation data were merged on 
to the SURFMET data. To avoid problems associated with averaging wind 
direction over time, the relative wind speed, ship's heading and course made 
good were converted to eastward (u) and northward (v) components, using the 
script muvsd.m. The true wind direction was calculated and the data were 
averaged into 1-minute bins. The average directions were calculated by their 
respective u and v components and contained in the file 
(met_jc031_d***_avg.nc).


10.4  Sensor Performance

10.4.1  Air Temperature and Humidity

The Vaisala sensor was located on the starboard side of the foremast 
platform. A possible bad connection between the two sections of the sensor 
produced negative temperatures and very low humidity measurements on day 65. 
This was fixed before sailing. Unfortunately the sensor failed again on day 
73 with similar problems. The wiring was checked and the connection between 
the sensor sections cleaned on day 77 and remained stable for the rest of the 
cruise.

10.4.2  Wind Speed and Direction

The Gill Windsonic was located on the foremast platform. Only data from one 
anemometer was logged so no comparisons with other anemometers were made. A 
large spotlight has been placed on the front edge of the foremast platform 
potentially increasing the flow distortion in that region (Yelland et al., 
1998; Moat and Yelland, 2008). This will bias the wind speed measurements 
made from foremast anemometers, especially when the anemometers are directly 
downwind of the spotlight.

10.4.3  TIR and PAR Sensors

The ship carried two total irradiance sensors, one (PTIR) on the port side of 
the foremast platform and the other (STIR) on the starboard. These measure 
downwelling radiation in the wavelength ranges given in Table 7. The STIR and 
SPAR sensor channels were logged through the wrong channels during the start of 
the cruise. This was corrected on day 68. A comparison of the TIR short-wave 
sensors showed that both sensors were in good agreement. The daily mean 
difference in the measured short-wave values was below 1.7W/m2 (standard 
deviation 10W/m2). In addition to the TIR sensors the ship carried two PAR 
sensors, which measured downwelling radiation in the wavelength ranges given in 
Table 7. The difference between the two PAR sensors increased linearly with 
increasing short wave radiation (offset = -0.039*SPAR-1.1), e.g. the starboard 
PAR sensor over-reads the port PAR sensor by 14.5W/M2 at an incoming shortwave 
of 400W/m2. It was not possible to check the serial numbers on the PAR sensors 
during the cruise so it is not clear if the correct calibrations were applied. 
The instrument was not replaced during the cruise.


Figure 63: Schematic diagram showing the instruments on the foremast 
           platform.


Table 7: SURFMET instrument details

                             Calibration 
                  Serial    Y=C0+C 1*x+C2      Sensor               Parameter 
  Instrument      number     *X^2+C3*X^3      position              (Accuracy)
---------------  ---------  -------------  --------------  ----------------------------
Vaisala HMP45A   D1330038   C0=0           Starboard       Air temperature and humidity
                            C1=1           side foremast   Humidity ±1.0%
                                                           Temperature ±0.13°C
---------------  ---------  -------------  --------------  ----------------------------
PAR              28563      C1=0.9285      Port side       PAR sensors
Skye energy      28558      C1=0.8453      Starboard side  1.077mV/100W/m2
sensor                                                     1.049mV/100W/m2
(400-700nm)
---------------  ---------  -------------  --------------  ----------------------------
TIR
Kipp and Zonen   047462     C1=0.8453      Port side       11.83 µV/W/m2
CMB6             047463     C1=0.9425      Starboard side  10.61 µV/W/m2
(335 to 2200nm)
---------------  ---------  -------------  --------------  ----------------------------
Vaisala PTB100A  RO45005    C0=4.79732E-1  ?
Atmospheric                 C1=9.99417E-1
pressure
---------------  ---------  -------------  --------------  ----------------------------
Gill Windsonic   064537                    Foremast        Wind speed and direction
anemometer


10.5  References

Moat, B.I. and M.J. Yelland, (2008), Going with the flow: state of the art 
    marine meteorological measurements on the new NERC research vessel, 
    Weather, 63(6), 158-159.

Yelland, M.J., Moat B.I., Taylor P.K., Pascal R.W., Hutchings J. and Cornell 
    V.C., (1998), Wind stress measurements from the open ocean corrected for 
    airflow distortion by the ship, Journal of Physical Oceanography, 28, 
    1511-1526.





                    APPENDIX A:  LIST OF SIGNIFICANT EVENTS



Day 65: (in Montevideo): Intermittent Vaisala air temperature humidity 
        sensor fault. Check connections on foremast. No reason found but 
        sensor functioning.

Day 68: Starboard PAR/TIR radiation sensors changed to correct SURFMET 
        logging streams.

Day 73 to 77: Vaisala air temperature humidity sensor failed. 
        Possible loose connection. Repaired on Day 77.





              APPENDIX B:  TIME SERIES OF MEAN METEOROLOGICAL DATA



Figures 64 - 72 show time series of 1 minute averages of the mean 
meteorological data. Only basic quality control criteria have been applied to 
these data. Each page contains five plots showing different variables over a 
five-day period.

Top panel - the air temperature from the Vaisala sensor plus sea surface 
temperature (temp_r) from the FSI thermosalinograph.

Upper middle panel - downwelling radiation from the two shortwave TIR and PAR 
sensors, all in W/m2.

Central middle panel - relative wind direction (reldd = 180° for a wind on the 
bow) and true wind direction (TRUdir) from the starboard R3 anemometer. The 
ship's true heading is also shown.

Lower middle panel - relative (RELspd) and true wind (TRUspd) speeds in 
m/s from the anemometer. The ship's speed over the ground is also shown in m/s.

Bottom panel - Atmospheric humidity from the Vaisala sensor and the atmospheric 
pressure.


Figure 64: Meteorological data for days 65 to 70. Note the change of channels 
           in the irradiance sensors on day 65.
 
Figure 65: Meteorological data for days 70 to 75
 
Figure 66: Meteorological data for days 75 to 80
 
Figure 67: Meteorological data for days 80 to 85
 
Figure 68: Meteorological data for days 85 to 90
 
Figure 69: Meteorological data for days 90 to 95
 
Figure 70: Meteorological data for days 95 to 100
 
Figure 71: Meteorological data for days 100 to 105
 
Figure 72: Meteorological data for days 105 to 109



11.  NAVIGATION
     (Lorna McLean and Ben Moat)


11.1  Instrumentation

11.1.1  POSMV

The Applanix POSMV is the primary GPS system used for science. Three data 
streams are output by the RVS system at 1 Hz. 'posmvpos' contains the ships 
position whilst the 'posmvtss' contained heading information. The 'gyropmv' 
data stream contains the posmvtss heading information rounded to 1 decimal 
place and is not analysed in this report. Occasional dropouts of the DGPS 
would happen, particularly towards the centre of the basin. The posmvpos data 
were used in the LADCP processing and as a position in the bathymetry and 
SBE45 data files.

11.1.2  Seapath systems

Two Seapath systems are used on the ship. The Seapath dps 116 is the primary 
GPS unit for the ship's dynamic positioning system and is believed to be very 
accurate. The data are logged via the 'dps 116' rvs data stream. In addition 
the ship possesses a Seapath 200 system as a secondary unit for the dynamic 
positioning system. The Seapath 200 data are not made available via the rvs 
data stream and are only available via the TECHSAS system. Even though the 
systems are classed as primary and secondary the ship's dynamic positioning 
system takes input from both systems.

11.1.3  Ashtech

On previous ships, the Ashtech used to be the primary system for obtaining 
the most accurate measurement of the ship's heading, but has been replaced by 
the posmv system. Accurate heading is required by the ship's ADCP systems. 
The Ashtech heading will be compared to the headings from other systems in 
Section 4. The Ashtech heading defaulted to 0 on day 070 and was not reset 
until day 087. The data stream was then checked daily as occasional dropouts 
to zero were observed during the remainder of the cruise.

11.1.4  Ship's Gyro

The ships gyro on the bridge was logged via the rvs data stream as 'gyros'. 
The data were used to remove any large outliers in the Ashtech system.


11.2  Routine processing

All data streams were processed in a similar manner. Data were transferred 
daily from the TECHSAS system using the script mday_00_get_all.m. Raw data 
files were copied to files with the suffix 'edit' and manually despiked using 
the mplxyed function. Data were averaged into 1 minute bins and appended into 
final files named '_jc032_01.nc'. Before averaging, the headings were split 
into east and north components to prevent errors arising from averaging a 
direction.


11.3  GPS positional accuracy

Figure 73 shows the difference in position between the different systems. It 
is clear that the posmv and the dps 116 positions drift more than the other 
systems. The posmv exhibits excursions of up to 200m off position (top panels 
in figure). The drift in the dps116 position was smaller than the posmv. A 
major feature can be seen in Figure 73c and d as a circular track. This is 
seen in Figure 73a in the top right quadrant. The difference between the 
Ashtech and Seapos positions is small and exhibits little drift (Figure 73e).

 
Figure 73: Differences between latitude and longitude measured from different 
           GPS systems.


11.4  Heading accuracy

Ashtech data were subject to more detailed editing. The 1Hz data were merged 
with the ship's gyro and edited using the following criteria:

Heading                   0 < heading < 360
Pitch                    -5 < pitch < 5
Roll                     -7 < roll < 7
Measumient RMS error   10-8 < mrms < 0.01,
Baseline RMS error     10-8 < brms < 0.01
Astech-Gyro heading      -7 < a-g < 7

The posmv and gyro heading was merged onto the Ashtech data and averaged in 2 
minute bins. Figure 74 shows that the three systems generally agree with each 
other to within about ±1°.


Figure 74: Comparison of GPS headings during dayofyear 80.



12.  BATHYMETRY
     (Lorna McLean, Ben Moat and Peter Keen)


12.1  Kongsberg EA600 Single Beam Echo Sounder

Bathymetry data are measured at 1Hz by an EA600 echo sounder and are 
processed daily.

The raw data were initially copied into a file named sim_jc032_d???_edit.nc 
(where ??? refers to the 3 digit Julian day number) using medit_sim_jc032. 
During the cruise the EA600 often lost the bottom and either reported zeros 
or inaccurate depths. These spurious depths were removed by manual despiking 
using the mplxyed function. This process was helped enormously by a hard copy 
screen dump of the 4-hour depth trace from the EA600.

The position data from the posmvpos system were merged on the bathymetry data 
and the corrected depths calculated from the carter tables using 
mmerge_sim_nav_jc032. A file named sim_jc032_d???_merged.nc was created.

There was still noise at depths close to the bottom, which biases the mean 
towards a shallower value. Therefore the median average over a period of 5 
minutes was calculated using mavg_sim_jc032 and gave a better representation 
of the data. On occasions where the instrument could not locate the bottom, 
gaps are present in the data (Figure 75). Each day the averaged files 
(sim_jc032d???_avg.nc) are appended using mday_02 and creates a final 
appended file named sim_jc032_01.nc. 'Distance run' was calculated from the 
navigation files and this was merged onto the bathymetry file. The data were 
then averaged over 5km to create the file sim_jc03201_dist_5km.nc.


12.2  Kongsberg EM12O Swath System

The EM120 swath system was running throughout the cruise. It is known that 
the flow of water over the ship's hull produces bubbles that are detrimental 
to the swath depth measurements. However, the instrument was reliable in calm 
seas or on station when the number of bubbles passing over the hull was 
reduced. The instrument was generally more constant in measuring the actual 
station depth than the single beam EA600 when the sea floor was steeply 
sloped or the CTD was flown into narrow valleys, e.g. the EA600 depth 
measurements were occasionally 400m shallower than the actual bottom depth.

It would be useful for future cruises to record the centre beam depth 
directly beneath the hull via the TECHSAS system.


Figure 75: Five minute averaged bathymetry data for the duration of the 
           cruise




13.  LOWERED ACOUSTIC DOPPLER CURRENT PROFILER (LADCP)
     (Lorna McLean, David Hamersley, Paul Provost and Peter Keen)


13.1  Instrument Setup

Following incidents on the previous cruise only one LADCP was available for 
use on JC032. The instrument in question was a downward looking titanium 
casing RDI 300kHz Workhorse ADCP (serial number 10607) and this was mounted 
just offcentre at the bottom of the CTD frame. The LADCP was configured to 
have a standard 16 x 10m bins, with one water track and one bottom track ping 
in a two second ensemble. There was also a 5m blank at the surface.

Prior to each station the ADCP was connected to a laptop in the deck lab (via 
a serial port - USB adapter) for pre-deployment tests and the instrument was 
programmed. After each station the instrument was reconnected to the laptop 
for the retrieval of the data. The battery package was charged between 
stations.


13.2  Instrument Performance

The LADCP exceeded expectations with respect to beam failure. It is believed 
that over 160 'deep' casts have now been completed in the past two months and 
this far exceeds aluminium pressure cased units. Although on a few stations a 
weak beam signal was detected (Figure 76), the correlation between the 4 
beams remained tight and the beam strength always returned to normal strength 
at the following station.

 
Figure 76: Example plot of echo amplitude with depth from Station 40 indicating 
           a weak beam on the LADCP and the corresponding plot showing the 
           correlation of all 4 beams.


The main issue regarding the technical performance of the LADCP occurred in 
the downloading of the data. On a number of stations it required numerous 
attempts to download the data, as the instrument was not communicating with 
the laptop. On three of these Stations (46, 48 and 50) the retrieval of the 
data had to be abandoned which led to incomplete upcast profiles (Figure 77). 
A number of actions were taken to try to solve the problem. Originally the 
LADCP was connected to this laptop via a USB - serial port adapter that was 
replaced by a PCMCIA - serial adapter to improve the data transfer but the 
download problems persisted. On day 87 after Station 51 the original laptop 
was replaced with a newer machine and the LADCP was plugged directly into the 
COM1 serial port. Subsequently, there were fewer problems with downloading 
the data.

On day 84 during Station 48, problems with the winch left the CTD at 3000m 
for a period of approximately 10 hours. Whilst at depth the LADCP continued 
to log data and this was downloaded on recovery to see if any evidence of 
internal waves could be detected.

On day 91 the CTD was dropped on the deck due to another failure of the winch 
mechanism as it was being deployed for Station 61. The LADCP was removed from 
the frame to check for damage but the instrument was not opened up as it was 
thought that this would increase the risk of flooding when put back into the 
water. The face of the instrument was checked visually for signs of damage 
and only a small chip on the powder coating of the transducer head was 
noticed. It was not clear when this happened but was thought to have been 
present before the dropping of the CTD. The chip was touched up with nail 
varnish and no other damage to the instrument was found and therefore 
considered suitable for redeployment. The instrument was also connected up to 
the laptop to run tests to ensure it was operating well. The technicians were 
happy with the performance of the LADCP and so it was reattached to the frame 
ready to be redeployed.

 
Figure 77: A plot of the u component of the flow on Station 44 measured in the 
           downcast (dashed blue line) and the upcast (dotted green line). The 
           mean is shown by the solid red line. Note that the upcast ends at 
           approximately 3250 m.


The performance of the LADCP deteriorated with depth as can be seen from 
plots of the sample number and shear standard deviation (Figure 78). Below a 
depth of 1500m sample numbers reduced to significantly low levels and the 
shear standard deviation became highly variable between bins. This is thought 
to be due to the lack of scatterers at depth. Therefore data recorded by the 
LADCP below 1500m may be considered unreliable.
 

Figure 78: Plots from Station 51 displaying the number of pings with depth and 
           the corresponding shear standard deviation


13.3  Data Processing

The data collected by the instrument were downloaded after each cast and 
stored as RDI binary files and corresponding text files in the directory 
/data32/JC032/LADCP/WHMaster. Both the binary (ctd*.000 ) file and the text 
file were copied into the directory 
/data32/cruise/pstar/data/ladcp/uh/raw/jc0903/ladcp where the text file was 
then moved into the directory txtfiles and the binary file was renamed using 
the format jc032???m.000 (where ??? represents the 3 digit station number).

The data were then processed using two different tools. Primarily a software 
package from the University of Hawaii (UH) was used to calculate the current 
velocities and provide information about the heading and tilt of the CTD 
package. The second piece of software originates from Lamont-Doherty Earth 
Observatory (LDEO) and was used for obtaining bottom track profiles and to 
monitor the beams of the instrument.

All the processing for the LADCP was carried out on the RAPID terminal and 
therefore used Solaris rather than Linux versions of the software.

The sequence of the routine processing for the LADCP data is outlined below.
13.3.1  UH Processing

The initial stages of processing allow the user to examine the quality of the 
data and to calculate relative velocity profiles in the absence of CTD data.

1. After navigating to the directory /data32/cruise/pstar/data/ladcp/uh, 
   type source LADall to set up the paths required for the processing.
2. Type cd proc/Rlad and linkscript to create symbolic links from the 
   binary *000 files to the real raw file.
3. Navigating back up to the directory /data/ladcp/proc type perl -S 
   scan.prl???_02 to scan the raw data and create a station specific 
   directory in the proc/casts directory. Data printed to screen should be 
   checked to ensure the details of the cast (i.e. depth, downcast/up cast 
   times) agree approximately with the CTD log sheet.
4. Station position and the magnetic variation correction are entered by 
   typing putpos2???02. This updates stations.asc and magvar.tab using 
   Matlab.
5. perl-Sload.prl???_02 loads the raw data, correcting for magvar.tab to 
   start processing. It is very important that this step is only carried 
   out once. If it needs to be repeated the database files 
   (~/proc/casts/j???_02/scdb) must be deleted first.
6. Next type perl-Sdomerge.prl-c0???_02 to merge the velocity shear 
   profiles from individual pings into full upcast and downcast profiles. 
   The option -c0 refers to the fact that CTD data has not yet been 
   included.
7. Enter the Rnav directory and run updatesm.exec to update the navigation 
   file. Then backup one level to the proc directory.
8. Open a Matlab session in this directory and set the variable 
   plist=???.02 and run do_abs to calculate relative velocity profiles. 
   Check that these plots look sensible, i.e. reasonable agreement between 
   downcast and upcast and that the vertical velocity changes sign between 
   downcast and upcast (it may be necessary to rescale some of the plots). 
   Also check the plot on Figure 78 to monitor the number of pings 
   throughout the profile.

Once the CTD data has been processed this can be incorporated into the LADCP 
processing to make more accurate estimates of depth and sound velocity and to 
obtain a final absolute velocity profile.

9.  The inclusion of CTD data requires an ASCII file containing 1Hz CTD 
    data for the station created in Matlab. If this is present navigate to 
    ~/proc/Rctd and open a Matlab session. Run the script mk_ctdfile 
    entering the station number when prompted. ctd_in(???_02) will read 
    the 1Hz CTD data in. Set plist=???. 02 and run fd to align the LADCP 
    and CTD data sets in time.
10. Exit Matlab and navigate back to ~/ladcp/proc. Type 
    perl-Sadd_ctd.prl???_02 to add the CTD data to the *.blk LADCP files 
    in the scdb directory.
11. Merge the single pings into corrected shear profiles by running 
    pen-Sdomerge.prl-ci???02 where the -ci option now states that we have 
    included CTD data.
12. Finally in Matlab, once again set plist=???.02 and run do_abs to 
    produce the final absolute velocity profiles.

13.3.2  LDEO Processing

As with the UH processing the LDEO processing can first be carried out 
without the CTD data to monitor the results and performance of the beams.

1. Navigate to /data32/cruise/pstar/data/ladcp/ldeo/jc0903 and start a 
   Matlab session.
2. Type sp and when prompted enter the station number and the run letter 
   ('noctd' for no ctd data and 'wctd' when CTD data are included).
3. Next type lp and this will run the processing scripts.
4. Print required plots.

The steps above should then be repeated to include the CTD data after it has 
been processed. The format of the CTD data required is the same for both LDEO 
and UH processing and when CTD data are available the processing will 
automatically use it.

13.3.2.1  Inclusion of True Depths

During the LDEO processing with CTD data, a corrected bottom depth was 
recorded. This was found by typing grep found */*wctd.log | grep bottom in 
the ladcp/ldeo/jc0903 directory. The second depth for the station in question 
was then noted along with its error and the proc.dat file located in 
~ladcp/proc was edited to include these values. The original depths were left 
in place but commented out so they were not used when the file was read. The 
perl-Sdomerge.prl-ci??? step was repeated to incorporate the new depth and in 
Matlab plist=???.02 and do_abs was re-run. The plots produced then show the 
corrected depth and may be printed.


13.4  Comparison of LADCP (UH and LDEO) with VMADCP

The opportunity to compare the velocity data from the two different types of 
LADCP processing and also the VMADCP (75Hz) was presented on this cruise, as 
was the case on JC031. There were four different components plotted in these 
graphs; UH velocities, LDEO velocities, bottom track velocities (calculated 
by the LDEO software), and the VMADCP velocities. The 75Hz VMADCP is capable 
of penetrating to a depth of approximately 800m and from the majority of the 
plots comparing velocities, it can be observed that the VMADCP plots are more 
consistent with those created by the LDEO processing. However, it must be 
stated that this is not always the case, because for certain stations the UH 
processing appears to have better agreement with the VMADCP. In all stations 
affected greatly by shear, the VMADCP is generally the most reliable reading, 
and this is complimented by the fact that the bottom track is well aligned 
with these velocities. This is a good indication that the outputs from the UH 
and LDEO processing should not strictly be taken at face value. The UH 
processing is particularly severe with the editing of 'bad' data points and 
may reject data that would be found perfectly acceptable by the LDEO 
software. As one might expect, the bottom track velocities are generally in 
best agreement with the LDEO velocities, since they are both processed by the 
same program. However, as was the case with comparison of the LADCP and the 
VMADCP velocities, that bottom track is not consistently in best agreement 
with the LDEO software. Again, shear plays a large role in heightening the 
ambiguity of any agreements that may exist between the bottom track and the 
UH and LDEO velocities. Bottom velocity is a reliable reading because it has 
a reference point with a reference velocity (the sea bed), which can be used 
to achieve more accurate velocities. No bottom track data is available for 
Stations 4 or 51. Reasons for this have not been firmly deduced, but it is 
possible that the slope of the seabed is such that it did not scatter the 
pings back to the instrument.

There was a minor problem during the processing which meant that all of the 
VMADCP data had the wrong time series applied to it, but this was corrected 
after investigation by Alex Brearley, who found that the time series was out 
by approximately 24hrs from Station 52 onwards. The velocity comparisons were 
replotted for these stations. It is possible to observe from the plots that, 
in deeper stations, below approximately 1500m the ability of the programs to 
process the data in a reliable manner is reduced by the significant lack of 
scatterers in the water, such as zooplankton. Due to these conditions, the 
pings made by the LADCP are not scattered back to the instrument, thus the 
number of samples collected can be negligible. However, the number of samples 
is increased on the upcast due to the time spent at each of the bottle firing 
stops, which allows the instrument to collect more samples. Comparison is not 
possible for Station 48 as this was an incomplete cast and was abandoned due 
to winch failure.

 
Figure 79: An example of the ADCP comparison plots produced.


13.5  Shear

As can be observed from the graph below, the shear velocities agree very well 
in the range of comparison. It should be noted that in the deeper ocean, the 
agreement was not as good, but this was largely due to the fact that there 
was little good data below 1500m depth. There does not appear to be any great 
difference between the agreements of the shear velocities in the u and v 
components. This shear was calculated using a filtering method in Matlab, 
which allowed the data to be made as smooth as desired. This comparison will 
be improved later on by using polyfit linear regression on different sections 
of the shear.

 
Figure 80: An example of the plots produced for ADCP shear velocities


13.6  Accumulation of Turns

The LADCP programming was used to keep track of the number of turns that were 
being put into the wire on each station. This was made possible because of 
the log of the heading that was recorded due to the need for the LADCP to 
know its orientation. Although the number of turns could be counted from the 
LDEO and UH processing of the LADCP data, additional scripts were constructed 
by Brian King to provide an 'unwrapped' station by station view and also a 
cumulative view of all the stations.

Assuming the number of turns on the winch cable to be zero at the start of 
the cruise, it can be seen from the cumulative graph produced that the number 
of turns on the cable started to increase from approximately Station 5 
onwards. There was a brief reprieve between Stations 19 and 24 where there 
was no change in the number of turns (+10 turns, where a positive value 
indicates a clockwise motion). After this station the twists in the wire 
increased to +37 by Station 42. Due to the winch failure on Station 48, the 
winch drum and thus the wire was switched and the wire was re-terminated, 
therefore effectively resetting the number of turns in the wire to zero. The 
new wire is represented on the graph by the red line. The trend visible after 
Station 48 is a progressive increase in the number of decreasing turns 
(turning of the package in an anticlockwise direction). This appeared to show 
some signs of improvement after Station 84 but the increase in anticlockwise 
turns resurfaced after Station 95. Consequently, after Station 108 was 
completed, the wire had accumulated approximately -100 turns at which point 
the wire developed a kink and therefore required a re-termination. However, 
after discussing this matter with Brian King it was decided that this number 
of turns in the wire was likely to have been insufficient to be the cause of 
the kink. Each break between the different coloured lines on the graph 
represents the point where a re-termination had to be carried out. By the end 
of the cruise the wire had accumulated a total of 79 turns in the 
anticlockwise direction.

 
Figure 81: Representation of the cumulative number of turns on the CTD. A 
           break between the different coloured lines on the graph represents 
           a re-termination of the wire. Black line = Stations 1 to 47, red 
           line = 48 to 108, green line = 109 to 118.




14.  VESSEL MOUNTED ADCP INSTRUMENTS
     (J Alexander Brearley)


14.1  Introduction

The two vessel-mounted Acoustic Doppler Current Profilers (ADCPs) onboard RRS 
James Cook were used throughout the cruise to estimate the horizontal 
velocity field. These instruments, installed on the port drop keel of the 
ship, are 75kHz and 150kHz Ocean Surveyor (OS) instruments supplied by 
Teledyne RD Instruments, Poway, California. The instruments can be operated 
with the keel either retracted or lowered (hereafter known as 'keel up' and 
'keel down' respectively). The keel up position allows greater ship speed, as 
the vessel is limited to 10 knots with the keel down, but also exposes the 
instrument to more bubbles, which significantly reduces its profiling range. 
By contrast, in the keel down position, the keel extends 2.8m below the hull, 
which itself has a draft of 6.9 m. Thus when the keel is lowered, the depth 
of the transducer is 9.7 m. We chose to run the instruments with the keel 
down throughout the cruise, except for short periods entering and leaving 
port.

The different frequencies of the two instruments affect both their depth 
range and resolution. The 150kHz allows smaller depth bins and consequently 
higher vertical resolution, but the signal is more rapidly attenuated and 
typically only penetrates to 500m. The 75kHz lacks such good vertical 
resolution but penetrates to ~1000m.


14.2  Real Time Data Acquisition

The data from the two instruments were acquired using the RD Instruments 
VmDas software package version 1.42. This software is installed on two PCs in 
the main laboratory, which control the 75kHz and 150kHz Ocean Surveyor 
instruments respectively. The software allows data acquisition in a number of 
configurable formats and performs preliminary screening and transformation of 
the data from beam to Earth coordinates.

In order to collect data in VmDas:

1. Open VmDas from the Start Menu and click on "Collect Data" in the File 
   Menu.
2. Under Options, click "Edit Data Options" and then set the configurable 
   parameters to the values outlined in the JC029 cruise report (Section 
   9.3.2). Under the ADCP setup tab, specify the relevant control file in 
   Table 8. It is important each time the ADCP is restarted to increase 
   the number in the recording tab by 1; otherwise VmDas may overwrite 
   previously written files.
3. Recording commences by clicking the blue record button in the top left 
   of the screen.
4. Collection stops by pressing the blue stop recording button in the top 
   left of the screen. Data collection was typically stopped and restarted 
   with a new ensemble number every 1-3 days during the cruise. Leaving it 
   on the same file for more than three days allows the files to become 
   too large and postprocessing in CODAS becomes slow.


14.2.1  Files Produced by VmDas

The files we produced have names of the form 

                    OS<inst>_JC032<nnn>_<filenumber>.<ext>,

where <inst> is the instrument name (75 or 150), 
      <nnn> is the file sequence number, 
      <filenumber> is the number of the file in the sequence and 
      <ext> is the extension. We set a new 
      <filenumber> to occur every time a file size of 10Mb was reached.

The list of files produced is given below:

• .ENR files are the binary raw data files.
• .ENS files are binary ADCP data after being screened for RSSI and 
   correlation and with  .navigation data included.
• .ENX files are ADCP single ping data and navigation data after having 
   been bin-mapped, .transformed to Earth coordinates and screened for 
   error velocity and false targets.
• .STA files are binary files of short-term average ADCP data (120s, 
   user-specified in VmDas).
• .LTA files are binary files of long-term average ADCP data (600s, user-
   specified in VmDas).
• .N1R files are ASCII text files of raw NMEA navigation data from the 
   NMEA1 stream.
• .N2R files are ASCII text files of raw NMEA navigation data from the 
   NMEA2 stream.
• .NMS files are binary files of navigation data after screening.
• .VMO files are ASCII text files specifying the option settings used for 
   the data collection.
• .LOG files are ASCII text files logging all output and error messages.

These files were stored in the C: \ADCP\Data\JC032 directory.

14.2.2  Real Time Data Monitoring

The 'R', 'S' and 'L' tabs on the VmDas menu bar allow you to swap between 
graphical output from the ENR, .STA and LTA files. When in 'R' mode, the 
default upper left hand display in VmDas is the raw velocity parallel to each 
beam, but this can be difficult to interpret as it is shown in beam 
coordinates. A more useful plot can be made in either the 'S' or the 'L' 
mode, displaying the current at a specified depth level as a stick plot in 
Earth coordinates. To produce these plots, ensure 'Ship Track 1' and/or 'Ship 
Track 2' is ticked in the Chart menu. The bins used in the stick plot are 
specified within "Options", "Edit Display Options". We used the NAV as the 
ship's position source throughout.

The data can also be inspected in real-time using the WinADCP software, which 
loads the ENX, STA or LTA files and displays the output as contour plots. The 
Monitor Option should be switched on with a suitable time interval (120s), 
meaning the contour plot is regularly updated. Plots of u and v were 
routinely examined throughout the cruise to check the data stream and to 
inform the bridge of ADCP measurements as required on station.

Several other things were also regularly checked whilst the ADCPs were 
recording:

1. We made sure the ensemble number in the real time display of VmDas was 
   increasing and that the size of the files in the C: \ADCP\Data\JC032 
   directory was increasing. The ensemble number check routinely took 
   place every 4 hours as part of the watchkeeping log.
2. We checked the deviation of the PC clock from the ship's clock. This 
   synchronisation occurs through the "Meinberg Network Time Protocol", a 
   piece of software installed on the hardware of each PC. The deviation 
   is recorded as the last entry on each $PADCP line of the N2R file. 
   Although the deviation was generally small (~0.10 s) throughout the 
   cruise, a short period of larger deviations did occur in 
   OS75_JC032028_000000.N2R and OS75_JC032029_000000.N2R (~5 s). Upon 
   further investigation, it was found that this occurred when the 
   instrument was started immediately after restarting the PC. It 
   generally takes a few minutes after Windows starts for the 
   synchronisation to be fully correct.
3. We ensured that records of the files created are kept up-to-date. A 
   full list of filenames can be found in Appendix II.
4. The LOG file records any problems such as timeouts and navigation 
   problems and was occasionally inspected. A frequent error regarding the 
   source of heading did occur, as discussed in the JC029 cruise report. 
   However, this once again did not appear to affect the data.

14.2.3  Alignment

As outlined in the JC029 cruise report, it is known that the OS75 instrument 
is roughly 90 out of alignment, in spite of the installation report stating 
that both ADCPs are perfectly aligned with the ship's axis. We once again 
used the EA00900 command setting in the control file to enable real time 
monitoring of the currents and for internal VmDas processing.

14.2.4  General Settings

During JC032, we ran both instruments in narrowband single-ping mode, with 
transducer depth adjustments made in the control file when the drop keel was 
lowered (9.7m compared to 6.9m). Where depth permitted, we ran both 
instruments in bottom track mode to obtain the most accurate phase and 
amplitude calibrations. Typically, the instruments were switched between 
bottom tracking and water tracking close to 1000 m. A table of the filenames 
and configurations used is given below:


Table 8: Configurations of individual control files used on JC032. Bottom and 
         water tracked files are denoted in the filename by 'BTon' and 'BToff' 
         respectively.

                                        Bin    Time between    Coarse        Max bottom
                          Time between  Depth  bottom and      transducer    search depth
Control file name         ensembles(s)  (m)    water pings(s)  Misalignment  (m)
------------------------  ------------  -----  --------------  ------------  ------------
OS75NBBTonJC32down.txt         3         16        1.5              9°          1200
OS75NBBToffJC32down.txt        3         16        1.5              9°          1200
OS75NBBTonJC32up.txt           3         16        1.5              9°          1200
OSJ50NBBTonJC32down.txt        2          8        1                0°           800
OSl50NBBToffJC32down.txt       1          8        1                0°           800
OS150NBBTonjC32_up.txt         2          8        1                0°           800


On both instruments, 60 bins were used, with a bin size of 16m for the OS75 
and 8m for the OS150. A blanking distance of 8m was used for the OS75 and 6m 
for the OS150, in order to avoid ringing from the transmit pulse. During 
JC031, both instruments had been run with a 2s 'time between ensembles' and a 
1s is 'time between BT and WT pings' whilst in water track mode. We were 
unsure why this had been done and so chose to test identical times (1s) using 
the OS150. It was found that the data did not appear to be compromised and so 
the instrument remained in this configuration for the rest of the cruise. We 
did not, however, alter the water track control file for the OS75. The 
control files in full are printed in Appendix I.

14.2.6  Sound Speed Considerations

There was initial concern at the start of the cruise about the effect on 
inaccurate sound speed estimates on the quality of the data. It was known 
that the temperature at the transducer face is measured for each ping, as 
water temperature is the largest variable in the calculation of sound speed, 
but we were worried that there was no accounting for salinity changes. Using 
the simple sw_svel Matlab routine (part of the Seawater package), it was 
found that a salinity change of 1 at 20°C produced a 1.1 m/s change in sound 
speed, whilst a temperature change of 1°C at S = 35 produced a 2.7 m/s 
change. Our fears were compounded when it was found that the temperatures of 
the OS75 and OS 150 instruments disagreed with each other by up to 1°C and 
with CTD temperatures by up to 2°C.

However, close inspection of the ADCP Principles of Operation Primer, 
supplied by Teledyne with the instrument, revealed that the measurement of x 
and y velocities is independent of sound speed for a phased array instrument 
(page 46). Each of the Ocean Surveyor ADCPs on RRS James Cook is of the 
phased array type, comprising a single ceramic assembly that produces 4 
acoustic beams simultaneously from the same aperture. Each element in the 
array is driven with the same signal except for a phase shift, which is 
constant for a given frequency and element spacing. If the speed of sound 
changes, the angle of the beam will consequently change. Fortunately, this 
beam angle change occurs in the same ratio as the Doppler shift equation, 
meaning that a change in the Doppler frequency shift of a particle moving 
parallel to the face is compensated entirely by the corresponding beam angle 
shift, rendering the horizontal velocity component independent of sound speed 
(although the vertical component is more sensitive than in a conventional 
transducer). As a result of these findings, accuracy of the sound speed 
measurements did not require further consideration.


14.3  Post-Processing

The final processing of the data was done using the CODAS (Common Ocean Data 
Access System) suite of software provided by the University of Hawaii. This 
suite of Unix and Matlab programs allows manual inspection and removal of bad 
profiles and provides best estimates of the required rotation of the data, 
either from water profiling or bottom tracking.

14.3.1  Transferring the Data

CODAS was run on the noseal terminal, so the files had to be transferred from 
the ADCP PCs to this Linux box. This was done using the psflp application on 
the desktop of both PCs. At the command window within sftp, the local 
directory was changed to C: \ADCP\Data\JC032 using the lcd command, and we 
logged into cook3 using open cook3.cook. local. The raw data were moved into 
either the /data32/JC032/cruise/pstar/data/vmadcp/jc032_os75/rawdata 
directory or the /data32/JC032/cruise/pstar/data/vmadcp/jc032_os150/rawdata 
directory, depending on the instrument.

14.3.2  Setting Up the Directories and Using quick adcp

Once loaded into the rawdata directory, the following steps were followed:

1. movescript was typed in the Unix command window. This short script 
   creates a new directory called rawdata <nnn> (nnn denotes the file 
   sequence) and moves the data loaded into the rawdata directory to the 
   appropriate rawdata<nnn> directory.
2. The command adcptree.py jc032<nnn>nbenx -datatype enx was typed at the 
   command window. This command sets up a directory tree for the codas 
   dataset and an extensive collection of configuration files, text files 
   and m files.
3. The directory was then changed to jc032<nnn>nbenx using the cd command, 
   and the control files q-py.cnt, q_pyedit.cnt and q_pyrot.cnt were 
   copied into that directory. We then used the command: 
   'quick_adcp.py-cntfile q_py.cnt', which loads the data into the 
   directory tree, performs routine editing and processing and makes 
   estimates of both water track and (if available) bottom track 
   calibrations. The raw ping files are also averaged into 5 minute 
   periods. The calibration values are stored in the adcpcal.out and 
   btcaluv.out files found in the cal/watertrk and cal/botmtrk directory 
   and are appended each time quick_adcp.py is run.

14.3.3  Gautoedit

The gautoedit package within CODAS allows the user to review closely the data 
collected by VmDas and flag any data that is deemed to be bad. These flags 
can then be passed forward and, using the qpyedit.cnt control file, the data 
removed. Typically, the data were reviewed as follows:

1. Matlab was opened in the jc032<nnn> nbenx directory (for the portion of 
   data we wished to process). In the command window, typing:

   codaspaths
   cd edit
   gautoedit

This started up an editing GUI, shown in Figure 82. The editing was done from 
here.

 
Figure 82: The gautoedit editing window within the CODAS suite of programs 
           in Matlab.


2. To get an initial feel for the data, the start time of the ENX file was 
   entered in the decimal day (start) box and the length of the dataset (in 
   days) was entered in the decimal day step box. Upon pressing Show Now, two 
   plots are displayed. One contains four subplots: the first displays the 
   absolute east-west velocity component, the second shows the absolute 
   north-south component, the third shows the percentage good parameter and 
   the fourth shows the ship speed (in m/s) and an editing parameter called 
   jitter. The second figure contains subplots of the ship's track and mean 
   absolute velocity vectors at the reference layer. By default, this 
   reference layer is set at bin 2 using the First Reference Layer Bin 
   command. An error command will appear if there are no data in the selected 
   time range. This initial review of the data allows the user to confirm the 
   direction of steaming, identify the position of on-station and off-station 
   parts of the file and spot any areas with low percentage good. It is also 
   useful to identify the maximum and minimum values of u and v to allow a 
   suitable colour bar to be used when examining the data more closely (by 
   default -60 to +60 is used). To change this, use the maximum u and v and 
   minimum u and v boxes.

3. To inspect the data more closely and to start applying edits, the data must 
   be inspected in shorter time sections. Typically, we worked from the start 
   of the data in 0.4 day portions as this allowed us to see the individual 
   5-minute bins. Once the edits were finished on one portion, the List to 
   Disk option was selected to save the flags before using Show Next to 
   advance onto the next 0.4 day section. Routine editing for each section 
   included:

     (i) looking for bad profiles (i.e. those in which the u and/or v had a 
         systematic offset over all depth levels). These were flagged using 
         the del bad times command.
    (ii) looking for bad levels. This is common at the bottom of profiles 
         where the amplitude return is small and the profiles commonly have a 
         low percentage good. These bad 'tails' are removed most easily using 
         the rzap bins command, which allows the user to flag all data within 
         a defined rectangular box.
   (iii) looking at the jitter parameter in the bottom subplot. A high level 
         of jitter either indicates noise in the navigation and/or rapidly 
         changing velocities. Generally, the default jitter threshold (set in 
         the Jitter: reject profile if jitter in measured velocity) of 15 cm/s 
         seemed to be a reasonable value for flagging potentially bad profiles 
         and did not need to be changed.

4. More specialised editing was required for some parts of the dataset where 
   we suspected velocity biases were present. In particular, the presence of 
   either enhanced scattering layers in the profiles or bubbles directly 
   beneath the ship are known to bias the underway velocities in the affected 
   layers in the direction of steaming. These biases are discussed at more 
   length in Section 4, but the typical steps taken to remove them were:

     (i) inspecting the echo amplitude plot, which shows the magnitude of the 
         return at each depth. Enhanced scattering layers can be distinguished 
         clearly in this plot.
    (ii) inspecting the bias parameter plot. This shows the vertical gradient 
         in the demeaned amplitude, multiplied by the ship velocity. The 
         demeaning removes the mean amplitude at the particular depth level, 
         so the plot is really the vertical derivative of the amplitude 
         anomaly multiplied by velocity. In an enhanced scattering layer (e.g. 
         due to zooplankton) the bias parameter tends to have positive (red) 
         values towards the top of the layer (as the anomaly increases with 
         depth) and negative values below (as the anomaly decreases), though 
         the sizes of these anomalies need not be symmetric. On station the 
         parameter, by definition, has a value of zero. Positive values in the 
         top two or three bins often indicate bubbling. The bias parameter 
         thus indicates the potential for velocity bias, but does not show 
         bias in itself.
   (iii) inspecting the alongtrack velocities on steaming sections. For most 
         of the cruise (along 24°S), this was the u velocity component. 
         Regions of potential bias highlighted with the bias parameter were 
         then examined for underway bias in the velocity. If bias in the 
         direction of travel whilst the ship was steaming could be found, the 
         bad bins were flagged using rzap bins. In the presence of anomalous 
         scattering, it was common to find a layer of positive velocity bias 
         above a layer of negative bias. In these cases, both layers were 
         removed.
         
         Although it is possible to edit data using other thresholds (e.g. 
         percentage good and number of neighbours), this was not found to be 
         necessary during JC032. Further details of gautoedit capabilities can 
         be found at:

         http://currents.soest.hawaii.edu/docs/adcp_doc/edit_doc/index.html

5. Once satisfied with the changes made, the List to Disk option is selected 
   which creates and updates a*.asc files in the jc032<nnn>nbenx/edit 
   directory.

14.3.4  Applying the Edits

Once the a*.asc files have been created, the edits are applied using the 
following command at the Unix terminal prompt from within the jc032<nnn> 
nbenx directory:

quick_adcp.py -cntfile q_pyedit.cnt

The q_pyedit.cnt file has to have the correct instname command line (i.e. 
OS75 or OS150).

14.3.5  Calibration

In order to obtain accurate horizontal velocities, it is vital to correct for 
heading errors. These can either occur as a result of transducer misalignment 
with respect to the hull, or from errors in navigation. Fortunately, the 
navigation is fed directly into VmDas from the Applanix POSMV, which 
incorporates a GPS heading source that is not sensitive to many of the 
heading errors that occur when gyrocompasses are used in isolation (e.g. 
Schuler Oscillations).

The best calibration estimates are obtained when the velocity data are 
referenced to the bottom. However, bottom track calibration estimates are 
only obtainable when the water depth is within 1.5 times the depth of the 
ADCP profiling range. We were able to obtain five separate periods of bottom 
tracking during the cruise, four on the Brazil/Uruguay shelf and one on the 
Namibian shelf. Unfortunately, the need to raise the drop keel for our 
unscheduled stop in Anaial do Cabo meant that two separate calibrations were 
required for each instrument (one for Stations 1-35 and one for Stations 
36-118). We examined both bottom track and water track calibrations for 
consistency on each section before deciding on best amplitude and phase 
corrections for each instrument.

The quick_adcp.py script estimates amplitude and phase corrections for each 
set of data. The values for these are presented in Appendices III and IV. By 
default, the water track estimates have an ensemble length of 7, meaning that 
seven individual five-minute ensembles bracket each turn or acceleration. The 
bottom track estimates have a default step size of 1, meaning that the 
individual ensembles are used to evaluate the calibration. Step sizes of 2 
and 3 are also permissible, meaning that adjacent profiles of length 2 or 3 
are averaged to obtain the amplitude and phase. By changing the control file 
timslip.tmp using the vi editor and the Matlab file calladcpcal_tmp.m, water 
track ensembles of length 5, 7 and 9 were evaluated for each section. It was 
found that varying the choice of ensemble length did not substantially change 
the values of amplitude and phase obtained. By modifying the Matlab file 
callbtcaluv_tmp.m, the sensitivity of each bottom track calibration was also 
tested by altering the step size to 2 and 3. Once again, it was found that no 
substantial changes occurred, and as a result we chose to study the water 
track estimates based on ensemble length 7 and the bottom track estimates 
based on ensemble length 1.

14.3.5.1  First Calibration: Montevideo to Arraial do Cabo

OS75: The individual bottom track calibrations for file sequence numbers 002, 
010 and 014 were compared with the water track calibrations from file 
sequences 002, 003, 004, 008, 009, 010, 012 and 013. It was found useful to 
have all the water track calibrations plotted together on the same axes to 
allow us to inspect for any large outliers and/or drift over time. To do 
this, a script was created called watertrackall.m (Appendix V), which loads 
the individual estimates of phase and amplitude from each file sequence and 
then plots the estimates together on the same axes along with the time 
differences between the navigation and PC. The single best estimate water 
track calibration was then derived, given in Table 9 (bold figures). The best 
estimate for bottom track was based on a mean value of the three individual 
estimates from 002, 010 and 014, weighted by the number of ensembles used. 
The result is also given in Table 9.

Both estimates agree closely as the difference between them only gives very 
small velocity differences. The maximum possible error in water velocity 
caused by employing one estimate of amplitude instead of the other (assuming 
a ship speed of 500 cm/s) is only 0.8 cm/s. The associated error for phase is 
only 0.45 cm/s. Given the larger number of ensembles and better quality of 
bottom tracking estimates, we choose the median values of bottom tracked 
amplitude and phase for as our final calibration. The total error in 
velocities obtained should not exceed 2 cm/s.


Table 9: Best estimates of OS75 calibration for the section from Montevideo to 
         Arraial do Cabo for water tracking and bottom tracking. The bold 
         figures are the final calibration applied.

                                Amplitude                    Phase (deg)
Calibration   Number of  ------------------------    --------------------------
  Method      ensembles  Median   Mean   Std Dev.     Median   Mean    Std Dev.
------------  ---------  ------  ------  --------    -------  -------  --------
Water track       59     1.0040  1.0044   0.0083     -0.0880  -0.1191   0.5080
Bottom track     474     1.0024  1.0025   0.0035     -0.1392  -0.1329   0.1963


OS150: The individual bottom track calibrations for file sequence numbers 
002, 009 and 013 were compared with water track calibrations from file 
sequences 002, 003, 007, 008, 009, 011 and 012. Using the same methodology as 
for the OS75, the results are given in Table 10. The maximum error resulting 
from the difference in amplitude of the calibrations is 1.1 cm/s and for the 
phase difference is 0.56 cm/s. Once again, the expected total error is less 
than 2 cm/s.


Table 10: Best estimates of OS150 calibration for the section from 
          Montevideo to Arraial do Cabo for water tracking and bottom 
          tracking. The bold figures are the final calibration applied.

                                Amplitude                    Phase (deg)
Calibration   Number of  ------------------------    --------------------------
  Method      ensembles  Median   Mean   Std Dev.     Median   Mean    Std Dev.
------------  ---------  ------  ------  --------    -------  -------  --------
Water track      63      1.0060  1.0057   0.0070     -0.6290  -0.6315   0.6013
Bottom track    478      1.0038  1.0040   0.0034     -0.5644  -0.5652   0.2321



14.3.5.2  Second Calibration: Arraial do Cabo to Walvis Bay

OS75: This time, the periods of bottom tracked data were confined to file 
sequence numbers 016 on the steam-out from Anaial do Cabo and 033 on the steam 
into Walvis Bay. Water track calibrations were available across the entire 24°S 
section. Initially, we used the bottom tracked section leaving Anaial do Cabo 
and the water tracked sections 017-024 up to Station 78 to estimate the 
calibrations (Table 11). It was found that there was a more noticeable 
difference between the bottom track and water track estimates of amplitude than 
for the period between Montevideo and Arraial do Cabo. As a result, we chose to 
use values mid-way between the water track and bottom track calibrations for 
our final calibration. These values were reviewed after a 27-hour period of 
bottom tracking on the continental shelf of Namibia. This was started after 
Station 115 and included the last three stations followed by three six-hour 
periods steaming at 10 knots, 9 knots and 8 knots respectively. The keel was 
finally raised at 0815GMT on 21st April 2009.


Table 11: Best estimates of OS75 calibration for the section from Arraial 
          do Cabo to Walvis Bay for water tracking and bottom tracking The 
          bold figures are the final calibration applied

                                Amplitude                    Phase (deg)
Calibration   Number of  ------------------------    --------------------------
  Method      ensembles  Median   Mean   Std Dev.     Median   Mean    Std Dev.
------------  ---------  ------  ------  --------    -------  -------  --------
Water track       65     1.0060  1.0071  0.0073      -0.1520  -0.1163   0.3450
Bottom track
(Arraial)         80     1.0016  1.0015  0.0029      -0.0906  -0.0913   0.2375
Bottom track
(Namibia)        256     1.1037  1.1203  0.0986      -0.1631  -0.1667  -0.2226
Final choice      -      1.004      -       -        -0.12       -        -


The long section of bottom tracking on the continental slope of Namibia gave 
an unrealistic amplitude calibration, which differed markedly from the water 
track calibration of the same period. Furthermore, the standard deviation of 
the bottom-tracked amplitude estimates was very large. Inspection of the 
individual plots (Figure 83) suggests that the period between decimal days 
108.35 and 108.52 (either side of Station 118) gave realistic values close to 
zero, but elsewhere the estimates are generally bad. We suspect that there 
may have been a problem in the navigation given the noisy speed and heading 
estimates in the second part of the period (third and fourth panels), but 
this has not been confirmed. In light of these concerns, we decided not to 
use this section to estimate our final calibration and hence the values of 
the final calibration remained unchanged.

On the 20th April 2009, the port keel was raised and the ADCP was run for the 
final day using the control file for BT on and keel up (file sequences 034 
and 035). The bottom track calibration from file sequence 34 was applied to 
both sequences (1.0043, -0.1796). These values are only slightly different 
from the keel down values used on the rest of the section (1.004, -0.12), 
suggesting the orientation of the transducer face did not change dramatically 
during the keel raising process.

OS150: The same procedure was used for the OS150, with the bottom tracked 
file sequences being 015 and 031 respectively. The water tracked file 
sequences used were 016-023. The final calibration was once again reviewed 
after the collection of data on the continental shelf of Namibia (Table 12). 
This time, the bottom tracking on the Namibian shelf gave reasonable 
estimates of amplitude, but a large negative phase correction. Had we chosen 
to apply this to the rest of the data, on and off-station striping would have 
occurred. Once again, we chose not to use this period of bottom tracking when 
making our final calibration estimate. It remains to be determined why this 
period of bottom tracking gave such poor estimates.

After the keel was raised on the April 2009, two further file sequences were 
written (032 and 033). The bottom track calibration from sequence 032 was 
applied to both sequences (1.0071, -0.6693). Once again, these do not differ 
by a large amount from the keel down values used on the rest of the section. 
The phase estimate of sequence 033 (-4.24) is clearly bad, but the reason for 
such a bad value is unclear and warrants further investigation.


Table 12: Best estimates of OS150 calibration for the section from Arraial 
          do Cabo to Walvis Bay for water tracking and bottom tracking The 
          bold figures are the final calibration applied

                                Amplitude                    Phase (deg)
Calibration   Number of  ------------------------    --------------------------
  Method      ensembles  Median   Mean   Std Dev.     Median   Mean    Std Dev.
------------  ---------  ------  ------  --------    -------  -------  --------
Water track       60     1.0075  1.0076   0.0073     -0.5265  -0.6018   0.3287
Bottom track
(Arraial)         80     1.0024  1.0022   0.0037     -0.4308  -0.4298   0.2118
Bottom track
(Namibia)        252     1.0056  1.0062   0.0059     -1.5443  -1.5258   0.7115
Final choice      -      1.005                       -0.48     


Figure 83: Amplitude scale and phase calibrations for 0575 instrument for the 
           period of bottom tracking on the continental shelf of Namibia. Speed 
           and heading (from nay) are given in the lower panels.


14.3.5.3  Applying the Rotation

The final calibrations discussed above were applied to each file sequence 
using:

quick_adcp.py -cntfile qpyrot.cnt

in the jc032<nnn>nbenx directory in the Unix terminal window. This rotates 
the datanby the phase and amplitude specified by the user in the control file 
q_pyrot.cnt. A recalculated calibration (after taking the first calibration 
into account) is printed to the *.out file(s). The data were then double 
checked in gautoedit to ensure that any vertical striping associated with 
on/off station differences had been removed by application of the 
calibration.

14.3.6  Creating the Output Files

Once the editing and rotation was complete, the final velocities were 
collated into Mstar files (*.nc) using the following commands in the 
jc032<nnn nbenx directory of a Matlab command window:

m_setup
m_addpath
mcod_01jc32
mcod_02jc32 (type os75_jc032<nnn>nnx or os150_jc032<nnn>nnx as the input file 
when prompted).

The first two commands set up the Mstar suite of programs and the relevant 
paths. The other two commands (derivatives of mcod_01 and mcod_02 
respectively) load in the final data for the file sequence and save it as two 
Mstar files. The first command produces a file of the form 
os75jc032<nnn>nnx.nc that includes the variables:

time - (in seconds since [2009 11 0 0 0]) 
lon - (0 to 360) 
lat - (-90 to 90) 
depth - (of bin) 
uabs - (absolute u velocity in cm/s) 
vabs - (absolute v velocity in cm/s) 
uship - (u velocity of ship over ground) 
vship - (v velocity of ship over ground) 
decday - (decimal day of year)

The second file is of the form os75jc032<nnn>nnx.nc and includes, in addition 
to the above variables:

speed - (scalar water speed in cm/s) 
shipspd - (scalar ship speed over ground in cm/s).

The individual os75_jc032<nnn>nnx.nc and os150_jc032<nnn>nnx.nc files are then 
appended together into a single output file for the cruise using the mapend 
command. This command relies on an input file containing the paths of all the 
individual files to be merged. These are to be found in the /jc032_os75 and 
/jc032_osl50 directories and are named merge_days.dat. The final output files 
are os75_jc032_apended.nc and os150_jc032_apended.nc.

In order to compare the vessel-mounted ADCP velocities on station with those 
derived from the lowered ADCP, the command mcod_03 was run using the appended 
file as the input. A loop was written to automate this process, named 
mcod_03rep (Appendix V), which is stored in both the /jc032_os75 and 
/jc032_os050 directories. The mcod_03 routine relies on an input file 
stations.dat, which contains the start and end times (in seconds since start 
of year) for each station. This dat file is found in the 
/data32/JC032/cruise/pstar/data/rnexec_processing_scripts_0902021711 
directory and is created using the stations.m script. The output files from 
mcod_03 are of the form os 75_jc032<sta>nc where <sta> denotes the station 
number.


14.4  Data Quality Issues

Whilst carrying out gautoedit editing, several quality control issues were 
identified that warrant discussion.

14.4.1  Bubble Contamination and Bias

Two potential issues arise from the presence of bubbles immediately below the 
transducer face. The first is that bubbles can prevent penetration of the 
transmit pulse and lead to truncated or bad quality profiles. This was not 
widely observed on our cruise. The second is the problem of bubble bias. It 
is known that the high amplitude return from bubbles can cause anomalous 
velocities in the direction of ship steaming (i.e. towards the east on the 
main 24°S section). It is commonly identified by a relatively low percentage 
good in the top few bins, and a red surface stripe in the along-track bias 
parameter (see Section 14.4.2). It typically does not affect lower bins of 
the profile, which remain good.

Bubble contamination was not a frequent problem when the keel was down on 
either instrument, but occasional periods of strong velocities in the surface 
associated with anomalously high returns were observed and the top few bins 
were discarded as a result (Figure 85).

14.4.2  Anomalous Scattering Bias

A more extensive problem is the presence of anomalous scattering layers 
leading to along-track velocity bias. The presence of layers of scatterers 
such as zooplankton in the water can cause severe bias in the direction of 
travel whilst the ship is steaming. This is observed as horizontal stripes in 
the velocity field, which disappear when the vessel is on station. If the 
layers are very strong, a layer of negative bias will also appear immediately 
below the scattering layer. Such features have been observed on previous 
subtropical cruises, such as Cruise 324 on RRS Discovery.

On this cruise, a large anomalous scattering layer was found on the OS75 
instruments for bins 28-40 (460-660 m) across much of the section (Figure 
84). This resulted in extensive red-over-blue striping in the along track 
bias parameter. The affected bins were removed using rzap bins within 
gautoedit. For much of JC032, there was no obvious evidence for a diurnal 
cycle in the depth of this layer, as is commonly found in zooplankton layers. 
However, close examination of some days (e.g. decimal days 71 and 93) show an 
enhanced amplitude layer moving downwards during the day from 150m to 500m, 
before returning to its original level in the evening (Figure 86). On some 
days (e.g. decimal day 93), there is an abrupt cut-off in percentage good 
below this depth (Figure 87), which does not occur for the deeper scattering 
layer at 500m. Whilst it is likely to be caused by the diurnal vertical 
migration of zooplankton, further investigation is required to find out why 
the percentage of good bins below this layer sometimes drops as low as 50%.

 
Figure 84: Amplitude return for the OS75 for file sequence 025. The 
           anomalously high scattering layer can be seen close to Layer 30.

Figure 85: Bias parameter for the same period. Note the strong red-over-blue 
           striping during the steaming periods at the depth of the anomalous 
           scattering layer. Note also the enhanced near-surface amplitude 
           return after day 98.5, most likely the result of bubbles below the 
           ship.
 
Figure 86: Anomalous region of low percentage good below bins 15-20 on decimal 
           day 93. This is thought to be caused by a diurnally migrating 
           zooplankton scattering layer.

Figure 87: Abrupt cut-off in percentage good around bin 16 for profiles 
           collected between decimal day 93.3 and 93.4 using the OS75.
 
Figure 88: Amplitude return for beam 1 for decimal day 93.3 to 93.4. Two 
           scattering layers are seen: one coincident with the sharp drop off in 
           percentage good and the deeper layer around bin 30.


Strong scattering layers are seen less frequently with the OS150. This is 
most likely because the beam does not penetrate as deep as the OS75 and the 
zooplankton are too large to act as strong scatterers on this instrument.

14.4.3  Interference Issues

No obvious evidence of interference with other instruments was seen in the 
amplitude returns during the cruise, despite the use of other acoustic 
instruments (e.g. the EM120 and EA600 echo sounders). There was some concern 
at the start of the cruise that the two ADCPs may be interfering with one 
another, as the amplitude returns of the raw ENX files did show some periodic 
green blocks in certain pings. However, these appeared to be removed by CODAS 
processing and we thus chose not to change any of the settings. CTD wire 
interference, which generally results in enhanced error velocities on 
station, was not observed during JC032.


14.5  Results

14.5.1  Brazil Current Crossings

The median on-station velocities at 98m (bin 5) are displayed for the three 
Brazil Current crossings in Figures 89, 90 and 91 respectively. In each case, 
the core of the Brazil Current is found close to the 1500m isobath, although 
the maximum velocity and alignment with respect to the topography varies 
between the sections. The strongest velocities were recorded in the first 
section off the coast of Uruguay (Figure 89), with values exceeding 40cm/s 
found at Stations 3-7. The flow is generally parallel to the topography.
 

Figure 89: Median on-station VMADCP velocities from the OS75 at 98m for the 
           first Brazil Current Crossing. The Brazil Current is seen flowing 
           towards the southwest, with a north-eastward recirculation 
           offshore.


The two northern crossings of the Brazil Current have a more complex 
structure. The second crossing (Figure 90), to the west of the Santos 
Plateau, has smaller absolute velocities in the Brazil Current (20cm/s), with 
the flow directed offshore at 45° to the topography. On the final crossing to 
the east of the Santos Plateau, the Brazil Current is stronger (40cm/s), but 
the direction is highly variable across the shelf (Figure 91). Northward 
recirculation offshore of the main current is observed on all three sections.

 
Figure 90: Median on-station VMADCP velocities from OS75 at 98m for the second 
           Brazil Current crossing. Note the different arrow size to that used 
           in Figure 89.

Figure 91: Median on-station VMADCP velocities from OS75 at 98m for the third 
           Brazil Current crossing. The Brazil Current closely follows the 
           isobaths above 1000m but becomes perpendicular to them at around 
           2500m.


14.5.2  24°S Mid-Ocean Section

The 98m velocities for the mid-ocean section are shown in Figure 92. 
Relatively weak northward flows are generally observed across the section, 
with the exception of the Mid-Atlantic Ridge near 15°W and the Walvis Ridge 
near 5°E.

 
Figure 92: Median on-station VMADCP velocities from 0575 at 98m for the 24°S 
           section.


14.5.3  The Continental Slope of Namibia

The north-south component of velocity at the eastern boundary (using the 
off-station OS75 data) is shown in Figure 93. The northward flowing Benguela 
Current is seen in the upper 250m between Stations 111 and 112, with peak 
velocities of around 30cm/s and a width of around 100km. However, several 
reversals in flow direction are seen on the rest of the slope, with southward 
flow both inshore and offshore of the main boundary current.
 

Figure 93: Off-station VMADCP v velocity in cmls at the eastern boundary of 
           the 24°S section. Triangles show station position (107 to 118), 
           with distances calculated relative to Station 107. The blank 
           regions are areas where bad data were removed using gautoedit.


14.6  Conclusions

We have successfully used two Ocean Surveyor phased array VMADCPs to obtain 
absolute velocities in the upper 1000m during JC032. The velocity errors 
associated with the calibration are less than 2cm/s. A comparison between the 
vessel-mounted and lowered ADCPs is given in David Hamersley's LADCP section 
of the cruise report (Section 13).



15.  BIOLOGICAL AND ADDITIONAL NUTRIENT BIOGEOCHEMISTRY SAMPLING
     (Mark Moore and Sinhue Torres)


15.1  Introduction

Oceanic productivity is ultimately constrained by the availability of 
nutrients at both local and global scales. Simultaneously, the activity of 
microorganisms in the ocean exerts a fundamental control on the 
biogeochemical cycles of the nutrient elements involved. Within different 
regions of the ocean the elements nitrogen (N), phosphorous (P) and iron (Fe) 
are thought to play the most important role in limiting productivity. 
However, there remain many gaps in our understanding of the interactions 
between the linked biogeochemical cycles of these elements, as well as the 
response of organisms and communities to shifts in nutrient abundance. An 
important example concerns the oceanic fixed nitrogen cycle. At global and 
potentially local scales, (Deutsch et al. 2007) the fixed nitrogen, which is 
lost from the oceans as a result of denitrificationlanammox in anoxic 
regions, must be replenished by the activity of nitrogen-fixing organisms 
(diazotrophs). This balance between nitrogen inputs and losses is crucial for 
maintaining productivity in the predominantly N-limited oceans. However, 
fundamental questions remain concerning both the spatial and temporal scales, 
as well as the mechanism, by which this process operates (Deutsch et al. 
2007). In particular, the relative influence of P and/or Fe availability in 
controlling of nitrogen fixation and hence the coupling of the N to P is 
still debated (Falkowski, 1997; Deutsch et al. 2007; Moore et al. submitted).

Cruise JC032 crossed the sub-tropical South Atlantic along a nominal latitude 
of 24°S. In marked contrast to the Northern sub-tropical gyres in the 
Atlantic and Pacific the southern sub-tropical gyres are highly under-sampled 
and in particular very little work has been performed in the South Atlantic. 
Consequently, JC032 represented an ideal opportunity to collect samples for 
the investigation of upper ocean and deep-water nutrient biogeochemistry and 
consequent influences on biological productivity in an under sampled region. 
Moreover, the cruise track crosses from west to east along a known marked 
gradient in upper ocean phosphorus availability which we hypothesise to 
result from the fixed nitrogen removal within anoxic regions of the Benguela 
current system on the eastern side, not being replaced by the action of 
diazotrophs until the waters have been transported around the gyre 
circulation to the western boundary where atmospheric Fe inputs are thought 
to be higher. Simultaneously, we wished to investigate what influence this 
gradient in P availability has on the upper ocean biota.

Samples were collected for a number of different analyses, most of which will 
be performed on return to the laboratory in Southampton.


15.2  Overall Sampling Strategy

Given the available manpower and the volumes of water available, compared to 
the high requirements for some of the desired measurements it was never going 
to be possible to collect samples for every parameter at each CTD station. A 
decision was thus taken to concentrate efforts on acquiring samples for the 
analysis of as many parameters as possible at one CTD station per day. To 
supplement the volumes of water available, samples were also collected from 
the ships underway (UW) non-toxic seawater supply at each station sampled. 
Additional sampling was also undertaken with a surface bucket in order to 
estimate the abundance of the nitrogen fixing colonial cyanobacterium 
Trichodesmium and using a General Oceanics Go-Flo bottle for collection of 
trace metal samples.

15.2.1  Total Chlorophyll a

Water samples (250m1) were collected from CTD bottles and the underway (UW) 
surface water supply and were filtered onto 25mm glass fibre filters 
(Fisherbrand, equivalent to Whatman GF/F). Filters were then placed in vials 
and extracted in 8m1 90% acetone for 24 hours in a darkened fridge. Total 
chlorophyll a was then measured with a TD-700 Turner Designs fluorometer 
following the procedure of Welschmeyer (1994) which minimises interference by 
chlorophyll b. The fluorometer was calibrated with dilutions of a solution of 
pure chlorophyll a (Sigma, UK) in 90% acetone before JC031. Blanks of 90% 
acetone were analysed daily. Additionally, 2 bulk samples with differing 
concentrations of chlorophyll were filtered onto multiple filters then stored 
at -80°C. Sub-sets of these samples were then thawed and analysed throughout 
the cruise at 1-2 week intervals to check for drift in the instrument 
response. A number of these filters, alongside duplicate profiles from a 
selection of stations will also be returned to the lab (frozen at -80°C) for 
analysis, as a second overall check on the accuracy of the calibration. The 
limit of detection calculated as 3 standard deviations of the blank was 
0.003mg m3 and differences measured between duplicate samples were <0.001mg 
m3 in all cases, both of which were satisfactory, given the measured 
chlorophyll concentrations ranging from 0.006 and 3.09mg m3. A total of 140 
samples were collected at 34 stations (Table 13). The upper water column 
chlorophyll concentration is mapped in Figure 94.

 
Figure 94: Preliminary contoured section of chlorophyll a measured on 
           discrete samples collected across the 24°S section.


15.2.2  Samples for δ15NPON

Particulate organic material (POM) was collected from the ships UW supply for 
the measurement of the natural abundance ratio of 15N:14N. Replicate 4.5L water 
samples were collected on station and filtered onto pre-ashed Whatman GF/F 
filters under gentle vacuum (<200 mbar). Filters were then placed in plastic 
vials and dried for 24-48 hours at 50-60°C before being stored for transport 
back to NOCS. On return samples will be analysed by isotope ratio mass 
spectrometry (IRMS) and used for the calculation of the δ15N (‰) (=1000 x 
(15N:14Nsample/15N:14Nstandard - 1), where the standard is N2 gas) of 
particulate organic nitrogen (PON). This data will in turn be used as a tracer 
of nitrogen cycling and the initial condition for direct incubation based rate 
measurements of nitrogen fixation.

15.2.3  Nitrogen Fixation Rate Measurements

Samples for water column nitrogen fixation rate measurements were collected 
from the CTD. Typically the top 3-4 Niskins were sampled corresponding to 
depths within the surface layer and within and above the DCM. Occasionally 
samples from the first bottle below the DCM were also incubated. Rate 
measurements were performed according to the methods detailed elsewhere 
(Montoya et al. 1996; Mills et al. 2004). Briefly, samples were drawn into 
4.5L Nalgene polycarbonate bottles and sealed ensuring that no air bubbles 
were present with a silicone septum lid. Bottles were then injected with 
either 3m1 or 4m1 of 99% 15N2 gas, sealed in clear plastic zip-lc bags and then 
transferred to an on-deck incubator cooled with flowing surface seawater. The 
incubator and individual bottles were shaded so as to approximate the 
irradiance at the sampling depth. After 24 hours, the incubations were 
terminated by gentle filtration (<200 mbar) onto precombusted GF/F filters, 
and the samples dried (24 hours at 50-60°C) and once again stored for IRMS 
analysis. A total of 36 stations were sampled (Table 13).

15.2.4  Samples for Intact Polar Lipids

Samples for intact polar lipids were drawn from Niskin bottles corresponding 
to both the near surface (~5m) and the DCM. Intact polar lipids are very 
labile and the goal was to have samples frozen within 1 hour of collection. 
Due to the time taken to sample the CTD it was typically only possible to 
filter 1L of sample from Niskins within a reasonable time frame. Consequently 
samples were also collected from the ships UW supply on station, such that a 
surface sample of 2L could be filtered and frozen within 1 hour. Samples were 
filtered onto anodized aluminium disks under gentle vacuum (<200 mbar). As 
soon as the filtrations were finished, discs were quickly taken and placed 
onto ashed foil which was then folded into an envelope, labelled and placed 
in the -80°C freezer for transport back to NOCS. Samples will be analysed by 
Patrick Martin (PhD student) during his participation in the Woods Hole 
exchange programme where he will be visiting the laboratory of Dr. Ben Van 
Mooy. In total 86 samples were collected from 33 stations (Table 13).

15.2.5  Samples for Protein Analysis

Samples were also collected for quantification of major metabolic proteins 
(including the photosystems, nitrogenase and Rubisco) via quantitative 
immunoblotting using global antibodies. Water samples were drawn from Niskin 
bottles (1L) or the ships UW system (2L) and gently filtered (<200 mbar) onto 
Advantec glass fibre filters. Filters were then quickly transferred to a 
-80°C freezer for return to NOCS where they will be analysed by a PhD student 
(Miss Anna Macey) under the supervision of Dr. Tom Bibby and Dr. Mark Moore 
(NOCS). In total, 86 samples were collected from 33 stations (Table 13).

15.2.6  Samples for the Enumeration of Trichodesmium

At each station sampled for nitrogen fixation rate measurements a surface 
bucket sample was collected for the enumeration of Trichodesmium. This 
organism forms large (~10,000 cell) colonies, which can be a significant 
component of the nitrogen fixing community even at relatively low abundance, 
frequently (<1 colony F1). Consequently, a large volume must be filtered. 10L 
samples from the surface collected with a bucket were gently filtered through 
a 10µm mesh, then re-suspended in filtered seawater and preserved in 2% 
lugols iodine solution for return to NOCS and enumeration by light microscopy 
(Tyrrell et al. 2003). A total of 34 samples were collected (Table 13).

15.2.7  Samples for Trace Metal Analysis

Clean samples for the analysis of trace metals were collected at a total of 
20 stations using a General Oceanics Go-Flo sampler deployed using a handheld 
Kevlar line. The Go-Flo is deployed closed and empty (air filled). A 
hydrostatic release then triggers at a depth of 1Om, flooding the bottle. The 
sampler was then lowered on down to 20m and a messenger sent down the line to 
close the bottle. On recovery the bottle was taken to a dedicated clean 
laboratory environment (the isotope container which had been loaded for 
JC031). Samples were then drawn from the Go-Flo into pre acid-washed 125m1 
LDPE bottles for both total dissolvable (i.e. unfiltered) and dissolved 
(filtered) trace metal analysis. Filtered samples were collected by gravity 
filtering ~100ml through SarbortanTM filter cartridges. Both filtered and 
non-filtered samples were then acidified by adding 60µl of ultra clean HNO3. 
Sample filtration and acidification were performed within glove bags flushed 
with air passed through an in-line HEPA filter.

15.2.8  Samples for Scanning Electron Microscopy Analysis

Samples were collected on behalf of Dr. Alex Poulton for the identification 
and enumeration of coccolithophores. Around 1-2L of water were collected 
either from the CTD or the UW system and gently filtered (<200 mbar vacuum) 
onto 0.4µm polycarbonate filters. Filters were subsequently dried for 12-24 
hours at 50-60°C, then stored for return to NOCS where they will be analysed 
by scanning electron microscopy (SEM).

15.2.9  Samples for δ15NNO3-

In addition to the δ15N of PON, the δ15N of NO3- can also be used as a tracer of 
the relative influence of nitrogen fixation and denitrification within a 
water body. We are currently investigating setting up methods for the 
analysis δ15N of NO3- at NOCS along with collaborators elsewhere. Consequently, 
given the ideal location of the JC032 transect for studying nitrogen dynamics 
it was prudent to collect frozen samples for potential future isotopic 
analysis. Water was collected directly from Niskin bottles into acid-washed 
and Milli-Q rinsed 125m1 or 250m1 plastic bottles following 3 sample rinses. 
These samples were then frozen at -20°C for return to NOCS. A total of 162 
samples for the potential assessment of δ15NO3- were collected at 15 stations. 
Where possible, sampling depths and stations were chosen to coincide with 
those sampled for DOM (see below) and where a CFC sample was also taken. The 
latter may eventually allow assessment of changes in δ15NO3- as a function of 
tracer age.

15.2.10  Samples for DOM

Samples were also drawn from a limited set of CTDs for the analysis of 
dissolved organic matter (DOM). Water was drawn directly from the CTD into 
Sterilin pots which were first rinsed 3 times with sample. Samples were then 
frozen for the return to NOCS. Samples will be stored with the intention of 
analysis at some future date for dissolved organic nitrogen and phosphorus by 
Dr. Sinhue Torres. One station a day was typically sampled. DON and DOP 
gradients are strongest in surface waters and due to a limited supply of 
sampling pots, on alternate days sampling concentrated on the upper water 
column, with a full (24 bottle) profile taken every other day. A total of 445 
samples were taken at 26 stations.


Table 13: Simple overview of sampling giving listings of stations sampled for 
          each parameter. A more detailed spreadsheet has been saved within the 
          cruise data directory or can be requested directly from C. M. Moore 
          (e-mail: cmm297@noc.soton.ac.uk).
                                                                    No.     Total
Parameter      Stations sampled                                  stations  samples
-------------  ------------------------------------------------  --------  -------
N2 fixation    8,10,15,25,29,30,34,37,38,41,44,47,49,51,54,         36       132
               56,59,63,65,68,71,75,78,80,83,86,88,90,93,95,
               101,105,108,110,117,118
15PON          8,10,15,25,30,34,37,41,44,47,49,51,54,56,59,         33        33
               63,65,68,71,75,78,80,83,86,88,90,93,95,101,
               105,108,110,118
Protein        8,10,15,25,30,34,37,41,44,47,49,51,54,56,59,63,      33        86
               65,68,71,75,78,80,83,86,88,90,93,95,101,105,
               108,110,118
Lipids         8,10,15,25,30,34,37,41,44,47,49,51,54,56,59,63,      33        86
               65,68,71,75,78,80,83,86,88,90,93,95, 101,105,
               108,110,118
Chlorophyll a  8,10,15,25,30,34,37,41,44,47,49,51,54,56,59,63,      34       140
               65,68,71,75,78,80,83,86,88,90,93,95,101,105,
               108,110,117,118
SEM            10,15,25,37,44,49,51,54,56,59,63,65,68,71,75,        27        44
               78,80,83,86,88,90,93,95,105,108,110,118
Trichodesmium  10,15,25,29,30,34,37,38,41,44,47,49,51,54,56,        34        34
               59,63,65,68,71,75,78,80,83,86,88,90,93,95,101,
               105,108,110,118
Trace metals   30,34,38,41,44,47,49,54,59,63,68,75,78,83,86,        20        20
               88,93,101,108,118
15NO3          25,30,37,43,46,53,59,65,77,88,93,100,108,115,118     15       162
DOM            37,43,46,51,53,56,59,62,65,68,71,74,77,80,83,85,     26       445
               88,90,93,95,100,104,108,110,115,118


15.3  References

Deutsch C., Sarmiento J.L., Sigman D.M. et al. (2007), Spatial coupling of 
    nitrogen inputs and losses in the ocean, Nature, 445, 163.

Falkowski P.G. (1997), Evolution of the nitrogen cycle and its influence on 
    the biological sequestration of CO2 in the ocean, Nature, 387, 272.
    Mills M.M., Ridame C., Davey M. et al. (2004), Iron and phosphorus co-limit 
    nitrogen fixation in the eastern tropical North Atlantic, Nature, 429, 
    292.

Montoya J.P., Voss M., Kahler P. et al. (1996), A simple, high-precision, 
    high-sensitivity tracer assay for N-2 fixation, Applied and Environmental 
    Microbiology, 62, 986.

Moore C.M. et al. (Submitted), Interactions between iron supply and large 
    scale circulation control the coupling of Nitrogen to Phosphorous in the 
    Atlantic Ocean.

Tynell T., Maranon E., Poulton A.J. et al. (2003), Large-scale latitudinal 
    distribution of Trichodesmium spp. in the Atlantic Ocean, Journal of 
    Plankton Research, 25, 405.

Welshmeyer N.A. (1985-1992), Fluorometric analysis of chlorophyll a in the 
    presence of chlorophyll b and phaeopigments, Limnol. Oceanogr., 39.




Acknowledgments 

Mark would particularly like to thank the principal scientist of JC032 (Dr. 
Brian King) for allowing me to participate in what has been an enjoyable 
cruise and being supportive in the collection of what will hopefully prove to 
be a very interesting dataset. I was also hugely impressed with the overall 
professionalism of the core science team that made the cruise run so 
smoothly. As ever Mark would like to thank all the crew of the RRS James Cook 
and the NMF technical staff for the cooperation and assistance.








16.  CONTINUOUS O2 CONCENTRATION MEASUREMENTS FROM THE UNCONTAMINATED SEAWATER 
     SUPPLY
     (Alba Gonzalez-Posada)


16.1  Objectives

• To measure the O2 concentration continuously from the uncontaminated 
  seawater supply (USW) using an oxygen optode sensor (Aanderaa Model No. 3835).
• To calibrate the optode data with discrete samples collected from the USW.

Dissolved O2 concentrations are measured from the sea surface water. Surface 
seawater is pumped to the laboratory by the uncontaminated system supply (USW) 
on board the RRS James Cook. The intake of the surface seawater (SS) is located 
at the bow of the ship at a nominal depth of 5m. Continuous dissolved O2 
measurements were done using an Aanderaa Oxygen optode sensor (AOO, Model No. 
3835, Serial No. 329).

The optode sensor measurements are based on the ability of selected 
substances to act as dynamic fluorescence quenchers. A fluorescent indicator 
with a special platinum porphyrin complex embedded in a gas permeable foil is 
exposed to the surrounding water. The foil is excited by modulated blue 
light, and the phase of a returned red light is measured. By linearising and 
temperature compensating with an incorporated temperature sensor, the 
absolute O2 concentration can be determined.

The continuous O2 concentration data from the optode was calibrated against 
the total O2 concentration from USW discrete samples. These were determined by 
the Winkler titration method (Dickson, 1996), using a Winkler Ω-Metrohm 
titration unit (716 DMS Titrino).


16.2  Underway Oxygen Measurements by an Aanderaa Optode.

The optode sensor was kept in a 1L dark bucket fed by the continuous USW flow 
in the controlled temperature laboratory (CTL) of the RRS James Cook. The USW 
was kept on at all times, except when approaching and leaving port.

Continuous temperature, not calibrated dissolved O2 and O2 saturation were 
recorded at a rate of 1 reading every 10 seconds. This produced a data set of 
more than 250,000 measurements for the whole of the cruise, comprising 42 
days between Julian days 67 to 110 (8th of March to 20th of April, 2009).

In general the optode sensor was stable; however, it may have been affected 
by external perturbations such as the presence of bubbles in the USW. Bubbles 
in the system were mainly produced by the ship pitching during bad weather 
(Figure 95).


Figure 95: Optode O2 concentration and temperature over time. The circle is 
           showing periods with bubbles.


16.3  Calibration of the Underway Oxygen Optode

The oxygen concentration measured by the optode represents the partial 
pressure of the dissolved oxygen. Since the foil is only permeable to gas, 
the optode sensor is not affected by dissolved salts. This is comparable to 
if the optode measurement is made in fresh water. Salinity corrections must 
be performed to obtain more accurate values.

Measurements of discrete samples were taken from the same supply feeding the 
sensor. These were collected directly into pre-calibrated glass bottles. The 
total dissolved O2 concentration was quantified following the Winkler 
titration method described by Dickson (1996), using a Winkler Ω-Metrohm 
titration unit (716 DMS Titrino) with amperometric end point detection.

A total of 326 samples were taken during the cruise. In general 4 samples 
were taken in duplicate per day, and were analysed after a crate of 28 
samples were accumulated. This represented 13 measurement sessions. Standards 
and blanks were prepared with the nutrients and oxygen team in 11 sessions 
(see methods in oxygen and nutrients report). The typical standard deviation 
of a duplicate analysis was 0.31µmol kg-1.

The calibration was carried out using a temperature-dependent fourth-order 
calibration polynomial called "DPhase", which is stored in the optode. In 
order to compare the sensor data with the discrete samples, these were 
transformed to a solved "DPhase". The resulting calibration function will be 
used to compute 'calibrated' optode data. Figure 96 shows the comparison 
between the sensor raw data and the solved "Dphase" for the samples 
collected.

 
Figure 96: Optode Dphase raw against Dphase solved for the discrete USW 
           samples collected for O2 continuous calibration. The worst data 
           comparison (Series 3 and 4) comes from the periods were there were 
           bubbles in the USW.


Differences are originated both from uncertainties in the optode and in the 
Winkler measurements.


16.4  Dissolved O2 Concentration From USW and CTD Surface Niskin Bottle

To evaluate the effect of the pipes over the O2 concentration in the surface 
seawater, a comparison between surface Niskin bottles and the laboratory USW 
will be done when USW oxygen concentration is completely calibrated.



Acknowledgements

I am grateful to the crew, officers and scientific party of RRS James Cook 
during cruise JC032. I am also grateful to Niki Silveira and Sinhué Tones for 
helping with the collection of the discrete O2 samples. Many thanks to the 
chemistry team for allowing me to use the Winkler titration unit and 
reagents.


16.5  References

Dickson, A.G. (1996), Determination of dissolved oxygen in seawater by 
    Winkler titration, in WOCE Operations Manual. Volume 3: The Observational 
    Programme. Section 3.1: WOCE Hydrographic Programme. Part 3.1.3: WHP 
    Operations and Methods, edited by World Ocean Circulation Experiment, 
    Woods Hole, Massachussetts, USA.



17.  NET COMMUNITY PRODUCTION ESTIMATES FROM DISSOLVED OXYGEN/ARGON RATIOS 
     MEASURED BY MEMBRANE INLET MASS SPECTROMETRY (MIMS)

     Gross Productivity Estimates From 17O/16O and 18O/16O Isotope Ratios of 
     Dissolved Oxygen


17.1  Rationale and Objectives

The dissolved oxygen (O2) concentration of seawater is affected by fundamental 
physical and biological processes. These include; photosynthesis (P) and 
respiration (R), diffusive and bubble-mediated gas exchange with the 
atmosphere, temperature and pressure changes, lateral mixing and vertical 
diffusion. In the absence of physical effects, dissolved O2 constrains the 
difference between P and R, i.e. net community production (N). Thus, O2 can be 
used as a geochemical tracer that reflects carbon fluxes integrated over 
characteristic response times. Warming and bubble injection lead to O2 
supersaturation, posing a challenge to this approach.

Craig and Hayward (1987), Dickson (1995) used oxygen/argon (O2/Ar) ratios to 
separate O2 supersaturations into a biological and physical component. This 
method is based on the similar solubility characteristics of O2 and Ar with 
respect to temperature and pressure changes as well as bubble injection. One 
can define an O2/Ar supersaturation, ∆O2/Ar, as:

                               c(O2)   / csat(O2)
                      ∆O2/Ar = -----  /  -------- -1
                               c(Ar) /   csat(Ar)  

∆O2/Ar essentially records the difference between photosynthetic O2 production 
and respiration. c is the dissolved gas concentration (in mol m-3) and csat is 
the saturation concentration. csat is a function of temperature, pressure and 
salinity. This method, in which discrete samples are collected at sea, 
stored, and analyzed in the lab, has been widely used in subsequent work 
(Spitzer and Jenkins 1989; Quay, Emerson et al. 1993; Luz and Barkan 2000; 
Hendricks, Bender et al. 2004).

Recently presented was an advance of this method for continuous underway 
measurements of O2/Ar by membrane-inlet mass spectrometry (MIMS) (Kaiser, 
Reuer et al. 2005), extending earlier oceanographic MIMS applications (Kana, 
Darkangelo et al. 1994; Tortell 2005). The measured ∆O2/Ar values can be used 
in conjunction with suitable wind-speed gas-exchange parameterizations to 
calculate biologically induced air-sea O2 fluxes and, where conditions are 
appropriate, N. The inferred N values represent rates integrated over the 
characteristic mixed layer gas exchange times (ratio of mixed layer thickness 
and piston velocity), typically between 2 and 4 weeks.

The O2/Ar method has the advantage not to involve potential biases associated 
with incubating water samples in a bottle. The N estimates from the JC032 
cruise will be used to quantitatively study the autotrophic or heterotrophic 
nature of different marine ecosystems in the South Atlantic subtropical gyre.

In addition to the continuous underway measurements, discrete samples from 
the same source of water were taken for calibration purposes and to measure 
the 17O/16O and 18O/16O isotope ratio analysis of dissolved oxygen. Triple 
oxygen isotope measurements combined with O2/Ar data can be used to estimate 
the ratio of net community production (N) to gross production (P) and the 
ratio of gas exchange to gross production. Again, in combination with 
suitable wind-speed gas-exchange parameterizations this can be used to 
estimate gross production over large regional scales at timescales of weeks 
to months.


17.2  Methodology

Continuous measurements of dissolved N2, O2, Ar and CO2 were made by MIMS on 
board RRS James Cook. The ship's uncontaminated system supply of seawater 
(USW) was used to pump water through an exchange chamber with a tubular 
Teflon AF membrane (Random Technologies) mounted on the inside. The membrane 
was connected to the vacuum of a quadrupole mass spectrometer (Pfeffer Vacuum 
Prisma). The intake of the USW is located at the bow of the ship at a nominal 
depth of 5m. The water first passed through a 50µm filter to remove 
macroscopic particles that can obstruct the flow in the degassing membrane. 
The inlet of seawater to the MIMS was kept in a 1L dark bucket that was 
filled up with the continuous USW flow from the aft starboard sink in the 
control temperature laboratory (CTL) (deck level) of the RRS James Cook. A 
flow of about 60m1/min was continuously pumped from the bucket through the 
membrane chamber, using a gear pump (Micropump). In order to reduce O2/Ar 
variations due to temperature effects and water vapour pressure variations, 
the exchange chamber with the membrane was held at a constant temperature of 
15°C. The flight tube was in a thermally insulated box maintained initially 
at 70°C.

The O2/Ar ratio measurements will be calibrated with discrete water samples 
taken from the same seawater outlet as used for the MIMS measurements. 
200-300cm3 samples were drawn into pre-evacuated glass flasks poisoned with 
7mg HgCl2 (Quay, Emerson et al. 1993). These samples will be later analyzed 
with an isotope ratio mass spectrometer at the School of Environmental 
Sciences, University of East Anglia, for their dissolved O2/Ar ratios and the 
oxygen triple isotope composition relative to air (Hendricks, Bender et al. 
2004). Raw O2/Ar ion current ratio measurements were made every 10 s and had a 
short-term stability of 0.05%. Absolute Ar supersaturation will be calculated 
from the absolute O2 supersaturations measured by Winkler titration and the 
O2/Ar ratios measured by MIMS.


17.3  Results

In total 77 discrete water samples were collected for calibration purposes 
and to analyze oxygen triple isotopes, 60 of them were taken from the USW and 
17 from the CTD. The water was sampled into evacuated bottles with 
compression O-ring valves (Glass Expansion). From Jan Kaiser's experience, 
this type of valve is more watertight than previously used high-vacuum valves 
(Louwers Hapert). These samples will be analyzed at the University of East 
Anglia after our return.

Membrane inlet mass spectrometry (MIMS) was used to analyze dissolved gases 
continuously, namely oxygen (O2), nitrogen (N2), argon (Ar), and carbon 
dioxide (CO2). The general performance of the instrument was good. However 
there are some unstable periods due to the contamination of the membrane with 
air usually after running discrete samples on station.


Acknowledgements 

Many thanks to crew, officers and scientific party of the RRS James Cook 
during JC032, particularly to David Cooper for helping with the collection of 
samples.


17.4  References

Craig, H. and Hayward, T. (1987), Oxygen supersaturation in the ocean: 
    Biological versus physical contributions, Science, 235, 199-202.

Hendricks, M.B., Bender, M.L., and Barnett, B.A. (2004), Net and gross O2 
    production in the Southern Ocean from measurements of biological O2 
    saturation and its triple isotope composition, Deep-Sea Res. I, 51, 
    1541-1561.

Kaiser, J., Reuer, M.K., Barnett, B., and Bender, M.L. (2005), Marine 
    productivity estimates from continuous oxygen/argon ratio measurements by 
    shipboard membrane inlet mass spectrometry, Geophys. Res. Lett., 32, 
    L19605, doi: 10.1 029/2005GL023459.

Kana, T.M., Darkangelo, C., Hunt, M.D., Oldham, J.B., Bennett, G.E., and 
    Cornwell, J.C. (1994), Membrane inlet mass spectrometer for rapid 
    high-precision determination of N2, O2, and Ar in environmental water 
    samples, Anal. Chem., 66, 4166-4170.

Luz, B. and Barkan, E. (2000), Assessment of oceanic productivity with the 
    triple-isotope composition of dissolved oxygen, Science, 288, 2028-2031.

Quay, P.D., Emerson, S., Wilbur, D.O., and Stump, C. (1993), The d18O of 
    dissolved oxygen in the surface waters of the subarctic Pacific: A tracer 
    of biological productivity, J. Geophys. Res., 98, 8447-8458.

Spitzer, W.S. and Jenkins, W.J. (1989), Rates of vertical mixing, gas 
    exchange and new production: Estimates from seasonal gas cycles in the 
    upper ocean near Bermuda, J. Mar. Res., 47, 169-196.

Tortell, P.D. (2005), Dissolved gas measurements in oceanic waters made by 
    membrane inlet mass spectrometry, Limnol. Oceanogr.: Methods, 3, 24-37.




18.  FAST REPETITION RATE FLUOROMETRY (FRRF) FROM THE UNCONTAMINATED SYSTEM 
     SUPPLY
     (Alba Gonzalez-Posada)


A Fast Repetition Rate Fluorometer (FRRF) (Chelsea Instruments Ltd.) was used 
to measure active fluorometry from the uncontaminated system supply (USW) 
onboard the RRS James Cook. The fast repetition rate fluorometry (FRR) is 
based on variable fluorescence characteristics of the phytoplankton 
(chlorophyll a). The FRRF has been introduced as a potential tool to evaluate 
the primary productivity in aquatic systems. Active chlorophyll a fluorometry 
provides a non-destructive and minimally intrusive method for probing 
oxygenic photosynthesis, in general, and the functioning of photosystem II in 
particular (Raateoja, 2004).

The FRRF was fitted to a protective rack in one of the sinks of the deck 
laboratory on the deck level onboard the RRS James Cook. A constant flow of 
surface water from the USW was kept acquiring data for the duration of the 
JC031 oceanographic cruise (ID 34 to 61) including the transits before and 
after the CTD casts. The USW pumps sea surface water from a nominal depth of 
5m. The intake is located at the bow of the ship.

The acquisition of discrete samples (data resolution) was every 10 seconds 
operating in a bench-top mode. A single file per 24 hours of data was created 
in txt format.

The variables of interest from the FRRF data are Fo and Fm that corresponds 
to the initial and maximal in vivo fluorescence yield (relative) in the 
dark-adapted state in the absence of non-photochemical quenching. Since there 
are non-homogeneous regions with high variation in phytoplankton 
concentration, a photomultiplier (PMT) variable is also considered. This 
variable was set to auto-ranging mode in the protocol (see below) set for the 
USW analysis.

A copy of the boot protocol followed is shown below.

FRRF boot protocol:

***Boot Protocol = 9***
6.  65535     Acquisitions
7.  16        Flash sequences per acquisition (averaged)
8.  100       Saturation flashes per sequence
9.  4         Saturation flash duration
A.  0         Saturation interflash delay
B.  ENABLED   Decay flashes
C.  20        Decay flashes per sequence
D.  4         Decay flash duration
E.  120       Decay interfiash delay
F.  10000     Sleep-time between acquisition sequence (mS)
G.  16        PMT Gain in Autoranging mode
H.  DISABLED  Analogue output
I.  ENABLED   Desktop (verbose) Mode
J.  INACTIVE  Light Chamber
K.  ACTIVE    Dark Chamber
L.  ENABLED   Logging mode to internal flashcard
M.  95        Upper Limit Autoranging Threshold value
N.  5         Lower Limit Autoranging Threshold value


18.1  References

Raateoja, M.P. (2004), Fast repetition rate fluorometry (FRRF) measuring 
    phytoplankton productivity: A case study at the entrance to the Gulf of 
    Finland, Baltic Sea, Boreal Environment Research, 9: 263-276.


Acknowledgements 

I am very grateful to Mark Moore for his advice and help with the FRRF system 
and also for providing me with a script to process the data.



19.  AEROSOL SAMPLING
     (Alba Gonzalez-Posada)


Aerosol samples were collected throughout the cruise using a high volume 
(lm3min-1) collector, with each sample collected over a period of approximately 
24 hours.

The apparatus for the collection of this data was situated on Monkey Island 
at the very top of the RRS James Cook. It was necessary to consult the bridge 
crew every time access was required to Monkey Island due to the operation of 
the large radar dish, which was a source of ionizing radiation. The bridge 
crew would not only ensure that the access to Monkey Island was safe, but 
also would keep an eye on the weather and provide notification of when the 
conditions such as the wind direction changed, or if it was likely to start 
raining.

Aerosol samples collected will be analysed at UEA for their major ion 
content, with the main focus being the estimation of atmospheric nutrient (N 
and P) fluxes into the South Atlantic. Rainwater samples were also collected 
whenever possible using a 40cm diameter polypropylene funnel. These samples 
will also be analysed at UEA for their major ion/nutrient content.



20.  ARGO FLOATS
     (David Hamersley and Gerard McCarthy)


20.1  Introduction

One of the operations that the physics team was involved with on JC032 was 
the preparation and launch of APEX type Argo floats (provided by the MET 
Office). APEX stands for Autonomous Profiling EXplorer, and this particular 
float is equipped with an array of sensors, which measure parameters such as 
salinity/conductivity, temperature, and pressure, whilst tracking the 
position of the float via the contingent of ARGOS satellites orbiting the 
Earth. The data collected by the floats is automatically transmitted to these 
satellites when the float surfaces. The floats manoeuvre vertically through 
the water column by means of pumping fluid into and out of an external 
bladder. This particular type of float is designed to be neutrally buoyant at 
a depth of 1000m (park pressure). The float then descends to a depth of 2000m 
and then rises back up to the surface. The process of inflating and deflating 
the bladder is repeated over and over, resulting in a continuous cycle from 
which high quality data of the ocean profile from 2000m depth to the surface 
can be recorded. The cycle length is programmable, but these particular 
floats have a cycle that carries out 1 profile every 10 days.


20.2  Objectives

During this cruise, 16 Argo floats were launched at different locations along 
the 24°S transect in the South Atlantic. The principal aim of this venture 
was to increase the population of Argo floats in the South Atlantic, in order 
to augment the quantity and quality of ocean profile data in this location. 
The launch positions largely depended on the positions of floats that were 
currently active near the 24°S transect. Out of the 16 Argo floats that were 
launched during the cruise, 4 of these were designed for near-surface 
temperature monitoring.


20.3  Float Identification

Each float had its own unique serial number on the hull. All the information 
for each of the floats, including pre-deployment tests and also when the 
float was actually launched was recorded in a log. The main information has 
been compiled in the following table.


Table 14:  Key Argo Float Information

D  | C |  T   |  H   |         |  S  |   A  T (J   |   E  D (J   |   D  T (J   | 
e  | r |  y   |  u   |         |  t  |   c  i  k   |   x  i  k   |   e  i  k   | 
p  | a |  p   |  l   |         |  a  |   t  m  a   |   p  v  a   |   p  m  a   | 
l  | t |  e   |      |         |  t  |   i  e  y   |   e  e  y   |   l  e  y   | 
o  | e |      |  S   |         |  i  |   v     /   |   c     /   |   o     /   | 
y  |   |      |  e   |         |  o  |   a     h   |   t  T  h   |   y     h   | 
m  |   |      |  r   |         |  n  |   t     h   |   e  i  h   |   m     h   | 
e  |   |      |  i   |         |     |   i     m   |   d  m  m   |   e     m   | 
n  |   |      |  a   |         |     |   o     m)  |      e  m)  |   n     m)  | 
t  |   |      |  l   | WMO ID  |     |   n         |             |   t         |   Latitude     Longitude
-- | - | ---- | ---- | ------- | --- | ----------- | ----------- | ----------- | -----------   -----------
 1 | 1 | Norm | 4364 | 1901228 |  36 | 080 / 23:46 | 080 / 05:46 | 080 / 01:31 | 23°S 59.96' | 037°W 29.85'
 2 | 1 | Norm | 4439 | 1901229 |  40 | 082 / 04:40 | 082 / 10:40 | 082 / 06:55 | 23°S 59.92' | 034°W 57.95'
 3 | 2 | Norm | 4440 | 1901230 |  46 | 084 / 04:35 | 084 / 10:35 | 084 / 06:12 | 23°S 59.98' | 031°W 10.13'
 4 | A | Surf | 4480 | 1901240 |  51 | 087 / 11:07 | 087 / 17:07 | 087 / 12:38 | 23°S 59.92' | 028°W 27.90'
   |   | Temp |      |         |     |             |             |             |                    
 5 | 2 | Norm | 4469 | 1901231 |  59 | 090 / 09:51 | 090 / 15:51 | 090 / 11:51 | 24°S 00.07' | 022°W 43.93'
 6 | 3 | Norm | 4471 | 1901233 |  63 | 092 / 13:32 | 092 / 19:32 | 092 / 15:12 | 24°S 00.03' | 019°W 52.13'
 7 | A | Surf | 4481 | 1901241 |  67 | 094 / 00:14 | 094 / 06:14 | 094 / 01:49 | 23°S 24.59' | 017°W 00.03'
   |   | Temp |      |         |     |             |             |             |                    
 8 | 3 | Norm | 4470 | 1901232 |  72 | 095 / 14:19 | 095 / 20:19 | 095 / 16:07 | 22°S 54.41' | 013°W 46.00'
 9 | 4 | Norm | 4473 | 1901235 |  77 | 097 / 05:00 | 097 / 11:00 | 097 / 06:25 | 22°S 21.09' | 011°W 00.53'
10 | B | Surf | 4482 | 1901242 |  82 | 099 / 00:25 | 099 / 06:25 | 099 / 01:50 | 23°S 41.01' | 007°W 25.05'
   |   | Temp |      |         |     |             |             |             |                    
11 | 4 | Norm | 4472 | 1901234 |  86 | 100 / 13:31 | 100 / 19:31 | 100 / 14:43 | 23°S 59.95' | 004°W 11.78'
12 | 5 | Norm | 4475 | 1901237 |  89 | 101 / 20:08 | 102 / 02:08 | 101 / 21:35 | 24°S 00.08' | 001°W 53.13'
13 | B | Surf | 4483 | 1901243 |  95 | 104 / 06:05 | 104 / 12:05 | 104 / 07:25 | 23°S 59.98' | 003°E 48.01'
   |   | Temp |      |         |     |             |             |             |                    
14 | 5 | Norm | 4474 | 1901236 | 103 | 105 / 22:48 | 105 / 04:48 | 106 / 00:21 | 23°S 59.91' | 007°E 02.52'
15 | 6 | Norm | 4477 | 1901239 | 107 | 107 / 11:02 | 107 / 17:02 | 107 / 11:35 | 24°S 00.00' | 009°E 42.00'
16 | 6 | Norm | 4476 | 1901238 | 111 | 108 / 11:51 | 108 / 17:51 | 108 / 13:13 | 24°S 00.00' | 012°E 04.00'



20.4  Launch Positions

This map shows the positions where the Argo floats were deployed, and it also 
highlights the positions of older floats in the vicinity.

 
Figure 97: Map of the South Atlantic Ocean with locations of old floats (*) 
           and the launch positions of floats on JC032 (x)


20.5  Pre-deployment checks

Tests were run on each float in advance of each deployment to ensure that the 
float was functioning as expected. These checks were performed using a laptop 
computer with a COM1 port to which the cables could be connected. It was 
necessary to ensure that the clamps were touching only the terminals 
protruding from the float and not the hull of the float itself otherwise 
random symbols would be generated in the terminal window on the screen. The 
program used for talking to the float was Hyper-terminal, saved under the 
alias 'apex_talk'.

Firstly, the parameters for communication with the float had to be selected, 
such as the terminal parity (none), transfer rate (9600 bits). Gerard 
McCarthy created log sheets and instructions for the pre-deployment checks. 
To start the program recording information, the capture text → start function 
in the menu toolbar was selected.

The list of values for the parameters of the float e.g. park pressure, Argos 
repetition period, up-time, down-time, etc. were displayed by typing L into 
the terminal, and the values were checked off, and were also noted if 
different to those displayed on the sheet.

Typing P displayed the pressure table of the float. There was a difference in 
the pressure tables between the normal and surface floats, as the near 
surface floats had an additional pressure level (58) to the normal floats.

The time offset (GMT - float was recorded), and it was generally found that 
the offset was in the order of 5-9 seconds. To test if the float was able to 
transmit data, a transmit command was sent to the float which would generate 
a beep from a receiver in confirmation.

The high pressure pumps were tested by monitoring the original positions of 
the pistons (should be 100 counts for shipping), and then the pump was 
extended and retracted by 4 counts. The battery voltage was checked, and was 
supposed to be higher than 15.2V. The internal vacuum was checked for a value 
between 78-87 counts.

The pneumatic system test was run in two stages due to the need to wait for 
five minutes before the second stage. Firstly the pumps were run for 6 
seconds and the vacuum counts were observed to check that they had risen by 
20-30 counts. The pumping continued until the vacuum had reached 120 counts, 
and once this value was reached the time was recorded concluding the first 
stage of the pneumatic system test. The second stage of the pneumatic system 
test consisted of checking that the vacuum counts had held at a relatively 
constant level (1-2 counts).

During the 5-minute wait, it was found to be an efficient use of time to 
carry out the CTD check where the current values of temperature, salinity and 
pressure were displayed just to check that they were sensible. All that was 
left after this was to run a self-test, which passed for every float. The 
float could then be made to hibernate and the text capture could be stopped.


20.6  Pre-deployment Issues

Several issues arose during the pre-deployment tests that are worth noting. 
These issues are listed below:

• The transmission beep was very faint on floats 4473 and 4475
• Float 4482 was given five minutes extra time to check vacuum counts
• The CTD pressure test had to be retaken on 4483; first reading = 0.00db; 
  second reading = 0.02db
• Floats 4439 and 4469 had higher test salinities (0.03 psu) than the other 
  floats.
• Floats 4470 and 4474 had 226 piston full extension 4481 had 225 piston 
  full extension as opposed to the prescribed 227 counts.


20.7  Deployment

Several hours before deployment (usually when the CTD package had reached 
maximum depth) the float was activated by rubbing a magnet across the reset 
panel of the Argo float, which tripped a reed switch inside. This started the 
float transmitting, which could be audible from the beep of the cat's meow 
receiver. The activation time was recorded in the log sheet. By the time the 
CTD had been brought back up to approximately 1000m depth, the float was 
checked again just to ensure that the receiver was beeping every 2 minutes.

The procedure of deployment would occur immediately after a station had 
surfaced and the ship had begun steaming slowly. Usually about three people 
were required to be present for a launch, two scientific staff to deploy the 
instrument and one of the deck crew to communicate the progress of the 
deployment with the bridge. The float was prepared on deck by removing the 
sensor covers and threading a rope through the plastic damper plate with one 
end of the rope attached securely to the ship with a bowline. Two people from 
the physics watch would lift the float over the side, keeping it upright, and 
then one person would take the weight of the float on the rope and start 
lowering it slowly into the water. When the float was in the water, it was 
allowed to stream out behind the ship and the rope was released to let the 
float go. When the rope was recovered an announcement would be made to the 
bridge to say all lines were clear. The time and coordinates of the float 
deployment were recorded.

On at least two occasions the floats deployed were not observed to float in 
the upright position, but were seen to remain horizontal in the water. It is 
likely that they managed to right themselves. Conditions during float 
launches on this cruise have been favourable, with minimal swell and a fair 
head wind to carry the float away from the ship.


20.8  Additional Notes

Upon investigation of the crates containing the Argo floats in Montevideo, it 
was found that none of them had cat meow receivers in them (receivers used to 
sound the beep during the transmission test). Luckily a spare receiver was 
brought by Brian King and has subsequently been used during the tests of all 
the floats.

So far we are aware of at least one APEX float that has failed to transmit 
its location 24 hrs after deployment. This is float, hull serial number 4439, 
(WMO ID 1901229). It will not be known if the remaining floats are 
successfully transmitting until at least 10 days after the final float has 
been deployed.

 

 


Diary

J064 4th March in port
     Cruise JC031 made port on the 3rd March 2009. Once all personnel from the 
     previous cruise had disembarked, the handover was made to the Master Peter 
     Sarjeant and Principal Scientist Brian King.
     
J064 5th March in port
     Workstations and labs were already setup from JC031 so there was sufficient 
     time to thoroughly test that the processing scripts were running properly by 
     running test data.
     
J065 6th March - In port
     A scientific meeting with was held at 9:00am, followed by a safety briefing 
     at 10:00am.
     
     It was noticed that the heading on the Ashtech system was reading 0. The unit 
     was rebooted and is now functioning well.
     
     The Vaisala temperature and humidity sensor has been temperamental since it 
     was previously dismantled. The instrument was giving negative velocities of 
     windspeed when tape was wrapped around the join between the two parts of the 
     instrument. The instrument was taped up then put back into its screen.
     
J066 7th March (departed Montevideo)
     In the morning emergency generator tests were run by powering the systems 
     down. We set sail from our berth in Montevideo at approximately 13:00 local 
     time (15:00 UTC).
     
     A muster drill was performed soon after departure at 16:15 local time (18:15 
     UTC) to ensure that all personnel were acquainted with the emergency 
     procedures. Fortunately this took place before a heavy downpour occurred at 
     16:50 local time (18:50 UTC).
     
     The retractable keels were lowered at 18:45 local time (20:45UTC). This meant 
     that the VMADCP instrument had to be restarted with the appropriate keel down 
     configuration files (20:45 UTC).
     
     Once far enough away from port the flow through the TSG was turned on (03:07 
     UTC). The conductivity of FSI initially read as 0. Subsequently, the FSI was 
     reset, however, this then gave too high a salinity reading when compared to 
     the SBE. Therefore the salinity from the SBE will be used for SVP records.
     
J067 8th March
     CTD station sampling started first thing in the morning. Most people from all 
     watches sampled the first station in order to get a feel for the sampling 
     procedures. These stations comprised the first of our three planned Brazil 
     current sections. A list of the first 5 stations demonstrates the frequency 
     with which stations were sampled.
     
     CTD Station 1:  200m water 09:03 UTC
     CTD Station 2:  560m water 11:59 UTC - delay after winch problem.
     CTD Station 3:  992m water 14.07 UTC
     CTD Station 4: 1441m water 17:14 UTC
     CTD Station 5: 2102m water 20.18 UTC
     
J068 9th March
     CTD Station 6: 2500m of water 23:53 UTC
     CTD Station 7: 3000m of water 04:27 UTC
     At 14:58 UTC the position on the POSMV view briefly went red. It was noted 
     that we should see whether the RTCM DGPS drops out at the same time if so 
     then Paul Duncan our computer technician should be consulted.
     
     It is possible that the Starboard TIR and PAR sensors are possibly 
     mislabelled. Therefore at 16:07 UTC: Paul Duncan swapped the plugs around for 
     the improperly fed sensors.
     
     CTD Station 8: 3572m water 10:51 UTC
     CTD Station 9: 4000m water 17:29 UTC
     
J069 10th March
     We are currently steaming to Station 10, which will be the start of the 
     Southern Brazil current section. Strong winds and a moderate swell have 
     slowed the ship down to around 7/8 knots.
     
J070 11th March
     We are continuing to steam to Station 10. As was the case yesterday strong 
     winds and a moderate swell has slowed our progress to around 7/8 knots. 
     However this is giving the science teams plenty of time to analyse the 
     samples collected from the first nine stations and prepare for the next 
     section.
     
J071 12th March 2009
     One more day of steaming should bring us to Station 10 by tomorrow morning.
     
J072 13th March 2009
     Normal scientific sampling resumed today as we arrived at Station 10. 
     CTD Station 10: 3043m water 10:18 UTC 
     CTD Station 11: 2861m water 16:06 UTC 
     CTD Station 12: 2594m water 22:30 UTC
     
J073 14th March
     CTD Station 13: 2544m water 03:32 UTC 
     CTD Station 14: 2357m water 08:13 UTC 
     CTD Station 15: 2222m water 12:17 UTC 
     CTD Station 16: 2076m water 16:41 UTC 
     CTD Station 17: 1878m water 20:55 UTC
     
J074 15th March
     CTD Station 18: 1512m water 00:52 UTC
     CTD Station 19: 996m water 04:06 UTC
     
     Due to a shallowing of the water depth, the VMADCP has been turned onto 
     bottom tracking mode (04:23 UTC).
     
     CTD Station 20: 504m water 06:36 UTC
     CTD Station 21: 254m water 08:34 UTC
     
     Whilst steaming to Station 21 we overshot our intended position by 1.4 miles 
     in order to find the 250m contour.
     
     LADCP processing of Station 20 indicates that beam 2 on the present 
     transducer is weak.
     
     An ADCP survey was carried out between Stations 21 to 22 to examine the 
     extent of the Brazil current.
     CTD Station 22: 127m water 12:12 UTC (only salinity samples were collected).
     
     This completes this section of the Brazil current. Begin passage northwards 
     towards the final Brazil current section.
     
J075 16th March
     Steaming over night and should reach Station 23 (start of the Northern Brazil 
     Current Section) just after midday.
     
     CTD Station 23: lOOm 13:32 GMT
     CTD Station 24: 500m 14:42 GMT
     CTD Station 25: 1000m 16:30 GMT
     CTD Station 26: 1500m 19:27 GMT
     
J076 17th March
     CTD Station 28: 2500m 02:02 GMT
     CTD Station 29: 2864m 07:24 GMT
     CTD Station 30: 3019m 12:49 GMT
     CTD Station 31: 3014m 10:06 GMT
     
J077 18th March
     Over the last couple of days there have been concerns over the ships 
     freshwater production, as we seem to be consuming vast quantities more than 
     we are producing. Despite attempts to try to conserve water the problem is 
     deemed too serious to attempt a trans-Atlantic crossing without fixing this 
     first. Therefore the decision has been taken by the Captain to put into port 
     in Arraial do Cabo, Brazil in order to take on more fresh water and attempt 
     to rectify the problem.
     
     CTD Station 32: 3424m 00:59 GMT
     CTD Station 33: 3489m 07:29 GMT
     CTD Station 34: 3560m 13:36 GMT
     
     Humidity is being read as very low by the sensor (9%). The sensor cap was 
     replaced and realigned in the housing and is now giving stable measurements. 
     (12:45 GMT).
     
     Paul Duncan finished cleaning Vaisala connections at 16:39 GMT. All readings 
     now appear stable.
     
     CTD Station 35: 4061m 20:11 GMT
     
     We stopped running salts through Autosal at ~02:45 GMT (1 bottle into Station 
     31) because of large jumps in the readings. The standby value is oscillating 
     between values in the range of 45 - 88. We emptied the cell drain carboy and 
     checked the machine but we have been unable to detect the cause of the 
     problem.
     
     At 00:05 GMT, the non-toxic underway supply was turned off in preparation for 
     our steam into port. Also a swath survey was conducted on our way into port.
     
J078 19th March
     
     Steaming to Brazil for water. Although an unfortunate turn of events with the 
     freshwater situation, the steaming period has once again allowed all the 
     scientific teams to get rid of some of the backlog of samples that has been 
     building up over the last few stations.
J079 20th March (on passage to Station 36)
     
     It was extremely clear and starry last night so the night-watch had the 
     fantastic opportunity of observing the space shuttle and the ISS.
     
     We came alongside in Cabo Frio 08:30 to take on freshwater and disembark 
     Phillipe (our Brazilian observer). Three hours of shore leave were granted, 
     which was unexpected but very welcome. Departed at 16:30 GMT with varying 
     degrees of sunburn.
     
     The non-toxic supply was switched back on at 23:00 ship's time.
     
J080 21st March (Start of long transect and voyage to Africa)
     
     After steaming throughout the night and most of the day, we arrived at 
     Station 36, which was a repeat of Station 35.
     
     CTD Station 36: 4061m 21:56 GMT
     
     Sinhue Torres reported strange results from bottle 5. Fired at 3750m and a 
     duplicate of bottle 4, bottle 5 displayed a low oxygen value, (l99µmols/l 
     compared to 230µmols/l) a higher temperature, (10.5°C compared to 8.4°C) and 
     no nutrients were found in the sample. CFCs and carbon were not sampled from 
     this bottle. As far as we are aware the bottle had closed and was not leaking 
     when brought on deck.
     
     Bottle 5 has since been checked and caps seated correctly before next cast. 
     Keep an eye on this bottle.
     
J081 22nd March
     CTD Station 37: 4001m in water 05:13 GMT
     CTD Station 38: 4112m in water 12:23 GMT
     CTD Station 39: 4200m in water 17:30 GMT
     
J082 23rd March
     CTD Station 40: 4250m water
     
     We deployed Argo float 2 (platform No. 1901229): This was reset at 04:40 GMT 
     and deployed on station at 06:55 GMT. The float was affectionately named 
     "Lorna"
     
     CTD Station 41: 4427m 10:54GMT
     CTD Station 42: 4616m 18:37GMT
     
J083 24th March
     CTD Station 43: 4750m 02:05 GMT
     
     Deployed Argo float 3 ("Millie"): Reset at 04:35 GMT and deployed at 06:12 
     GMT. Platform Number: 1901230.
     
     CTD Station 44: 4990m in water 095 3GMT
     CTD Station 45: 5060m 17:59GMT
     
J084 25th March
     CTD Station 46: 5146m 01:54GMT 
     CTD Station 47: 5241m 10:O3GMT 
     CTD Station 48: Up until now everything has been running relatively smoothly, 
     but at 19:25, the gearbox on CTD drum 1 failed. 3000m of wire have been paid 
     out, and the CTD package is now halted at this depth, whilst we try to figure 
     out the best way to resolve the problem.
     
J085 26th March
     From 10:00 GMT the CTD wire was hauled by the traction system and spooled 
     onto the storage drum which was turned by hand. A very dedicated effort by 
     the CTD technicians and the ship's crew.
     
     16:28 UTC a red light was noticed on the posmv viewer POSITION. This happened 
     again at 18:43 UTC.
     
J086 27th March
     CTD 49 came on board at around 17:30 UTC
     CTD Station 50: 5440m in water 21:55 GMT
     
J087 28th March
     CTD 50 on board at 03:19 GMT
     
     Argo float 4480 was reset at 11:07 UTC and deployed at 12:38 UTC. Argo float 
     number 4: platform number 1901240 (4480).
     
     CTD Station 51: 5443m in water 07:50 GMT
     CTD Station 52: 5480m in water 17:04 GMT
     
J088 29th March
     CTD Station 53: 5668m in water 02:34 GMT 
     CTD Station 54: 5660m in water 11:45 GMT 
     CTD Station 55: 5671m in water 20:52 GMT.
     
J089 30th March
     Hump day
     
     CTD Station 56: 5210m in water 05:42 GMT
     CTD at Station 56 was close to a steep cliff face of a seamount therefore we 
     made a slow approach to the bottom. To aid this the swath was left on until 
     the CTD was on the upcast. Various swath angles showed good instrument 
     performance. The SWATH System was left logging when on station.
     
     CTD Station 57: 5219m in water 14:33GMT
     CTD Station 58: 5209m in water 23:02GMT
     
J090 31st March
     CTD Station 59: 5122m in water 07:38 GMT
     
     Argo float number 5: 4469 (WMO 1901231) ("Sarah") was reset at 09:50 UTC and 
     deployed 11:50 UTC.
     
     CTD Station 60: 4970 in water 16:09 GMT
     
J091 1 April
     At 00:30 GMT the Winch failed to stop when lifting off deck for deployment. 
     The package was hauled up to the block the wire parted, and the CTD hit the 
     deck in the water bottle annex. All CTD systems were checked and tested and 
     don't appear to have sustained any damage. All the Niskin bottles were 
     checked. Bottle number 21 was broken into two pieces so was replaced with 
     Bottle 11 and renamed 21. The tap needed replacing on 14.
     
     Alternatives to using the winch control 'belly' boxes were investigated.
     
     CTD Station 61: 5100m in water 17:53 GMT
     
J092 2nd April
     CTD Station 62: 4785m in water 02:22 GMT 
     Deployed float 6: platform number 1901233
     
     CTD Station 63: 4446m in water 10:57 GMT 
     CTD Station 64: 4809m in water 19:47 GMT 
     The Ashtech heading read as 0 from 15:17 GMT onwards, so was reset.
     
J093 3rd April
     CTD Station 65: 4676m in water 04:23 GMT 
     CTD Station 66: 4716m in water 13:20 GMT 
     CTD Station 67: 4969m in water 21:35 GMT
     
J094 4th April
     Deployed float 7: "MONTY and the clan McLEAN" Platform number: 1901241.
     
     It was noted that a large front was crossed in the NADW between Stations 68 
     and 69.
     
     CTD Station 68: 4606m in water 06:20 GMT 
     CTD Station 69: 3905m in water 14:32 GMT 
     CTD Station 70: 4200m in water 21:44 GMT
     
J095 5th April
     CTD Station 71: 4057m in water 05:11 GMT 
     CTD Station 72: 3818m in water 12:40 GMT 
     CTD Station 73: 3978m in water 20:19 GMT
     
     Deployed float 8: platform number 1901232
     
J096 6th April
     CTD Station 74: 4414m in water 02:55 GMT 
     CTD Station 75: 4385m in water 10:38 GMT 
     CTD Station 76: 4360m in water 18:00 GMT
     
J097 7th April
     CTD Station 77: 4165m in water 02:36 GMT
     
     Deployed float Number 9: "CHARLIE", platform number 1901235. This was reset 
     at 05:00 GMT and deployed at 06:25 GMT.
     
     CTD Station 78: 4072m in water 11:10 GMT 
     CTD Station 79: 4465m in water 19:25 GMT
     
     
J098 8th April
     CTD Station 80: 5243m in water 04:16 GMT 
     CTD Station 81: 4426m in water 13:17 GMT 
     CTD Station 82: 4890m in water 21:42 GMT
     
     Deployed float Number 10: Platform number 1901242 reset at 00:25 GMT and 
     deployed at 01:50 GMT.
     
     1099 9th April
     The EA600 echo sounder lost contact with GTP transceiver (0 depth recorded) 
     at approximately 02:30GMT so the system was rebooted.
     
     CTD Station 83: 4881m in water 07:00 GMT
     CTD Station 84: 4592m in water 16:02 GMT
     
     The TECHSAS system froze at 20:40 GMT. The length of outage is unknown as 
     watch keepers were out on deck sampling. Red panels were present throughout 
     the entire no. of frames column. Paul Duncan rebooted the system at 20.45 
     GMT.
     
J100 10th April
     CTD Station 85: 5234m in water 00:50 GMT
     
     Ship time advances 1 hour today, a sign that we are slowly but surely making 
     our way across the Atlantic.
     
     CTD Station 86: 5137m in water 10:36 GMT
     CTD Station 87: 4826m in water 21:05 GMT
     
J10l 11th April
     CTD Station 88: 5021m in water 06:57 GMT
     CTD Station 89: 5273m in water 17:02 GMT
     
     The CT lab flooded due to a pipe flowing out of sink. The pipe was secured 
     and the water was mopped up.
     
J102 12th April
     The flow rate out of the TSG pipe was found to be low for some reason. The 
     TSG flow rates were checked but it seems that we will have to live with the 
     low rate for the time being.
     
     CTD Station 90: 5476m in water 03:10 GMT
     
     Easter Sunday. The chefs prepared a fantastic lunch, which was enjoyed by 
     all. Nobody is happier than Gerard who has been observing Lent.
     
     CTD Station 91: 4367m in water 13:31 GMT
     CTD Station 92: 5199m in water 22:35 GMT
     
     1103 13th April
     The Ashtech system was rebooted at 01:39GMT.
     
     A quick repair had to be made to Niskin bottle in place 21, before the cast 
     as the nylon lanyard had snapped.
     
     CTD Station 93: 5264m in water 08:17 GMT.
     
     The bottom end-cap lanyards were found not to be attached to the brass clips 
     on bottles 16, 17 and 18.
     
     The primary conductivity cell on the CTD was changed.
     
     CTD Station 94: 5156m in water 18:05 GMT.
     
J104 14th April
     The Niskin bottle in position 3 on the CTD was swapped.
     
     CTD Station 95: 5010m in water 03:32 GMT.
     
     Deployed float number 13 'KEEN MARINE' Platform number 1901243. Reset at 
     06:05 GMT and deployed at 07:25 GMT
     
     CTD Station 96: 4183m in water 08:58 GMT. 
     CTD Station 97: 3661m in water 15:20 GMT. 
     CTD Station 98: 3025m in water 20:23 GMT.
     
J105 15th April
     CTD Station 99: 2481m in water 01:13 GMT. 
     CTD Station 100: 1999m in water 05:40 GMT. 
     CTD Station 101: 1895m in water 11:21 GMT. 
     CTD Station 102: 2380m in water 16:07 GMT. 
     CTD Station 103: 1967m in water 21:36 GMT.
     
     Deployed float number 14 Platform number 1901236. Reset at 22:48 GMT and 
     deployed at 00:21 GMT.
     
J106 16th April
     CTD Station 104: 3504m in water 01:49 GMT. 
     CTD Station 105: 4246m in water 05:58 GMT. 
     CTD Station 106: 4678m in water 14:19 GMT
     
J107 17th April
     CTD Station 107: 4620m in water 23:10 GMT.
     
     SVP probe sent down on CTD 107.
     
     CTD Station 108: 4313m in water 08:04 GMT.
     
     Deployed float number 15 Platform number 1901239. Reset at 11:02 GMT and 
     deployed at 11:35 GMT.
     
     The CTD cable needs 5 meters cutting off at the end because of bird caging. 
     The re-termination took place at 13:19 GMT).
     
     Finally after many attempts we managed to have a BBQ on deck without it 
     raining.
     
     CTD Station 109: 4051m in water 18:49 GMT
     
     
J108 18th April
     The Ashtech needed rebooting again.
     
     CTD Station 110: 3559 in water 02:57 GMT
     CTD Station 111: 2831 in water 10:47 GMT
     CTD Station 112: 2260m in water 16:05 GMT.
     CTD Station 113: 1937m in water 19:10 GMT.
     CTD Station 114: 22:18m in water 22:18 GMT
     
     
J109 19th April
     CTD Station 115: 1013m in water 01:42 GMT
     CTD Station 116: 503m in water 04:39 GMT
     CTD Station 117: 305m in water 07:09 GMT
     CTD Station 118: 205m in water 10:01 GMT
     
     With the completion of Station 118 all CTD sampling is now over.
     
J110 20th April
     VMADCP switched back to bottom tracking mode for calibration of the 
     instrument.
     
J111 21st April
     Arrived in Walvis Bay at approximately 09:00 local time. No berth available 
     so anchored off shore with tens of other ships. All day was spent backing up 
     data, packing up the labs and loading the containers. Boat transfer to shore 
     was at about 1800 local time.






CCHDO DATA PROCESSING NOTES


Event Date  Person              Date Type      Action     Summary 
----------  ------------------  -------------  ---------  ---------------------
2009-06-08  King, Brian         CTD            Submitted  data are public 
            revised upload; data can be public once upload confirmed. SD has 
            advised expocode 740H20090307, but expocode in files is 740H032_1. 
            Expocode will be revised at NOC for any further file updates. 

2010-06-10  King, Brian         Cruise Report  Submitted  pdf format 
            The final copy of the James Cook 032 (A095) cruise report is now 
            available online. Its a few 10s of MB, so suggest you pull it from 
            http://www.noc.soton.ac.uk/ooc/TRANSPORTS/JC032_REPORT.pdf instead 
            of my making it an email attachment. 



