CRUISE REPORT: A05
(Updated JUN 2014)






Highlights




                           Cruise Summary Information

          WOCE Section Designation  A05
Expedition designation (ExpoCodes)  74DI20100106
                             Alias  74DI346_1
                  Chief Scientists  Brian King / NOCS
                             Dates  2010-JAN-06 - 2010-FEB-19
                              Ship  RRS Discovry
                     Ports of call  Freeport, Bahamas - Lisbon, Portugal

                                                  27° 55' 39" N
             Geographic Boundaries  79° 56' 51" W               13° 22' 9" W
                                                  23° 15' 1" N

                          Stations  135
      Floats and drifters deployed  0
    Moorings deployed or recovered  0

                             Contact Information:

                                 Brian A. King
    Institute of Oceanographic Sciences • Southampton Oceanography Centre
            Empress Dock • Southampton • SO14 3ZH • UNITED KINGDOM
             Phone:  (44) 23 8059 6438 • Fax:  (44) 23 8059 6204
                        Email:  b.king@noc.soton.ac.uk












                         National Oceanography Centre

                             Cruise Report No. 16

                           RRS Discovery Cruise 346
                             05 JAN - 19 FEB 2010

                      The 2010 transatlantic hydrography
                               section at 24.5°N

                             Principal Scientist
                                   B A King

                                    Editor
                               D R C Hamersley







                                      2012







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

Tel: +44 (0)23 8059 6438
Email: b.king@noc.ac.uk
© National Oceanography Centre, 2012









DOCUMENT DATA SHEET


AUTHOR                                                       PUBLICATION DATE

    KING, B A et al                                                      2012

TITLE

    RRS Discovery Cruise 346, 05 Jan - 19 Feb 2010. The 2010 transatlantic 
    hydrography section at 24.5°N.

REFERENCE

    Southampton, UK: National Oceanography Centre, Southampton, l77pp. 
    (National Oceanography Centre Cruise Report, No. 16)

ABSTRACT

    A Hydrographic section was occupied at a nominal latitude of 24.5°N in 
    the Atlantic Ocean during January - February 2010 on Cruise 346 of RRS 
    Discovery. 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, and to infer decadal 
    variability.


    A total of 135 CTD/LADCP stations were sampled, with two additional 
    bottle blank stations. In addition to temperature, salinity and oxygen 
    profiles from the sensors on the CTD package, water samples from a 24 x 
    20 litre 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, CFCs, 
    DIC, alkalinity, and filtering. In addition, samples were collected from 
    the ships' underway system to calibrate and compliment the data 
    continually collected by the TSG (thermosalinograph). Full depth velocity 
    measurements were made at every station by 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, which is attached to the hull. 
    However, whilst steaming it was found that switching over to the fish 
    instrument produced a cleaner dataset.


    This report describes the methods used to acquire and process the data on 
    board the ship during cruise D346.

KEYWORDS

    ADCP, Atlantic Ocean, carbon, CFC, circulation, cruise D346 2010, CTD, 
    Discovery, Lowered ADCP, Meridional Overturning Circulation, meteorology, 
    MOC, nutrients, oxygen, shipboard ADCP

ISSUING ORGANISATION  National Oceanography Centre
                      University of Southampton Waterfront Campus
                      European Way
                      Southampton S014 3ZH	UK
                      Tel: +44(0)23 80596116  Email: nol@noc.soton.ac.uk

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




Contents

List of Figures 
List of Tables 
Scientific Personnel 
Technical Personnel 
Ship's Personnel 
Acknowledgements 
Background and Objectives 
Summary 
Itinerary and Cruise Track 
Diary 
1.  CTD Systems Operation 
    1.1.  CTD and Sensors 
    1.2.  LADCP 
    1.3.  20L Niskin Bottles 
2.  CTD Data Processing and Calibration 
    2.1.  Initial Processing Using SeaBird Programs 
    2.2.  Mstar CTD Processing 
    2.3.  Processing Procedure Used on D346 
    2.4.  Sample Files 
    2.5.  CTD files 
    2.6.  Temperature-Conductivity Sensor 
    2.7.  Calibration of the Oxygen Sensor 
    2.8.  Addition of Metadata to the Mstar Files 
    2.9.  Niskin Bottles 
3.  Water Sample Salinity Analysis 
    3.1.  Sampling 
    3.2.  Laboratory Setup 
    3.3.  Analysis
    3.4.  Initial Standardisation 
    3.5.  Procedure 
    3.6.  Differences and Adjustments 
    3.7.  Salinometer Performance 
    3.8.  Secondary Standards 
    3.9.  Processing 
4.  Inorganic and Total Nutrient Analysis 
    4.1.  Method 
    4.2.  Observations (inorganic and total nutrient analysis) 
5.  Dissolved Oxygen 
    5.1.  Methods 
    5.2.  Observations 
    5.3.  References 
6.  Inorganic Carbon 
    6.1.  Methods 
    6.2.  References 
7.  Chlorofluorocarbons and Sulphur Hexafluoride measurements 
    7.1.  Sample collection 
    7.2.  Equipment and technique 
    7.3.  Calibration 
    7.4.  Precision and accuracy 
    7.5.  Data
    7.6.  References 
8.  Computing, Sea-Surface and Meteorological Instrumentation 
    8.1.  Primary Logger - hardware and software 
    8.2.  Level C 
    8.3.  CLAM 
    8.4.  Surfmet 
    8.5.  Simrad EA-500 Echo Sounder 
    8.6.  Chernikeeff EM Log
    8.7.  Printing 
    8.8.  Backups 
9.  Lowered Acoustic Doppler Current Profiler (LADCP) 
    9.1.  Instrument Setup and Performance 
    9.2.  Data Processing 
    9.3.  M* Formatting 
    9.4.  Data Quality 
10. Underway Temperature, Salinity, Fluorescence & Transmittance 
    10.1.  Instrumentation 
    10.2.  Routine Processing 
    10.3.  Calibration of Underway Sea Surface Salinity 
    10.4.  References 
11. Surface Meteorological Sampling System (SURFMET) 
    11.1.  Instrumentation 
    11.2.  Routine Processing 
    11.3.  References 
12. Navigation 
    12.1.  Navigation Summary 
    12.2.  Comparison of GPS accuracy 
    12.3.  Gyrocompass 
    12.4.  Ashtech 3DF GPS Attitude Detection Unit (ADU) 
    12.5.  Daily Processing Steps 
    12.6.  Chernikeeff Doppler Log Calibration 
13. Bathymetry 
    13.1.  Instrumentation 
    13.2.  Routine Processing 
14. Vessel Mounted ADCP Instruments 
    14.1.  Introduction 
    14.2.  Real Time Data Acquisition 
    14.3.  Post-Processing 
    14.4.  Data Quality Issues 
    14.5.  References 
15. Iron, Nitrogen Fixation and Filtering 
    15.1.  Background and cruise objectives 
    15.2.  Sampling and methods 
    15.3.  Evaluation 
    15.4.  References 
16. Inorganic Nitrate and Phosphate at Nanomolar Concentrations 
    16.1.  Cruise objectives 
    16.2.  Method 
    16.3.  System 
    16.4.  Performance 
    16.5.  Results 
    16.6.  References 
17. Near-surface and Sea Surface Salinity Study for SMOS Cal/Val 
    17.1.  Introduction 
    17.2.  Handheld CT sensor 
    17.3.  Tethered buoy system 
    17.4.  Validation using the non-toxic supply 
    17.5.  Results of near surface salinity investigations 
Appendix.  CTD station listing 


List of Figures


Figure 1:  Station positions across the North Atlantic basin for Cruise D346 
Figure 2:  Western Boundary of the North Atlantic Basin 
Figure 3:  Sampling scheme along the Kane Fracture Zone 
Figure 4:  Eastern Boundary of the North Atlantic Basin 
Figure 5:  0-5 anomaly during the Station 12 downcast 
Figure 6:  Final offsets between bottle salinities and calibrated CTD 
           salinities 
Figure 7:  Final offsets between bottle oxygen and calibrated CTD oxygen 
Figure 8:  CTD potential temperature, salinity, oxygen and fluorescence 
           across the Florida Straits transect 
Figure 9:  CTD potential temperature and salinity along the Atlantic 24°N 
           hydrographic section 
Figure 10: CTD oxygen and fluorescence along the Atlantic 24°N hydrographic 
           section 
Figure 11: Salinity difference and adjustment for each station 
Figure 12: Residuals and ratio of the bottled and CTD conductivities for all 
           points below 3000db for each station 
Figure 13: Guildline conductivity ratio for primary and secondary seawater 
           standards during the same time period as Stations 69-75
Figure 14: 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 15: Baselines time series 
Figure 16: Calibration slope time series 
Figure 17: Calibration correlation coefficients 
Figure 18: Low Nutrient Seawater (LNSW) time series 
Figure 19: Time series of bulk nutrient seawater (from the South Atlantic 
           Subtropical Gyre) concentrations
Figure 20: The efficiency of the cadmium column 
Figure 21: Calibrations for dissolved oxygen analysis 
Figure 22: Absolute replicate difference for oxygen bottles in each CTD cast 
Figure 23: Depth-longitude grid of samples analysed for DIC and TA 
Figure 24 (a): Calibrated CRM-DIC values for the VINDTA #004 
Figure 24 (b): Calibrated CRM-DIC values for the VINDTA #007 
Figure 25 (a): Mean DIC difference and precision for the VINDTA #004 
Figure 25 (b): Mean DIC difference and precision for the VINDTA #007 
Figure 26 (a): Calibrated CRM-TA values for VINDTA #004 
Figure 26 (b): Calibrated CRM-TA values for the VINDTA #007 
Figure 27 (a): Mean TA difference and precision for the VINDTA #004 
Figure 27 (b): Mean TA difference and precision for the VINDTA #007 
Figure 28: Example of calibration curves 
Figure 29: Sensitivity of the system over time 
Figure 30: Countour plots of CFC-11, CFC-12, CFC-113, CCl4 and SF6data from the 
           main D346 24°N transect 
Figure 31: Instrument performance of the three LADCPs used on D346 
Figure 32: Gridded velocities through the Florida Straits from the UH 
           software (upper) and the LDEO software (lower) 
Figure 33: Three profiles illustrating different behaviour of the LADCPs used 
           on D346 
Figure 34: Location of RRS Discovery underway seawater supply 
Figure 35: Non-toxic supply pumps in forward hold and enlargement showing 
           temperature probe 
Figure 36: Photograph showing route of underway water supply through 
           instruments located in the Water Bottle Annex of RRS Discovery 
Figure 37: Comparison of Seabird TSG and bottle salinities during D346 
Figure 38: First order calibration of the TSG salinity sensor by comparison 
           with the non-toxic water supply samples 
Figure 39: Calibrated TSG salinity plotted with bottle data used in 
           calibration 
Figure 40: First order calibration of the TSG temperature sensor by 
           comparison with the sensor mounted on the CTD frame 
Figure 41: Calibrated TSG temperature plotted with CTD data used in 
           calibration
Figure 42: 5km mean calibrated TSG salinity during D346 
Figure 43: 5km mean calibrated TSG temperature during D346 
Figure 44: Time series of 1-minute (median) averages of the meteorological 
           data for the duration of D346 
Figure 45: Comparisons between positions measured by (a) Ashtech and GPS G12, 
           (b) Ashtech and GPS 4000, (c) GPS G12 and GPS 4000 
Figure 46: Calibration curves for the previous two calibrations of the 
           Chernikeeff EM log on RRS Discovery 
Figure 47: Scatter plot of Chernikeeff displayed speed against speed measured 
           by the VMADCP second bin, before any calibration was applied 
Figure 48: As Figure 47, but after first calibration 
Figure 49: As Figure 47, but after second calibration 
Figure 50: As Figure 47, but after final calibration 
Figure 51: Bathymetry data averaged over 5km intervals of the distance run, 
           plotted as a function of longitude for the duration of the cruise 
Figure 52: The Gautoedit window within the CODAS suite of programs in Matlab
Figure 53: Example of scattering near the surface due to bubble contamination 
Figure 54: Example of the amplitude return for the OS75 instrument 
Figure 55: Strong red-over-blue striping during the steaming periods at a 
           similar depth to the anomalous scattering layer 
Figure 56: V component for the 24°N section 
Figure 57: Example of the VMADCP data processed using ENS files instead of 
           the ENX files 
Figure 58: A cold core eddy identified using the OS75 VMADCP instrument 
Figure 59: A profile of the first transect across the Florida Straits using 
           data from the OS75 instrument 
Figure 60: A profile of the return transect across the Florida Straits using 
           data from the OS75 instrument 
Figure 61: The nitrate+nitrite SCFA-LWCC system below the phosphate system. 
           The glass coils used are 1.6-mm ID 
Figure 62: The Phosphate SCFA-LWCC system. The glass coils used are 1.6-mm ID 
Figure 63: Phosphate calibration curve 
Figure 64: Contour plots of nitrate and phosphate concentrations in the upper 
           layer along the transect 
Figure 65: Photographs showing a) internal arrangement of sensor 'pot'; b) 
           sensor attached to buoy and c) close up of sensors on rope (also 
           showing handheld CT probe) 
Figure 66: Photographs of showing the development of the near surface 
           salinity buoy system showing a) 2 sensors mounted on initial 5m 
           long chain-weighted rope; b) and c) showing later shallower, 
           lighter system 
Figure 67: Diagrammatic representation of final system for near surface 
           salinity measurements 
Figure 68: Scatterplots of mean a) SSS and b) SST from the TSG versus results 
           from the handheld CT probe for all deployments 
Figure 69: Comparison of a) salinity and b) temperature of water from 
           non-toxic supply in the WBA and from sensors #4 and #5 










List of Tables


Table 1:  The position of primary and secondary conductivity-temperature 
          sensors during D346 
Table 2:  Niskin bottle flags 
Table 3:  Bottle salinity analysis information 
Table 4:  Set of calibration standards used for dissolved inorganic nutrient 
          analysis. 54
Table 5:  Compounds used to prepare stock standard solutions, weight 
          dissolved in 1L of Milli-Q water and molarity of the solution 
Table 6:  Means and variations of all the standards measured, and the 
          precision of the analysis at each concentration 
Table 7:  D346 02 determinations 
Table 8:  CFC precision table 
Table 9:  Results of the test station 200 
Table 10: Results of the test station 202 
Table 11: Concentrations over time of the sparged Niskin test 
Table 12: Underway SST, SSS, fluorescence and transmittance instrument 
          details. 98
Table 13: Meteorological instrument details 
Table 14: Navigation processing steps with descriptions of their function 
Table 15: Calibration values entered into both 'table 1' and 'table 2' in the 
          Chernikeeff EM log's calibration menu 
Table 16: Bottom track calibration data for the OS75 instrument 
Table 17: Bottom track calibration data for the OS 150 instrument 
Table 18: Water track calibration data for the OS75 instrument 
Table 19: Water track calibration data for the OS 150 instrument 
Table 20: OS75 filenames_readme 
Table 21: OS150 filesnames_readme 
Table 22: The sequence log of the OS150 instrument 
Table 23: The sequence log of the OS75 instrument 
Table 24: List of Samples collected for nitrogen fixation and filtering 
Table 25: Times, dates, locations and summary data for deployment of handheld 
          CT sensor during D346 
Appendix: Details of Stations Sampled during Cruise D346 








Scientific Personnel

Name                     Role                 Affiliation
-----------------------  -------------------  -----------------------------
Brian King               Principal Scientist  NOCS
Gerard McCarthy          Physics              NOCS
David Hamersley          Physics              NOCS
Chris Atkinson           Physics              NOCS
Gavin Evans              Physics              NOCS
Helen Pillar             Physics              Oxford University
Ben Webber               Physics              UEA
Chris Banks              Physics              NOCS
Sinhue Tones Valdes      Nutrients & Oxygen   NOCS
Ekaterina Chernyavskaya  Nutrients & Oxygen   Arctic and Antarctic Research 
                                              Institute, St. Petersburg
Claire Powell            Nutrients & Oxygen   UEA
Laura Casburn            Nutrients & Oxygen   NOCS
Helen Smith              Nutrients & Oxygen   NOCS
Francois-Eric Legiret    Nano-nutrients       NOCS
David Honey              Biology              NOCS
Ute Schuster             Carbon               UEA
Adriaan Louwerse         Carbon               UEA
Gareth Lee               Carbon               UEA
Oliver Legge             Carbon               NOCS
Marie-Jose Messias       CFC                  UEA
Peter Brown              CFC                  UEA
Stephen Woodward         CFC                  UEA
Andrew Brousseau         CFC                  UEA


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


Technical Personnel

Paul Duncan    Technician  NMF
Peter Keen     Technician  NMF
Alan Sherring  Technician  NMF
David Teare    Technician  NMF


Ships Personnel

                      Name                      Rank
                      William Richardson        MASTER
                      John Leask                C/O
                      lain Macleod              2/0
                      Richard Callender         3/0
                      Peter Griffin             MENG
                      Stephen Bell              2/E
                      Gary Slater               3/E
                      Geraldine O'Sullivan      3/E
                      Dennis Jakobaufderstroht  ETO
                      Graham Bullimore          PCO
                      Greg Lewis                CPOD
                      John Smyth                ERPO
                      Mark Squibb               CPOS
                      Philip Allison            POD
                      John Brodowski            SG1A
                      Cohn Birthwhistle         SG1A
                      Mark Duthie               SG1A
                      Philip Alford             SG1A
                      Mark Preston              H/CHEF
                      Lloyd Sutton              Chef
                      Jacqueline Waterhouse     STWD



Acknowledgments

It is a pleasure for the Principal Scientist to acknowledge the outstanding 
contributions by the ship's and scientific personnel. Over a long cruise, the 
Deck Officers efficiency in station keeping saves enough time for many extra 
stations; The deck crew managed overside operations with minimal 
interruptions, and the CPOS and CPOD ensured winch operations were smooth and 
efficient apart from the winch system failures documented elsewhere. The 2/E 
Officer and ETO kept the winch operational, without which the cruise could 
not have proceeded. While there were many important individual contributions 
on the technical side, none was more critical than Paul Duncan's simulation 
of the failed CLAM system, without which the cruise would have been 
terminated after less than a week. The Engineer Officers came up with an 
ingenious solution to the problem of waste management and local port 
regulations. This enabled Discovery to dock in Lisbon and use sea freight to 
transfer equipment to RRS James Clark Ross, thereby saving the logistical 
nightmare of transhipment by air freight. The combined effort of the entire 
scientific party enabled a complete dataset to be uploaded to the 
international data centre the day after the cruise ended. This is a unique 
achievement for a UK cruise of which all contributors should be proud, and 
was a result of the sustained efforts by sample analysts and data processors 
throughout. The Principal Scientist noted that the catering was of a high 
standard throughout, but particularly so on the occasion of his 50th birthday 
party. Finally the Principal Scientist is particularly indebted to David 
Hamersley, who assembled and edited this report, and to the Master, for his 
leadership, support and cooperation throughout his first major expedition 
with NERC.




Background and Objectives

RRS Discovery Cruise 346 was a repeat occupation of the Atlantic hydrographic 
section at a nominal latitude of 24.5°N. As such it will enable the study of 
decadal variability, of the present circulation, and the present transports 
of heat, freshwater, and biogeochemical tracers. The previous occupations of 
this line include Discovery Cruise D279 (2004), Ronald H Brown (1998) and 
Hesperides HE06 (1992). The cruise was a contribution to the CLIVAR/GO-SHIP 
repeat hydrography program, and end-of-cruise data have been submitted to the 
CLIVAR and Carbon Hydrographic Data Office (CCHDO).

The data collected during D346 came from four main scientific teams, physics, 
chemistry (nutrients and oxygen), carbon, and CFCs.


Summary

In total 137 CTDO (conductivity-temperature-depth-oxygen) stations were 
occupied. Two of these stations (assigned 200 and 202) were bottle blank 
stations run for the CFC team. Therefore, 135 stations comprised the 
principal data collected along the 24.5°N section.

A 24-bottle rosette, with 20 litre externally-sprung Niskin bottles, was used 
to take water samples at CTD stations. Samples were analysed for salinity, 
dissolved oxygen, inorganic and organic nutrients, carbon system and CFCs. 
Nanonutrient and biological samples were drawn and analysed as guest 
projects. A suite of instruments was mounted on the underwater package, 
including LADCP (Lowered acoustic Doppler current profiler), fluorometer, 
transmissometer, and altimeter for nearbottom detection. Those instruments 
not pressure rated below 6000m were removed for the duration of the deepest 
casts. Therefore data for certain parameters (LADCP, fluorometer and 
transmissometer) are unavailable for these stations. There were several 
problems with malfunctioning sensors (LADCPs, conductivity sensors, and an 
oxygen sensor), which are discussed in the CTD technicians' report (Section 
1). In particular three out of four conductivity sensors failed before the 
midpoint of the cruise. In addition, the winch telemetry logging and display 
system (CLAM) failed early in the cruise so software had to be written in 
order to maintain a log and display of the wire-out and wire tensions. This is 
also discussed in further detail in Section 1 and Section 8.3. Continuous 
underway data were collected from the VMADCP (vessel mounted ADCP), 
thermosalinograph (TSG), the SURFMET system, multiple navigation sources, and 
the Simrad single-point precision echo sounder.



Itinerary and Cruise Track

Depart from Freeport, Bahamas, 5th January 2010 - arrive in Lisbon, Portugal, 
19th February 2010.


Figure 1: Station positions across the North Atlantic basin for Cruise D346 
          highlighted by white crosses.

Figure 2: Western Boundary of the Atlantic Basin where Cruise D346 began

Figure 3: A focused view of the sampling scheme along the Kane Fracture Zone

Figure 4: Eastern Boundary of the North Atlantic Basin where Cruise D346 
          finished




Diary


Fri 1 Jan (Local time is initially UTC-5).
Although some of the scientific party had taken a few days vacation in 
Freeport before the cruise, the majority had a very early start on New Years 
Day in the UK, arriving via Nassau.


Sat 2 Jan
The scientists arrived promptly at the ship to start mobilization. Most of 
the boxes had been made ready in the hangar, but there was no sign of the UEA 
Carbon and CFC containers. The Master had been pressuring the agent to get 
them brought over from the container port for some days. Continued pressure 
produced the improbable result that they arrived at about 17:00 on Saturday 
afternoon, to be swung on board immediately. Space was cleared to enable the 
installation and commissioning of the Liquid Nitrogen generator. It became 
apparent that despite frequent questions from the UK, the agent would be 
unable to secure a starting stock of LN2 in the extra storage dewars brought 
for the purpose. It was therefore a great relief when the LN2 generator 
started producing stock the next day.

It was discovered that there was neither a transmissometer nor a fluorometer 
for the CTD. This oversight apparently arose because the rest of the CTD 
equipment had been loaded for D344, for which these instruments were not 
required. When packing the small number of extra items required for D346, it 
was thought that the main instruments were already on board. The fluorometer 
was particularly important to provide context and to guide David Honey's 
measurements, and arrangements were put in place to have the instruments sent 
from NOC. It was agreed that UPS or an equivalent dispatch company could not 
guarantee their arrival and release from customs in a timely manner. The 
arrangement was therefore made for someone to fly to Freeport, bringing the 
items as accompanying baggage. Since a fluorometer was the most important 
instrument, it was agreed that two fluorometers and one transmissometer would 
be brought.


Sun 3 Jan (Local = UTC-5)
Container services were connected first thing, to enable the CFC and CO2 teams 
to start mobilization. An early and major failure was the transformer for the 
power supply for the CFC analyzer. The ETO arranged a makeshift replacement, 
and while this enabled mobilization to start, it was considered a temporary 
repair. Mobilisation of other groups continued.


Mon 4 Jan
Mobilisation continued. Extensive enquiries confirmed that no spare 
transformer for the CFC analyzer was available in Bahamas. A correct spare 
was sourced in USA, to be shipped by overnight courier to Ft. Lauderdale. No 
US supplier could guarantee next-day shipment to Bahamas. The solution was to 
arrange for Andrew Brousseau to fly to Ft. Lauderdale to collect it. Andrew 
returned the next day via Miami after being bumped from his confirmed seat on 
the Ft. Lauderdale return flight. Back at NOC, John Wynar collected the 
missing instruments and was due to arrive late that evening after flying from 
LHR via Miami. Around mid afternoon, we received the unwelcome news that his 
flight from LHR to MIA had been cancelled due to mechanical problems. He 
would instead arrive the following evening (5 Jan). It was agreed that 
sailing would be delayed to enable delivery of these instruments.


Tue 5 Jan
Sailing planned for midnight departure local time.

Andrew Brousseau returns early afternoon with CFC transformer, which was 
fitted by the ETO.

J Wynar arrives from LHR via MIA early evening, carrying one fluorometer and 
one transmissometer. A second fluorometer has been misdirected, even though 
it was collected and rechecked in MIA.


Wed 6 Jan
RRS Discovery moved away from berth for cruise D346 just after midnight local 
time, at 0519Z. Test station number 001, at 27°50'N, 78°50'W, was reached and 
a test station to 844dbar was conducted between l649Z and 1758Z. The latitude 
of the Florida Current section will be 27°20'N. This allows access to shallow 
water while remaining outside the US 12 mile limit. We returned to that 
latitude at 2320Z. After a bathymetric survey into shallow water to the east 
to establish water depths for the subsequent CTD stations, a VMADCP survey 
with bottom tracking was conducted on a heading of 2700 on that latitude.


Thu 7 Jan
The Florida Current section started in 100m water depth at 07/0420Z (Station 
002).


Fri 8 Jan
The Florida Current section ended in 150m water depth at 08/0418Z (Station 
013).

The ship steamed round to the north of Grand Bahama and Great Abaco Island to 
start the main section at 26°30'N, 76°56'W, arriving to start Station 014 at 
1854Z. The station positions out to Station 43 (26°30'N, 71°00'W) follow 
those previously occupied on D279 in 2004, and in many other occupations by 
colleagues from Miami. The maximum station spacing was 20nm (nautical miles). 
Station 032 would be completed at 0343Z on 16 Jan.

While hauling Station 016 in water depth 1600m, the CLAM system failed at 
09/0026Z, when the wire-out was 971m. After a pause the station was completed 
without the CLAM system, ending at 09/013 OZ.

Sat 9 Jan
Subsequent investigation of the CLAM system revealed that the CLAM computer 
hard drive had failed and was unrecoverable. Stations continued without the 
CLAM, since the water depths meant that wire tension did not exceed the 5:1 
Factor of Safety. It was agreed that a winch data logging system was needed 
to fulfill obligations of the agreement that allows NERC ships to operate 
wires with FoS less than 5:1. Inspection of tension data from D344 showed 
that this gave a practical operating limit of about 4000m, which would be 
exceeded on Station 020, which would occur about 12 hours later.

A spare CLAM computer was found in the tape store. However, this was ex-RRS 
Darwin, and did not have software for the RRS Discovery winch system. It had 
clearly been brought from the RRS Darwin, but had never been configured for 
RRS Discovery. No backup copy of the software on the failed hard drive was 
available on board. Documentation for the communication between the CLAM and 
the winch PLC was incomplete, mainly taking the form of the spec provided to 
Caley in advance of delivery, and not providing a complete description of the 
final system. The Caley PLC does not simply output serial data for logging. 
It requires to be polled by sending the correct characters to its serial 
port. After a certain amount of experimentation, Paul Duncan devised a system 
(subsequently referred to as CLAD) that enabled the winch PLC to be polled, 
with the output logged to a local and networked hard drive. The system 
consisted of the Windows PC borrowed from the P50 office, reconfigured to 
boot into Linux, with a 4-way USB/serial converter. A compiled 'C' program 
then generating polling characters (uppercase 'S') for the winch PLC at 5Hz. 
The return string of winch telemetry was logged to the local hard drive and 
also to the Drobo shared network drive. CLAD simulated all the RS232 serial 
ports of the CLAM, and enabled clock messages to be interspersed with the 
winch data in the logged file. Thus satisfied that we were fulfilling the 
winch logging obligations, we were able to proceed with Station 020 on 
schedule. The CLAD logging system came online during the downcast of Station 
020 before the limiting tension was reached. A complete winch telemetry 
record has been kept from Station 021 onwards. The initial display was a 
scrolling text echo to the screen of the $CTD3 strings sent by the winch. 
Considering the non-negotiable necessity of a winch logging system, it is not 
an exaggeration to say that the assembly of this system rescued the cruise 
from a massive delay and setback and even possibly a premature end.

The second function of the CLAM system was to provide a data display for the 
winch drivers and the bridge. This includes a graphical display of tension 
data for recent minutes, as well as real-time digital display of tension, 
wire-out and haul/veer rate. In parallel with Paul Duncan's development of the 
CLAD logger, the PSO programmed a Matlab figure display comparable to the old 
CLAM display, updating the digital values and with a graphical display of 5 
minutes of recent tension data. The CLAD display program ran on NOSEA1, 
pulling data in real time (up to 3 seconds delay) off the Drobo shared disk. 
The first version was available in time for Station 021. Initially, the CLAD 
Linux box had not been configured to run X windows displays, so the CLAD 
display was run on the PSO's laptop, feeding the video splitter box near the 
old CLAM system. Later, the CLAD Linux box was configured so that it could 
run remote X shells on NOSEA 1 and took over that function as well.


Mon 11 Jan
A short weather delay was experienced while waiting to start Station 026.


Wed 13 Jan
Further development of the CLAD had been difficult, since the machine was in 
regular use during stations with little time in between for experimentation. 
Station spacing at this stage was between 5 and 10 miles. Initial effort had 
been expended in trying to resurrect either of the original CLAM computers, 
but all efforts were thwarted by lack of correct software, even though some 
software had been sent from NOC. The CLAM software was written in Lab View, 
and we were unable to ascertain why it would not interrogate and then parse 
the return from the winch PLC. Colleagues at NOC were unable to tell us 
whether the replacement software sent to the ship worked correctly at NOC 
when offered simulated PLC output. However, by l3/l8l6Z, in time for Station 
035, the CLAD output had been further modified so that it sent a correctly 
formatted serial output message on a port connected to the TECHSAS system, so 
TECHSAS logging was resumed. Logging to local drive (for security) and 
network drive (for CLAD display) continued. Files for Stations 021 to 034 
were read into Matlab from the /Drobo data logs, and Mstar files produced 
equivalent to those taken from TECHSAS for other stations. The CLAD system 
continued in use for the remainder of the cruise.


Fri 15 Jan
Today it was noticed that primary conductivity sensor had failed, thus was 
consequently replaced with a spare.


Sat 16 Jan
Clocks advance on the night of 15 Jan, so ship time is now UTC-4.


Mon 18 Jan
The secondary conductivity sensor failed, but the decision was taken not to 
replace this as we only have one spare conductivity sensor remaining and the 
primary sensor is still working well so we will continue to use that for now.


Fri 22 Jan
Clocks advanced on the night of 21 Jan, so ship time is now UTC-3.


Sat 23 Jan
The LADCP and other units such as the fluorometer and transmissometer were 
removed before Station 64 as these instruments are not pressure rated to 
below 6000m.

After Station 064, a test station, referred to as number 200 to distinguish 
it from the main stations in the section, was undertaken for CFC bottle 
blanks. It commenced at 23/1 l20Z and ended at 23/l729Z. It reached 6349db, 
and all bottles were closed at the bottom of the cast. Shortly after starting 
to haul, at 6046db, the winch cut out. The compensator between the winch and 
the storage drum had reached the end of its travel and operated a stop. The 
winch remained stopped from l320Z to 1455Z, while the 2nd Engineer and ETO 
investigated. No fault was found, and the conclusion was that the storage 
drum was struggling to provide sufficient back tension as required by the 
winch at high wire-outs. Accordingly, slower hauling speeds were used at high 
wire-outs in subsequent stations, to reduce the likelihood of a repeat. The 
wire was recovered on this station without further abnormal behaviour. A 
thorough investigation was carried out by the 2' Engineer and ETO while 
steaming to Station 065, and on arrival the winch was declared fit for normal 
use, subject only to the limitation of lower haul rates at greatest depths.


Sun 24 Jan
Station 066 was the deepest station on the section. The maximum CTD depth was 
6450m, at a pressure of 6592db. As far as we are aware, this is the greatest 
depth achieved with the present winch system. It slightly exceeds the depth 
of the equivalent station on D279. Bottom of the cast was reached at 24/0742Z 
and the cast ended at 24/l05lZ. The maximum tension spike on this station was 
2.86T, with a mean of 2.7lT when first hauling from 6450m wire-out. This is 
well within the agreed SWL for the wire.

Ironically, the echo sounder was not working during this station. On arrival 
at station 066, the echo sounder was swapped from the PES fish to the 
starboard hull transducer, which was the custom throughout the cruise. The 
fish gave better data underway, but often gave poor or absent data whilst on 
station. It was supposed that this was due to trim of the fish being poor 
when stationary. Apparently when the swap was made, the plug may not have 
been properly seated in the socket, so when the echo sounder was reactivated 
it caused a failure of the system. Data were lost after 24/0442Z. Various 
replacement boards were tried without success. At 0535Z, Station 066 was 
commenced with the echo sounder u/s, relying solely on the CTD altimeter. The 
echo sounder had provided a reliable bottom depth before failing. The 
altimeter was used as normal, supplying height-off from a range of 97m, and 
the CTD approached to 10m off the seabed. During and following Station 066, 
the echo sounder was extensively investigated. Various boards (10kHz and 
12kHz) were tried in the three operating slots available in the instrument. 
It was presumed that the original board had been damaged by being operated 
while the transducer selection plug was not properly seated. No obvious fault 
was found, and after various swaps the instrument was once again working. 
Mysteriously, it continued working when reassembled with the original boards 
in the original slots, and worked normally for the remainder of the cruise. 
We can only presume that multiple power cycling cleared whatever problem had 
originally occurred, where single power cycling had not.

A short weather delay was experienced while waiting to commence Station 067.


Tues 26 Jan
The original Aluminium-casing LADCP unit was replaced on Station 70 with a 
titanium-casing unit. This proved a bad move as the unit failed on Station 
72. A very poor piece of equipment.


Wed 27 Jan
The termination failed early on the downcast of Station 073. The station was 
abandoned, the package was recovered and the wire re-terminated. A 
replacement Station 073 resumed at 27/l2l8Z


Thurs 28 Jan
The primary conductivity sensor, which had previously been replaced, failed, 
so we had to use our last remaining spare to replace it. It seems to have 
been a wise decision to save it for this moment; We must hope that this is a 
good one that behaves itself for the rest of the cruise.


Fri 29 Jan
The CTD was grounded at the bottom of Station 081, and approximately 200m of 
further wire paid out. A combination of poor depth echo, and no bottom return 
from either the pinger or the altimeter allowed the event to occur. No damage 
or loss occurred. The package evidently tipped over onto the seabed. Several 
Niskin bottles came back containing sediment. A detailed account of the 
events was prepared by the PSO and sent to NOC.


Sun 31 Jan
Clocks advance on the night of 30 Jan, so ship time is now UTC-2.


Thu 4 Feb (035)
The PSO's upcoming birthday on the 5th was marked with a BBQ. Strong winds 
underway between Stations 098 and 099 rendered outdoor cooking impossible, so 
the ship hove to between 35/2106Z and 35/2235Z so that most of the scientists 
and ships' personnel could enjoy an excellent selection of BBQ food prepared 
by the catering team, and anticipate the landmark of Station 100 due the 
following morning.


Fri 5 Feb (036)
A second CFC bottle blank station was conducted, designated 202 (since 201 
had been reserved for use elsewhere), falling between Stations 100 and 101. 
This time the level chosen was 3500m. The station began at 36/1534Z and ended 
at 36/1738Z.


Mon 8 Feb (039)
Clocks advance on the night of 7 Feb, so ship time is now UTC- 1.


Wed 10 Feb (041)
For the last run of stations the LADCP has been replaced with the original 
unit that started the cruise because this performed well.


Sun 14 Feb (045)
Clocks advance on the night of 14 Feb, so ship time is now UTC. This is the 
correct time zone for Lisbon.

Last station (number 135) completed


Fri 19th Feb (050)
We arrived in Lisbon early morning, approximately 06:30 UTC. Since finishing 
the sampling big efforts have been made by all the scientific teams to finish 
analysing the backlog of samples, write their sections of the cruise report 
and pack their equipment away. Today, both the ships' crew and the scientific 
contingent are working hard to finish packing away equipment for either 
freight back to the UK or to Montevideo for the ANDREX cruise scheduled to 
take place in 3 weeks time. Both Sinhue Tones and Andrew Brousseau will be 
taking part in ANDREX.




1.  CTD SYSTEMS OPERATION
    David Teare, Peter Keen and Alan Sherring

1.1.  CTD and Sensors

The CTD system comprised of the following equipment:

• Seabird 911+ CTD with dual pumped temperature and conductivity sensor pairs
• Seabird SBE43 dissolved oxygen sensor
• Seabird SBE32 carousel with twenty-four OTE, externally sprung, twenty 
  litre water bottles
• Downward looking RDI 300kHz workhorse ADCP
• Chelsea Instruments Alphatracka (transmissometer)
• Chelsea Instruments Aquatracka (fluorometer)
• Tritech P200 altimeter
• IOS 10kHz pinger
• Sonardyne location beacon

One pair of temperature\conductivity sensors were mounted on the 
stabilisation vane, the other pair, with the oxygen sensor, were mounted 
conventionally onto the CTD frame.

Overall the system worked well with only a small amount of time lost due to 
breakdowns. There were, however, a number of problems worthy of mention, 
these are listed below.

  1. For the first half of the cruise the carousel repeatedly returned 
     'error, unsupported carousel message', this had been reported on the 
     previous cruise. On several very early casts, bottles failed to fire, or 
     fired but failed to return a valid code. The 11+ deck unit was changed 
     which appeared to resolve the problem, although on one later cast the 
     problem reappeared. After the sea cable was reterminated the error 
     message disappeared.

  2. Near the end of the cruise there were several mechanical jams of the 
     release levers. This was rectified by fitting "diverter" tie-wraps to 
     provide a more direct pull on the levers. This problem is due to an 
     alignment error between the release lever and the bottle position.

  3. Three out of four conductivity sensors failed, due to cracking of the 
     cells, at depths in excess of 5500m. After contacting Seabird it appears 
     that a problem with the bonding of the cell to the unit is the cause. 
     The cells will be replaced, free of charge, using the new bonding 
     technique.

  4. The original oxygen sensor was replaced due to an electronic error in 
     the gain ranging.

The starting sensor configuration is as follows, with subsequent 
configuration files in the raw data directory.

T1 = 4872
C1 = 3258
P = 90573
T2 = 438i
C2 = 3052
Oxy =1624
Alt = 6198.118171
Fluor = 088095
Trans = 161048

Salient cast and sensor changes are listed below.

Cast 36  Oxygen sensor 1624 swapped for 0621. 
Cast 41  Conductivity sensor 3258 swapped for 3054. 
Cast 50  Conductivity sensor 3052 failed but not replaced.
Cast 51  The physical position of the vane and CTD mounted sensors swapped.
         The channel allocation remained the same.
Cast 68  Suspect temperature sensor 4381 replaced with 2674.
Cast 69  Sensor 4381 checked ok, returned to replace 2674.
Cast 73  Sea cable terminated, carousel error messages disappeared.
Cast 77  Conductivity sensor 3054 failed, replaced with 2231.



1.2.  LADCP

A single 300kHz Workhorse downward looking ADCP was operated on the frame in 
the lowered mode. Three units were available for this purpose and all were 
deployed at some point during the cruise. The ADCP was removed for casts 
deeper than 6000m. Instrument performance analysis on this cruise is dealt 
with in other reports though in general, two functioned reasonably well and 
one failed on its third cast. The unit which failed (s/n 13399) had had a 
small amount of water ingress through the main bulkhead connector, which came 
in contact with components on the top board where the main power supply comes 
in, causing these to short circuit.



1.3.  20L Niskin Bottles

Prior to commencement of the cruise the original silicon-fluoride O-rings 
were replaced with decontaminated 'Nitrile' O-rings. Decontaminated 'Viton' 
equivalents were also available and were substituted for the Nitrile versions 
where sealing of the bottle was considered an issue on the supposition that 
the Nitrile versions were too unyielding to affect a good seal.

As mentioned in the previous CTD section there were some issues early on 
associated with communications problems with the carousel leading to misfires 
on some of the earlier casts. This problem was eventually solved through 
re-termination of the cable. Later there were also problems with latches on 
the carousel hanging up, after returning a positive firing confirmation code, 
this being attributed to misalignment between the carousel and the rosette.

In addition to these problems there were frequent occasions where bottles did 
not seal properly or appeared to have closed at depths out of sequence with 
the order in which they were fired. Often this was revealed in anomalous 
temperatures when the bottle was being sampled. Records were kept of these 
occasions and are reported in detail elsewhere. Bottles that showed 
consistent failure were replaced. This amounted to changing three bottles 
over the course of the cruise.




2.  CTD DATA PROCESSING AND CALIBRATION
    Chris Atkinson, Gerard McCarthy and Gavin Evans

2.1.  Initial Processing Using SeaBird Programs

The files output by Seasave (Version 7.19) 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 7.19. 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 D346_nnn.hex where nnn 
refers to the threedigit 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.

Output files were copied to NOSEA1 from Drobo using the UNIX exec 
ctd_linkscript. Symbolic links were created for each file named 
ctd_di346_nnn_ctm.cnv, where nnn is the station number.

As part of Data Conversion, an algorithm that attempts to reduce hysteresis 
between downcast and upcast oxygen measurements is available. This was 
initially applied to the oxygen data as part of routine processing using the 
default parameters recommended by SeaBird. Using this algorithm a noticeable 
reduction in upcastdowncast oxygen residuals was observed relative to data 
from cruise JC032 where processing was carried out using an earlier version 
of the SBE Data Processing suite where no hysteresis correction was 
available. To further tune the hysteresis parameters, a decision was taken to 
apply the SeaBird hysteresis algorithm to the oxygen data within the Mstar 
CTD processing suite. This eliminated the need for cumbersome reprocessing of 
data using the SBE Data Processing software each time a parameter change was 
tested. The final oxygen hysteresis correction was applied to 24Hz CTD files 
as part of Mstar CTD processing using the script mctd_02b.m.


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 D346

After having converted CTD with the SBE processes, there were two ASCII files 
to work on: ctd_di346_nnn_ctm.cnv and ctd_di346_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, m_setup was run in Matlab to add Mstar 
tools and information needed for the processing. The following scripts were 
then run:

msam_01: creates an empty sam file to store all information about rosette 
bottle samples. The set of variables are available in the  /templates 
directory and can be changed according to what it needs to store. This file, 
named as sam_di346_nnn.nc, stores data for each sample bottle, their flags, 
and some CTD data at firing time.

mctd_01: reads the raw data (ctd_di346_nnn_ctm.cnv) and stores it in a NetCDF 
file named ctd_di346_nnn_raw.nc, which becomes write protected.

mctd_02a: copies ctd_di346_nnn_raw.nc into ctd_di346_nnn_24hz.nc renaming the 
variables for the SBE sensor.

mctd_02b: using 24Hz data (ctd_di346_nnn_24hz.nc), applies oxygen hysteresis 
correction to variable oxygen she to create new variable oxygen.

mctd_03: using 24Hz data (ctd_di346_nnn_24hz) it averages to 1Hz data. Then, 
using the 1Hz file (ctd_di346_nnn_1hz) it calculates salinity and potential 
temperature (ctd_di346_nnn_psal). This script also calls 
mctd_sensor_choice.m, which records the first choice CT sensor pair for each 
station. First choice sensor data is then stored in the variables temp and 
cond (which are subsequently used to calculate variables potemp and psal).

mdcs_01: creates an empty file named as dcs_di346_nnn to store information 
about the start, bottom and end of the cast.

mdcs_02: populates dcs_di346_nnn with information from the bottom cast. It 
takes the highest pressure point as bottom.

mdcs_03: selects and shows surface data < 20db (ctd_di346_nnn_surf) allowing 
the analyst to choose 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 10db and then the point where is it was 
brought back to the surface for the start of the downcast. The scan number at 
which the pressure begins to increase and temperature, salinity and oxygen 
data show reasonable values is selected as the start point of the downcast.

To find the end of upcast, the data were scrolled up from the bottom to 
identify where the CTD came back onboard. The operator chooses the last 
available point where sensor values are reasonable before an abrupt change in 
measurements occurs as the CTD is lifted out of the water.

mctd_04: using information on dcs_di346_nnn it selects the CTD downcast data 
from ctd_di346_nnn_psal file and averages it into 2db resolution 
(ctd_di346_nnn_2db).

mdcs_04: loads position from navigation file and merges it on the cast's 
points previously defined in mdcs_03, and stores it on dcs_di346_nnn_pos.nc.

mfir_01: extracts information about fired bottles from ctd_di346_nnn.bi and 
copies them into a new file named fir_di346_nnn_bl.nc.

mfir_02: using fir_di346_nnn_bl and ctd_di346_nnn_1hz it merges the time from 
the CTD using scan numbers and puts it into a new file 
(fir_di346_nnn_time.nc).

mfir_03: stores the CTD data at each bottle firing time in fir_di346_nnn_ctd. 
The CTD data are taken from ctd_di346_nnn_psal and selected according to the 
firing time information stored in fir_di346_nnn time.

mfir_04: copies information of each bottle from fir_di346_nnn_ctd onto 
sam_di346_nnn.

mwin_01: creates a new file named win_di346_nnn.nc to store information about 
winch working (for e.g. angles, rate and tension).

mwin_03: using time stored in fir_di346_nnn_time, it selects wire-out from 
win_di346_nnn at each bottle firing location to fir_di346_nnn_winch.

mwin_04: pastes wire-out information from fir_di346_nnn winch into 
sam_di346_nnn.nc.

mbot_01: creates a bottle file (bot_di346_nnn) to store information regarding 
the state of each Niskin bottle. It uses a text file named as 
bot_di346_001.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_di346_nnn to sam_di346_nnn.nc.

mdep_01: applies the full water depth to all files. The depth is taken from 
the LDEO processing of the LADCP. Where this is not possible, mdep_02 was 
used to create the full water depth using package depth combined with 
altimeter data or echo sounder data.

mdcs_05: applies positions from dcs_di346_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_di346_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 
station - 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 using similar format, e.g. 
oxy_di346_nnn.nc in the case of oxygen. The second step was to merge these 
individual Mstar files onto the master sam file for each station. This was 
performed by the programs moxy_02, mnut_02 etc. For nutrient data, a further 
script, mnut_03 was run to calculate organic nitrate and phosphate values 
from total nutrient and inorganic nutrient measurements and input these 
variables to the master sam file for each station. For oxygen data, a further 
script, msam_oxykg was run to convert bottle oxygen data from µmol/l to 
µmol/kg and input this variable to the master sam file for each station.

This approach provides a flexible method of assimilating data from the 
various teams contributing to D346. The sam files were periodically appended 
together to form the master file sam_di346_all.nc, which, along with the 2db 
CTD files, was used by run_mgridp_ctd.m to produce gridded and interpolated 
section data in NetCDF format. This gridded data was then plotted using 
plot_cont_di346.m. This allowed cruise progress to be continuously monitored 
and provided a useful first step for identifying bad data whose flags may 
need adjustment.


2.5.  CTD files

Due to failure of the CLAM winch logging system during Station 16, some winch 
data was lost until a temporary solution was found. The introduction of the 
CLAD system from Station 36 onward allowed data to be logged again via the 
TECHSAS data streams. For Stations 1-16 and 36-135, winch data was therefore 
obtained using TECHSAS data using mwin_01. From Stations 17-20, no winch data 
was available. For Stations 21-35, winch data was saved in ASCII format 
before transformation to Mstar format by the script mwin_00_get_time.

Processed CTD sensor data was viewed using the script mplotxy_ctdck.m. This 
uses des, psal and 2db CTD files to allow CTD data to be viewed and compared 
with data from previous casts. Ideally, CTD data should be viewed immediately 
after each cast to identify any degradation in sensor performance so that a 
solution can be quickly found. Unfortunately, this system only became common 
practice several stations after initial degradation of the first oxygen 
sensor. This data was recovered following station-by-station calibration to 
bottle oxygen samples.

In addition to sensor degradation or failure, several minor spurious features 
were identified in the psal and 2db CTD and oxygen data. These included 
spikes associated with CTD telemetry failure, spikes at the start and end of 
a cast where bad start and end scan numbers were chosen in mdcs_03, 
unreasonable CT and oxygen values in the upper few decibars of a downcast 
relative to the surrounding water and bad CT and oxygen values where the 
pumps were temporarily switched off at the start of a downcast. Problems were 
solved on a case-by-case basis, either by adjusting start and end scan 
numbers in the dcs_di346_nnn files to omit bad data or by removing spikes 
using a median de-spiking routine to identify and set bad data to NaN values. 
In the latter case, corrections were made to the 24Hz files before re-
processing CTD data through to the 2db stage.

Two CTD data corrections are highlighted. The first was to Station 81 where 
the CTD was temporarily grounded. Because the bottom of a downcast is 
identified using the deepest pressure value, several bad data scans were 
included in the downcast. The end downcast scan number was therefore edited 
in dcs_di346_081 to exclude downcast data within 2db of the sea floor. The 
second was an anomalous TS spike generated by a pause in winching when 
switching to the autopilot during Station 12 (Figure 5). In this case water 
entrained in the wake of the CTD overtook the package leading to a warm and 
saline TS anomaly. The TS properties suggest the entrained water came from 
15m above the package and passed within ~20 seconds of the pause in winching. 
In this case bad scan values were set to NaN in the 24Hz files before 
re-processing CTD data through to the 2db stage. Whilst similar anomalies 
almost certainly exist in other files, these are difficult to identify in the 
final 2db CTD files that also retain some natural spikiness in TS space. 
Station 12 stood out as an interesting feature due to the clear kink produced 
in TS space and is highlighted here merely as a case study in wake effects 
generated by motion of the CTD package.

Final calibrated CTD sensor data for the Florida Straits and main 24°N 
section are shown in Figures 8-10.


2.6.  Temperature-Conductivity Sensor

2.6.1.  First Choice Sensor Data

The CTD used on D346 was equipped with two conductivity and temperature 
sensors. Initially the primary conductivity-temperature sensor was attached 
to the fin of the CTD and the secondary sensor was attached near the bottom 
of the main frame (Table 1). Both temperature sensors were found to compare 
well (< 0.001°C difference) and no evidence of significant upcast-downcast 
difference was found in either sensor. For Station 1-49, prior to failure, 
the secondary conductivity sensor was seen to possess less hysteresis between 
upcast and downcast (< 0.001 on potential temperature levels) and therefore 
was the initial sensor of choice.

The secondary conductivity-temperature sensor remained the first choice 
sensor to Station 49. During Station 50 the secondary conductivity sensor 
failed at the start of the upcast and was not replaced. From Station 50 
onwards the (second) primary conductivity-temperature sensor therefore became 
the first choice sensor pair and from Station 51 onwards was swapped to a 
position on the bottom of the CTD frame. On Station 78 a new (third) primary 
conductivity sensor was installed following failure of the previous sensor at 
the start of the upcast on Station 77. Subsequently, the first choice 
temperature-conductivity sensor was positioned on the bottom of the main CTD 
frame for all stations except 50 (Table 1).

Due to no data being available from the secondary conductivity sensor on 
Station 77, upcast data were recovered by interpolation of downcast data on 
density surfaces. Four iterations on pressure, potential temperature, and 
potential density were carried out so that interpolations were successively 
less vulnerable to the broken conductivity sensor.

The primary conductivity sensors used from Stations 50-77 and 78-135 showed 
differing hysteresis properties to both the secondary conductivity sensor 
used for Stations 1-49 and to each other. However, in all cases the 
difference between upcast and downcast data on potential temperature levels 
was seen to be < 0.001 at pressures > 2000db.


Table 1: The position of primary and secondary conductivity-temperature 
         sensors during D346 for Stations 1-135. Number in brackets denotes 
         sensor number (this increments when a new sensor is fitted following 
         failure of previous sensor). Stars denote the first choice sensor 
         pair.

Frame                  Fin                                        Stations
---------------------  -----------------------------------------  --------
Secondary Sensor (1)*  Primary Sensor (1)                         1-41
Secondary Sensor (1)*  Primary Sensor (2)* (Only for Station 50)  42-50
Primary Sensor (2)*    Secondary Sensor (1 - broken)              51-77
Primary Sensor (3)*    Secondary Sensor (1 - broken)              78-135


2.6.2.  Conductivity Calibration

Upcast conductivity from the first choice sensors (Table 1), present in the 
SAM file at bottle depths as 'ucond', was calibrated against conductivity 
derived from bottle samples. Final calibrations were applied using 
mcond_fix.m to the 2411z file conductivities before cascading through to 1Hz, 
psal, 2db and SAM files. As the calibration was applied at the transition 
between the raw files and the 24Hz files, it was necessary to do a 
conductivity (not salinity) calibration.

A multiplicative correction factor applied to conductivity is associated with 
a deformation of the conductivity cell. The ratio between conductivity 
derived from bottle samples and upcast conductivity was investigated at 
depths > 3 000db where vertical salinity gradients are small and CTD-bottle 
comparison is less susceptible to bottle flushing issues. In the deep ocean 
(potential temperatures < 2°C) where horizontal salinity gradients are small, 
bottle salinities showed greater spread about the mean TS properties (std. 
dev. ~ 0.001-0.0015) than CTD salinities (std. dev. ~0.0005), which appeared 
to be more stable over time.

For the three first choice sensors used during D346, while bottle/CTD ratios 
were close to unity, offsets still existed for each sensor roughly equivalent 
to 0.001-0.002 in salinity. The final calibration ratios applied to the 
secondary, second primary and third primary conductivity sensors (Table 1) 
were 0.9999719, 1.0000574 and 1.0000285 respectively. For the second primary 
conductivity sensor, a small negative trend in conductivity ratio was 
observed over time (a change of 0.00002 over 27 stations). However, only a 
mean ratio correction was chosen as calibration using a ratio trend 
introduced greater spread of CTD salinities about the mean TS curve in the 
deep ocean (potential temperatures <2°C).

Following conductivity ratio calibration, bottle-CTD conductivity residuals 
showed some structure against pressure. The structure of the residuals was 
seen to be different for each sensor though in all cases offsets were 
equivalent to a maximum of ~0.001psu at pressures > 1500db. In the 
thermocline and surface-ocean, large gradients in temperature and salinity 
occur, and bottle-CTD residuals are of greater magnitude and less coherent 
with pressure. Bottle conductivities in this region often read lower than 
those of the CTD, which is partly interpreted as a bottle flushing issue. 
However, consistent bottle-CTD offsets observed in the surface mixed layer 
suggest some of the offset is related to sensor performance and therefore 
corrections against pressure were applied to the CTD sensor data throughout 
the water column. It is noted that although the pressure offsets are 
comparable in magnitude to the sensor downcast-upcast hysteresis, the 
structures against pressure are different and as such are considered a 
beneficial correction. No trends were noted in conductivity residuals against 
temperature or conductivity.

The calibration was applied by correcting conductivities using an additive 
factor decided by a pressure lookup table. The pressure lookup table was 
created for each sensor by calculating median offsets in pressure bins. 
Application of the calibration ratios and pressure corrections reduced rms 
offset of salinity offset from 0.00128, 0.00238 and 0.00202 to 0.00073, 
0.00119 and 0.00064 for the secondary, second primary and third primary 
conductivity sensors respectively. Most of the remaining offset is found in 
the upper ocean (< 1000db). Final offsets for all CTD-bottle pairs are shown 
in Figures 6 and 7.

Note that the performance of the third primary conductivity sensor was 
observed to be stable and calibration parameters calculated for Stations 
78-106 were applied to all data from Stations 78-135.


2.7.  Calibration of the Oxygen Sensor

The oxygen sensor was attached to the conductivity-temperature sensor on the 
CTD frame. Following a period of sensor degradation, the first oxygen sensor 
was swapped for a second oxygen sensor before Station 37. The second sensor 
was seen to perform well and remained stable for the rest of the cruise.

As discussed in section 1.1, a correction for downcast-upcast sensor 
hysteresis was made during Mstar processing by mctd_02b. This applies an 
algorithm provided by Sea-Bird for oxygen concentration values measured by 
the SBE 43 sensor.

The algorithm has the form:


Oxnew    = {(Oxygen   (i) + (Oxnew   (i -1) x C x D)) - (Oxygen   (i -1) x c)}/D
    conc          conc           conc                         conc


Where: D = 1 + H1 x (exponential(P(i)/H2) - 1)

       C = exponential(-1 x (Time(i) - Time(i - 1))/H3)


i=indexing variable, P=pressure (db), Time=time (seconds), H1=amplitude of 
hysteresis correction function (default -0.033), H2=function constant or 
curvature function for hysteresis (default 5000), H3=time constant for 
hysteresis (seconds, default 1450).

Following experimentation, values for H1, H2 and H3 of -0.028, 5000 and 2500 
respectively were chosen for the first oxygen sensor. Values for H1, H2 and 
H3 of -0.037, 5000 and 1450 respectively were chosen for the second oxygen 
sensor. Downcast-upcast hysteresis was successfully reduced to typically a 
few µmol/kg by this procedure.

Following the hysteresis correction, upcast oxygen concentrations from each 
sensor was calibrated against oxygen concentrations derived from bottle 
samples. Final calibrations were applied using moxy_fix.m to the 24Hz file 
oxygen data before cascading through to 1 Hz, psal, 2db and SAM files.

For the first oxygen sensor, bottle oxygen and CTD oxygen showed a clear 
linear relationship. As such a multiplicative correction factor calculated as 
the median ratio between bottle and CTD oxygen was applied to CTD oxygen. 
This was calculated and applied in bulk for Stations 1-22. For Stations 
23-36, the correction was calculated and applied on a station-by-station 
basis to account for the gradual degradation in sensor performance over this 
period prior to removal of the sensor.

This reduced bottle-CTD residuals from > 10µmol/kg to ±5µmol/kg. After 
application of this correction, bottle-CTD residuals retained clear structure 
against pressure. Below 1500db, botoxy-CTD residuals were generally positive, 
whilst upper ocean residuals differed depending on the stage of sensor 
degradation. For Stations 1-22, upper ocean residuals were generally 
positive, for Stations 23-25, upper ocean residuals were nearer zero and for 
Stations 26-36 upper ocean residuals were typically negative. For each of the 
three groups of stations, an additive correction was made to CTD oxygen 
calculated using a third order polynomial fit of bottle-CTD residuals against 
pressure. Following this procedure, bottle-CTD residuals were reduced to 
±2µmol/kg for the first oxygen sensor.

For the second oxygen sensor, bottle oxygen and CTD oxygen concentration 
offset was typically > 10µmol/kg however a linear relationship was less 
obvious than for the first sensor. In this case, bottle-CTD offset was 
reduced to ±2µmo1/kg by applying a combined second order pressure and first 
order temperature dependent offset to all data with potential temperature < 
7.5°C. The coefficients of the pressuretemperature offset function were 
calculated using a least-squares approach. For data with potential 
temperature > 7.5 °C, a simple offset of 7µmol/kg was added.

Final offsets for all CTD-bottle pairs are shown in Figure 7.

Note that the performance of the second oxygen sensor was observed to be 
stable, and that calibration parameters calculated for Stations 37-100 were 
applied to all data from Stations 37-135.


2.8.  Addition of Metadata to the Mstar Files

Position, time and full water depth were added to the headers 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 were pasted into the files. The time 
corresponding to the bottom of the cast was found from the DCS files with the 
GPS4000 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 backup approach 
was used for Stations 1, 15, 16, 53, 64-70, 72, 100, 101 and 200. Depth from 
the echo sounder was used for Station 202 where distance between maximum 
package depth and the seafloor exceeded the range of both the LADCP and 
altimeter.


2.9.  Niskin Bottles

The Niskin bottles, on the whole performed well, however, problems were 
identified with regards to sealing the bottles, possibly related to a change 
in the seals used. This resulted in dribbling from some of the bottles, which 
although thought not to contaminate the sample, was still undesirable due to 
losing a potentially substantial amount of water as the CTD is drawn upwards 
through the water column. The slight dripping can be related to both a 
sealing problem and a pressure effect, as it was continuously witnessed that 
shallower Niskin bottles displayed a greater tendency to dribble. Another 
problem that was sometimes encountered was when water leaked from the bottom 
tap, prior to the top valve being opened, indicating a slight break in the 
vacuum within the Niskin bottles with a potential increase in sample 
contamination. In order, to maximise the number of bottles sampled, and limit 
the probability of contamination, bottles with minor leaks were sampled and 
given a flag of 10. Bottles were only immediately rejected if they were seen 
to be leaking when the CTD was removed from the water (flag 3), or if the 
bottle did not fire (flag 4). The bottle was also rejected if the temperature 
measurement taken by the oxygen team revealed an unusually high temperature, 
conducive with the Niskin bottle failing to seal correctly at its original 
depth, but sealing fully higher up the water column (flag 4).
Table 2:  Niskin bottle flags

           Flags  
           -----  --------------------------------------------
               2  No Problems noted
               3  Leaking profusely when taken from water
               4  Bad Bottles from salinity/temp measurements
               4  Did not fire
               9  Samples not drawn from bottle
              10  Slight drip/water leak when top valve opened


2.9.1.  Bottle Performance

Bottles 1 and 15 were removed from the rosette on Station 87 and replaced 
with two spare Niskin bottles, labeled as bottles 25 and 26 respectively, due 
to a perceived higher failure rate. Bottle 19 was also removed from the 
rosette on Station 115 for exclusive use by the CFC group, and replaced with 
another unused bottle (bottle 27). On Station 121, bottle 18 was retained for 
exclusive CFC use, and replaced with bottle 19 for the remaining stations. 
Re-analysis of the results from the bottled salinity and bottled oxygen 
datasets revealed that Niskin bottles labeled with a flag of 10 were 
uncontaminated, because although there was a small dribble of water, there 
was no exchange of water as the bottle traveled through the water column. The 
total percentage of Niskin bottles during the cruise given a flag of 3 or 4 
was ~4%.


Figure 5: Θ-S anomaly during the Station 12 downcast resulting from a pause 
          in winching (a) Θ-S anomaly (highlighted by rectangular box) (b) 
          Θ-S-Pressure against time centred on the anomaly.

Figure 6: Final offsets between bottle salinities and calibrated CTD 
          salinities for Stations 1-135 (also 200 and 202). Blue lines denote 
          ±0.002 offset range.

Figure 7: Final offsets between bottle oxygen and calibrated CTD oxygen for 
          Stations 1-135 (also 200 and 202).  Blue lines denote ±2µmol/kg 
          offset range.

Figure 8: CTD potential temperature, salinity, oxygen and fluorescence across 
          the Florida Straits transect.

Figure 9: CTD potential temperature and salinity along the Atlantic 24°N 
          hydrographic section.

Figure 10: CTD oxygen and fluorescence along the Atlantic 24°N hydrographic 
           section. White bands on fluorescence plots denote the deepest 
           stations where the sensor was removed.




3.  WATER SAMPLE SALINITY ANALYSIS
    Gavin Evans


3.1.  Sampling

Bottle salinity sampling was undertaken as a secondary source of salinity 
measurements. Samples were collected in 200m1 glass bottles from each Niskin 
bottle fired at each station. TSG samples were also collected at 4-hourly 
intervals and recorded within the watchkeeping logs. Ten crates were 
designated for general use and three crates for TSG. The standard procedure 
for sampling both the CTD and the TSG samples was to rinse the sample bottle 
and lid thoroughly three times using sample water from the appropriate Niskin 
bottle or using surface water from the TSG system. The sample water was then 
filled approximately to the neck of the glass bottle. The rim and inside of 
the lid was subsequently wiped using disposable paper towels to prevent salt 
crystals forming around the rim of the bottle and providing an artificial 
salinity enhancement. Each sample bottle was sealed with a disposable plastic 
stopper and its respective screw cap. After a station had been completed, the 
crate of salinity bottles was taken to the constant temperature (CT) 
laboratory and left for a minimum of 24 hours to allow for temperature 
equilibration. The time that the crate was left in the laboratory was 
recorded in UTC in order to readily identify it for later sample analysis.


3.2.  Laboratory Setup

For the purpose of salinity analyses, two Guildline 8400B laboratory 
salinometers were used, serial numbers 68958 and 60839. The temperature of 
the laboratory was maintained at a temperature between 22-23°C for Stations 
1-94, and between 2021°C for Stations 94 onwards, therefore keeping the air 
temperature lower than the water bath temperature within the Autosal. The 
temperature of the CT laboratory was recorded as part of the watchkeeping 
logs.


3.3.  Analysis

Autosal analysis of the salinity samples was shared between the members of 
the physics watch: Gavin Evans, Chris Atkinson, Gerard McCarthy, Benjamin 
Webber, David Hamersley and Helen Pillar. The methodology for using the 
Autosal was explained to each of the new analysts, so that the task of 
running salinity samples could be shared between the physics team members. 
The data-logging software for the most part provided good guidance to the 
analyst when recording salinities.


3.4.  Initial Standardisation

The first two bottles of the test station were run as part of the 
standardisation process. A number of standard seawater samples were used to 
reaffirm the values produced by the salinometer. Initially, the values given 
for the standard seawater samples were fluctuating at an unacceptable level. 
However, after running four bottles of standard seawater through the Autosal, 
the Guildline conductivity ratio appeared to have stabilised. The 
conductivity ratio was set to be a little lower than the Autosal intended, to 
avoid the issue of alternation above and below the 2.0 suppression setting 
(i.e. 1.99973 in correspondence with the Autosal recommended 1.99994). A 
positive value of the suppression was needed for the Autosal software to be 
able to read it correctly. The test station crate was run as a practice to 
ensure that the Autosal was giving reasonable values.


3.5.  Procedure

In order to use the Guildline 8400B salinometer for salinity samples, first 
the air pump system needs to be switched on so that the system is primed for 
drawing through the seawater samples. A standard sample of seawater is placed 
in the holding position on the Autosal with the intake tube inserted into the 
sample bottle. The tubing is handled using blue roll, to avoid unnecessary 
contamination. It is advisable to flush the system with old standard seawater 
samples before flushing three times using the new standard, in order to bring 
the salinity of the cell closer to that of the new sample.

To begin the analysis the peristaltic pump is switched on and draws water 
into the system, filling the cell. The system is then flushed three times 
whilst the read/standby knob is set to 'standby' mode. Once the three flushes 
are complete, seawater is drawn through the system a fourth time and the 
conductivity ratio of the sample is read. The standard number and bottle 
numbers were recorded on the salinometer logsheets, as well as automatically 
using the data logging software.

The conductivity ratio of the sample, as given by the Autosal was usually 
recorded within the 1.9-2.1 suppression range. To record the conductivity 
value the suppression dial on the Autosal is rotated to produce values within 
the correct suppression range, otherwise inaccurate results will be recorded. 
One potential improvement to the current software would be an on-screen 
warning to alert the user that the current suppression range is incorrect. 
After one value for the conductivity ratio of the sample is recorded, the 
system is flushed and another sample from the sample bottle is drawn through. 
The conductivity ratio of this sample is then recorded. The flush, draw and 
analyse process is repeated once more so that three values for the 
conductivity are obtained. The average of these three samples is then 
calculated automatically and recorded.

A sample of standard seawater must be run through the salinometer before and 
after every crate to ensure that there has not been any drift of the 
instrument and that the conductivities of the samples recorded are reliable. 
The standard seawater samples produced by Ocean Scientific Instruments Ltd. 
(OSIL), were used throughout the cruise- Batch number: P151, and K15 ratio: 
0.99997, 2*K15: 1.99994. In the data logging software, standards were 
recorded using a sequential numbering order. An ID number is given to the 
standard sample used using the naming convention '9' followed by the number 
of standard samples used i.e. the first standard sample used is referred to 
as '9001'.


3.6.  Differences and Adjustments

The set procedure is to run a standardisation after each crate to ensure that 
the salinometer was not excessively skewing the conductivity ratio read-outs, 
and in order to remain within budgetary constraints given the cost of one 
sample of standard seawater. Each batch of standard seawater has a prescribed 
value for the conductivity ratio. The difference between twice the prescribed 
value and the actual value for the conductivity ratio recorded by the 
salinometer is known as the difference. The adjustment that is assigned as a 
result of the difference is done so as to smooth out any jumps in the 
salinometer readings. When applying adjustments, difficulty exists in 
assessing drift from the beginning of a crate to the end; therefore the 
adjustment is somewhat subjective. Once the adjustment is applied, the 
validity of the value chosen can be reaffirmed by comparing the 
bottle-measured conductivity with the CTD measured conductivity. The onboard 
CTD conductivity measurements appeared to show a high degree of structure, 
and hence a plot of the residuals of the bottled and CTD data could reveal a 
misjudged adjustment.


Figure 11: Salinity difference and adjustment for each station. The black 
           line shows the difference given by the standard seawater samples 
           that were analysed. The coloured lines show the adjustments that 
           were applied i.e. blue line for the first Autosal/red line for the 
           second Autosal.


3.7. Salinometer Performance

Initially the Guildline 8400B Autosal (Serial No: 68958) was used giving a 
robust performance for the first 40 stations. However, after witnessing an 
increasing spread in the residual dataset, the decision was made to change to 
the second Guildline 8400B (Serial No: 60839 at Station 65. This decision was 
based on analysis of the graph of the residuals of the bottle and CTD 
conductivities for each station. As the CTD conductivities were believed to 
be stable throughout this time period. The spread in the residuals was 
attributed to the bottle salinities. In order, to minimise the reasons for an 
increase in the distribution of the bottle salinities, a decision was made on 
the advice given by Brian King, to switch the peristaltic pump off when a 
reading was being taken. This was seen to limit the noise within the samples, 
and avoid any electrical bias that could be attributed to water being 
continually pumped through as the measurement is undertaken. All analysts 
reported a substantial difference in the conductivity values measured after 
changing to a 'pump-off' approach to measurement as opposed the readings 
before this change when the measurements could fluctuate by up to '15 counts. 
A switch was added to the pump to improve the functionality for the analysts.

The change in Autosal and the technique of the analysts was seen to a make a 
genuine improvement in reducing the distribution of the residuals allowing it 
to be easier to apply an offset value to the CTD salinities. The offset would 
be different for the different salinometers, and the different conductivity 
sensors that were used on the CTD. The final plot of the conductivity 
residuals (Guildline ratio offset) is shown in Figure 11 for all samples 
collected deeper 3000dbar.


Figure 12: Residuals and ratio of the bottled and CTD conductivities for all 
           points below 3000db for each station of the total 135 stations. 
           The blue x show the first Autosal and the red x indicate the 
           second Autosal.


The peristaltic pumps presented some issues, firstly due to bubbles forming 
within the cell of the Autosal, and also due to leaking from the plastic 
tubing. Formation of bubbles within the cell increases the analysis time, 
because additional flushing is required to remove the bubbles, and also 
bubbles have the potential to alter the conductivity readings. Leaks can 
reduce performance, further increasing analysis time. Three peristaltic pumps 
were used during the cruise and the tubing on two of them was changed due to 
leaks.


3.8.  Secondary Standards

Secondary standards were briefly used to assess the stability of the second 
Autosal, to ensure reasonable residuals. A crate of 24 salinity bottles was 
drawn from one Niskin bottle (Niskin bottle 1) containing deep water (6146m) 
at Station 69. The secondary standards were run at the start, middle and end 
of each crate, accompanying the standards that were already being run.

The use of the secondary standards, Figure 13, seemed to provide no clear 
indication of a linear drift of the Autosal during an individual crate with a 
correlation coefficient of 0.1 between the primary and secondary standards 
for the test analysis.

Hence, a single adjustment value per crate is still the preferred method, as 
opposed to correcting for a linear drift of the Autosal during individual 
crates.


Figure 13: Guildline conductivity ratio for primary and secondary seawater 
           standards for the same time period of Stations 69-75



3.9.  Processing

The data logging software outputs a Microsoft Excel spreadsheet containing 
the salinity of each sample. The spreadsheets were then manually edited. A 
sample number was assigned based on the station number and the position that 
the sample was taken from on the CTD rosette. For example, if the Niskin 
bottle in the first position was sampled at Station 32, the sample number 
would be 3201. Consultation of the CTD log sheets was required to account for 
any bottles that had failed to close or fire. The seawater standards were 
given an individual ID with one nine added to the sequential standard number 
(e.g. '9001', would be the sample number for the first standard used on the 
cruise). The TSG spreadsheets were edited to include a sample number based 
from the time at which the sample was taken, in the following format, 
'ddhhmmss'. After editing, the files were saved as comma delimited csv files 
for input into Matlab.

Using the adjustments chosen for each station and the data spreadsheets it 
was now possible to process the data using Matlab scripts: msal_01.m and 
msal_02.m. The adjustments are chosen based on the difference between the 
standard seawater sample measured by the Autosal and the actual conductivity 
ratio of the seawater. Adjacent difference values were also taken into 
account when deciding the adjustment. For the TSG, the Matlab script 
mtsg_01_di346.m was used. Similarly this requires an adjustment based on the 
standard seawater values.


Table 3: Bottle salinity analysis information

ID    Station  Crate  Run pos       Standard  Measured  Difference  Adjustment
----  -------  -----  ------------  --------  --------  ----------  ----------
9001      1      35   Before start  1.99994   1.99974    0.00020     0.00013
9002      1      35   End           1.99994   1.99981    0.00013     
9003      5      15   End           1.99994   1.99981    0.00013     0.00013
9004      7      19   End           1.99994   1.99981    0.00013     0.00013
9005     10      12   End           1.99994   1.99981    0.00013     0.00013
9006     11      24   Before start  1.99994   1.99969    0.00025     0.00017
9007     15      11   End           1.99994   1.99977    0.00017     0.00017
9008     15      11   End           1.99994   1.99977    0.00017     
9009     16       1   Before start  1.99994   1.99973    0.00021     0.00017
9010     17      40   Midway        1.99994   1.99975    0.00019     0.00019
9011     18      15   End           1.99994   1.99976    0.00018     0.00019
9012     19      19   Before start  1.99994   1.99970    0.00024     0.00018
9013     19      19   End           1.99994   1.99976    0.00018     
9014     20      35   End           1.99994   1.99977    0.00017     0.00018
9015     21      12   Before start  1.99994   1.99976    0.00018     0.00018
9016     22      24   End           1.99994   1.99981    0.00013     0.00015
9017     23      40   End           1.99994   1.99984    0.00010     0.00014
9018   TSG001   901   End           1.99994   1.99976    0.00018     0.00016
9019     23      40   End           1.99994   1.99982    0.00012     0.00015
9020     24       1   Before start  1.99994   1.99976    0.00018     0.00016
9021     24       1   End           1.99994   1.99978    0.00016     
9022     25      19   End           1.99994   1.99974    0.00020     0.00017
9023     26      15   End           1.99994   1.99977    0.00017     0.00017
9024     27      35   Before start  1.99994   1.99978    0.00016     0.00017
9025     27      35   End           1.99994   1.99978    0.00016     
9026     28      40   End           1.99994   1.99976    0.00018     0.00017
9027     29      11   Before start  1.99994   1.99978    0.00016     0.00017
9028     29      11   End           1.99994   1.99977    0.00017     0.00017
9029     30      12   Before start  1.99994   1.99974    0.00020     0.00017
9030     30      12   End           1.99994   1.99982    0.00012     
9031     31      21   End           1.99994   1.99981    0.00013     0.00014
9032     32      19   Before start  1.99994   1.99980    0.00014     0.00014
9033     33       1   End           1.99994   1.99975    0.00019     0.00017
9034     33       1   End           1.99994   1.99976    0.00018     
9035     34      10   Before start  1.99994   1.99975    0.00019     0.00017
9036     34      10   End           1.99994   1.99973    0.00021     
9037     35      15   End           1.99994   1.99977    0.00017     0.00017
9038     36      24   Before start  1.99994   1.99974    0.00020     0.00017
9039     37      11   End           1.99994   1.99977    0.00017     0.00017
9040     37      11   End           1.99994   1.99984    0.00010     0.00012
9041     38      12   End           1.99994   1.99984    0.00010     0.00012
9042     39      40   End           1.99994   1.99988    0.00006     0.00011
9043     40       1   Before start  1.99994   1.99986    0.00008     0.00014
9044     40       1   End           1.99994   1.99977    0.00017     
9045   TSG002     1   End           1.99994   1.99977    0.00017     0.00015
9046     41      19   End           1.99994   1.99979    0.00015     0.00015
9047     42      21   End           1.99994   1.99979    0.00015     0.00015
9048     43      24   Before start  1.99994   1.99973    0.00021     0.00017
9049     43      24   End           1.99994   1.99973    0.00021     
9050     44      15   End           1.99994   1.99980    0.00014     0.00017
9051     45      11   End           1.99994   1.99977    0.00017     0.00017
9052     46      40   Before start  1.99994   1.99980    0.00014     0.00014
9053     46      40   End           1.99994   1.99986    0.00008     
9054     47      19   End           1.99994   1.99988    0.00006     0.00012
9055     48       1   Before start  1.99994   1.99972    0.00022     0.00020
9056     48       1   End           1.99994   1.99976    0.00018     
9057     49      21   End           1.99994   1.99974    0.00020     0.00020
9058     50      12   End           1.99994   1.99973    0.00021     0.00020
9059     51      11   Before start  1.99994   1.99989    0.00005     0.00012
9060     51      11   End           1.99994   1.99972    0.00022     
9061     52      40   End           1.99994   1.99973    0.00021     0.00020
9062     53      19   Before start  1.99994   1.99989    0.00005     0.00012
9063     53      19   End           1.99994   1.99974    0.00020     
9064     54      15   End           1.99994   1.99988    0.00006     0.00006
9065     55      21   End           1.99994   1.99984    0.00010     0.00011
9066     56      12   Before start  1.99994   1.99984    0.00010     0.00011
9067     56      12   End           1.99994   1.99992    0.00002     
9068     57      10   End           1.99994   1.99982    0.00012     0.00011
9069     58      40   Before start  1.99994   1.99977    0.00017     0.00013
9070     58      40   End           1.99994   1.99978    0.00016     
9071   TSG003   901   Before start  1.99994   1.99978    0.00016     0.00013
9072   TSG003   901   End           1.99994   1.99977    0.00017     
9073     59      15   End           1.99994   1.99983    0.00011     0.00011
9074     60       1   Before start  1.99994   1.99984    0.00010     0.00016
9075     60       1   End           1.99994   1.99975    0.00019     0.00016
9076     61      24   End           1.99994   1.99977    0.00017     0.00016
9077     62      12   End           1.99994   1.99976    0.00018     0.00016
9078     63      21   Before start  1.99994   1.99975    0.00019     0.00016
9079     63      21   End           1.99994   1.99980    0.00014     
9080     64      19   End           1.99994   1.99978    0.00016     0.00016
9081    200      15   End           1.99994   1.99972    0.00022     0.00020
9082     65      11   Before start  1.99994   1.99984    0.00010     0.00013
9083     65      11   End           1.99994   1.99979    0.00015     
9084     66      40   End           1.99994   1.99979    0.00015     0.00015
9085     67      21   Before start  1.99994   1.99979    0.00015     0.00014
9086     67      21   End           1.99994   1.99980    0.00014     
9087     68      19   End           1.99994   1.99983    0.00011     0.00011
9088     69      12   Before start  1.99994   1.99977    0.00017     0.00017
9089     69      12   End           1.99994   1.99976    0.00018     
9090     70      10   End           1.99994   1.99981    0.00013     0.00013
9091     71      21   End           1.99994   1.99979    0.00015     0.00015
9092   TSG004     1   Before start  1.99994   1.99975    0.00019     0.00014
9093   TSG004     1   End           1.99994   1.99984    0.00010     
9094     72      11   End           1.99994   1.99980    0.00014     0.00014
9095     73      19   End           1.99994   1.99984    0.00010     0.00011
9096     74      12   Before start  1.99994   1.99975    0.00019     0.00016
9097     74      12   End           1.99994   1.99979    0.00015     
9098     75      24   End           1.99994   1.99986    0.00008     0.00010
9099     76      40   End           1.99994   1.99983    0.00011     0.00011
9100     77      10   Before start  1.99994   1.99976    0.00018     0.00016
9101     77      10   End           1.99994   1.99978    0.00016     
9102     78      21   End           1.99994   1.99979    0.00015     0.00015
9103     79       1   Before start  1.99994   1.99977    0.00017     0.00016
9104     79       1   End           1.99994   1.99978    0.00016     
9105     80      15   End           1.99994   1.99978    0.00016     0.00016
9106     81      40   Before start  1.99994   1.99973    0.00021     0.00016
9107     81      40   End           1.99994   1.99980    0.00014     
9108     82      24   End           1.99994   1.99980    0.00014     0.00014
9109     83      21   End           1.99994   1.99982    0.00012     0.00012
9110     84      10   Before start  1.99994   1.99995   -0.00001     0.00012
9111     84      10   End           1.99994   1.99980    0.00014     
9112   TSG005   901   End           1.99994   1.99982    0.00012     0.00012
9113     85      12   Before start  1.99994   1.99978    0.00016     0.00014
9114     85      12   End           1.99994   1.99981    0.00013     
9115     86      15   End           1.99994   1.99979    0.00015     0.00015
9116     87      40   End           1.99994   1.99979    0.00015     0.00015
9117     88      19   Before start  1.99994   1.99980    0.00014     0.00014
9118     88      19   End           1.99994   1.99981    0.00013     
9119     89      11   End           1.99994   1.99975    0.00019     0.00019
9120     90      35   End           1.99994   1.99976    0.00018     0.00018
9121     91      40   Before start  1.99994   1.99972    0.00022     0.00019
9122     91      40   End           1.99994   1.99975    0.00019     
9123     92      10   End           1.99994   1.99976    0.00018     0.00018
9124     93      12   Before start  1.99994   1.99953    0.00041     0.00019
9125     93      12   End           1.99994   1.99975    0.00019     
9126     94      11   End           1.99994   1.99973    0.00021     0.00021
9127     95      19   Before start  1.99994   1.99972    0.00022     0.00020
9128     95      19   End           1.99994   1.99975    0.00019     
9129     96      35   End           1.99994   1.99978    0.00016     0.00016
9130     97      15   End           1.99994   1.99977    0.00017     0.00017
9131     98      12   Before start  1.99994   1.99967    0.00027     0.00017
9132     98      12   End           1.99994   1.99978    0.00016     
9133     99      11   End           1.99994   1.99977    0.00017     0.00017
9134    100      21   Before start  1.99994   1.99973    0.00021     0.00019
9135    100      21   End           1.99994   1.99977    0.00017     
9136   TSG006     1   End           1.99994   1.99973    0.00021     0.00021
9137    101      19   End           1.99994   1.99974    0.00020     0.00020
9138    102      40   Before start  1.99994   1.99975    0.00019     0.00021
9139    102      40   End           1.99994   1.99971    0.00023     
9140    103      11   End           1.99994   1.99977    0.00017     0.00017
9141    104      24   Before start  1.99994   1.99973    0.00021     0.00020
9142    104      24   End           1.99994   1.99975    0.00019     
9143    105      12   End           1.99994   1.99973    0.00021     0.00021
9144    106      10   Before start  1.99994   1.99970    0.00024     0.00023
9145    106      10   End           1.99994   1.99972    0.00022     
9146    107      35   Start/End     1.99994   1.99972    0.00022     0.00022
9147    108      11   Before start  1.99994   1.99976    0.00018     0.00018
9148    109      24   End           1.99994   1.99973    0.00021     0.00021
9149    113      24   Before start  1.99994   1.99967    0.00027     0.00025
9150    113      24   End           1.99994   1.99969    0.00025     
9151    110      12   End           1.99994   1.99977    0.00017     0.00017
9152    111      21   End           1.99994   1.99973    0.00021     0.00021
9153    112      40   Before start  1.99994   1.99968    0.00026     0.00021
9154    112      40   End           1.99994   1.99978    0.00016     
9155   TSG007   901   End           1.99994   1.99973    0.00021     0.00021
9156    114      11   Before start  1.99994   1.99971    0.00023     0.00022
9157    114      11   End           1.99994   1.99973    0.00021     
9158    115      19   End           1.99994   1.99972    0.00022     0.00022
9159    116      24   End           1.99994   1.99974    0.00020     0.00020
9160    117      35   Before start  1.99994   1.99973    0.00021     0.00018
9161    117      35   End           1.99994   1.99978    0.00016     
9162    118      40   End           1.99994   1.99978    0.00016     0.00016
9163    119      10   Before start  1.99994   1.99972    0.00022     0.00020
9164    119      10   End           1.99994   1.99976    0.00018     
9165    120      15   End           1.99994   1.99975    0.00019     0.00019
9166    121      24   Before start  1.99994   1.99969    0.00025     0.00023
9167    121      24   End           1.99994   1.99972    0.00022     
9168    122      21   End           1.99994   1.99970    0.00024     0.00024
9169    123      35   End           1.99994   1.99971    0.00023     0.00023
9170    124      11   Before start  1.99994   1.99965    0.00029     0.00020
9171    124      11   End           1.99994   1.99980    0.00014     
9172    125      10   Before start  1.99994   1.99973    0.00021     0.00021
9173    125      10   End           1.99994   1.99972    0.00022     
9174    126      40   End           1.99994   1.99972    0.00022     0.00022
9175    127      15   End           1.99994   1.99977    0.00017     0.00017
9176    128       1   Before start  1.99994   1.99974    0.00020     0.00016
9177    128       1   End           1.99994   1.99982    0.00012     
9178    129      19   End           1.99994   1.99982    0.00012     0.00012
9179    130      21   Before start  1.99994   1.99972    0.00022     0.00019
9180    130      21   End           1.99994   1.99977    0.00017     
9181    131      35   End           1.99994   1.99981    0.00013     0.00013
9182    132      11   End           1.99994   1.99980    0.00014     0.00014
9183    133      10   End           1.99994   1.99976    0.00018     0.00018
9184   134/35  15/40  End           1.99994   1.99976    0.00018     0.00018
9185   TSG008     1   Before start  1.99994   1.99966    0.00028     0.00026
9186   TSG008     1   End           1.99994   1.99969    0.00025     





4.  INORGANIC AND TOTAL NUTRIENT ANALYSIS
    Sinhue Torres, Laura Casburn, Ekaterina Chernyavskaya, Claire Powell and 
    Helen Smith


4.1.  Method

Seawater was collected for analysis of micro-molar concentrations of 
dissolved nutrients; nitrate and nitrite (hereafter nitrate), phosphate and 
silicate. Samples for inorganic nutrient analysis were collected directly 
into either 30mL plastic pots or 60mL Sterilin pots. 60mL pots were used for 
collection of seawater for total nutrient analysis. The pots were rinsed with 
sample water at least three times before drawing the sample. When required, 
samples were stored in a fridge at approximately 4°C until analysis.

In general analyses were started within 1-4 hours of sample collection using 
a segmented continuous-flow Skalar Sans 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 the reproducibility and peak shape of the results.

For D346 the analysis was calibrated using the set of standards shown in 
Table 4. Table 4 shows target and actual standard concentrations. Target 
concentrations were values that were desired when preparing working standards 
(i.e., standards used everyday). Actual concentrations were values corrected 
by taking into account i) the weight of the dry chemical used to prepare a 
given standard (Table 4) and, ii) the calibrated volume of the pipettes used 
for diluting stock standards (i.e., high concentration standards).

5µmol L(^-1) stock standard solutions prepared in Milli-Q water were used to 
produce working standards. Working standards were prepared in a saline 
solution (40g NaCl in 1L of Milli-Q water, hereafter artificial seawater), 
which was also used as diluent for the analyses.

Total nutrients, total nitrogen (TN) and total phosphorus (TP), were measured 
as nitrate and phosphate, respectively, after photo-oxidation for 2 hours 
using a Metrohm 705 digester (Sanders and Jickells, 2002). The oxidation 
efficiency of the method was monitored using a Guanosine standard at two 
different N and P concentrations; i) 2 and 5µmol L(^-1) nitrogen, ii) 0.4 and 
1µmol L(^-1) phosphorus, which produced i) 2±0.3 and 4.1±0.8 (efficiency 
higher than 80%) and ii) 0.2±0.3 and 0.8±0.2 (efficiency higher than 50%). 
The UV systems were installed inside the fume hood of the chemistry lab and a 
flow meter was attached in order to monitor the water flow for cooling.


Table 4: 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  40.80  2.5  2.54  60   61.22
                 Std 2  20  20.40  2.0  2.03  40   40.81
                 Std 3  10  10.10  1.5  1.52  20   20.41
                 Std 4   5   5.10  1.0  1.01  10   10.20
                 Std 5   1   1.02  0.5  0.51   2.5  2.55


Table 5: Compounds used to prepare stock standard solutions, weight dissolved 
         in 1 L of Milli-Q water and molarity of the solution.

             Compound  Weight (g)  Molarity 1 L stock solution
             --------  ----------  ---------------------------
              KH2PO4     0.6813              5.0064
             Na2SiF6     0.9468              5.0346
              NaNO3      0.4278              5.0332
              NaNO2      0.3493              5.0626



4.2.  Observations (inorganic and total nutrient analysis)

4.2.1.  General observations

Prior to the cruise, all labware was washed with 10% HCl and rinsed with 
Milli-Q water several times. The labware was then rinsed again once onboard 
the ship.

The autoanalyser was washed through with 10% Deacon 90 then Milli-Q water for 
at least 30 minutes respectively after each run when the time between 
stations allowed, otherwise the autoanalyser was left with the reagent tubing 
connected ready for the next run. However, it was noticed that after each 
wash the baseline displayed a slight drift, with a decreasing trend as the 
run progressed. Therefore, the autoanalyser was usually left with the reagent 
tubing connected to avoid this problem. New pump tubing and lamps were fitted 
at the start of the cruise, along with a new cadmium column. After one and a 
half weeks the pump tubing was turned around to prevent the section in the 
pump from wearing out. By two and a half weeks, all tubing and lamps were 
replaced, and the cadmium column was replaced for the second half of the 
cruise. The new tubing was turned around at 5 weeks.

New batches of artificial seawater were prepared almost once a week and 2 
sets of calibration standards were produced and used, with the first used up 
until CTD081 and the second from CTD082. Both artificial seawater and 
standards were analysed prior to use in order to check for contamination and 
consistency.

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 and 
are shown in Figures 14 to 20.


4.2.2.  Autoanalysers

Originally two autoanalysers were set up to allow inorganic and total 
nutrient concentrations to be analysed separately. A second aim for a double 
setup was to test whether both instruments produced results consistent with 
each other. However, there was a communication issue very early on with the 
autoanalyser set up for inorganic nutrient analysis, which caused the 
calibration of nitrate to fail. The computer set for this autoanalyser 
crashed and it required reformatting, which caused the first couple of 
analysis files to be lost. The problem persisted even after the computer was 
reformatted, and it remains unclear whether the problem was related to the 
Flow Access software, a malfunction of the computer communication port, or a 
malfunction of the interface (integrator) between the light detectors and the 
computer. Samples for both inorganic and total nutrient analysis were 
therefore run through the same analyser for most of the cruise period, which 
also contributed to slowing down the turnover of sample processing and 
subsequently, of the results.


4.2.3.  Total Nutrient Analysis

At the start of the cruise all samples from all stations were UV oxidised in 
duplicates. However, since the two UV units were first switched on, they 
started failing, despite being sent to the manufacturer (Metrohm) for 
maintenance prior to the cruise. This delayed the progress of the analysis 
and soon after the Florida Straits transect, these delays resulted in a large 
backlog of samples.

Ideally total nutrients should be analysed together with the respective 
inorganic fraction in the same autoanalyser run, but the large backlog 
prompted us to run all inorganic nutrient samples as soon as possible and the 
total nutrients as soon they became available upon UV oxidation (from Station 
1 to Station 39). This suggested analysing total nutrients in separate runs.

In order to reduce the pressure on the lamps and clear the backlog of 
samples, it was decided to reduce the number of samples being analysed for 
total nutrient concentrations to every third station. From Station 39 and 
starting with Station 42, 1 out of 3 CTD casts were thus sampled for total 
nutrients. Whenever a Niskin bottle misfired, the available space on the UV 
unit racks was used for either a replicate or for the analysis of a Guanosine 
standard.

Once the backlog was cleared and the time between stations increased, it was 
decided that samples for total nutrient analysis should be taken from all 
casts again. However, this was not possible, due to the continuous failure of 
the UV systems.

Repeats of whole profiles were also run for a number of stations to check the 
reliability of the 15V digester units and accuracy of the total nutrient 
concentrations. In the case of total nitrogen, repeats produced similar 
results, mostly within the error of the technique. However, results were not 
always consistent for total phosphorus concentrations. There were cases where 
the first run produced results inconsistent with the inorganic fraction, yet 
the results from the second run were consistent and vice versa. There were 
also cases where both runs produced either consistent or inconsistent results 
relative to the inorganic fraction. This suggests that the methodology may be 
flawed or is subject to error.

4.2.4.  UV systems

UV digesters were unreliable throughout the duration of the cruise. Failure 
was originally due to the units overheating. It was discovered that the flow 
of the cooling system was insufficient to maintain the required temperature. 
Both UV units were initially washed out several times with 4M HCl and rinsed 
with Milli-Q, which improved the flow, indicating that the problem may have 
been accumulation of limescale inside the cooling system. However, the units 
soon became blocked again and so were washed out with 5M H2SO4 followed by 
Milli-Q. This procedure was repeated frequently throughout the cruise to 
maintain a good flow through the cooling system. The pump unit was elevated 
to increase its efficiency. The units were also set to run for 1 hour at a 
time with a minimum of a 30 minutes cooling period between runs, thereby 
further reducing the potential for overheating and loss of the samples. In 
addition to the cooling system, a fan was used to improve airflow inside the 
fume hood and further reduce the potential of overheating.

The original bulbs fused early on and were replaced by brand new bulbs. 
However, the new bulbs also fused within a few uses. The melted end and 
surrounding glass were filed away to expose the undamaged connection wire. A 
copper disc was then placed at the base connection to provide the extra 
height needed for the lamp to reach the upper connection of the lamp unit. 
This fix functioned well, although the copper discs needed replacing every 
couple of days when the lamps were seen to fail more frequently than usual. 
The copper disc oxidised very quickly, most likely due to the high voltage 
passed though it when the unit is switched on. By the start of the fifth week 
of the cruise two of the 15V bulbs were completely fused.

4.2.5.  Performance of the Analyser

The performance of the autoanalyser was monitored by producing time series 
plots of the following parameters: standard concentrations, 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 more than 2 
stations and UV oxidised samples.

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 6 and shown in Figure 16. 
Triplicate analyses were performed on the first, mid and last sample of every 
station. This revealed the sample variability of replicates from a given mean 
concentration, which 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 D346 were 0.09 
µmol L-1 for PO43-, 0.10µmol L-1 for NO3- and 0.14µmol L-1 for Si(OH)4.


Table 6: Means and variations of all the standards measured, and the 
precision of the analysis at each concentration (µmol L-1).

               NO3-      Prec.  PO4(^3-)   Prec.   Si(OH)4   Prec.
             ----------  ----  ----------  -----  ---------  -----  
      Std 1  40.8 ±0.3   0.1%  2.53 ±0.05   1.8%  61.4 ±0.4  0.7%
      Std 2  20.4 ±0.2   0.9%  2.03 ±0.06   3.1%  40.9 ±0.3  0.7%
      Std 3  10.1 ±0.9   8.8%  1.53 ±0.08   5.0%  20.6 ±1.8  8.7%
      Std 4   5.0 ±0.1   1.6%  1.04 ±0.17  16.7%  10.2 ±0.1  0.7%
      Std 5   1.1 ±0.05  4.6%  0.50 ±0.06  12.3%   2.6 ±0.1  2.7%


Figure 14: 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 15: Baselines time series. The baseline for nitrate was fairly 
           consistent all through the cruise. The phosphate baseline changed 
           dramatically after changing the autoanalyser tubing and the 
           silicate baseline shows a slight increased with time.

Figure 16: Calibration slope 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 remain fairly constant with time, with phosphate 
           increasing towards the end of the cruise.

Figure 17: Calibration correlation coefficients. All r2 were better than 
           0.999.


Low Nutrient Seawater: Certified Ocean Scientific International (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.


Figure 18: Low Nutrient Seawater (LNSW) time series. Black dots represent 
           silicate, green dots represent nitrate and grey dots represent 
           phosphate concentrations.

Figure 19: Time series of bulk nutrient seawater (from the South Atlantic 
           Subtropical Gyre) concentrations. The average concentration was 
           -0.14±0.1µmol L(^-1), 1.26±1.2µmol L(^-1), 0.08±0.O8µmol L(^-1) 
           for nitrate, silicate and phosphate respectively. Given the low 
           nutrient concentration of the surface South Atlantic Subtropical 
           Gyre, the negative concentration of nitrate and phosphate 
           indicates this water has less nitrate and phosphate than the 
           background levels of our artificial seawater solution.


Seawater collected in 2009 during the JC032 (24°S) cruise from the surface 
subtropical South Atlantic Ocean (henceforth referred to as Bulk Nutrients) 
was used as an additional 'Low Nutrient' standard. The purposes of measuring 
bulk nutrients are i) to test for the consistency of low nutrient 
measurements throughout the cruise and ii) to test artificial seawater (ASW) 
batches for contamination (i.e. by comparing these with the baseline produced 
by ASW).


Figure 20: 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). This figure 
           shows the ratio of nitrate to nitrite for all analysis carried 
           out. The nitrate standard though, was slightly lower than 
           targeted, with an average concentration of 39.4µmol L-1.





5.  DISSOLVED OXYGEN
    Sinhue Torres, Laura Casburn, Ekaterina Chernyavskaya, Claire Powell and 
    Helen Smith


All stations occupied during D346 were sampled for dissolved oxygen (DO) just 
after CFCs were sampled. Seawater was collected directly into pre-calibrated 
glass bottles using a Tygon® tube. Before the sample was drawn, the bottles 
were flushed with seawater for several seconds (for about 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, and a water 
seal was used after the sample was fixed. Samples were thoroughly mixed 
following the addition of the fixing reagents and were then kept in a dark 
plastic crate for 30-40 min 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 2 hours of sample collection.


5.1.  Methods

DO determinations were made using a Winkler -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 previously 
prepared 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 week 
using a 1.667µmol L-1 certified OSIL iodate standard. Calibration values are 
summarised in Table 7 and shown in Figure 21. Thiosulphate solutions were 
prepared by dissolving 50g of sodium thiosulphate in IL of Milli-Q water. 
These solutions were left to stabilise for 24 hours and a new calibration was 
carried out before using it. Calculation 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 
pipettes' calibrated dispensing volumes (i.e., reagents and iodate standard 
additions have been calibrated). Figure 22 shows a time series of replicates.


5.2.  Observations

1. In general, replicate measurements of selected samples were carried out in 
order to test for reproducibility. At least one Niskin bottle was always 
sampled in duplicate, typically the deepest Niskin bottle. Any misfires were 
used to duplicate further Niskin bottles. The mean difference between 
replicates was 0.4±0.3µmol O2 L-1, results are shown in Figure 22.

2. In many cases the first oxygen measurement produced lower concentrations 
than expected (e.g., relative adjacent samples or replicate). In order to 
avoid this problem, a dummy sample was run previous to the analysis of 
samples. It seems the electrode needs to stabilise for some seconds inside 
the solution of seawater with the three different reagents mixed. It was also 
observed, that leaving the electrode inside the sample for some seconds 
before starting a titration also produced good results.

3. In addition to showing calibration results, Table 7 also indicates the 
station numbers where a given calibration was used to calculate oxygen 
concentrations. Three stocks of thiosulphate were prepared during the cruise 
(also shown in Table 5).


Table 7: D346 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).

  Calibration     Date      BLK     STD     STD-   Thiosulphate  Used from
    number                  (mL)    (mL)    BLK      Molarity     CTD No.
  -----------  ----------  ------  ------  ------  ------------  ---------
      1*       05/01/2010  0.0015  0.2556  0.2541     0.3970         1
      2        11/01/2010  0.0022  0.2558  0.2536     0.3977        26
      3        18/01/2010  0.0019  0.2558  0.2539     0.3972        51
      4*       21/01/2010  0.0017  0.2567  0.2550     0.3956        59
      5        28/01/2010  0.0021  0.2560  0.2539     0.3973        76
      6*       06/02/2010  0.0011  0.2552  0.2541     0.3970       103
      7        13/02/2010  0.0016  0.2552  0.2536     0.3977       124


Figure 21: Calibrations for dissolved oxygen analysis. Blank volume titre 
           (upper panel), standard volume titre, standard minus blank (middle 
           panel) and thiosulphate molarity (lower panel). Black lines 
           indicate when a new solution of thiosulphate was prepared. Values 
           plotted here are shown in Table 7.

Figure 22: The absolute replicate difference for oxygen bottles in each CTD 
           cast. The mean (0.4µmol L-1) and the standard deviation (±1) are 
           specified with solid and dash lines respectively. Black symbols show 
           replicate values flagged as good and red symbols show all data, 
           included values flagged as dubious or bad.


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





6.  INORGANIC CARBON
    Ute Schuster, Arie Louwerse, Gareth Lee and Ollie Legge


The carbon parameter analytical equipment 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).


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 
Niskin bottles on the 24 Niskin CTD rosette and collected in 500m1 and 250m1 
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). Samples were 
stored in the dark until they were put into a 25°C water bath to bring the 
sample to an ambient temperature prior to analysis. In addition to station 
samples, 125 samples were taken for secondary standards from Stations 83, 85, 
and 86 and 2 stations used for tracer testing (Stations 200 and 202). Samples 
for DIC and TA were not taken from all depths at each station. Generally, 16 
depths were sampled from each station, including the shallowest and deepest 
Niskins with the other depths selected to allow for optimum interpolation 
across the section. Initially, every station was sampled in 500ml bottles. 
However, this strategy proved unsustainable, as analysis could not keep pace 
with the frequency of the sampling. Therefore, from Station 34 until Station 
129, every third station was sampled in 250m1 bottles and initially stored. 
Stations sampled in 500m1 bottles were analysed as a priority and once 
profiles for these stations had been obtained, selected 250m1 bottles were 
analysed in order to strengthen areas of missing or suspect data. Whereas 
500m1 bottles allow both DIC and TA to be measured twice per sample (thereby 
providing information on the precision of measurements), 250m1 bottles only 
allow one DIC and one TA measurement per sample. Therefore, four Niskins at 
each of the stations sampled with 250m1 bottles were sampled in duplicate to 
provide a measure of consistency. Figure 23 shows the depth-longitude grid of 
samples analysed for DIC and TA during D346, for which values of both DIC and 
TA were available after the first shipboard quality control (1st QC).

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.

DIC analysis was performed using two Versatile INstrument for the 
Determination of Titration Alkalinity (VINDTA version 3C, Marianda, Germany, 
SN # 004 and # 007, Mintrop, 2004), each connected to a coulometer (UIC, USA, 
model 5011). Samples were brought to 25°C prior to analysis, and the pipette 
(volume approximately 20m1), has a water jacket around it, keeping it at 
25°C. Two replicate analyses were made on each 500 ml sample bottle and the 
coulometer counts were calibrated against Certified Reference Material (CRM, 
batch 97).


Figure 23: Depth-longitude grid of samples analysed for DIC and TA during 
           D346, for which values of both DIC and TA were are available after 
           shipboard first quality control (1st QC).


On 28th January, valve 11 on VINDTA #007 started leaking and had to be 
replaced, which affected the calibrated volume in the DIC pipette. The DIC 
pipette, having started to hold back drops of seawater on the inside, was 
also replaced and the volume of the new pipette was measured by dispensing 
Milli-Q water from the pipette into 15 pre-weighed vials for weighing at the 
UEA. Between 5th and 7th February there was considerable downtime on VINDTA 
#007 due to electrical/mechanical problems. The fault was traced to a printed 
circuit board, which was replaced and sample analysis was resumed on 8th 
February 2010 (post-cruise QC will include the apparent shift in TA 
calibration on #007, see Figure 24(b)). Analysis was also interrupted on 
several occasions by power-cuts in the container.

Initial DIC calibration was done during the cruise for each instrument by 
correcting all sample data by the difference between the mean of all CRM 
measurements and the certified reference value of CRM batch 97 (2002.52µmol 
kg-1; preliminary value in September 2009). Figure 24 shows these calibrated 
CRM values for (a) VINDTA #004 and (b) VINDTA #007, together with the mean, 
control limits and warning limits (Dickson et al., 2007). Whole-cruise CRM 
values varied by ±3.0[µmol kg-1 for VINDTA #004 and by ±3.lµmol kg-1 for VINDTA 
#007 after on-board 1st QC.


Figure 24 (a): Calibrated CRM-DIC values for the VINDTA #004, showing the 
               mean, control limits and warning limits.

Figure 24 (b): Calibrated CRM-DIC values for the VINDTA #007, showing the 
               mean, control limits and warning limits.


The differences between replicates of all samples analysed for DIC are shown 
in Figure 25 (a) for the VINDTA #004 and (b) for the VINDTA #007. The mean 
difference was 0.6µmol kg-1 and the precision was 1.9µmol kg-1 for the VINDTA 
#004, whilst the mean difference was 0.6µmol kg-1 and the precision was 
2.4µmol kg-1 for the VINDTA #007.


Figure 25 (a): Mean DIC difference and precision for the VINDTA #004.

Figure 25 (b): Mean DIC difference and precision for the VINDTA #007.


Post-cruise data quality control will include calibration of the DIC readings 
for each coulometer cell used during D346, 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 (model 3C, S/N #004 and #007) 
(Mintrop, 2004). The systems use a highly precise Metrohm Titrino for adding 
acid, an ORION-Ross pH electrode, a Metrohm reference electrode, and an 
auxiliary electrode. The pipette (volume approximately 100 ml), and the 
analysis cell have a water jacket around them, keeping them at 25°C. The 
titrant (0.1M hydrochloric acid, HCl) was made in the home laboratory; batch 
A used throughout the cruise. Replicate analyses were run for 500 ml samples 
brought to 25°C. Alkalinity values were calibrated using CRM batch 97 
(certified at 2210.5µmol kg-1, preliminary values September 2009).

As previously mentioned, between 5th and 7th February there was considerable 
downtime on VINDTA #007 due to electrical/mechanical problems. The fault was 
traced to a printed circuit board, which was replaced and sample analysis was 
resumed on 8th February 2010 (post-cruise QC will include the apparent shift 
in TA calibration on #007, see Figure 24(b)).

Figure 26 shows alkalinity CRM values recorded by (a) VINDTA #004 and (b) 
VINDTA #007, showing a whole-cruise variation of ±2.1µmol kg-1 on VINDTA #004 
and ±3.1µmol kg-1 on VINDTA #007 after on-board 1st QC

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 QC will then include 
identifying and removing further outliers, and accounting for drift in the 
instruments' alkalinity, especially the apparent drift in TA calibration on 
#007 after 8th Feb 2010.


Figure 26 (a): Calibrated CRM-TA values for VINDTA #004. Mean, control and 
               warning limits.

Figure 26 (b): Calibrated CRM-TA values for the V1INDTA #007, showing the 
               mean, control limits and warning limits.


The differences between replicates of all samples analysed for alkalinity are 
shown in Figure 27, (a) for the VINDTA #004 and (b) for the VINDTA #007. For 
the VINDTA #004 the mean difference was -0.2µmol kg-1 and the precision was 
1.3 µmol kg-1, whilst for the VINDTA #007 the mean difference was -0.1 µmol kg-
1 and the precision was 1.l µmol kg-1.


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. 1 91

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.I., and Braendstroem, 
    L. (1987), Coulometric total carbon dioxide analysis for marine studies: 
    automation and calibration, Marine Chemistry, 21, pp. 117133

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


Figure 27 (a): Mean TA difference and precision for the VINDTA #004.

Figure 27 (b): Mean TA difference and precision for the VINDTA #007.





7.  CHLOROFLUOROCARBONS AND SULPHUR HEXAFLUORIDE MEASUREMENTS
    Marie-José Messias, Andrew Brousseau, Peter Brown, and Stephen Woodward


7.1.  Sample collection

As per WOCE protocol, seawater sample for Chlorofluorocarbons (CFCs) and 
Sulphur Hexafluoride (SF6) measurements were the first samples drawn from the 
Niskin bottles.

The Nitrile 'O' rings of the Niskins were washed in isopropanol and baked in 
a vacuum oven for 24 hours prior to the cruise. The trigger system of the 
bottles was external stainless steel springs. Water samples were collected in 
500 ml ground glass bottles. The bottles were rinsed with sample water, then 
filled from the bottom using Tygon® tubing. The bottles were overflowed at 
least twice before being stoppered and then stored in cool boxes containing 
seawater close to their sampling temperature (13°C, 16°C and 20°C) until 
analysis was performed.

For air sampling, a ¼ inch OD Dekabon tubing was run from the analysis system 
to the mast of the ship. The air was pump through the line using a DA1 SE 
Charles Austen pump.


7.2.  Equipment and technique

The samples were analyzed using an automated coupled CFC-SF6 purge and trap 
system developed and built at the University of East Anglia from a design 
proposed by Bill Smethie [LDEO, 2004, personal communication]. This system 
has the advantage of simultaneous analysis of SF6 and four 
chlorofluorocarbons, namely CFC-11, CFC-12, CFC-113, CCl4 (carbon 
tetrachloride also classified as CFC-10) from the same water sample.

The system combines the LDEO CFC method (W. Smethie et al., 2000) and the PML 
SF6 method (Law et al., 1994) with a common valve for the introduction of 
water samples. 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 a 
separate purge and trap circuit. Each purge and trap circuit was interfaced 
with an Agilent 6890 gas chromatograph equipped with an electron capture 
detector (GC-ECD). The compounds were extracted from the water by passing N2 
through the sparging chambers and then transferred at 85m1 mn-1 to a Unibeads 
trap at -100°C for the CFCs and at up to 120m1 mn-1 to a Porapak Q trap at 
-80°C for the SF6. The headspace of liquid nitrogen was used to cool the 
traps. After 4 mins (3 mins for SF6) of sparging, the traps were heated to 
100°C for the CFCs and 65°C for SF6 and injected into the respective gas 
chromatograph. The separation of the various CFCs was achieved using a 1m 
Porasil B packed pre-column and a 1.5m carbograph AC main column. The SF6 
separation was achieved using a molecular sieve packed 2m main column and 2m 
buffer column. The carrier gas was pure oxygen-free nitrogen, which was 
cleaned by a series of purifiers.


7.3.  Calibration

The CFCs and SF6 concentrations in air and water were calculated using an 
external gaseous standard. The standard supplied by NOAA (Brad Hall, December 
2009) corresponds to clean dry air slightly enriched in SF6, CFC-11 and CCl4 
in 29L Aculife-treated aluminum cylinders (SN AAL-072073). 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 28. Calibration curves were made 
approximately every 2 days whereas the changes in the sensitivity of the 
system was checked by measuring a fixed volume of standard gas every 8 runs 
(Figure 29). The temporal drift of the ECD between two calibration curves was 
assumed to be linear in time. Particular difficulty was noted for CCl4, where 
significant variation in standards was noted. In this report, dissolved CFCs 
and SF6 are given in units of [pmol/l] and [fmol/l] respectively, calibrated 
on the NOAA 2009 scale. The final data set will be converted to mol/kg on the 
SIO-98 scale using NOAA's comparison tables.


7.4.  Precision and accuracy

7.4.1.  Precision or reproducibility

The precision of the measurements can be determined from duplicate samples 
drawn on the same Niskin bottles. 80 duplicate samples were analysed, from 
which we calculated the following precision, expressed as the square root of 
the variance of the duplicates differences.


Table 8: CFC precision table

             SF6      ±1.05%         for surface values
                      ±0.011 fmol/l  for values < 0.1 fmol/l
             CFC-12   ±0.95%         for surface values
                      ±0.003 pmol/l  for values < 0.1 pmol/l
             CFC-11   ±1.1%          for surface values
                      ±0.006 pmol/l  for values < 0.1 pmol/l
             CFC-113  ±1.5%          for surface values
                      ±0.001 pmol/l  for values < 0.1 pmol/l
             CCl4     ±3%            for surface values
                      ±0.015 pmol/l  for values < 0.3 pmol/l


7.4.2.  Test stations and sample blank correction

The sample blank includes Niskin bottle blanks and other blanks associated 
with transferring, storing and analyzing the sample. This blank is best 
determined from analyses of CFC-free water. In order to assess the sample 
blank we tripped all the bottles in the lowest CFC water found of the two 
major basins crossed along the cruise-tract, respectively at 6300m in the 
western basin (Table 9, test Station 200) and at 3500m in the eastern basin 
(Table 10, test Station 202). We also took samples from a Niskin bottle 
sparged with nitrogen for up to 30 hours, until concentrations had reached a 
steady-state value (Table 11). The comparison of the station tests with the 
samples from the sparged Niskin test shows that:

1- The CFC concentrations from test Station 200 are too high; the water 
   appears to contain CFCs and those results are therefore not considered as 
   a blank.

2- The CFC concentrations from test Station 202 are reasonably closed to the 
   concentrations from the sparged Niskin test and those results are 
   therefore considered as the blank concentration for the full cruise.


Table 9: Results of the test Station 200.

              Niskin    SF6      F12     F11    F113    CCl4
              -------  ------  ------  ------  ------  ------
                 1     0.016   0.0726  0.1102  0.0152  0.5270
                 2     0.016   0.0637  0.1018  0.0143  0.5128
                 3     0.016   0.0728  0.1102  0.0150  0.5299
                 4     0.016   0.0676  0.1093  0.0147  0.5217
                 5     0.016   0.0651  0.1076  0.0124  0.5120
                 6     0.027   0.0643  0.1003  0.0129  0.4882
                 7     0.016   0.0624  0.1041  0.0120  0.4511
                 7     0.011   0.0624  0.0981  0.0113  0.3958
                 8     0.027   0.0671  0.1111  0.0137  0.4293
                 9     0.027   0.0699  0.1104  0.0141  0.4322
                10     0.027   0.0677  0.1126  0.0145  0.4054
                11     0.033   0.0665  0.1074  0.0121  0.4068
                12     0.016   0.0658  0.1080  0.0118  0.4313
                13     0.016   0.0643  0.1083  0.0116  0.4420
                14     0.032   0.0711  0.1111  0.0124  0.4207
                15     0.032   0.0693  0.1104  0.0126  0.4752
                15     0.006   0.0682  0.1045  0.0131  0.3645
                16     0.018   0.0714  0.1134  0.0137  0.4068
                17     0.011   0.0655  0.1057  0.0125  0.3926
                18     0.024   0.0714  0.1119  0.0127  0.4312
                19     0.017   0.0695  0.1104  0.0142  0.4127
                20     0.033   0.0631  0.1042  0.0118  0.4097
                21     0.009   0.0690  0.1127  0.0137  0.4264
                22     0.031   0.0706  0.1127  0.0158  0.3938
                23     0.015   0.0682  0.1065  0.0123  0.3646
                24     0.027   0.0683  0.1099  0.0121  0.4356
              -----------------------------------------------
              AVERAGE  0.0205  0.0676  0.1082  0.0133  0.4363
              STDEV    0.0082  0.0032  0.0042  0.0013  0.0477


Table 10: Results of the test Station 202. The average and standard deviation 
          of CCl4 does not include the anomalously high concentration from 
          Niskin 4.

              Niskin    SF6      F12     F11    F113    CCl4
              -------  ------  ------  ------  ------  ------
                 1     0.000   0.0083  0.0165  0.0056  0.0600
                 1     0.000   0.0107  0.0163  0.0050  0.0504
                 2     0.009   0.0124  0.0185  0.0069  0.0569
                 3     0.014   0.0092  0.0174  0.0043  0.0493
                 4     0.000   0.0086  0.0189  0.0079  0.2444
                 5     0.000   0.0055  0.0139  0.0055  0.0562
                 6     0.009   0.0074  0.0114  0.0052  0.0457
                 7     0.000   0.0074  0.0118  0.0053  0.0464
                 8     0.000   0.0071  0.0130  0.0049  0.0428
                 9     0.000   0.0060  0.0120  0.0040  0.0490
                10     0.000   0.0074  0.0112  0.0061  0.0401
                11     0.009   0.0072  0.0123  0.0051  0.0446
                12     0.000   0.0069  0.0114  0.0048  0.0421
                13     0.000   0.0102  0.0127  0.0059  0.0439
                14     0.014   0.0083  0.0128  0.0039  0.0497
                15     0.014   0.0086  0.0153  0.0054  0.0499
                16     0.005   0.0099  0.0146  0.0052  0.0457
                17     0.000   0.0081  0.0130  0.0058  0.0378
                18     0.000   0.0078  0.0120  0.0028  0.0354
                19     0.000   0.0085  0.0117  0.0034  0.0417
                20     0.000   0.0072  0.0137  0.0048  0.0403
                21     0.000   0.0064  0.0128  0.0050  0.0320
                22     0.000   0.0088  0.0139  0.0039  0.0385
                23     0.000   0.0094  0.0156  0.0040  0.0446
                24     0.000   0.0100  0.0170  0.0037  0.0446
              -----------------------------------------------
              AVERAGE  0.0032  0.0082  0.0138  0.0051  0.0453
              STDEV    0.0053  0.0016  0.0023  0.0011  0.0067
              
              
Table 11:  Concentrations over time of the sparged Niskin test.

             SAMPLING TIME   SF6    F12     F11    F113    CCl4
           ----------------  ---  ------  ------  ------  ------
           10/02/2010 08:00   0   0.0097  0.0179  0.0041  0.0549
           10/02/2010 13:00   0   0.0102  0.0161  0.0047  0.0383
           10/02/2010 18:00   0   0.0114  0.0192  0.0068  0.0264
           11/02/2010 08:00   0   0.0114  0.0217  0.0049  0.0394
           AVERAGE            0   0.0107  0.0188  0.0051  0.0398
           STDEV              0   0.0009  0.0024  0.0012  0.0118


7.4.3.  Sparging efficiency

The sparging efficiency was evaluated by re-stripping high concentration 
surface water samples and comparing the residual concentrations to the 
initial concentrations. The re-sparge values were approximately <2% of the 
initial sample concentration for CFC-12 and CFC-11 and below <7% for CFC-113 
and CCl4 for a sparging of 4 min at 85 mL/min. The SF6 re-sparge value was 
zero for a 3 min sparging going up to 120mL/min. A fit of the re-sparging 
efficiency as a function of temperature and flow rate will be applied to the 
final data set.



7.5.  Data

The contour plots for all 5 tracers are presented in Figure 30. A small 
number of water samples with anomalously high concentrations relative to 
adjacent samples are included in the sections but are given a quality flag of 
3 or 4 in the data set. When not associated with anomalies in other 
parameters, it suggests that these samples were probably contaminated with 
CFCs during the sampling or analysis processes. This affected more often 
CFC-113 and CCl4. Note that CFC-113 and CCl4 were mostly not measured in the 
200-500m depth range to save on analytical time.

As expected, the sections show high concentrations for all five tracers at 
the surface and within the North Atlantic Deep Water in the Western Basin. A 
puzzling feature is the high core of SF6 above the Mid-Atlantic Ridge centred 
around 1500m, which is not associated with a CFC maximum. Another interesting 
feature is the invasion of CCl4 in the deep eastern basin.


Figure 28: Example of calibration curves.

Figure 29: Sensitivity of the system over time expressed as the area divided 
           by the amount of standard injected into a 1ml loop.

Figure 30: Countour plots of CFC-11, CFC-12, CFC-113, CCl4 and SF6 data from 
           the main D346 24N transect.



7.6.  References

Law C.S., Watson A.J. and Liddicoat MI. (1994), Automated vacuum analysis of 
    sulphur hexafluoride in seawater: derivation of the atmospheric trend 
    (1970-1993) and potential as a transient tracer, Marine Chemistry, 48, 
    pp. 57-69.

Smethie, W. M., Schlosser Jr., P., Bönisch G., and Hopkins T. S. (2000), 
    Renewal and circulation of intermediate waters in the Canadian Basin 
    observed on the SCICEX 96 cruise, I Geophys. Res., 105(C1), 1105-1121.






8.  COMPUTING, SEA-SURFACE AND METEOROLOGICAL INSTRUMENTATION
    Paul Duncan


8.1.  Primary Logger - hardware and software

As in earlier cruises, the primary data logging is performed by IFREMER's 
TECHSAS data logging system.

At present the operating system is the third release of Red Hat's Enterprise 
Linux Workstation product. The reason for using this old version of the 
operating system is that the kernel it uses supports the National Instruments 
PCI serial cards used by the systems.

Chris Barnard has been doing some research with later kernels, and has also 
been communicating with National Instruments about the issue, and we hope to 
have a newer operating system, along with upgraded motherboards, processors, 
RAM in use in the near future. We are also hoping to switch over from an 
IDE-based hardware RAID solution, to one based on SATA drives.


8.2.  Level C

The Level C software is still running on a Sun Blade 1500 SPARC-based 
workstation. The fromtechsas program is used to take data broadcast by the 
TECHSAS system over the ships' LAN, and then save it in individual data 
streams, which can then be examined in the graphical data editor, and/or have 
processing performed on them.

During the cruise, the graphical data editor was used to remove the worst of 
the spikes (including zero values) from the EA-500 bathymetry data, and the 
prodep program was then used to correct it for Carter Area. The 
relmov/bestnav navigation processing software was also run to create the 
bestnav and bestdrf streams. Finally the windcalc program was run to 
calculate the absolute wind speed and direction.


8.3.  CLAM

The CLAM system, used to monitor and record data from the ships' winches, 
failed on the evening of Friday, 8th January.

Initial investigations revealed that the system's 3.4GB hard drive had 
failed. After all efforts to recover data from the drive had failed, the top 
was removed, and the drive head could be seen repeatedly traveling rapidly 
from the innermost area of the drive surface, to the outermost area.

Another CLAM system was located in the tape store, but unfortunately it was 
not identical to the system that had been in use. It had been used on RRS 
Charles Darwin, and had not been modified since. Therefore it had the wrong 
version of the CLAM software, and could not be used to monitor the winch 
systems on RRS Discovery. It also had only a third of the RAM of the RRS 
Discovery CLAM system.

A version of the CLAM software was sent out from NOCS, and loaded onto the 
SBWR computer. A 4-port USB-serial converter was used to provide the 
necessary serial ports. We were unable to make this software read the data 
coming from the winch system.

Eventually, a system was cobbled together by taking the computer from the 
PSO's cabin, an Edgeport 4-port USB-serial converter. The computer's original 
hard disk was removed, and a spare hard drive (kept onboard for the TECHSAS 
systems) was put in its place. Ubuntu Linux was loaded, along with a terminal 
emulation program called Minicom.

Minicom was used to set the baud rate, parity, handshaking etc. on each port 
that the system needed to use. This was basically a cheat, to ease the 
programming load - the programs would simply use the serial ports in their 
last-used configuration.

It had been determined, through looking at the CLAM documentation and 
examining the CLAM code, that the Caley winch system was polled for data by 
sending an "5" character at 19,200 baud, about once every 200ms. Initially a 
shell-script was written that simply sent S characters to the serial port 
every second, whilst in a second terminal the UNIX tail -f command was used 
to read the responses from the winch. An example of these responses is shown 
below:

    $CTD3, .69, 1 224, 52.0385, 0,
    $CTD3, .68, 1 223, 52.0385, 0,
    $CTD3, .67, 1 222, 52.0385, 0,
    $CTD3, .66, 1 221, 52.138,  0,
    $CTD3, .67, 1 220, 52.0385, 0,
    $CTD3, .68, 1 220, 52.0385, 0,

Eventually a small C program was written to poll the winch at 200ms, read the 
date/time from the clock port, and write these data to the standard output, 
and also simulate the SMP message, which was sent to the TECHSAS logger. The 
output of this program was piped through the UNIX tee program to enable the 
winch data to be saved to the local hard disk, and also to some online disk 
storage.

The principal scientist wrote a program in Matlab, running on his NOSEA1 Sun 
workstation that read the data from the online storage area and used it to 
generate a CLAM-like display on the PC. The video output from this PC was 
then hooked up to the video distribution system so that the winch cab and 
bridge had a good visual and numerical representation of the winch load, and 
also access to the wire-out and rate data.


8.4.  Surfmet

The Surfmet system is used to log the following instrumentation:

• Seabird 45 (TSG) and Seabird 38 (sea surface temperature)
• WET Labs Fluorometer
• WET Labs Transmissometer
• Gill Windsonic sonic anemometer
• Vaisala HMP45 temperature/humidity sensor
• Vaisala PTB 100A air pressure sensor
• 2 x Kipp & Zonen CMB6 total irradiance sensors
• 2 x Skye Photosynthetically Active Radiation (PAR) sensors

The Surfmet system provides an easy way to check on these instruments, with 
both graphical and numerical displays. In addition it also timestamps the 
data and sends it to the TECHSAS data loggers.


8.5.  Simrad EA-500 Echo Sounder

Despite its age, this system worked fairly well until one of the transducers 
was improperly connected when switching over between the fish and the hull 
transducers. We initially thought that the transceiver board might have been 
blown, but after lots of playing around it came back to life.

The fish seems to be a little nose heavy, despite moving the weight in the 
tail boom fully aft. This caused problems with achieving good bathymetry data 
whilst the vessel was on station, and meant it was necessary to change over 
the transducers when arriving on and departing from stations.


8.6.  Chernikeeff EM Log

For the past two cruises the EM Log has been reading quite high at the top 
end of the speed range.

The scientific party used the data from the ships' ADCP systems to derive new 
calibration data for the Chernikeeff. Once these were entered, the log gave a 
much more believable speed.


8.7.  Printing

Both HP LaserJet 2605dn printers performed faultlessly throughout the cruise, 
with the only problem being a shortage of A4 paper towards the end of the 
cruise. Thankfully the UEA CFC team kindly donated three bags of paper, which 
helped a lot.

The DeskJet 1220C was only used briefly and worked fine, except that the 
colour cartridge ran out. The only other working colour cartridge on board 
was found in the other DeskJet l220C in the technician's office.

When the DeskJet l220C was found to be short of ink, an attempt was made to 
use the DesignJet 1055CM. Unfortunately this developed a fault in detecting 
the magenta ink cartridge. However, on 18th February it was turned on just to 
verify which ink cartridge was causing the problem, but was found to be 
working. Prior to this, this particular plotter must have been power cycled 
over a dozen times - some of them by the Master, who has used this plotter a 
lot in his previous post on cable ships. The plan is still to have it looked 
at by an HP service engineer during the coming rest period.


8.8. Backups

Two backups were performed every day. Firstly the Level C and TECHSAS files 
were backed up on the Level C's directly connected LTO2 drive. Secondly, the 
NOSEA1 workstation was backed up over the network to a second LTO2 drive 
connected to the discovery3 workstation. Unfortunately, towards the end of 
the cruise, the LTO2 drive on discovery3 started to generate errors during 
the write process, even when the cleaning tape, and re-tensioning of the data 
tape were used. The intention is to replace this drive with a spare.





9.  LOWERED ACOUSTIC DOPPLER CURRENT PROFILER (LADCP)
    Gerard McCarthy


9.1.  Instrument Setup and Performance

Three RDI 300kHz Workhorse LADCP units were available on D346: one aluminium 
cased unit and two titanium-cased units. The LADCP was configured to have a 
standard 16 x 10 m bins, and to ping in water track mode. There was also a 5m 
blank at the surface. Data were collected in beam co-ordinates and rotated to 
earth co-ordinates in post-processing. The instruments were mounted in a 
downwardlooking orientation on the CTD frame.

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.

The cruise began with the aluminium-cased unit mounted on the CTD frame. This 
instrument performed well. All beams were correlated and of similar strength 
(Figure 31). On cast 21, the instrument stopped and restarted itself halfway 
up the upcast, which led to two files for this station. Concatenating the two 
files together and then processing normally successfully processed these 
files. This instrument was removed after Station 63 as casts 64 - 69 were all 
deeper than 6000m and the LADCP is not depth rated beyond this depth.

At cast 70, the aluminium unit was replaced with one of the titanium-cased 
units, S/N 13399 (Figure 31). This unit was found to have one beam with a 
much greater strength than the others, however correlation between the beams 
was good. This unit failed on cast 72.

Another titanium-cased unit, S/N 13400, replaced it. This unit was found to 
have one beam weaker than the others. This beam was also not correlated with 
the others (Figure 31). In spite of this, this unit produced good data. It 
was replaced before Station 114 when the original instrument was put onto the 
frame again.


9.2. 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 
/Drobo/D346/LADCP.

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

Data were collected in beam coordinates, as this is the recommended method of 
collection. The UH software handled this format with no modifications. The 
LDEO software required an updated version of their loadrdi.m program.

All the processing for the LADCP was carried out on the NOSEA1 Linux 
terminal.

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

9.2.1.  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 ~/cruise/data/ladcp/uh, source LADall 
    sets up the paths required for the processing.
 2. cd proc/Rlad; linkscript creates symbolic links from the binary *.000 
    files to the real raw file. As processing was performed on the local disk 
    of NOSEA1, the raw files were copied from the network and symbolic links 
    were created to the required filenames. The UH software requires a 
    filename of d_NNN_02.000, where NNN is the station number. The LDEO 
    software requires a filename of D346_NNNm.000. The suffix 02 refers to 
    the LADCP being down-looking.
 3. cd proc; perl -S scan.prl NNN_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/upcast times) agree approximately with the CTD logsheet.
 4. matlab; m_setup; putpos(NNN,02) gets position of the cast by accessing 
    the TECHSAS data streams. magvarsm(NNN.02) applies the magnetic 
    correction to the compass on the LADCP. Quit Matlab.
 5. perl -S load.prl NNN_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/dNNN_02/scdb) must be deleted first.
 6. perl -S domerge.prl -c0 NNN_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. cd Rnav; matlab; make sm makes a smoothed navigation file for the cast. 
    Quit Matlab.
 8. cd proc; matlab; plist = NNN.02; do_abs; calculates the 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).

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 cd proc; cd Rctd 
    and open a Matlab session. Run m_setup and the script mk_ctdfile(NNN). 
    Quit Matlab.
10. cd proc/Pctd; ctd_in(NNN,02) will read the 1Hz CTD data in. plist=NNN.02; 
    fd aligns the LADCP and CTD data sets in time. Quit Matlab.
11. cd proc; perl -S add_ctd.prl NNN_02 adds the CTD data to the *.blk LADCP 
    files in the scdb directory.
12. perl -S domerge.prl -c1 NNN_02 merges the single pings into corrected 
    shear profiles. The -cl option now states that we have included CTD data.
13. matlab; plist=NNN.02; doabs; calculates the velocities again with the 
    merged pings.

9.2.2.  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. cd ladcp; cd ldeo/di1001; 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.

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 the 
LDEO and UH processing paths and when CTD data are available the processing 
will automatically use it.

The LDEO processing extracts the useful bottom track velocities. These 
velocities were not used to constrain the full velocity profile but existed 
as a method of verifying the reality of the near bottom velocities calculated 
by the standard LDEO inverse calculation.

The LDEO processing also extracts an estimate for the full ocean depth by 
combining the bottom ping with the CTD data. This was used to add to the 
headers of the CTD data. It was also used to add a better estimate of the 
full ocean depth to the proc.dat file in the proc/ directory. The domerge -c1 
and the do_abs steps of the UH processing were rerun with this new proc.dat 
file to cut out sub-bottom pings.


9.3.  M* Formatting

The data from both processing routes were read into M* files. Three M* files 
were created for each station: one for the UH profile, one for the full LDEO 
profile and one for the LDEO bottom track velocities. Three files were 
produced for ease of gridding. Figure 32 shows the gridded velocities from 
the LADCP through the Florida Straits.


9.4.  Data Quality

Three main categories of profiles were observed. The first, evident in the 
survey of the Florida Straits and early profiles in the west of the section, 
was of the LDEO, UH, bottom track and VMADCP profiles all matching (Figure 
33, top). Secondly, as the section moved over the abyssal plain and 
scatterers in the deep ocean diminished, profiles began to disagree (Figure 
33 centre). Often the LDEO and UH would give different answers in the upper 
ocean and neither would agree with the bottom tracking velocities. The VMADCP 
was seen to agree more often with the UH software. Thirdly, using the third 
LADCP instrument which had a weak beam, the UH profile would drop out between 
1000 and 1500 m (Figure 33, bottom). The LDEO gave a full profile but with 
often wild velocities of up to two or three metres per second. These profiles 
never agreed with the bottom track velocities. The VMADCP agreed much better 
with the UH processed data.


Figure 31: Instrument performance of the three LADCPs used on D346. From the 
           top, the first instrument had four beams of similar strength and 
           close correlation. The second had one beam stronger than the 
           others but retained close correlation. The third had one beam 
           weaker than the others and this beam had poor correlation with the 
           other beams.

Figure 32: Gridded velocities through the Florida Straits from the UH 
           software (upper) and the LDEO software (lower).

Figure 33: Three profiles illustrating different behaviour of the LADCPs used 
           on D346: (top) Station 008, (centre) Station 039 and (bottom) 
           Station 085.





10.  UNDERWAY TEMPERATURE, SALINITY, FLUORESCENCE & TRANSMITTANCE
     Chris Banks and Helen Pillar


10.1.  Instrumentation

Near surface temperature, salinity, fluorescence and transmittance were 
measured throughout the cruise by instruments located in the non-toxic 
supply. The inlet for this supply is situated on the underside of the hull, 
close to the bow (Figure 34). The underway supply is pumped past a Seabird 38 
temperature sensor (Figure 35), mounted within a few metres of the inlet, 
before reaching the fluorometer, transmissometer and thermosalinograph in the 
water bottle annex (WBA)/wetlab (Figure 36). Details of the instrumentation 
are given in Table 12.


Figure 34: Location of RRS Discovery underway seawater supply (depth -5-6 m).

Figure 35: Non-toxic supply pumps in forward hold and enlargement showing 
           temperature probe (estimated to be - 5 m from inlet).

Figure 36: Photograph showing route of underway water supply through 
           instruments located in Water Bottle Annex of RRS Discovery.


Table 12: Underway SST, SSS, fluorescence and transmittance instrument 
          details.
                                       Serial      Sensor 
     Variable          Instrument      number     position    Accuracy
-------------------  ---------------  --------  ------------  --------
Thermosalinograph -       SBE45         0229    Water bottle 
housing temperature     Micro TSG                  annex  

Thermosalinograph -       SBE45         0229    Water bottle 
   conductivity         Micro TSG                  annex 

    Sea surface       SBE38 Digital     0476    Near intake  
    temperature        Thermometer  

   Fluorescence          Wetlabs      W535-247  Water bottle  ± 0.66mV
                       Fluorometer                 annex  

   Transmittance         Wetlabs      CST-112R  Water bottle 
                     Transmissometer               annex  


10.2.  Routine Processing

Data from the Seabird TSG was logged in both the di346/data/met/surftsg and 
di346/data/tsg/ directories. The processing steps applied to the data in the 
two locations varied and are detailed below in the Surfmet Processing and TSG 
Processing sections respectively. Other variables were only processed in the 
Surfmet Processing only. Files were transferred from the onboard logging 
system

(TECHSAS) to the UNIX system on a daily basis using the script 
mday_00_get_met.m.


10.2.1.  Surfmet Processing

The raw data (file extension d***_raw.nc) were copied to d***_edit.nc files 
for editing, using the function mday_mk_met_edit.m. Manual despiking of data 
was then performed using the Mstar function mplxyed.

Values of salinity were calculated in real-time in the tsg/ directory but had 
to be computed from the conductivity and housing temperature (temp_h) 
variables in the met/surftsg/ data stream. The logged conductivity ratio was 
converted to a salinity value by implementing the UNESCO algorithm of 
Fofonoff and Millard (1983) in sw_salt.m. The function mavg_surflsg_di346.m 
was used to call this script and average the data into 1-minute median bins. 
The smoothed output was saved with the extension d***_avg.nc and appended to 
the file met _tsg_di346_01.nc using the script mapend_surflsg. m.


10.2.2.  TSG Processing

In order to utilise the daily despiked and averaged data, the individual 
NetCDF files were processed from /data/tsg/. Navigation data are found using 
a similar naming convention (e.g., pos_di346_d006_raw.nc) in 
/data/nav/gps4000.

The Matlab program mmerge was used by specifying, for each day, the 
navigation file and the TSG file.

TSG data are stored in the data/tsg directory where the naming convention 
follows the following pattern:

tsg_di346_d006_edit.nc or tsg_di346_d006_raw.nc

<data type_cruise_Julian day _ either raw data or despiked data (edit)>. The 
raw version is that obtained from the TECHSAS data stream and the edit 
version is a copy of this used for processing.

Processing of the TSG data was achieved using the Mstar suite of packages. 
First, using mplxyed.m, the data were examined visually and any obvious and 
significant spikes removed. Spikes were removed in the two temperature 
records (inlet and water bottle annex), the conductivity record and the 
salinity record. Note that the sound speed values (the other variable 
available in the data files) were not despiked.

The working directory for the processing from this stage onwards is 
/data/cjb_work/cb_underway where the next required Matlab script, 
changenantemps2salin.m, is located. This script recodes any value of salinity 
to be NaN if the temperature in the WBA was found to be NaN (i.e. as a result 
of the despiking exercise). A new variable, named salm_mcalib, is created and 
the original salinity values remain in the file. This script replaces the 
existing file with a new file of the same name, but containing a new 
variable.

The next script is new_merge_all_tsg.m and the first step is to combine 
(using mapend.m) all the TSG files (these are listed in 
files_of_interest_bestnav). When this stage is complete the data are merged 
(using mmerge.m) with the navigation data (taken from 
data/nav/g12/bst_di346_01). The resulting file is written to 
data/tsg/tsgwithbestnav/tsg_merged.

In order to ensure that all values of salinity that are NaN also represent 
cases where conductivity is NaN and vice versa, changenantemps2nansalinv2.m 
is run and produces two new variables (salin_new and cond_new).

The final processing stage in new_merge_all_tsg.m is to average the variables 
over a time span of two minute intervals using the mavmed.m function (i.e. 
the median values). The resulting file is written to 
data/tsg/tsgwithbestnav/tsg_merged_with_bestnav_smooth.nc. At this stage the 
NetCDF files are also read into Matlab format using mload.m. Both smoothed 
and unsmoothed files are saved in data_merged.mat as the structures named 
data_final and data_final_unsmoothed respectively.



10.3  Calibration of Underway Sea Surface Salinity

Both of the above methodologies use the same calibration approach detailed 
here. Water samples from the TSG outflow pipe were collected in 200m1 flat 
glass bottles at ~4 hour intervals throughout the cruise. Before each sample 
was taken, the hose connected to the outflow pipe was flushed for 
approximately 20 seconds to ensure that a fresh sample was drawn from the sea 
surface, and the sample bottles were rinsed thoroughly 3 times with the 
sample water. Bottles were filled halfway up the shoulder and the necks wiped 
dry to prevent contamination of the sample by salt crystallisation at the 
bottle opening. The bottles were then sealed using airtight, single-use 
plastic inserts before the bottle cap was refitted. The samples were stored 
in open crates and left in the controlled temperature laboratory for a 
minimum of 24 hours before analysis, ensuring full adjustment to the ambient 
temperature of the laboratory. A total of 193 TSG samples were taken during 
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 2010 using mtsg_01_di346.m. This script appends data from 
successive processed crates to the file tsg_di346.nc.

The script mtsg_02_di346. m averaged the continuous TSG data onto the 
discrete bottle samples for calibration of the SBE45. For each bottle data 
point, the corresponding TSG salinity was determined as the 10-minute mean of 
the ~0.5Hz data stream, centred on the time that the bottle sample was drawn. 
This approach smoothes noise in the continuous data and accounts for the 
occasional uncertainty in the exact time that the bottle sample was 
collected. A comparison of the bottle and TSG salinities is plotted in Figure 
37.

Figure 37: Comparison of Seabird TSG and bottle salinities during D346. The 
           TSG error bars (plotted in green) are computed as the standard 
           deviation of the 10-minute TSG data bin. Data points plotted in 
           red exceeded the tolerated discrepancy between bottle and TSG 
           data.


A maximum tolerated difference between the corresponding bottle and TSG 
salinities was set at 0.1 practical salinity units (psu). Six data points 
exceeded this difference and were subsequently omitted from the calibration 
calculation. The uncertainty (standard deviation of the 10 minute bin) 
associated with the discarded TSG data was not sufficiently large to account 
for the discrepancy in each case, suggesting a possible contamination of the 
bottle sample.

A first order calibration for the TSG salinity was employed to account for 
the constant offset of the Seabird sensor from the bottle samples and a small 
temporal drift:

             TSG_salinity_calibrated = -3.4l2e-9 * time + 0.0291

The linear fit to the retained data is shown in Figure 38. The calibrated 
salinity is plotted in Figure 39.


Figure 38: First order calibration of the TSG salinity sensor by comparison 
           with the non-toxic water supply samples.


An independent calibration of the TSG can be performed by comparing the 
Seabird sensor in the inlet pipe, to temperature and salinity data from the 
instruments mounted on the CTD frame. During cruise D346, 135 CTD casts were 
taken between days 6 and 45. The script mtsg_04_di346.m selected the CTD 
temperature and salinity data logged between 5 and 6db (assumed to be the 
approximate depth of the remote temperature sensor in the inlet pipe) for 
each CTD cast. This region is assumed to be well mixed so that the depth 
difference between the level sampled by the CTD probe and the level of the 
inlet pipe is negligible. Data obtained during the 10m dip preceding each 
cast was discarded before averaging the TSG data onto the CTD sample times. 
For each CTD data point, the corresponding TSG salinity was determined as the 
20-second mean of the ~0.5Hz data stream, centred on the time that the CTD 
probe sampled. This averaging bin is deliberately smaller than that selected 
for the TSG calibration with the bottle data, where the sample frequency was 
significantly lower and the collection time was rounded to the nearest 
minute.


Figure 39: Calibrated TSG salinity plotted with bottle data used in 
           calibration.

Figure 40: First order calibration of the TSG temperature sensor by 
           comparison with the sensor mounted on the CTD frame.


The SBE45 temperature and salinity sensors were found to have a small offset 
from the primary sensors mounted on the CTD. A comparison of the TSG and CTD 
temperatures is plotted in Figure 40. A first order calibration for the TSG 
temperature was employed to account for the discrepancy between the SBE3 8 
digital thermometer and the superior CTD mounted probe:

             TSG_temp_calibrated = 1.0268* TSG_temp_raw - 0.7512.

The calibrated TSG temperature is plotted in Figure 41.


Figure 41: Calibrated TSG temperature plotted with CTD data used in 
           calibration.
 
Figure 42: 5km mean calibrated TSG salinity during D346.


The SBE45 salinity measurements were also found to be weakly dependent on sea 
surface temperature (not shown). The Seabird TSG computes salinity using data 
from the temperature sensor collocated with the conductivity sensor in the 
water bottle annex. It is suggested the warmest SSTs were associated with the 
greatest ship-sea thermal contrast during D346. This contrast may have 
induced a more notable difference between the temperature read by the sensor 
in the hull and the sensor in the water bottle annex. However, the dominant 
uncertainty in the TSG salinity data was determined to be the instrument 
error previously accounted for by calibration with the bottle samples. As a 
result, no further adjustment to the salinity data was applied and the weak 
dependency on sea surface temperature was ignored.

Calibrated TSG salinity and temperature data averaged across 5km sections of 
the cruise track are shown in Figure 42 and Figure 43 below.


Figure 43: 5km mean calibrated TSG temperature during D346.



10.4.  References

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





11.  SURFACE METEOROLOGICAL SAMPLING SYSTEM (SURFMET)
     Helen Pillar


11.1.  Instrumentation

The RRS Discovery was equipped with a variety of meteorological sensors to 
measure air temperature and humidity, atmospheric pressure, total irradiance, 
photosynthetically active radiation, wind speed and wind direction throughout 
the cruise.


Table 13: Meteorological instrument details

                                  Serial    Calibration      Sensor 
  Variable       Instrument       number   Y = C0 + C1x +   position     Accuracy
                                            C2x2 + C3x3
------------  -----------------  --------  --------------  ---------  ---------------
Atmospheric       Vaisala                   C0 =-1.17483      Port
 Pressure         PTB100A        S3610008   C1 = 1.00152    Foremast        -
                 barometer                  

 Dry bulb         Vaisala        B4950010     C0 = 0.0        Port     Humidity ±1.5% 
 air temp +       HMP45A                      C1 = 1.0      Foremast   Temp ±0.15°C
 humidity    

Wind speed       Gill sonic       071123      C0 = 0.0        Port          -
+ direction      anemometer                   C1 = 1.0      Foremast

Total irra-     Kipp & Zonen      994133      C0 = 0.0        Port     9.60 µV/W/m2
diance (TIR)  CM6B (335-2200nm)               C1 = 1.0
                 pyranometer      962301      C0 = 0.0      Starboard  9.76 µV/W/m2
                                              C1 = 1.0

 Photosyn-      Skye energy       28557       C0 = 0.0        Port     11.04 µV/W/m2
thetically      sensor                        C1 = 1.0
  active        (400-700nm)       28556       C0 = 0.0      Starboard  10.53 µV/W/m2
 radiation                                    C1 = 1.0
   (PAR)  


The radiation and pressure variables were logged in the datalmet/surflight 
directory. The remaining data was logged in /met/surfmet.


11.2. 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_met.m. The raw data 
files have extensions of the form _di346_d***_raw.nc, where *** represents 
the day number. These were copied _di346_d***_edit.nc files for editing using 
the script mday_mk_met_edit.m. The data were plotted using the scripts 
mday_plot_surfmet.m and mday_plot_surflight.m, before being manually despiked 
using the function mplxyed. The data were then averaged into 1-minute 
(median) bins using mavg_surfmet_di346.m and mavg_surflight_di346.m and 
appended to the files met_di346_01.nc and met_light_di346_01.nc using the 
scripts mapend_surfmet.m and mapend_surflight.m respectively.

The barometer data was the only stream that required adjustment; a 1st order 
calibration, (as given in the instrument documentation) and a correction to 
account for the ~16m offset of the mounted barometer from the sea level. 
These adjustments were performed by running the script mcal_atmpress.m, which 
assumes the atmospheric boundary layer is both hydrostatic and well mixed 
(isothermal) between the surface and the instrument level. This is likely to 
be a reasonable assumption for the convective boundary layer (Stull, 1988) 
but may be unrepresentative of the nocturnal boundary layer in the absence of 
mechanical stirring. The corrected pressure was then averaged into 1-minute 
(median) bins and appended to press_correct_di346_01.nc using the scripts 
mavg_press_di346.m and mapend_press.m respectively.

Once the meteorology and navigation data had been processed, the true (Earth 
relative) wind speed and direction was computed from the cleaned, ship 
relative wind data using the script mtruewind_di346.m and saved in the file 
met_di346_truewind.nc. It is noted that 19 hours of anemometer data was lost 
on 19/01/2010 when sustained spuriously high wind speeds were logged. The 
cause of this instrument error was not determined.


11.3.  References

Stull, R.B. (1988), 'An Introduction to Boundary-Layer Meteorology', Kluwer, 
    pp. 666


Figure 44: Time series of 1-minute (median) averages of the meteorological 
           data for the duration of D346 (Julian day 5 - 47). The time 
           annotation is completed decimal days, so the first panel begins at 
           midnight at the end of day number 5 (5 Jan) and the last panel 
           ends at midnight at the end of day number 47 (16 Feb) 





12.  NAVIGATION
     Ben Webber


12.1.  Navigation Summary

High quality navigation data were necessary to orientate all the measurements 
made during the cruise. In addition, accurate ship speed and heading were 
important for making accurate underway measurements of ocean currents as well 
as wind speed and direction, since small heading errors while steaming can 
lead to large anomalies when calculating absolute velocities from 
ship-relative measurements.

The RRS Discovery has three GPS receivers: the Trimble 4000, which is a 
differential GPS; the Ashtech; and the GPS Gl2. The ship also uses a 
gyrocompass and Chernikeeff Electromagnetic (EM) log to measure ship heading 
and speed. Data from the Trimble 4000 and G12 GPS streams as well as position 
and attitude data from the Ashtech GPS were processed daily as outlined 
below.


12.2.  Comparison of GPS accuracy

A comparison of the position data produced by all three GPS streams was 
carried out (Figure 45). Differences in latitude and longitude were converted 
to metres for a more meaningful comparison. The G12 and the Trimble agree 
best; there is considerably more scatter in the comparisons of both with the 
Ashtech. However, there were several occasions during the cruise when the 
Trimble GPS froze, leading to gaps in the data. Therefore, the G12 was chosen 
as the most accurate and reliable GPS stream, and was used for creating the 
final 'bestnav' (bst_di346_01.nc) file.


12.3.  Gyrocompass

The ships' gyrocompass provides a reliable estimate of the ships' heading 
that is not dependent on transmissions external to the ship. However, the 
instrument is subject to latitude- and velocity-dependent errors and has an 
inherent oscillation following a change of heading. This is known as the 
Schuler oscillation with a period of approximately 86 minutes.

Because the gyrocompass calculates heading based on the rotation of the 
Earth, it needs to be configured for the ships' latitude and average speed. 
At the start of the cruise the primary gyrocompass failed at 05:45:12 GMT on 
06/02/2010; the data stream was then changed to the secondary gyrocompass. 
However, this had not been correctly calibrated to the ships' latitude 
leading to a period of adjustment when the data were considered unreliable, 
until 06:43:48 GMT.

Although the gyrocompass is reliable, the time-dependent errors need to be 
corrected for using the less reliable but more accurate Ashtech Attitude 
Detection Unit (ADU) heading data. The data for both these systems and the 
heading correction were calculated in daily segments before being applied to 
calibrate the VMADCP data.


Figure 45: Comparisons between positions measured by (a) Ashtech and GPS G12, 
           (b) Ashtech and GPS 4000, (c) GPS G12 and GPS 4000.



12.4.  Ashtech 3DF GPS Attitude Detection Unit (ADU)

The Ashtech GPS comprises four antennae mounted above the bridge. Every 
second, the Ashtech calculates ship attitude (heading, pitch and roll) by 
comparing phase differences between the four incoming satellite signals. This 
is usually very accurate, but occasionally the Ashtech unit failed to pick up 
enough GPS signals to provide an accurate fix. These periods were usually 
identifiable by spikes in the heading, pitch and roll data. The largest of 
these spikes were automatically removed using the mash_01 script as outlined 
below, and the rest were manually removed using the mplxyed function. This 
avoids allowing spurious Ashtech heading data to contaminate the 
ashtech-minus-gyro (a_minus_g) heading correction used in the calibration of 
the VMADCP.


12.5.  Daily Processing Steps


Table 14:        Navigation processing steps with descriptions of their 
                 function

mday_00_get_nav  Get all the navigation data and convert from techsas data 
                 into daily files of mstar data. The filenames were in the 
                 format <dataname>_di346_d???_raw.nc, where <dataname> refers 
                 to a three-letter string, e.g., 'gyr' for gyrocompass data.

mgyr_0l          Remove non-monotonic times from the gyro data. Outputs 
                 gyr_di346_d???.nc files

mash_01          Merge the gyro heading into the ashtech data file then 
                 calculate the a-g heading correction.
                 Apply quality control using mdatpik such that data are 
                 removed outside the following limits:

                             head_ash       0          360
                             pitch         -5            5
                             roll          -7            7
                             mrms           0.00001      0.01
                             brms           0.00001      0.1
                             head_gyr       0          360
                             a_minus_g     -7            7

                 Apply 2 minute averaging to the data.
                 The output from this processing is in the ash_di346_d???.nc 
                 files.
                 Note that the purpose of this process is to provide reliable 
                 heading information to the VMADCP calculations. Therefore 
                 the emphasis is on removing bad data and smoothing over 
                 high-frequency variability. It is possible that the mdatpik 
                 stage removes good data, but it is expected that the amount 
                 of good data discarded will be relatively small.
                 Also note that although pitch and roll are carried through 
                 to the final files, the two-minute averaging means that 
                 these data should be extracted from the raw.nc files 
                 instead.

mplxyed          The a minus g data were manually de-spiked using this 
                 interactive plotting command in mstar. Care was taken to 
                 remove spikes that were due to errors in the ashtech data 
                 but leave spikes due to sudden changes in ships' heading.

mday_00_run_nav  Append the daily data into a single <dataname>_di346_01.nc 
                 file for each data set.

mbest_all        Wrapper script for the mbest_01, mbest_02, mbest_03 and 
                 mbest_04 scripts. These scripts run 30-second averaging on 
                 the position (GPS_4000 and GPS_G12) and gyrocompass data and 
                 then calculates speed and groundcourse from the GPS data, 
                 before merging the GPS and gyro data into a bst_di346_01.nc 
                 file.


11.6.  Chernikeeff Doppler Log Calibration

The Chernikeeff Doppler log records the ships' velocity through the water by 
measuring the voltage produced by seawater flowing through an alternating 
magnetic field. The velocities are measured in both the forward-aft and 
port-starboard directions. The amount of voltage produced is roughly 50 
µV/Knot, and this signal is scaled to produce the 'measured' speed. However, 
because this relationship is not perfectly linear, it is necessary to 
calibrate the Chernikeeff to convert this measured speed into a 'true' speed 
for the ship. This calibration is typically done by steaming out and back 
over a measured distance at a set engine RPM and then taking the average 
velocity calculated from the two runs. This is repeated for multiple speeds 
to create an empirical look-up table as an approximation to the true 
calibration curve.

On cruise D346, it became apparent early on that the Chernikeeff was over-
estimating the ships' speed considerably, especially at high velocities. It 
was decided that a practical solution would be to calibrate the Chernikeeff 
against the ships' velocity as measured by the VMADCP. The ships' forward-aft 
velocity from the second bin of the OS150 VMADCP was used for this purpose, 
corresponding to the ship-relative water velocity at approximately 16 m below 
the hull. It was assumed that any bias associated with calibrating between 
different depths would be negligible.

On examination of the previous calibration, it appeared that the reason for 
the Chernikeeff over-estimating the ships' speed was that the calibration 
value for the highest RPM was higher than would be expected from the previous 
points (Figure 46). Since the calibration is extrapolated from the last two 
points entered, any errors in this last point will be amplified at high 
speeds. When the Chernikeeff 'true' speed was plotted against the VMADCP 
measured speed, a kink was indeed evident at high speeds (Figure 47) that was 
assumed to be related to this apparent error.


Figure 46: Calibration curves for the previous two calibrations of the 
           Chernikeeff EM log on RRS Discovery. The upper curve is the most  
           recent calibration, the lower curve a previous calibration with a 
           linear  relationship. The pink line represents a 1:1 relationship 
           and is plotted for  comparison only. 
 
Figure 47: Scatter plot of Chernikeeff displayed speed against speed  
           measured by the VMADCP second bin, before any calibration was 
           applied.


Re-calibration of the Chernikeeff was performed by fitting a piecewise linear 
relationship with the VMADCP measured speed and using this best fit to adjust 
the values in the original look-up table. The values entered were adjusted by 
hand to make a smooth curve in the adjusted look-up table to reduce the 
possibility of inaccurate extrapolation from the final points. The resulting 
relationship between the Chernikeeff and the VMADCP is shown in Figure 48. It 
is apparent that the Chernikeeff was now under-estimating the velocities, but 
that the relationship was more linear than the previous. Thus a linear fit 
was applied to produce a third calibration, the result of which is shown in 
Figure 49. The gradient of the fit was now almost perfect, but there was a 
gradient in the cluster of points at high velocities. This appeared to be due 
to the value at around 9 knots being too low and the one at around 12 knots 
being too high. Thus these two values were adjusted by hand to give the final 
calibration, shown in Figure 50. There is some evidence that this final 
calibration may have been a slight over-correction for the gradient at high 
speeds in the previous calibration. However, given the relatively short 
period, during which rough weather was experienced, it is possible that this 
is not entirely representative. Further investigation on subsequent cruises 
may be worthwhile in order to establish additional improvements to this 
calibration.


Figure 48: As Figure 47, but after first calibration

Figure 49: As Figure 47, but after second calibration

Figure 50: As Figure 47, but after final calibration


The look-up table with the original and new calibration values is shown 
below. Note that the Chernikeeff requires two tables to be entered for 
calibration (corresponding to the outbound and return legs of the trial 
runs), so the values in the final column are entered for both 'table 1' and 
'table 2'.


Table 15: Calibration values entered into both 'table 1' and 'table 2' in the 
          Chernikeeff EM log's calibration menu.

RPM        EM-log      Original EM-log 'true' speed  VMADCP-calibrated true speed
     'measured' speed       before calibration        (after final calibration)
---  ----------------  ----------------------------  ----------------------------
 75         300                   439                            372
100         466                   626                            533
125         643                   833                            710
150         776                   979                            875
160         813                  1079                            980
180        1043                                                 1133





13.  BATHYMETRY
     Helen Pillar


13.1.  Instrumentation

The RRS Discovery was equipped with a Simrad EA500 echo sounder (10.2/12.0kHz 
'fish' and hull mounted system) to allow bathymetric profiling throughout the 
cruise. The estimated depth of the hull-mounted transducer was 5.3m. The 
Precision Echosounding (PES) transducer mounted in a 'fish' was towed at an 
estimated depth of 8.5m. Whilst steaming, the hull-mounted transducer was 
ineffective due to interference from bubbles generated by the ship 
propulsion. The PES fish transducer - towed at a lower depth - was used 
preferentially, proving less susceptible to this noise. At low towing speeds 
and whilst on station, the attitude and depth of the fish were less stable 
and the task of bathymetric profiling was switched to the hullmounted 
transducer.

The measured depth was logged by the TECHSAS system and displayed on the 
Simrad visual display unit, informing decisions to change the preset range 
and gain of the signal. A hardcopy of this display was also produced on a 
colour printout. A uniform sound velocity of 1500m1s was assumed throughout 
the cruise.


13.2.  Routine Processing

Files were transferred from the onboard logging system (TECHSAS) to the UNIX 
system on a daily basis using the Matlab function mday_00('sim ',day#). The 
raw data files have extensions of the form _di346_d***nc where *** is the 
number of the Julian day.

During the cruise, the echosounder often failed to detect the bottom and 
reported either zeros or spuriously large depths. The script msim_01.m was 
run to remove data outside a tolerated range and apply a 5-minute median 
despiking, outputting the file sim_di346_d***_smooth. nc. The script 
msim_plot.m copied the smoothed data to the file sim_di346_d***_edited.nc and 
called the function mplxyed to allow a manual removal of the remaining 
spikes. The paper record proved highly useful in detecting spurious depths 
resulting from side-echoes off steep topography and reflection off the CTD 
cable. Incorrect values for the bottom depth were also detected when the 
transmitted ping penetrated thick layers (up to ~200m) of soft sediment on 
the sea floor before being reflected by the underlying bedrock.

Following the manual edit of the smoothed data, the script mapend_sim.m was 
run to append all existing sim_di346_d***_edited.nc files to sim_di346_01.nc. 
Once a clean navigation file had been produced, mmerge_sim_navdi346.m was run 
to merge the position and bathymetry data and correct for the variable speed 
of sound using Carter table climatologies. The corrected depths were saved in 
the file sim_di346_01_withnav. Finally, the data were averaged across 5km 
along-track intervals using mavg_sim_di346.m. This data was saved in the file 
sim_di346_01_5km.nc and is shown plotted against longitude in Figure 51 
below. The most notable gap in the data is associated with discarded 
side-echoes generated whilst traversing the Abaco shelf.


Figure 51: Bathymetry data averaged over 5km intervals of the distance run, 
           plotted as a function of longitude for the duration of the cruise.





14.  VESSEL MOUNTED ADCP INSTRUMENTS
     David Hamersley


14.1.  Introduction

Two vessel-mounted Acoustic Doppler Current Profilers (ADCPs) onboard RRS 
Discovery were used throughout the cruise to measure the horizontal velocity 
field (cross-track and along-track). The 75kHz and 150kHz Ocean Surveyor (OS) 
instruments were supplied by Teledyne RD Instruments. Unlike RRS James Cook, 
RRS Discovery does not have retractable keels so these instruments are fitted 
to the hull of the ship. Cruise D345 did not have the 75kHz instrument 
fitted, so the transducer was installed by divers whilst docked in Freeport 
prior to D346. The depths of the transducers are 5.3m. Both transducers are 
phased-array, which means that they are made up of many elements each 
transmitting in different phase. This is advantageous, because it means that 
the accuracy of the velocities, derived from the Doppler shifted return 
signals, is not affected by speed of sound changes throughout the water 
column. However, the range and accuracy of the instruments has been observed 
in this cruise, as it has previously, to be affected by exposure to bubbles.

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 approximately 400-500m. The 75kHz lacks such 
good vertical resolution but penetrates to approximately 800-l000m.



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:

• Open VmDas from the Start Menu and click on "Collect Data" in the File 
  Menu.
• 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. 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.
• Recording commences by clicking the blue record button in the top left of 
  the screen.
• 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 file number everyday during the cruise. Leaving it on the same file for 
  too long allows the files to become too large and post-processing in CODAS 
  becomes slow.

14.2.1.  Files Produced by VmDas

The files we produced have names of the form 
os<inst>_<di346<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. This was 
helpful, because it meant that if problems were encountered in the data 
processing, they were more likely to be contained within a single file 
number. If more than one file number was affected, then they could quite 
easily be processed together because of the same file sequence number.

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 following directories:

/ADCP150/di346 (for 150kHz transducer data)
/ADCP75/di346  (for 75kHz transducer data)


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".

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:

• We made sure the ensemble number in the real time display of VmDas was 
  increasing during the 4 hourly watchkeeping log. Inspection of the 
  navigation input to VmDas was identified as a necessary watchkeeping task 
  after a 6hour dropout of navigation data was noticed.
• We ensured that records of the files created are kept up-to-date.
• The LOG file records any problems such as timeouts and navigation problems 
  and was occasionally inspected.

14.2.3.  Alignment

Zero offset for both sensors.

14.2.4.  General Settings

During D346, we ran both instruments in narrowband single-ping mode. Where 
depth permitted, for the first few days of the cruise, 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 900m. A table of the bottom track 
phase and amplitude calibrations is given below.


Table 16: Bottom track calibration data for the OS75 instrument. The 'after 
          tvrot' line is after applying the time-varying gyro minus ashtech 
          correction. The 'final' line are data from the end of the cruise 
          after applying the accepted adjustment of -2.88 for phase and 1.002 
          for amplitude.
  
                            Amplitude  Amplitude  Amplitude   Phase    Phase    Phase
File                         (median)   (mean)      (STD)    (median)  (mean)   (STD)
-------------  -----------  ---------  ---------  ---------  -------  -------  -------
di346005nbenx  Raw            1.0041    1.0034     0.0033    -4.1898  -4.1315  0.2493
               After tvrot    1.004     1.0032     0.0033    -2.8165  -2.8324  0.0733
di346006nbenx  Raw            1.0013    1.0015     0.0058    -2.6168  -2.7867  0.7168
               After tvrot    1.0012    1.0015     0.0053    -2.8837  -2.8806  0.2879
di346007nbenx  Raw            1.002     1.002      0.0037    -3.3616  -2.8444  1.5419
               After tvrot    1.0022    1.0021     0.26      -2.9398  -2.9308  0.244
di346008nbenx  Raw            1.0024    1.0027     0.0052    -3.6556  -3.8943  1.15
               After tvrot    1.0025    1.0024     0.0043    -2.8895  -2.9247  0.3157
di346009nbenx  Raw            1.005     1.0049     0.0021    -2.3513  -2.3066  0.7591
               After tvrot    1.0052    1.0049     0.0022    -2.8465  -2.8527  0.1366
di346050nbenx  Final          1.002     1.002      0.0021     0.0507   0.0768  0.2202


Table 17:	Bottom track calibration data for the OS150 instrument. As table 
16, but the accepted adjustments are -1.58 for phase and 1.005 for amplitude.

                             Amplitude  Amplitude  Amplitude   Phase    Phase    Phase
File                          (median)   (mean)      (STD)    (median)  (mean)   (STD)
--------------  -----------  ---------  ---------  ---------  -------  -------  -------
di346003nbenx  Raw              -          -          -         -        -         -
               After tvrot      -          -          -         -        -         -
di346004nbenx  Raw            1.0057    1.0038     0.0191    -1.215   -1.1278  1.4118
               After tvrot    1.0057    1.0021     0.0174    -1.6046  -1.5549  1.2753
di346005nbenx  Raw            1.0064    1.0059     0.0088    -1.965   -3.0424  4.8463
               After tvrot    1.0063    1.0062     0.0084    -1.6267  -2.7597  3.4155
di346006nbenx  Raw            1.0051    1.005      0.0031    -2.58    -2.5249  1.0367
               After tvrot    1.005     1.0051     0.0033    -1.5638  -1.5549  0.2815
di346007nbenx  Raw             NaN       NaN        NaN        NaN      NaN     NaN
               After tvrot     NaN       NaN        NaN        NaN      NaN     NaN
di346048nbenx  Final          1.001     1.0014     0.0028    -0.0079   0.0018  0.1504

The number of bins and the bin sizes on both instruments differed. On the 
OS75, 65 bins were used, with a bin size of 16m and for the OS150, 65 bins 
were used at a size of 8m. A blanking distance of 8 m was used for the OS75 
and 6m for the OS150, in order to avoid ringing from the transmit pulse. 
Using the VmDas options the instruments were switched between bottom track 
and water track mode on decimal day 009 when the sea floor was out of range 
of bottom tracking. However, as can be seen in Table 17, file di346007nbenx 
on the OS150 does not contain any bottom track calibrations, because the 
seafloor was already out of range for this instrument. The means of the 
amplitude and phase values in each of the respective tables were used in the 
control files of each of the respective instruments.

Table 18:  Water track calibration data for the OS75 instrument

File           Amplitude  Amplitude  Amplitude   Phase     Phase   Phase
                (median)   (mean)      (STD)    (median)   (mean)  (STD)
-------------  ---------  ---------  ---------  --------  -------  ------
di3460l0nbenx    1.001     1.001      0.0057    -3.1705   -3.1705  0.0969
di3460llnbenx    1.007     1.0077     0.005     -2.485    -2.7927  0.5723
di3460l2nbenx    0.9995    1.0018     0.008     -2.6375   -2.7057  0.3126
di3460l3nbenx    0.9985    1.0001     0.0049    -2.9185   -2.9157  0.2907
di3460l4nbenx    1.003     1.0024     0.0036     0.001     0.0056  0.2453
di3460l5nbenx    1.0025    1.0015     0.004     -2.936    -2.9075  0.3469
di3460l6nbenx    1.004     1.0034     0.0055    -3.122    -3.1313  0.601
di3460l7nbenx    1.003     1.0013     0.0062    -2.842    -2.8988  0.3792
di3460l8nbenx    1.008     1.0068     0.0055    -2.6775   -2.823   0.4323
di3460l9nbenx    1.0015    0.9972     0.0132    -2.9095   -2.9732  0.7464
di346020nbenx    0.9995    0.9992     0.0064    -2.7945   -2.857   0.2657
di346025nbenx    1.001     1.0067     0.0136    -2.42     -2.011   1.1285
di346030nbenx    0.996     0.9946     0.0074    -0.092     0.0316  0.299
di346035nbenx    1.001     1.0018     0.0026    -2.8      -2.854   0.4182
di346040nbenx    0.998     0.998      0.0029    -0.165    -0.213   0.18
di346045nbenx    1.001     1.002      0.0093     0.146     0.2154  0.5141


Table 19:  Water track calibration data for the OS! 50 instrument

File           Amplitude  Amplitude  Amplitude   Phase     Phase   Phase
                (median)   (mean)      (STD)    (median)   (mean)  (STD)
-------------  ---------  ---------  ---------  --------  -------  ------
di3460l0nbenx    1.002     1.0064     0.0145    -1.7625   -1.6661  0.5482
di3460llnbenx    1.0025    1.0017     0.0044    -1.553    -1.6243  0.5724
di3460l2nbenx    1.007     1.0072     0.0067    -1.6725   -1.7828  0.5053
di3460l3nbenx    1.004     1.0045     0.0056    -1.738    -1.8077  0.544
di3460l4nbenx    1.007     1.0063     0.0071    -1.633    -2.0193  0.9957
di3460l5nbenx    1.01      1.0055     0.0098    -1.5875   -1.6335  0.2401
di3460l6nbenx    1.003     1.0046     0.0072    -1.3      -1.3826  0.2153
di3460l7nbenx    1.0055    1.0045     0.008     -1.802    -1.507   1.4555
di3460l8nbenx    0.996     0.9982     0.0053    -1.691    -1.6452  0.604
di3460l9nbenx    1.0045    1.0032     0.0034    -1.5385   -1.4968  0.2499
di346020nbenx    1.0035    1.0035     0.0034    -1.52     -1.471   0.3949
di346025nbenx    1.0045    1.0055     0.0048    -1.7605   -1.8502  0.6372
di346030nbenx    0.997     0.998      0.0058    -0.054     0.1974  0.4708
di346035nbenx    1.006     1.0047     0.0072    -1.3195   -1.3815  0.4863
di346040nbenx    1.001     0.9972     0.0066    -1.837    -1.7614  0.2914
di346045nbenx    1.001     0.9998     0.0069     0.261     0.1977  0.4863



14.2.6.  Sound Speed Considerations

Measurements of x and y velocities are independent of the speed of sound for 
phased array ADCP instruments such as those used on D346. If the speed of 
sound changes in the vertical water column or in front of the transducer, the 
angle of the beam will consequently change. This change in 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, canceling out the 
change in the speed of sound. For a more in-depth account of speed of sound 
considerations when using ADCP units please refer to JC032 cruise report 
(King et al., 2010).


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 editing 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 NOSEA1 terminal, so the raw data files had to be copied 
over from the ADCP PCs. The raw data were moved into either the 
/vmadcp/di346_os75/rawdata directory or the /vmadcp/di346_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 creates a new 
   directory called rawdata<nnn> (nnn denoting the file sequence) and moves 
   the relevant data to this new location.

2. The command adcptree.py di346<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 di346<nnn>nbenx using the cd command, 
   and the control files q_py.cnt, q_pyedit.cnt q_pytvrot.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 respectively and are appended each time 
   quick_adcp.py is run.

4. The files were usually left at this point of the processing for at least a 
   day until the navigation processing had been completed for the appropriate 
   period.

14.3.3.  Calibration

The quick_adcp.py script estimates amplitude and phase corrections for each 
set of data. It is only by specifying a calibrated rotation in the 
q_pyrot.cnt file that accurate velocities could be obtained.

The best calibration estimates are obtained when the velocity data is 
collected using the seabed as a reference. However, bottom track calibration 
estimates are only obtainable when the water depth is within the ADCP 
profiling range. Bottom tracking was performed at the beginning of the 
section in the Bahamas from Julian day 006-009, and again when we reached the 
continental shelf of Morocco. The reason for running the ADCPs in bottom 
tracking mode at the end of the main section was to verify that the rotations 
applied to the data through the section had not changed since the first 
bottom tracking measurements obtained in the Bahamas. A table of the bottom 
tracking calibrations was created to calculate mean phase and amplitude of 
the instruments, which were then used as the rotation values in the 
q_pyrot.cnt control file. As can be seen from Tables 16 and 17 the final 
calibration check (highlighted in yellow) shows very little difference from 
the original rotations applied to the data and is well within acceptable 
limits (i.e. a tenth of a degree). The calibrations given were as follows: 
OS75 rotation angle = -2.88, amplitude = 1.002; OS150 rotation angle = -1.58, 
amplitude = 1.005.

Comparison with the water track rotations shows close similarity with the 
bottom track calibrations (Table 18 and 19). Here are the following means 
calculated from the water track data: OS75 rotation angle = -2.1194 amplitude 
= 1.0015; OS150 rotation angle = -1.4107, amplitude = 1.0032. The numbers are 
not identical, but this was not expected.

14.3.4.  Applying the Rotation

Applying the rotations to the data required several different steps. 
Initially a heading correction file was created in Matlab by typing m_setup 
and running the script make_g_minus_a(<os>,<nnn>) in order to subtract the 
Ashtech heading from that of the shipboard gyro.

Back in Unix, the processing continued in the cal/rotate directory where the 
rotate.tmp file was edited using vi in order to provide the appropriate time 
angle file for data which was created in the previous processing step. To 
apply the rotation to the database the following command was typed; rotate 
rotate.tmp.

Using quick_adcp.py --cntfile q_pytvrot.cnt the time dependant heading 
correction was then run.

The final calibrations discussed above were applied to each file sequence 
using quick_adcp.py --cntfile q_pyrot.cnt in the di346<nnn>nbenx directory in 
the Unix terminal window. This rotates the data by 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 checked in Gautoedit to ensure that any 
vertical striping associated with on/off station differences had been removed 
by application of the calibration. Any alterations that needed to be made to 
the files, for example due to bad profiles or bad bins were edited using 
Gautoedit.

14.3.5.  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 q_pyedit.cnt control file, the data 
removed. Typically, the data were reviewed as follows:

1. Matlab was opened in the di346<nnn> nbenx/edit directory (for the portion 
   of data we wished to process). In the command window, typing:

   m_setup; codaspaths; gautoedit

   An editing GUI, shown in Figure 52. The editing was done from here.


Figure 52: The Gautoedit window within the CODAS suite of programs in Matlab



2. Gautoedit was initially used after the first quick_adcp.py step to observe 
   whether the ENX files had processed correctly. 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 according to the default plot 
   selections. One contains four subplots: the first displays the absolute 
   east-west (U) velocity component, the second shows the absolute 
   north-south (V) 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 ships' track and 
   mean absolute velocity vectors at the reference layer. However, it was 
   noted that throughout the duration of the cruise there was bug within this 
   part of the software, as when show now was clicked, Gautoedit crashed 
   during the plotting of the ships' track and velocity vectors. This did not 
   present a problem to the processing because simply pressing show now once 
   more succeeded in plotting the vectors. 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 0.3 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 0.3 day section.

   Routine editing for each section included:

   • 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 and choosing the select time range option.
   • 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 
     pzap bins command, which allows the user to flag all data within a 
     defined polygon.
   • 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 l5cm/s seemed to be a 
     reasonable value for flagging potentially bad profiles and did not need 
     to be changed.

4. 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 further in Section 14.4.

   • 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 bias 
     due to bubbles. The bias parameter is therefore a useful tool that can 
     be used as a guide for identifying potential areas of velocity bias.
   • If particularly bad bias in the along-track velocities on steaming 
     sections could be found, the bad bins were flagged using pzap bins.

   However, in both cases it was deemed unhelpful to remove these areas of 
   data because the editing steps would remove the data in both the U and V 
   components for the corresponding bins. We were unwilling to remove 
   perfectly good data from one component just to remove potentially bad bins 
   in the other component that spanned virtually the entire length of the 
   dataset. Therefore, the scattering layers were left in.

5. Once satisfied with the changes made, the List to Disk option is selected 
   which creates and updates a*.asc files in the di346<nnn>nbenx/edit 
   directory.

14.3.6.  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 di346<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 OSl50).

14.3.7.  Creating the Output Files

Once the editing and rotations were completed, the final velocities were 
collated into Mstar files (*.nc) using the following commands in the 
di346<nnn>nbenx directory of a Matlab command window:
m_setup 
mcod_0l 
mcod_02 
(type the file number and instrument number when prompted to specify the 
input file).

The first command sets up the Mstar suite of programs and the relevant paths. 
The other two commands 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 
os75_di346<nnn>nnx.nc that includes the following variables:

• time - (in seconds since [2010 1 1 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 os75_di346<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_di346<nnn>nnx.nc and os150_di346<nnn>nnx.nc files are 
then appended together into a single output file for the cruise using a 
script called mcod_mapend. 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 /di346_os75 and /di346os150 directories and are named nc_files. This 
needed to be edited a number of times due to the bottle blank stations 
undertaken for the CFC team which were designated with file numbers 200 and 
202. The reason this needed to be altered is because otherwise the files 
would have been appended in numerical order, which would have not placed them 
in the correct position in the appended file. The final output files are 
os75_di346nnx_01.nc and os150_di346nnx_01.nc which contain appended 
on-station and underway data.

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 simple loop was usually written in the Matlab command 
window to automate this process. 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. Usually when the mcod03 step would not run, it 
meant that the stations.m file needed to be run again to update the 
station.dat file.

The output files from mcod_03 contain individual on-station data of the form 
os75di346nnx_stn<nnn>.nc where <nnn> denotes the station number.

Individual steaming sections (i.e. between two on-station sections) were 
created in a similar manner using the mcod_04 script. The files created from 
this step were named accordingly, e.g. os75di346nnx_stn<nnn>_to_stn<nnn>.nc.
Finally, the underway files created in mcod_04 were appended together with 
the mcod_mapend_uway script. This took the individual steaming sections 
listed in the input file uway_nc_files and appended them together to create 
the file os75_di346nnx_uway_01.nc.


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. Bubbles can prevent penetration of the transmit pulse and 
lead to truncated or bad quality profiles. This was not widely observed on 
cruise D346. It is also 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°N 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. It typically does not affect lower bins of the 
profile, which remain good.

There were relatively few incidences of bubble bias encountered on cruise 
D346 significant enough to warrant editing of the data. Figure 53 however, 
does show an incidence when it is thought that bubble bias may have been 
responsible for spurious high surface velocities. Fischer et al, (2003) 
relate an increase in bubble formation with increased inclement weather 
conditions, however this does depend on the location of the transducer on the 
ships' hull, as some areas may be more prone to bubble formation than others.


Figure 53: Example of scattering near the surface due to bubble contamination 
           (approx. dday 20.65)


14.4.2.  Anomalous Scattering Bias

A more extensive feature was the presence of anomalous scattering layers 
leading to along-track velocity bias. The presence 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 and Cruise JC032 on 
RRS James Cook.

On this cruise, a large anomalous scattering layer was found on the OS75 
instrument between 460-660 metres across much of the section (see Figure 54; 
evidence of this scattering layer is also present in Figures 53 and 55). In 
Figure 53 this feature resulted in extensive red-over-blue striping in the 
along track bias parameter. The affected bins were not removed within 
Gautoedit because this would have also removed perfectly good data from the 
cross track parameter, which was deemed to be unwarranted. For much of D346, 
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 show an enhanced amplitude layer moving downwards during the day, 
before returning to its original level in the evening.


Figure 54: Example of the amplitude return for the OS75 instrument. The 
           anomalously high scattering layer can be seen close to 500 metres.

Figure 55: Note the strong red-over-blue striping during the steaming periods 
           at a similar depth to the anomalous scattering layer. Note also 
           the enhanced near-surface amplitude returns, most likely the 
           result of bubbles below the ship.


Strong scattering layers are seen less frequently with the OS150. This is 
most likely because the beam does not penetrate as deeply as the OS75.


Figure 56: U component for the 24°N section. A strong scattering layer can be 
           identified at approximately 500 metres, most likely a continuous 
           zooplankton layer produces this feature.


14.4.3.  Other Issues

A further departure from routine processing was the result of a failure in 
the input of the navigation data to the raw ENX files.

It was noticed from the CTD display that the navigation had dropped out. The 
problem was investigated and traced to a plug that had fallen out of a 
splitter box in the computer room. Paul Duncan fixed this problem, and as a 
result it was realised that the navigation was also not being fed to VmDas 
for the shipboard Dopplers. This meant that no headings for the data were 
available. The problem was found to have begun at 23:15 on Julian Day 028. 
The navigation data was still logged in the TECHSAS system however, so Brian 
King wrote a script entitled fix_nav.m to rescue the navigation data and 
apply it to the VMADCP data using the ENS files instead of the ENX files.

On Julian day 28 the navigation source was switched over from the GP54000 to 
the GPSG12 at approximately 23:20, and at approximately 23:30 the 
differential input for the GPS4000 was switched off. However, upon attempting 
to process the ENX files after this period it was found that there was no 
heading data in the files. Brian King was also responsible for fixing this 
problem, creating repaired raw data directories called rawdata< nnn>_fixhead. 
The following files were affected 026-029 for the OS150 and 029-032 for the 
OS75. This covers a period from approximately 23:20 on Julian day 028 until 
14:54 on Julian day 030. At this point Paul Duncan switched the navigation 
input back to the GPS4000. Initially no NMEA1 messages were received and then 
it was realised that the baud rate needed changing back. The files for the 
OS75 and OS150 where thus started at ensemble 1414 (14:58) and ensemble 159 
(15:00) respectively.

The affected files were processed using the ENS files, which meant that 
certain steps of the processing had to be altered. The control file q_py.cnt 
has to be altered to support ENS files instead of ENX files and the 
appropriate raw data directory selected (i.e. rawdata<nnn>_fixhead). Also it 
was necessary to add the line '--ens_halign 0'. The 
make_g_minus_a(<os>,<nnn>) and mcod_01 and mod_02 files were also edited to 
accommodate the ENS files (i.e. make_g_minus_a_ens(<os>, <nnn>), mcod_01_ens, 
mcod_02_ens). To allow the mcod_mapend step to work properly, a symbolic link 
to the respective directory di346<nnn>nbens was created to parse the data 
through di346<nnn>nbenx. These data from these files were then available to 
be viewed, edited and appended just like any other ENX file.


Figure 57: Here is an example of VMADCP data processed using ENS files 
           instead of the ENX files


As a test, file 26 was processed using good ENX data and the repaired 
(heading added) ENS data and the velocities were then compared. They were 
found to be synchronous with differences in the standard deviation of 
~0.01-0.02cm/s which is considered to be sufficiently good.

Due to a discrepancy between the PC clock and UTC time some files contained 
segments that would not process properly. CODAS keeps track of the offset 
between the time on the PC acquiring data and UTC in navigation messages. 
(The individual ensembles are timestamped with PC time, but if navigation 
messages are available with UTC then the offset is recorded within the ENX 
files). Each ENX file is processed using a single clock offset, because this 
is expected to vary slowly. Data from each ENX file are reduced to 5-minute 
averages, with single pings (at intervals of a few seconds) unused at the end 
of each ENX file carried over to be processed with the next ENX file. If the 
PC minus UTC clock offset has changed sufficiently between ENX files, this 
can create a backwards time jump between carried-over pings and the first 
ping in the next file. This causes quick_adcp.py to fail. The PC minus UTC 
clock difference varied in the range ± 120 seconds. The solution is to 
process troublesome ENX files individually, rather than as a batch. It was 
found that once the individual ENX file was separated into its own rawdata 
directory (series 900 and following) and processed alone the processing ran 
smoothly and without problem. ENX files affected by this problem were 
recorded in a readme file in the OS75 and OS150 directories. Copies of these 
readme files can be found below in Table 20 and 21.

Another problem that was identified were anomalously high velocities found in 
the Florida Straits section. It was clear that these could not be true 
velocities so the data was investigated and it was realised in the end that 
the velocities were arising due to a doubling of the data. This occurred 
because of the existence of a bottom track directory that was created after 
the Florida Straits section in order to view the profile. Removing this 
directory, which was no longer needed, left only a single data source. 
Reprocessing this section of data after the removal of the redundant 
directory fixed the problem and yielded sensible velocities.


Table 20:  OS75 filenames readme

           Directory number           ENX file numbers
           ----------------  -----------------------------------
                  701             os75_di346007_000001.ENX
                  900        All bottom track ENX files for OS75
                  901             os75_di346010_000001.ENX
                  902             os75_di346011_000002.ENX
                  903             os75_di346011_000004.ENX
                  904             os75_di346009_000001.ENX



Table 21:  OS150 filenames readme

           Directory number           ENX file numbers
           ----------------  -----------------------------------
                  901             os150_di346009_000000.ENX
                  902             os150_di346009_000001.ENX
                  903             os150_di346009_000002.ENX
                  904             os150_di346009_000003.ENX
                  905             os150_di346009_000004.ENX
                  906             os150_di346009_000005.ENX
                  907             os150_di346009_000006.ENX
                  910             os150_di346023_000001.ENX
                  911             os150_di346023_000003.ENX
                  912             os150_di346024_000002.ENX
                  913             os150_di346038_000001.ENX
                  914             os150_di346038_000003.ENX
                  915             os150_di346039_000001.ENX



On a couple of occasions along the 24°N transect, features such as those seen 
in Figure 58 were identified. This is a cold core eddy. This was better 
defined using the OS75 due to the greater range of the instrument. Eddies 
born from the Gulf Stream as it travels northwards can have warm or cold 
cores. These can also be identified by observing satellite images of sea 
surface temperature. The eddy identified in Figure 58 is rotating in an 
anticlockwise direction, which means that it has a cold core. Eddies usually 
retain properties that differ from those of the surrounding water mass. For 
example the occurrence of this feature coincided with a drop in the surface 
mixed layer and surface layer salinity.


Figure 58: A cold core eddy identified using the OS75 VMADCP instrument.


Another interesting feature was revealed earlier in the cruise as a result of 
our passage across the Florida Straits. RRS Discovery performed two transects 
of the Florida Straits along the same latitude, which allowed us to collect 
sufficient data to produce profiles of the Gulf Stream. Figure 59 illustrates 
our first uninterrupted pass along the Florida Straits, whereas Figure 60 is 
created from the underway data of various durations appended together to 
compare the two sections. It is interesting to note the spatial changes in 
water transport velocity that occur over such a short timescale. The 
timescale between these figures is approximately 4-5 days maximum.


Figure 59: A profile of the first transect across the Florida Straits using 
           data from the OS75 instrument

Figure 60: A profile of the return transect across the Florida Straits using 
           data from the OS75 instrument


Table 22: The sequence log of the OS150 instrument.

         ENX File  Start  Start    End     End   End    BT/WT   Notes
          Number   Date   Time   Ensemble  Date  Time  
         --------  -----  -----  --------  ----  -----  -----  --------
             2       6    05:36    2032      6   07:31   BT    Bad Gyro
             3       6    07:31    1600      6   09:08   BT    Bad Gyro
             4       6    09:09   12416      6   21:03   BT    
             5       6    21:04   17175      7   13:03   BT    
             6       7    13:03   27892      8   13:50   BT    
             7       8    13:51   18355      9   05:16   BT    
             8       9    05:17   57051     10   12:58   BT    
             9      10    12:59   43648     11   13:14   WT    
            10      11    13:14   43122     12   13:12   WT    
            11      12    13:13   43549     13   13:24   WT    
            12      13    13:24   43148     14   13:23   WT    
            13      14    13:23   42735     15   13:08   WT    
            14      15    13:09     722     16   13:15   WT    
            15      16    13:16   40894     17   11:59   WT    
            16      17    12:00   45262     18   13:08   WT    
            17      18    13:09   47425     19   15:30   WT    
            18      19    15:32   37014     20   12:04   WT    
            19      20    12:05   43427     21   12:12   WT    
            20      21    12:13   41955     22   11:31   WT    
            21      22    11:33   42920     23   11:23   WT    
            22      23    11:23   45000     24   12:24   WT    
            23      24    12:24   43253     25   12:28   WT    
            24      25    12:28   43270     26   12:31   WT    
            25      26    12:31   41316     27   11:29   WT    
            26      27    11:29   42861     28   11:18   WT    
            27      28    11:18   44366     29   11:57   WT     GPSG12
            28      29    11:58   45837     30   13:26   WT    
            29      30    13:26    2621     30   14:54   WT    
            30      30    14:54   36290     31   11:04   WT     GPS4000
            31      31    11:05   41969     32   10:23   WT    
            32      32    10:25   42391     33   09:57   WT    
            33      33    09:59   43632     34   10:12   WT    
            34      34    10:12   43950     35   10:38   WT    
            35      35    10:39   43984     36   11:05   WT    
            36      36    11:06   41518     37   10:09   WT    
            37      37    10:10   42618     38   09:51   WT    
            38      38    09:52   30930     38   01:19   WT    
            39      39    01:21   16053     39   10:16   WT    
            40      39    10:17   42028     40   09:38   WT    
            41      40    09:39   42822     41   09:26   WT    
            42      41    09:27   42600     42   09:07   WT    
            43      42    09:08   43665     43   09:24   WT    
            44      43    09:25   43737     44   09:43   WT    
            45      44    09:43   42364     45   09:15   WT    
            46      45    09:16   43343     46   09:21   WT    
            47      46    09:21    8943     46   14:23   WT    
            48      47    14:23    9206     46   22:54   BT    
            49      46    22:54   24387     47   12:27   WT    
            50      47    12:28   39279     48   10:17   WT    
            51      48    10:18   43755     49   10:36   WT    
            52      49    10:36   14227     49   18:31   WT      END
 

Table 23: The sequence log of the OS75 instrument


         ENX File  Start  Start    End     End   End    BT/WT   Notes
          Number   Date   Time   Ensemble  Date  Time  
         --------  -----  -----  --------  ----  -----  -----  --------
            2        6    05:36     343      6   06:03   BT    Bad Gyro
            3        6    06:03      14      6   06:23   BT    Bad Gyro
            4        6    06:23     949      6   07:34   BT    Bad Gyro
            5        6    07:35     993      6   09:09   BT    
            6        6    09:09    7527      6   21:00   BT    
            7        6    21:02   11078      7   13:01   BT    
            8        7    13:02   16603      8   13:46   BT    
            9        8    13:47    5112      9   05:15   BT    
           10        9    05:15   40091     10   12:57   WT    
           11       10    12:57   30651     11   13:11   WT    
           12       11    13:12   30319     12   13:09   WT    
           13       12    13:10   30622     13   13:21   WT    
           14       13    13:22   30348     14   13:20   WT    
           15       14    13:20   30056     15   13:05   WT    
           16       15    13:06     723     16   13:10   WT    
           17       16    13:15   28759     17   11:58   WT    
           18       17    11:59   31866     18   13:09   WT    
           19       18    13:10     790     19   15:31   WT    
           21       19    15:31   25960     20   12:04   WT    
           22       20    12:06   30552     21   12:14   WT    
           23       21    12:14   29504     22   11:33   WT    
           24       22    11:33   30248     23   11:27   WT    
           25       23    11:28   31606     24   12:26   WT    
           26       24    12:27   30378     25   12:27   WT    
           27       25    12:27   30390     26   12:28   WT    
           28       26    12:28   29065     27   11:27   WT    
           29       27    11:27   30156     28   11:17   WT    
           30       28    11:17   31195     29   11:56   WT     GPSG12
           31       29    11:57   32197     30   13:22   WT    
           32       30    13:23    1843     30   14:51   WT    
           33       30    14:51   25568     31   11:03   WT     GPS4000
           34       31    11:03   29610     32   10:27   WT    
           35       32    10:28   29771     33   09:59   WT    
           36       33    10:00   30683     34   10:14   WT    
           37       34    10:14   30917     35   10:40   WT    
           38       35    10:40   30929     36   11:06   WT    
           39       36    11:07   29187     37   10:10   WT    
           40       37    10:10   29967     38   09:51   WT    
           41       38    09:53   30804     39   10:13   WT    
           42       39    10:13   29556     40   09:34   WT    
           43       40    09:35   30125     41   09:23   WT    
           44       41    09:24   29973     42   09:05   WT    
           45       42    09:05   30711     43   09:21   WT    
           46       43    09:22   30766     44   09:40   WT    
           47       44    09:40   29789     45   09:12   WT    
           48       45    09:13   30565     46   09:22   WT    
           49       46    09:23    8943     46   14:23   WT    
           50       46    14:23    6222     46   22:55   BT    
           51       46    22:55   17130     47   12:28   WT    
           52       47    12:28   27613     48   10:18   WT    
           53       48    10:18   30749     49   10:36   WT    
           54       49    10:38   10005     49   18:32   WT      END


14.5.  References

Fischer, J., P. Brandt, M. Dengler, M. Müller, and D. Symonds, (2003), 
    Surveying the Upper Ocean with the Ocean Surveyor: A New Phased Array 
    Doppler Current Profiler. J. Atmos. Oceanic Technol., 20, pp. 742-751.

McDonagh, E.L., et al, Hamersley, D.R.C. and McDonagh, E.L. (eds.) (2009), 
    RRS James Cook Cruise JCO3J, 03 Feb-03 Mar 2009. Hydrographic sections of 
    Drake Passage. Southampton, UK, National Oceanography Centre Southampton, 
    170pp. (National Oceanography Centre Southampton Cruise Report, 39)




15.  IRON, NITROGEN FIXATION AND FILTERING
     David Honey


15.1.  Background and cruise objectives

Cruise D346 provided the perfect opportunity to sample an area of specific 
interest to my PhD, the tropical North Atlantic, with respect to the 
influence of iron (Fe) on nitrogen fixation. Despite the vast abundance of 
molecular nitrogen (N2) in the atmosphere, fixed sources of nitrogen 
(nitrates, nitrites, ammonia, etc) in the oceans can often be in short 
supply. This is related to the strong triple bond between the two atoms of N, 
which results in its relatively inert behaviour. This can induce a limitation 
on biological production as nitrogen provides the fundamental building blocks 
of life, including DNA. The tropical North Atlantic is an area known to 
exhibit high levels of nitrogen fixation and the project aims to investigate 
the role Fe has to play in this system.

Organisms that are able to biologically fix nitrogen are known as diazotrophs 
and the most commonly known are from the genus Trichodesmium. The enzyme 
responsible for this reaction is nitrogenase, which has a high Fe 
requirement. It is believed that the marine diazotrophs provide a significant 
proportion of fixed nitrogen to the oceans. The term heme (or haem) refers to 
the Fe-porphyrin complex that acts as the prosthetic group for a wide range 
of Fe proteins, also known as the hemoproteins. However, it should be noted 
that hemes are not directly involved in the nitrogenase enzyme. There are 3 
specific heme structures commonly represented in biology: hemes a; b; and c. 
Heme b (also referred to as protoheme IX) is considered the most versatile 
form and is associated with globins, cytochrome P450, catalases, peroxidases 
and b-type cytochromes (Caughey (1973)). Therefore, hemeoproteins and 
nitrogenase could potentially highlight the allocation of Fe within these 
nitrogenfixing organisms.

It is undeniable that Fe plays a significant role in mediating phytoplankton 
blooms and, therefore, potentially influences carbon sequestration to the 
oceans. However, it has also been argued that the availability of nitrate 
(NO3-, classical 'biological' view) and/or phosphate (P043-, 'geochemical' 
view) could exclusively or co-limit biological growth and phytoplankton 
biomass (Smith (1984), Codispoti (1989), Tyrrell (1999)). In addition, it has 
been hypothesised that fluctuations in oceanic nitrogen concentration 
influence the atmospheric CO2 concentration over large time scales (i.e. 104 
years) (McElroy (1983)). Therefore, in addition to the obvious interest of CO2 
variation and climate change, it is interesting to note the significant 
relationship between Fe (including heme complexes) and the nitrogen cycle. It 
is hoped that results collected from the cruise will provide an insight 
regarding the allocation of Fe in the region, either to the photosynthetic 
apparatus (heme) or nitrogen fixation (nitrogenase).


15.2.  Sampling and methods

Samples from the surface, chlorophyll maximum and one further 'near-surface' 
depth (usually between the surface and chlorophyll maximum) were collected 
from the CTD which were then filtered onto GF/F's for heme, chlorophyll and 
nitrogenase, as well as POC using ashed-GF/F's. All filters were then stored 
in the -80°C freezer for analysis post-cruise. In addition, waters from 
surface and chlorophyll maximum depths were 'spiked' with 15N2 and incubated at 
sea-surface temperature for 24 hours, before also being filtered onto 
ashed-GF/F's and dried in an oven at 50°C for a further 24 hours. All 
incubation filters were stored in a dry place for analysis postcruise. In 
order to measure total Fe, a GOFLO was deployed once a day throughout the 
main section of the cruise to collect samples from 20m and 40m. Clean 
concentrated nitric acid was then added to the samples in preparation for 
analysis post-cruise.

15.2.1.  Heme

Heme samples were taken from the CTD at three depths per station (surface, 
chlorophyll maximum and one further 'near-surface' depth). Up to 4000ml of 
seawater was filtered onto GF/F filters. Filters were then folded into 
eppendorfs and kept in the -80°C freezer. Analysis will be conducted at NOCS, 
UK using the High Performance Liquid Chromatography (HPLC) with diode array 
spectrophotometry technique described by Gledhill (2007). In total, 388 heme 
samples were collected from 133 stations.

15.2.2.  Chlorophyll-a

Chlorophyll-a samples were taken from the CTD at three depths per station 
(surface, chlorophyll maximum and one further 'near-surface' depth). 500ml of 
seawater was filtered onto GF/F filters. Filters were then folded into 
eppendorfs and kept in the -80°C freezer. Analysis will be conducted at NOCS 
using a Turner fluorometer. In total, 401 chlorophyll-a samples were 
collected from 133 stations.

15.2.3.  FOG

POC samples were taken from the CTD at three depths per station (surface, 
chlorophyll maximum and one further 'near-surface' depth). Up to 4000m1 of 
seawater was filtered onto pre-ashed GF/F filters. Filters were then folded 
into eppendorfs and kept in the -80°C freezer. Filters are to be processed 
and dispatched to Proudman Marine Laboratory (PML) for analysis. In total, 
374 POC samples were collected from 133 stations.

15.2.4.  Nitrogenase

Nitrogenase samples were taken from the CTD at three depths per station 
(surface, chlorophyll maximum and one further 'near-surface' depth). Up to 
3000m1 of seawater was filtered onto GF/F filters. Filters were then folded 
into eppendorfs and kept in the -80°C freezer. When sampling for nitrogenase, 
it was always filtered immediately (i.e. before heme, POC and chlorophyll) 
and then immediately placed in the -80°C freezer in an attempt to minimise 
the degree of degradation of the enzyme. Analysis will be conducted at NOCS. 
In total, 110 nitrogenase samples were collected from 38 stations.

15.2.5.  Nitrogen fixation incubations

Once per day, samples were taken from the CTD at two depths (surface and 
chlorophyll maximum) for the preparation of nitrogen fixation incubations. 
4½L clear bottles were filled with sample water and spiked (injected) with 
4m1 of 15N2 through a septum closure. Filter film was used to adjust light 
levels: surface = 1 x blue; chl max = 1 x blue, 1 x black. The bottles were 
then placed in an incubator on the aft deck using water from the non-toxic 
underway supply, keeping them at approximately surface temperature. After 24 
hours, the bottles were removed and the contents filtered onto pre-ashed GF/F 
filters. Filters were then folded into eppendorfs and placed in a drying oven 
(50°C) for a further 24 hours. Once complete, the eppendorfs were stored in a 
dry place. Analysis will be conducted at NOCS. In total, 78 nitrogen fixation 
incubations were conducted from 39 stations.

15.2.6.  Trace metal analysis

The GOFLO bottle was used to collect water samples that would not be 
contaminated with Fe from the CTD (cable and rosette) or the ship (RRS 
Discovery). The 2L GOFLO was attached to climbing rope (thoroughly rinsed 
with seawater before use) and deployed to 20m and 40m whilst on station. 
These depths were chosen as the first (20m) was sufficiently away from the 
ship to avoid contamination, but to also provide a deeper sample (40m) 
somewhat closer to the chlorophyll maximum. As the instrument was entirely 
deployed by hand, it was not practical to allow the GOFLO to be lowered to 
greater depths. The added counter weight that would be required and possible 
water currents would make the operation too dangerous; especially considering 
it was conducted on the starboard aft-deck only 20m from the CTD. Once 
recovered, the bottle tap was rinsed with Milli-Q. Trace metal clean tubing 
was attached to direct the water samples into previously prepared trace metal 
clean bottles (60ml). 50µl of clean concentrated nitric acid was added to the 
samples in the fume cupboard to allow them to be analysed post-cruise at 
NOCS, UK. In total, trace metal samples were collected from 32 stations.


15.3.  Evaluation

In general, the cruise was extremely successful with over 3000L of water 
filtered across the transect, as well as numerous nitrogen fixation 
incubations and GOFLO samples collected. However, a few small issues were 
raised during the cruise.

15.3.1.  -80°C freezer

One major problem that was apparent throughout the cruise was the reliability 
of the -80°C freezer. Roughly once a week, the temperature would rise to 
approximately -30°C, obviously causing much concern for the affect on the 
samples it contained. The temperature would generally rise extremely quickly 
(50°C in around 2-3 hours) before recovering back to a more suitable 
temperature where it still regularly fluctuated (between -70°C and -80°C). A 
few theories were discussed for this including the warm temperature of the 
hold area where the freezers are stored (next to the engine room and 
incinerator), but also that the freezer was not particularly full (eppendorfs 
containing GF/F's utilise little space and it was only used for this purpose 
during the cruise) reducing the efficiency. The heme, chlorophyll and POC 
samples would not have been greatly affected by the temperature change as 
they can be stored at -20°C (albeit for differing time periods). However, the 
nitrogenase samples are fairly unstable once filtered and difficult to sample 
at the best of times, so are required to be keep at -80°C until analysis. It 
was decided that the freezer would be regularly monitored (every 4 hours) to 
ensure it was still working adequately; a task carried out by the physics 
team during their 4 hourly watchkeeping log. The instrument needs to be 
properly checked once back in port.

15.3.2.  Fume cupboard

Ideally, a fume cupboard was required to add the clean concentration nitric 
acid to the samples taken from the GOFLO bottle. This would allow the 
procedure to be undertaken safely (removes fumes) and reduces the risk of 
contamination. However, the fume cupboard was out of action and could not be 
repaired during the cruise. The problem was sorted by ensuring the acid was 
added in a well-ventilated area and extra precautions were taken to avoid 
contact with sources of contamination (i.e. Fe).

15.3.3.  Volume of water available

At certain stations, not enough water was available to filter at the 3 target 
depths (i.e. surface, chlorophyll maximum and one further 'near-surface' 
depth). Ideally, up to 4L each would be filtered for heme, POC and 
nitrogenase, 0.5L for chlorophyll as well as setting up an incubation, which 
requires another 4½L. Obviously, it cannot be expected that 17L will be made 
available for this sole purpose from 20L Niskin bottles. However, at times 
only 5L remained once all the other teams had sampled which left very little 
opportunity to adequately filter for these measurements. The situation was 
rectified by asking others to be less wasteful with the water, although it 
was understood that thorough rinsing was required (e.g. CFC, oxygen, carbon). 
In addition, specific bottle depths were replicated whenever possible (only 
at shallower stations) to ensure plenty of water was available.


15.4.  References

Caughey WS (1973), Iron porphyrins - hemes and hemins. In: Eichham GL (ed) 
    Inorganic Biochemistry. Elsevier, Amsterdam, pp 797-831

Codispoti LA (1989), Phosphorus vs. nitrogen limitation of new and export 
    production. In: Berger WH, Smetacek VS, Wefer G (eds) Productivity of the 
    ocean: Past and present: Report of the Dahlem workshop. John Wiley and 
    Sons, New York, pp 377-394

Gledhill M (2007), The determination of heme b in marine phyto- and 
    bacterioplankton. Marine Chemistry, 103, pp. 393-403

McElroy MB (1983), Marine biological controls on atmospheric CO2 and climate, 
    Nature, 302, pp. 328-329

Smith SV (1984), Phosphorus versus nitrogen limitation in the marine 
    environment, Limnology and Oceanography, 29, pp. 1149-1160

Tyrrell T (1999), The relative influences of nitrogen and phosphorus on 
    oceanic primary production, Nature, 400, pp. 525-531


Table 24: List of Samples collected for nitrogen fixation and filtering

                         Filtered Volume (L)                  N2 Fix
Stn  Samp  Btl  Depth  Heme   POC  Chlorophyll  Nitrogenase  Incubation  GOFLO
---  ----  ---  -----  -----  ---  -----------  -----------  ----------  -----
  1  1      24    10    1.5   1.5      0.5          0.0          No      No
     2      21    50    1.5   1.5      0.5          0.0          No      
     3      18   180    2.0   2.0      0.5          0.0          No      
  2  1      21     5    1.5   1.5      0.5          0.0          No      No
     2      13    50    1.0   1.0      0.5          0.0          No      
     3       4   101    1.0   1.0      0.5          0.0          No      
  3  1      20     5    1.5   1.5      0.5          0.0          No      No
     2      14    50    1.5   1.5      0.5          0.0          No      
     3       8   150    1.5   1.5      0.5          0.0          No      
  4  1      22     5    2.0   2.0      0.5          0.0          No      No
     2      18    50    1.5   1.5      0.5          0.0          No      
     3      14   100    2.0   2.0      0.5          0.0          No      
  5  1      23     5    2.0   2.0      0.5          0.0          No      No
     2      20    50    2.0   2.0      0.5          0.0          No      
     3      16   150    2.5   2.5      0.5          0.0          No      
  6  1      23    10    2.0   2.0      0.5          0.0          No      No
     2      21    50    2.0   2.0      0.5          0.0          No      
     3      16   200    3.0   3.0      0.5          0.0          No      
  7  1      24     5    2.5   2.5      0.5          0.0          No      No
     2      21    50    2.5   2.5      0.5          0.0          No      
     3      18   150    2.5   2.5      0.5          0.0          No      
  8  1      23    10    2.0   2.0      0.5          2.0          No      No
     2      21    50    2.0   2.0      0.5          2.0          No      
     3      19   100    3.0   3.0      0.5          2.0          No      
  9  1      24     5    2.0   2.0      0.5          0.0          No      No
     2      21    50    2.0   2.0      0.5          0.0          No      
     3      18   150    1.5   1.5      0.5          0.0          No      
 10  1      22    10    2.0   2.0      0.5          0.0          No      No
     2      18    50    2.0   2.0      0.5          0.0          No      
     3      14   100    2.5   2.5      0.5          0.0          No      
 11  1      21     5    2.5   2.5      0.5          0.0          No      No
     2      17    50    2.5   2.5      0.5          0.0          No      
     3      14   150    2.5   2.5      0.5          0.0          No      
 12  1      24    10    2.0   2.0      0.5          0.0          No      No
     2      14    50    2.0   2.0      0.5          0.0          No      
     3       9   100    1.5   1.5      0.5          0.0          No      
 13  1      23     5    2.0   2.0      0.5          0.0          No      No
     2      10    50    2.0   2.0      0.5          0.0          No      
     3       2   166    2.0   2.0      0.5          0.0          No      
 14  1      24     5    2.0   2.0      0.5          0.0          Yes     No
     2      21    25    2.0   2.0      0.5          0.0          Yes      
     3      18    50    1.5   1.5      0.5          0.0          No      
 15  1      24     5    2.0   2.0      0.5          0.0          No      No
     2      21    25    3.0   3.0      0.5          0.0          No      
     3      20    50    2.0   2.0      0.5          0.0          No      
 16  1      24     5    2.0   2.0      0.5          0.0          No      No
     2      21    50    2.0   2.0      0.5          0.0          No      
     3      19   100    2.0   2.0      0.5          0.0          No      
 17  1      24     5    2.0   2.0      0.5          0.0          No      No
     2      21    50    2.0   2.0      0.5          0.0          No      
     3      19   100    2.0   2.0      0.5          0.0          No      
 18  1      -     -     0.0   0.0      0.0          0.0          No      No
     2      -     -     0.0   0.0      0.0          0.0          No      
     3      -     -     0.0   0.0      0.0          0.0          No      
 19  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      22    50    2.5   2.5      0.5          0.0          No      
     3      20   100    2.5   2.5      0.5          0.0          No      
 20  1      24     5    1.5   1.5      0.5          0.0          Yes     20m
     2      23    50    1.5   1.5      0.5          0.0          Yes      
     3      22   100    2.0   2.0      0.5          0.0          No      
 21  1      24     5    3.0   2.5      0.5          2.0          No      No
     2      23    50    3.0   3.0      0.5          2.0          No      
     3      22   100    2.5   2.0      0.5          2.0          No      
 22  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 23  1      24     5    2.0   2.0      0.5          2.0          Yes     No
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22   100    2.5   2.5      0.5          3.0          Yes      
 24  1      24     5    2.0   2.0      0.5          3.0          No      No
     2      22   120    3.5   3.0      0.5          3.0          No      
     3      21   175    3.0   3.0      0.5          3.0          No      
 25  1      24    10    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   105    3.5   3.5      0.5          0.0          No      
 26  1      24    10    2.0   2.0      0.5          2.0          Yes     No
     2      23    50    2.5   2.5      0.5          3.0          No      
     3      22   100    2.5   2.0      0.5          3.0          Yes      
 27  1      24    10    3.0   3.0      0.5          3.0          No      No
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22   100    3.0   1.5      0.5          3.0          No      
 28  1      24    10    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 29  1      24    10    3.0   3.0      0.5          0.0          No      No
     2      22    50    3.0   3.0      0.5          0.0          No      
     3      20   100    3.0   3.0      0.5          0.0          No      
 30  1      24     5    0.0   0.0      0.5          0.0          Yes     No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    2.0   2.0      0.5          0.0          Yes      
 31  1      24     5    3.0   3.0      0.5          3.0          No      20m, 40m  
     2      22   100    3.0   3.0      0.5          3.0          No      
     3      21   175    4.0   3.0      0.5          3.0          No      
 32  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          0.0          No      
 33  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      22    50    3.0   2.5      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          0.0          No      
 34  1      24    10    3.0   3.0      0.5          0.0          No      No
     2      22   100    3.0   3.0      0.5          0.0          No      
     3      21   175    3.0   3.0      0.5          0.0          No      
 35  1      24    10    0.0   0.0      0.5          2.0          Yes     20m, 40m  
     2      22   100    0.0   0.0      0.5          2.0          Yes      
     3      21   175    3.0   3.0      0.5          3.0          No      
 36  1      24    10    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 37  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   130    3.0   3.0      0.5          0.0          No      
 38  1      24     5    2.5   2.5      0.5          2.0          No      No
     2      23    50    2.5   2.5      0.5          3.0          No      
     3      22   100    3.0   3.0      0.5          3.0          No      
 39  1      24     5    2.5   0.0      0.5          2.0          Yes     No
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22    80    3.0   3.0      0.5          3.0          Yes      
 40  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   120    3.0   3.0      0.5          0.0          No      
 41  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 42  1      24    10    1.25  0.0      0.5          0.0          Yes     20m
     2      22   100    3.0   3.0      0.5          3.0          Yes      
     3      21   175    3.0   2.5      0.5          3.0          No      
 43  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 44  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22    75    3.0   3.0      0.5          0.0          No      
 45  1      24     5    2.0   2.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          Yes      
 46  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 47  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 48  1      24     5    0.0   0.0      0.5          0.0          Yes     20m
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22   100    2.5   2.5      0.5          2.0          Yes      
 49  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   110    3.0   3.0      0.5          0.0          No      
 50  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 51  1      24     5    2.5   2.0      0.5          0.0          Yes     No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    2.5   2.5      0.5          0.0          Yes      
 52  1      24     5    3.0   3.0      0.5          3.0          No      No
     2      23    50    2.5   2.0      0.5          3.0          No      
     3      22   100    3.0   3.0      0.5          3.0          No      
 53  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 54  1      24     5    2.5   0.0      0.5          0.0          Yes     20m, 40m  
     2      22   100    1.5   0.0      0.5          0.0          Yes      
     3      21   175    3.0   3.0      0.5          0.0          No      
 55  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 56  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 57  1      24     5    2.0   2.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    2.0   2.0      0.5          0.0          Yes      
 58  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 59  1      24     5    3.0   3.0      0.5          0.0          Yes     No
     2      22   100    3.0   3.0      0.5          0.0          Yes      
     3      21   175    3.0   3.0      0.5          0.0          No      
 60  1      23    50    3.0   3.0      0.5          3.0          No      No
     2      22   100    3.0   3.0      0.5          3.0          No      
     3      21   175    3.0   3.0      0.5          3.0          No      
 61  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 62  1      24     5    0.0   0.0      0.5          0.0          Yes     No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          Yes      
 63  1      23    50    3.0   3.0      0.5          0.0          No      20m, 40m  
     2      22   100    3.0   3.0      0.5          0.0          No      
     3      21   175    3.0   3.0      0.5          0.0          No      
 64  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 65  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 66  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.5   4.0      0.5          0.0          No      
     3      22   100    3.0   3.5      0.5          0.0          No      
 67  1      24     5    2.5   0.0      0.5          0.0          Yes     No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    2.5   0.0      0.5          0.0          Yes      
 68  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 69  1      24    10    1.75  0.0      0.5          0.0          Yes     No
     2      22   100    2.5   2.5      0.5          0.0          Yes      
     3      21   175    3.0   3.0      0.5          0.0          No      
 70  1      24     5    3.0   3.0      0.5          3.0          No      No
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22   100    3.0   3.0      0.5          3.0          No      
 71  1      24    10    2.0   2.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   0.0      0.5          0.0          No      
 72  1      24     5    3.0   0.0      0.5          2.0          Yes     20m 40m 
     2      23    50    3.0   3.0      0.5          3.0          No      
     3      22   100    3.0   3.0      0.5          3.0          Yes      
 73  1      24     5    0.0   0.0      0.4          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.0   0.0      0.5          0.0          Yes      
 74  1      24     5    3.0   3.0      0.5          3.0          No      No
     2      22   100    3.0   3.0      0.5          3.0          No      
     3      21   175    3.0   3.0      0.5          3.0          No      
 75  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 76  1      24     5    3.0   3.0      0.5          3.0          Yes     20m, 40m  
     2      22    50    3.0   3.0      0.5          3.0          No      
     3      21   100    2.25  0.0      0.5          2.0          Yes      
 77  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      22   100    3.0   3.0      0.5          0.0          No      
     3      21   175    3.0   3.0      0.5          0.0          No      
 78  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          0.0          No      
 79  1      24     5    3.0   3.0      0.5          0.0          Yes     20m, 40m  
     2      22    50    3.0   3.0      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          0.0          Yes      
 80  1      24     5    2.5   2.5      0.5          2.0          No      No
     2      23    25    3.0   3.0      0.5          3.0          No      
     3      21   100    3.0   3.0      0.5          3.0          No      
 81  1      -     -     0.0   0.0      0.0          0.0          No      No
     2      -     -     0.0   0.0      0.0          0.0          No      
     3      -     -     0.0   0.0      0.0          0.0          No      
 82  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    25    3.0   3.0      0.5          0.0          No      
     3      22    50    3.0   3.0      0.5          0.0          No      
 83  1      24    10    2.0   1.75     0.5          0.0          Yes     20m, 40m  
     2      22   100    2.25  2.0      0.5          0.0          Yes      
     3      21   175    3.0   3.0      0.5          0.0          No      
 84  1      24     5    0.0   3.0      0.5          3.0          No      No
     2      23    25    3.0   3.0      0.5          3.0          No      
     3      21   100    2.0   2.0      0.5          3.0          No      
 85  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 86  1      24    10    3.0   3.0      0.5          3.0          Yes     20m, 40m  
     2      22    50    3.0   2.25     0.5          3.0          No      
     3      21   100    2.5   2.0      0.5          3.0          Yes      
 87  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      22    50    3.0   3.0      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          0.0          No      
 88  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    3.0   3.0      0.5          0.0          No      
 89  1      24     5    2.5   2.5      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.0   3.0      0.5          0.0          No      
     3      22   100    2.0   2.0      0.5          0.0          Yes      
 90  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 91  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 92  1      24     5    0.0   0.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          Yes      
 93  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      23    50    3.5   2.5      0.5          3.0          No      
     3      21   175    3.5   3.0      0.5          3.0          No      
 94  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 95  1      24     5    0.0   0.0      0.4          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    2.0   0.0      0.5          0.0          Yes      
 96  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.0      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 97  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
 98  1      24     5    3.0   3.0      0.5          3.0          Yes     20m, 40m  
     2      22    50    3.0   2.5      0.5          0.0          No      
     3      21   100    3.0   3.0      0.5          3.0          Yes      
 99  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
100  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      21   175    3.5   3.5      0.5          0.0          No      
101  1      24     5    2.5   2.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.0   1.75     0.5          0.0          Yes      
102  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
103  1      24     5    0.0   0.0      0.5          3.0          Yes     20m, 40m  
     2      23    50    3.5   3.25     0.5          3.0          No      
     3      22   100    3.5   3.0      0.5          3.0          Yes      
104  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22    88    3.5   3.5      0.5          0.0          No      
105  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   130    3.5   3.5      0.5          0.0          No      
106  1      23     5    3.5   3.5      0.5          3.0          Yes     20m, 40m  
     2      22    50    3.5   3.5      0.5          3.0          No      
     3      20   100    3.5   3.5      0.5          3.0          Yes      
107  1      24   5.0    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
108  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22    77    3.5   3.5      0.5          0.0          No      
109  1      24     5    3.5   0.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   0.0      0.5          0.0          Yes      
110  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
111  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      23    50    3.5   3.5      0.5          3.0          No      
     3      22   100    3.5   3.5      0.5          3.0          No      
112  1      24     5    3.5   0.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22    85    3.5   3.5      0.5          0.0          Yes      
113  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
114  1      24     5    2.5   2.25     0.5          0.0          Yes     20m, 40m  
     2      22    65    3.5   3.5      0.5          0.0          Yes      
     3      21   175    3.5   3.5      0.5          0.0          No      
115  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      22   100    3.5   3.5      0.5          0.0          No      
116  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      22    75    3.5   3.5      0.5          0.0          No      
     3      21   100    3.5   3.5      0.5          0.0          No      
117  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      23    50    3.5   3.5      0.5          3.0          No      
     3      22   100    3.5   3.5      0.5          3.0          No      
118  1      24     5    2.25  2.0      0.5          0.0          Yes     20m, 40m  
     2      23    50    3.5   3.5      0.5          0.0          No      
     3      21   100    3.5   3.5      0.5          0.0          Yes      
119  1      24     5    2.5   2.25     0.5          3.0          No      No
     2      23    25    3.5   3.0      0.5          3.0          No      
     3      21   100    3.5   0.0      0.5          3.0          No      
120  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      21    75    3.5   3.5      0.5          0.0          No      
     3      20   100    3.5   3.5      0.5          0.0          No      
121  1      24     5    3.5   3.5      0.5          0.0          Yes     20m, 40m  
     2      22    50    3.5   3.5      0.5          0.0          No      
     3      21   100    2.0   0.0      0.5          0.0          Yes      
122  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      20    75    3.0   2.25     0.5          3.0          No      
     3      19   100    3.5   3.5      0.5          3.0          No      
123  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      22    25    3.5   3.5      0.5          3.0          No      
     3      20   100    3.5   3.5      0.5          3.0          No      
124  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      21    50    3.5   3.5      0.5          0.0          No      
     3      19   100    3.5   3.5      0.5          0.0          No      
125  1      24     5    3.5   3.5      0.5          0.0          Yes     20m, 40m  
     2      19   100    0.0   0.0      0.5          0.0          Yes      
     3      18   175    3.5   3.5      0.5          0.0          No      
126  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      21    75    3.5   3.5      0.5          3.0          No      
     3      20   100    3.5   3.5      0.5          3.0          No      
127  1      24     5    3.5   3.5      0.5          0.0          No      No
     2      22    50    3.5   3.5      0.5          0.0          No      
     3      20    75    3.5   3.5      0.5          0.0          No     
128  1      24     5    3.5   3.25     0.5          3.0          No      20m, 40m
     2      23    25    3.5   3.5      0.5          3.0          No    
     3      21    80    3.5   3.5      0.5          3.0          No    
129  1      24     5    3.5   3.5      0.5          3.0          Yes     20m, 40m
     2      21    50    3.5   3.5      0.5          3.0          No    
     3      19    95    3.5   3.5      0.5          3.0          Yes    
130  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      22    25    3.5   3.5      0.5          3.0          No    
     3      19   100    3.5   3.5      0.5          3.0          No    
131  1      24     5    3.5   3.5      0.5          3.0          No      No
     2      20    60    3.5   3.5      0.5          3.0          No    
     3      17   175    3.5   3.5      0.5          3.0          No    
132  1      24     5    3.0   3.0      0.5          3.0          Yes     20m, 40m
     2      19    75    2.5   2.25     0.5          0.0          Yes    
     3      18   100    3.0   3.0      0.5          3.0          No    
133  1      24     5    3.0   3.0      0.5          0.0          No      No
     2      19    75    3.0   3.0      0.5          0.0          No    
     3      18   100    3.0   3.0      0.5          0.0          No    
134  1      24     5    3.0   3.0      0.5          3.0          No      No
     2      20    50    3.0   3.0      0.5          3.0          No    
     3      14   100    3.0   3.0      0.5          3.0          No    
135  1      24     5    3.0   3.0      0.5          3.0          Yes     20, 20m, 40m   
     2      20    40    3.0   3.0      0.5          3.0          Yes    
     3      13   100    3.0   3.0      0.5          3.0          No  





16.  INORGANIC NITRATE AND PHOSPHATE AT NANOMOLAR CONCENTRATIONS
     François-Eric Legiret


16.1.  Cruise objectives

My main objective for cruise D346 was to measure nanomolar concentrations of 
nitrate and phosphate. This will be the first time that accurate nutrient 
measurements at the surface are achieved.


16.2.  Method

Gas-segmented continuous-flow colorimetric method was used for both phosphate 
and nitrate. The chemical methods are described by Grasshoff et al., (1983). 
The autoanalyser is coupled with liquid waveguide capillary cells (LWCC) to 
achieve nanomolar levels of detection following the methods described by 
Patey et al. (2008).

Blanks were measured with Milli-Q and low nutrients seawater (LNSW), this 
water being aged several months in the lab at room temperature and with 
light. Standards were measured in Milli-Q and LNSW to correct for the salt 
effect from the seawater matrix.


Figure 61: The nitrate+nitrite SCFA-LWCC system below the phosphate system. 
           The glass coils used are 1.6-mm ID.

Figure 62: The Phosphate SCFA-LWCC system. The glass coils used are 1.6-mm 
           ID.


16.3.  System

Samples were drawn from Niskin bottles on the CTD into 10% HCl clean 60ml 
LDPE bottles from Nalgene and kept refrigerated at approximately 4°C until 
analysis.

An auto-sampler from Skalar has been added ahead of the system. Sampling time 
was 150 seconds and the wash time was 150 seconds leading to 1:1 ratio.

Analysis was undertaken on a modified Burkard Autoanalyser with one main 
peristaltic pump and reaction channels, one for phosphate and one for 
nitrate.

The detection cells were Liquid Core Waveguide Capillary Cells (LWCC) of 2m 
in length, from WPI instruments. Spectrophotometric detection was achieved 
using tungsten lamps as light sources and 2 spectrometers. These devices were 
linked with fiber-optic connections. All of this equipment was supplied by 
OceanOptics.

Data acquisition was undertaken using the software Spectrasuite in 2 steps. 
First the spectrum of the coloured complex provides a value of the signal 
intensity for each wavelength. The absorbance of the signal is measured for 
the wavelength of interest for each compound. The selected wavelengths for 
nitrate and phosphate are respectively 540nm and 710nm.


16.4.  Performance

The general performance of the analyser is monitored via the following 
parameters: sensitivity, baseline value, intensity of the signal, regression 
coefficient of the calibration curve and cadmium column efficiency. The 
efficiency of the cadmium column was checked and cleaned if required. The 
sensitivity of the analyser stayed relatively constant throughout the cruise.

NB: Channels were washed daily with 10% triethanolamine, methanol and 2M HCl.

Several problems have been encountered:

• The first was with the software's capability to read both channels 
  simultaneously. The software does not support the function of being given 
  two references, one for each channel. We had to add a reference monitor 
  required for the second acquisition.

• The second problem was due to contamination of samples in the lab. This 
  problem had been anticipated so a bag, flushed with oxygen-free nitrogen, 
  was successfully set around the sampler to prevent any contamination from 
  the air. The first sample read was repeated at the end of the run to make 
  ensure there was no contamination.


16.5.  Results

Overall 135 stations were sampled from the surface down to a depth of 300m. 
System calibrations enabled us to validate the quality of the signal.


Figure 63: Phosphate calibration curve


Further cross-linked analysis of this new dataset with parameters measured on 
the cruise will be conducted.


Figure 64: Contour plots of nitrate and phosphate concentrations in the upper 
           layer along the transect


16.6.  References

Grasshoff, K., Ehrhardt, M., and Kremling, K., (1983) Methods of Seawater 
    Analysis, Verlag Chemie, Weinheim.

Patey, M. D., Rijkenberg, M.J.A., Statham, P.J., Mowlem, M., Stinchcombe, 
    M.C. and Achterberg, E.P. (2008) Determination of nitrate and phosphate 
    in seawater at nanomolar concentrations, TrAC Trends in Analytical 
    Chemistry, 27 (2): 169-182. 





17.  NEAR-SURFACE AND SEA SURFACE SALINITY STUDY FOR SMOS CAL/VAL
     Chris Banks


17.1.  Introduction

In November 2009, ESA launched the Soil Moisture and Ocean Salinity satellite 
(SMOS). The payload of SMOS is the Microwave Imaging Radiometer using 
Aperture Synthesis (MIRAS) and this instrument is the first attempt to 
measure ocean salinity and soil moisture from space. Using complex 
cross-correlations of the 69 receivers, SMOS will provide global coverage of 
ocean salinity every three days with an estimated accuracy of '~1psu (pixel 
size 35-50km). This accuracy can be improved to ~0.lpsu by combining data 
over 10 days and 200 x 200km, or 30 days and 100 x 100km.

As part of the calibration and validation (Cal/Val) of the SMOS satellite the 
National Oceanography Centre, Southampton is studying the salinity of the 
North Atlantic during the initial data collection phase. In particular, data 
from the underway conductivity and temperature sensors during D346 is of 
importance. However, the salinity as measured by SMOS relates to the top few 
centimetres rather than the ~5.5m depth of the underway water inlet (or the 
depths of a few metres gathered by other underway systems, buoys or floats). 
Additional data have been gathered throughout the cruise with an aim of 
understanding salinity variability in the top 10m likely to impact on 
differences between SMOS and other measurement systems.

Two main approaches have been used for this purpose in addition to data from 
the underway system and CTDs. The first method comprised a handheld CT probe, 
and the second used a tethered buoy system both intended to look at 
variability at different depths. The two approaches are discussed in the 
following sections and the preliminary results are presented.


17.2.  Handheld CT sensor

The lower Sm of the cable of the YSI 30 handheld conductivity (salinity), 
temperature (CT) probe was marked at 1-metre intervals using different 
coloured tape. This probe provides salinity and temperature values to 1 
decimal place and was calibrated just before being air freighted for D346. 
During occupation of some CTD stations the probe was lowered into the water 
from the starboard side and values of salinity and temperature were noted on 
the way down and the way up for each of the intervals. In addition, an effort 
was made to hold the sensor as close to the surface as possible and this 
represented the surface value. Later on in the cruise (from 19 January), the 
number of markings and maximum depth were increased to 10m.

In order to reduce the depth at which surface salinity was measured (i.e. the 
top few cm), the probe was attached to a piece of wood using reusable cable 
ties from 26th January onwards. To prevent the cable sinking the sensor, an 
empty drink bottle was attached approximately 1m from the probe. This 
arrangement was deployed at the same time as the measurements to 10m depth.


17.3.  Tethered buoy system

In order to investigate the near surface salinity, it was planned to deploy a 
system of CT sensors vertically on a buoy tethered to the ship during the 
occupation of CTD stations. NOCS, in collaboration with the School of 
Electronics and Computer Science, University of Southampton, are developing a 
new 'lab-on-a-chip' salinitytemperature sensor and eight of these sensors 
were obtained for the purposes of the SMOS Cal/Val project. In addition, D346 
provided an opportunity for deployment of the sensors in an oceanic rather 
than laboratory setting.

The sensors are mounted at one end of a cylindrical pot (Figure 65) with a 
removable fixing disc at the other end. The sensors are held inside by 
screwing on the lid (with an integral guard to protect the sensor head) and 
sealed against the plate (Figure 65a) with an 'o' ring. The fixing disc has a 
channel into which the rope is placed and then held in place by attaching to 
the pot with four screws (Figure 65).

Shortly before the cruise, whilst the sensors were still in the UK, a problem 
was noted with the temperature sensor. To provide a working solution for the 
purposes of the cruise a thermistor was added to the arrangement by drilling 
through the plate holding the sensor (see Figure 65a).


Figure 65: Photographs showing a) internal arrangement of sensor 'pot'; b) 
           sensor attached to buoy and c) close up of sensors on rope (also 
           showing handheld CT probe)


In order to test the sensors, they were placed in a bucket being replenished 
by the non-toxic seawater supply on 6th January. After downloading the data 
it became clear that there were issues with the calibration of the sensors. 
In addition, one of the pots had leaked allowing seawater in. Other pots also 
leaked when the system was tested over the starboard side to a depth of ~5m.

One possible reason was that the difficulties were caused by the presence of 
bubbles in the channel (Figure 65a). Two of the sensors were then weighted 
down and then left to operate inside a coolbox in the Constant Temperature 
(CT) laboratory ensuring (by shaking and close inspection) that all bubbles 
had been removed. However, this failed to solve the issue and the temperature 
values, not dependent on the channel, were also incorrect.

As the thermistors were added after the calibration it was suggested that the 
calibration should be repeated. By using the coolbox in the CT laboratory 
with various salinity values, a calibration exercise was carried out using 
the four remaining sensors that had not leaked over the next few days. 
Unfortunately, one of the pots leaked during the calibration exercise leaving 
three working sensors.

On 18th January, two sensors were attached to a tethered buoy and deployed 
off the stem during CTD Station 51. Upon recovery, one of the pots had leaked 
and so the battery was disconnected and the electronics rinsed thoroughly in 
deionised water. The temperature measured by the remaining instrument was 
approximately -60°C. However, by taping the battery to the terminals the 
problem of the instrument resetting itself with the slightest loss in voltage 
was removed.

The two remaining instruments (#4 and #5) were now producing consistent 
values of salinity and temperature. The tethered system was deployed at 20 
subsequent CTD stations, at depths varying between ~0.3 - 3.0m. However, they 
will require an extensive post-cruise calibration and as such no values of 
SSS and SST are reported here.

Also developed throughout the cruise were a variety of different approaches 
to tethering the sensors to the ship. Initially the setup was simply a tether 
from the ship to a single Polyform A2 buoy weighted with a length of chain 
and the sensors attached onto the rope holding the chain. However, in order 
to reduce the snatch from the ship, as it moved relative to the sensors, a 
chain between buoys was used so that any movement of the ship was first taken 
up in the chain as the chain tended to sink and pull the buoys together. Two 
variations of the system are shown in Figure 66 and the final setup of the 
system is shown in Figure 67.

Figure 66: Photographs of showing the development of the near surface 
           salinity buoy system showing a) 2 sensors mounted on initial 5m 
           long chain-weighted rope; b) and c) showing later shallower, 
           lighter system.

Figure 67: Diagrammatic representation of final system for near surface 
           salinity measurements.


17.4.  Validation using the non-toxic supply

As the sensors were observed to be taking some time to equilibrate with the 
temperature of the sea, it was decided to place them in a bucket being 
replenished with the underway sea water supply. This had the additional 
benefit of providing useful validation data as the temperature and salinity 
of this supply are constantly monitored (see Section 10).

As there was limited variability in the temperature (and salinity) 
encountered on the trans-Atlantic section the sensors were left in the bucket 
for the northward leg of the cruise towards Lisbon. These data will provide 
additional useful validation of the sensors as they show the T/S properties 
of the surface water from 13:20 on 15th February (27°54.7N, 13°24.6W) to 
15:33 on 17th February (35°10.8N, 10°35.8W).


17.5.  Results of near surface salinity investigations

The summary data for the handheld CT sensor investigations are detailed in 
Table 25 for both salinity and temperature. The salinity and temperature 
values given as 010m represent the mean (and standard deviation) of all 
measurements from surface to 10m depth (but not floater measurements). As 
such, these values provide a basis of comparing near surface salinity with 
surface salinity as measured by the floater.

The relationship between the two estimates of SSS and SST from the handheld 
and that from the ships' underway TSG are shown in Figure 68. The underway 
TSG data in these plots represent the mean SST or SSS measured in a 20 minute 
interval either side of the time of the deployment of the handheld sensor. As 
the handheld system was only deployed when the ship was on station, the 
values from the TSG effectively remain constant (on the level of precision 
measured by the handheld probe, i.e. to 1 decimal place).

The values of salinity and temperature of the water in the water bottle annex 
(WBA) as measured by the underway system and sensors #4 and #5 during the 
northward cruise between 15th and 17th February are plotted in Figure 67. 
Whilst the values of temperature seem to be in general agreement, there 
clearly needs to be further investigation of the new sensors response to 
salinity.


Table 25: Times, dates, locations and summary data for deployment of handheld 
          CT sensor during D346

 Time and Date    CTD    Lon         Lat        S      T    Salinity  Sal.    Temp.   Temp.
                  Stn.                        float  float   0-10m    surf.   0-10m   surf.
----------------  ---  ----------  ---------  -----  -----  --------  ----  --------  -----
1920  08/01/2010   14  76°55.83W   26°30.03N    -     -     36.6±0.0   -    23.8±0.0   -
1415  13/01/2010   34  74°14.71W   26°29.82N    -     -     36.8±0.0   -    24.3±0.1   -
1900  13/01/2010   35  73°56.26    26°30.17     -     -     36.9±0.1   -    24.6±0.0   -
2050  14/01/2010   39  72°27.83W   26°30.15N    -     -     36.8±0.0   -    23.9±0.0   -
1840  15/01/2010   42  71°21.63    26°29.76     -     -     36.9±0.1   -    23.7±0.0   -
1735  16/01/2010   45  70°15.93W   25°42.20N    -     -     36.9±0.0   -    23.7±0.0   -
1730  17/01/2010   48 -68.85       24.5°        -     -     36.9±0.0   -    24.4±0.0   -
1738  18/01/2010   51  66°56.25    24°29.97     -     -     36.9±0.1   -    25.1±0.0   -
1130  19/01/2010   53  65°29.39    24°30.03     -     -     36.5±0.0   -    25.1±0.0   -
1730  19/01/2010   54  64°46.02    24°29.94     -     -     36.5±0.1   -    25.2±0.0   -
1125  20/01/2010   56  63°17.53    24°29.74N    -     -     36.4±0.1   -    25.4±0.0   -
1820  20/01/2010   57  62°33W      24°30N       -     -     36.3±0.0   -    25.4±0.1   -
1225  21/01/2010   59  61°5.38W    24°30.1      -     -     36.5±0.1   -    25.1±0.0   -
1820  21/01/2010   60  60°21       24°30        -     -     36.4±0.0   -    25.2±0.1   -
1300  22/01/2010   62  58°53.55W   24°29.98     -     -     37±0.0     -    24.9±0.0   -
1945  22/01/2010   63  58°9.21W    24°29.89N    -     -     37.1±0.0   -    25±0.0     -
1150  23/01/2010  200  57°3.13077  24°29.8716   -     -     37±0.0     -    24.3±0.0   -
1254  26/01/2010   71  52°50.43W   25°6.91N    37.4  24.3   37.4±0.0  37.4  24.3±0.0  24.3
1800  26/01/2010   72  52°17.37W   25°4.58N    37.2  24     37.3±0.0  37.2  24±0.0    24
1300  27/01/2010   73  51°44.42W   25°1.12N    37.3  23.4   37.3±0.0  37.3  23.5±0.0  23.4
2130  27/01/2010   74  51°11.11W   24°56.20N   37.4  23.7   37.3±0.0  37.4  23.8±0.0  23.7
1205  28/01/2010   76  50°5.37W    24°40.09    36.5  24     37.5±0.0  36.5  24.2±0.0  24
1850  28/01/2010   77  49°32.06W   24°31.25N   37.4  23.7   37.4±0.1  37.4  23.8±0.0  23.7
1130  29/01/2010   79  48°28.42W   24°11.77    37.2  23.7     -       37.2  #DIV/0!   23.7
1720  29/01/2010   80  47°56.10W   24°3.93N    37.3  23.6   37.4±0.1  37.3  23.6±0.0  23.6
1625  30/01/2010   83  46°20.06W   23°52.4N    37.2  23.9   37.4±0.1  37.2  23.9±0.0  23.9
1510  31/01/2010   86  44°43.94W   23°39.98N   37.5  23.8   37.5±0.0  37.5  23.9±0.0  23.8
2005  31/01/2010   87  44°12.39W   23°32.19N   37.1  23.6   37.5±0.0  37.1  23.7±0.0  23.6
1145  01/02/2010   89  43°8.35W    23°22.24N   37.5  23.8   37.5±0.0  37.5  23.9±0.0  23.8
1835  01/02/2010   90  42°35.96W   23°14.96N   37.5  23.8   37.5±0.0  37.5  23.9±0.0  23.8
0900  02/02/2010   92  40°56.30W   23°31.03N   37.6  23.8   37.5±0.0  37.6  23.8±0.0  23.8
1900  02/02/2010   93  40°6.22W    23°40.00N   37.5  23.9   37.5±0.0  37.5  23.9±0.0  23.9
1230  03/02/2010   95  38°25.96W   23°56.05N   37.7  23.6   37.6±0.0  37.7  23.6±0.0  23.6
2050  03/02/2010   96  37°36.21W   24°5.07N    37.5  23.6   37.6±0.0  37.5  23.6±0.0  23.6
1440  04/02/2010   98  35°55.67W   24°21.30N   37.5  23.5   37.6±0.1  37.5  23.5±0.0  23.5
1125  05/02/2010  100  34°24.90W   24°29.64N   37.5  22.8   37.6±0.1  37.5  22.8±0.0  22.8
1550  05/02/2010  202  34°02.95W   24°30.54N   37.6  23.2   37.6±0.0  37.6  23.3±0.0  23.2
2025  05/02/2010  101  33°43.90W   24°29.88N   37.6  23.1   37.6±0.0  37.6  23.1±0.0  23.1
1225  06/02/2010  103  33°21.28W   24°29.37N   37.4  23     37.5±0.1  37.4  23.1±0.1  23
1830  06/02/2010  104  31°41.12W   24°29.95N   37.4  23     37.5±0.0  37.4  22.9±0.0  23
1130  07/02/2010  106  30°19.29W   24°29.51N   37.3  22.85  37.4±0.0  37.3  22.9±0.0  22.85
2033  07/02/2010  107  29°39.42W   24°30.12N   37.5  23.3   37.4±0.0  37.5  23.4±0.0  23.3
1400  08/02/2010  109  28°16.82W   24°29.88N   37.3  22.8   37.3±0.0  37.3  22.8±0.1  22.8
0915  09/02/2010  111  26°55.18W   24°30.98N   37.3  23.2   37.2±0.0  37.3  23.3±0.0  23.2
1545  09/02/2010  112  26°13.40W   24°30.25N   37.2  23.2   37.1±0.1  37.2  23.2±0.0  23.2
1000  10/02/2010  114  24°50.82W   24°30.85    36.9  22.8   37.1±0.0  36.9  22.8±0.0  22.8
1620  10/02/2010  115  24°10.04W   24°30.14N   37.0  22.7   37.1±0.1  37.0  22.8±0.0  22.7
0920  11/02/2010  117  22°52.68W   24°43.25N   37.1  22.4   37.1±0.0  37.1  22.5±0.1  22.4
1515  11/02/2010  118  22°16.04W   24°55.16N   36.9  22.3   36.9±0.0  36.9  22.2±0.1  22.3
1155  12/02/2010  121  20°25.12W   25°32.78N   36.9  22.3   37.1±0.1  36.9  22.2±0.0  22.3
1800  12/02/2010  122  19°47.83W   25°44.58N   37.0  22.8   37±0.1    37.0  22.1±0.2  22.8
1315  13/02/2010  125  17°57.5W    26°22.59N   36.9  21.45  37±0.0    36.9  21.5±0.1  21.45
1935  13/02/2010  126  17°20.08W   26°34.60N   37.1  21.5   37±0.0    37.1  21.5±0.1  21.5
0910  14/02/2010  128  16°5.73W    26°59.13N   37.0  20.8   37±0.0    37.0  20.9±0.0  20.8
1357  14/02/2010  129  15°28.89W   27°12.12N   36.9  20.3   36.9±0.0  36.9  20.4±0.0  20.3
1045  15/02/2010  133  13°33.38W   27°52.01N   36.6  19.4   36.8±0.1  36.6  19.4±0.0  19.4
1325  15/02/2010  134  13°24.55W   27°54.66N   36.5  19.5   36.8±0.0  36.5  19.5±0.0  19.5
1540  15/02/2010  135  13°22.14W   27°55.65N   36.5  19.6   36.8±0.0  36.5  19.5±0.0  19.6


Figure 68: Scatterplots of mean a) SSS and b) SST from the TSG versus results 
           from the handheld CT probe for all deployments. The solid line is 
           the reference line showing equality.

Figure 69: Comparison of a) salinity and b) temperature of water from 
           non-toxic supply in the WBA and from sensors #4 and #5.




Appendix: Details of Stations Sampled during Cruise D346


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
  1|06/01/10 1649|        |        |     |    |   |     |     |   |   |   |   |   |    
   |06/01/10 1720|27 50.10|78 50.41| -999| 837| 15| 1851|  845|  8| 19| 20|  0| 12|  0
   |06/01/10 1758|        |        |     |    |   |     |     |   |   |   |   |   |      
  2|07/01/10 0419|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 0432|27 20.29|79 56.85|  113| 103|  8|   -3|  103|  3|  3| 17|  3|  3|  4
   |07/01/10 0444|        |        |     |    |   |     |     |   |   |   |   |   |      
  3|07/01/10 0554|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 0609|27 20.74|79 51.10|  265| 258|  5|   -2|  260|  4|  4| 19|  4|  4|  4
   |07/01/10 0627|        |        |     |    |   |     |     |   |   |   |   |   |      
  4|07/01/10 0751|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 0815|27 21.11|79 45.29|  407| 396|  9|   -2|  399|  6|  6|  6|  6|  6|  5
   |07/01/10 0840|        |        |     |    |   |     |     |   |   |   |   |   |      
  5|07/01/10 1004|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 1031|27 20.41|79 40.45|  554| 541| 11|   -2|  545|  7|  7|  7|  7|  7|  7
   |07/01/10 1102|        |        |     |    |   |     |     |   |   |   |   |   |      
  6|07/01/10 1241|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 1316|27 20.64|79 34.67|  741| 731|  9|   -1|  737|  9|  9|  9|  9|  9|  9
   |07/01/10 1355|        |        |     |    |   |     |     |   |   |   |   |   |      
  7|07/01/10 1533|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 1552|27 20.66|79 30.14|  725| 713| 10|   -2|  719|  9|  9|  9|  9|  9|  0
   |07/01/10 1626|        |        |     |    |   |     |     |   |   |   |   |   |      
  8|07/01/10 1753|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 1818|27 20.83|79 25.01|  678| 662| 14|   -2|  667|  9|  9|  9|  9|  9|  0
   |07/01/10 1902|        |        |     |    |   |     |     |   |   |   |   |   |      
  9|07/01/10 2023|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 2042|27 20.01|79 20.14|  587| 578|  7|   -1|  583|  8|  7|  7|  7|  7|  6
   |07/01/10 2114|        |        |     |    |   |     |     |   |   |   |   |   |      
 10|07/01/10 2231|        |        |     |    |   |     |     |   |   |   |   |   |      
   |07/01/10 2247|27 19.94|79 15.03|  449| 435| 12|   -2|  439|  6|  6|  6|  0|  6|  8
   |07/01/10 2307|        |        |     |    |   |     |     |   |   |   |   |   |      
 11|08/01/10 0016|        |        |     |    |   |     |     |   |   |   |   |   |      
   |08/01/10 0035|27 20.11|79 12.50|  362| 350|  9|   -3|  353|  5|  5|  5|  5|  5|  6
   |08/01/10 0053|        |        |     |    |   |     |     |   |   |   |   |   |      
 12|08/01/10 0204|        |        |     |    |   |     |     |   |   |   |   |   |      
   |08/01/10 0214|27 20.29|79 11.02|  256| 242|  9|   -4|  244|  4|  4|  4|  4|  4|  5
   |08/01/10 0229|        |        |     |    |   |     |     |   |   |   |   |   |      
 13|08/01/10 0401|        |        |     |    |   |     |     |   |   |   |   |   |      
   |08/01/10 0408|27 20.08|79 10.45|  177| 167|  7|   -4|  168|  3|  3|  3|  3|  3|  3
   |08/01/10 0418|        |        |     |    |   |     |     |   |   |   |   |   |      
 14|08/01/10 1854|        |        |     |    |   |     |     |   |   |   |   |   |      
   |08/01/10 1903|26 30.07|76 56.05|  249| 246|  9|    6|  248|  8|  8|  8|  8|  7|  7
   |08/01/10 1925|        |        |     |    |   |     |     |   |   |   |   |   |      
 15|08/01/10 2035|        |        |     |    |   |     |     |   |   |   |   |   |      
   |08/01/10 2109|26 29.94|76 51.89| 1318|1221| 79|  -19| 1232| 14| 14| 14| 15|  9|  9
   |08/01/10 2208|        |        |     |    |   |     |     |   |   |   |   |   |      
 16|08/01/10 2327|        |        |     |    |   |     |     |   |   |   |   |   |      
   |09/01/10 0006|26 31.97|76 48.97| 1689|1591| 77|  -21| 1607| 16| 16| 16| 16|  0|  9
   |09/01/10 0130|        |        |     |    |   |     |     |   |   |   |   |   |      
 17|09/01/10 0313|        |        |     |    |   |     |     |   |   |   |   |   |      
   |09/01/10 0407|26 30.19|76 46.93| 2289|2281| 80|   72| 2308| 18| 16| 16| 15| 10|  8
   |09/01/10 0525|        |        |     |    |   |     |     |   |   |   |   |   |     



   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
 18|09/01/10 0655|        |        |     |    |   |     |     |   |   |   |   |   |       
   |09/01/10 0737|26 29.93|76 48.05| 1501|1493|  5|   -2| 1508| 15| 11| 11| 11|  9|  9
   |09/01/10 0848|        |        |     |    |   |     |     |   |   |   |   |   |        
 19|09/01/10 1002|        |        |     |    |   |     |     |   |   |   |   |   |        
   |09/01/10 1140|26 29.74|76 45.68| 3778|3763|  3|  -12| 3822| 24| 24| 23| 24| 14| 15
   |09/01/10 1405|        |        |     |    |   |     |     |   |   |   |   |   |        
 20|09/01/10 1612|        |        |     |    |   |     |     |   |   |   |   |   |        
   |09/01/10 1743|26 29.95|76 40.96| 4574|4561| 11|   -3| 4641| 22| 21| 21| 21| 14| 14
   |09/01/10 2028|        |        |     |    |   |     |     |   |   |   |   |   |        
 21|09/01/10 2315|        |        |     |    |   |     |     |   |   |   |   |   |        
   |10/01/10 0100|26 29.83|76 37.79| 4698|4686| 10|   -2| 4769| 22| 20| 20| 20| 16| 17
   |10/01/10 0314|        |        |     |    |   |     |     |   |   |   |   |   |      
 22|10/01/10 0521|        |        |     |    |   |     |     |   |   |   |   |   |      
   |10/01/10 0652|26 29.76|76 32.28| 4839|4831|  7|   -2| 4919| 22| 19| 20| 18| 14| 13
   |10/01/10 0903|        |        |     |    |   |     |     |   |   |   |   |   |      
 23|10/01/10 1348|        |        |     |    |   |     |     |   |   |   |   |   |      
   |10/01/10 1522|26 29.02|76 26.60| 4837|4826|  9|   -2| 4914| 22| 23| 23| 21| 16| 18
   |10/01/10 1748|        |        |     |    |   |     |     |   |   |   |   |   |      
 24|10/01/10 1947|        |        |     |    |   |     |     |   |   |   |   |   |      
   |10/01/10 2129|26 29.75|76 18.18| 4835|4821| 11|   -2| 4909| 22| 21| 23| 24| 17| 20
   |10/01/10 2356|        |        |     |    |   |     |     |   |   |   |   |   |        
 25|11/01/10 0149|        |        |     |    |   |     |     |   |   |   |   |   |        
   |11/01/10 0333|26 29.22|76 13.50| 4810|4805|  4|   -1| 4892| 24| 23| 21| 24|  4| 18
   |11/01/10 0551|        |        |     |    |   |     |     |   |   |   |   |   |        
 26|11/01/10 1350|        |        |     |    |   |     |     |   |   |   |   |   |        
   |11/01/10 1520|26 29.75|76 06.52| 4805|4794|  9|   -2| 4881| 22| 23| 23| 24| 17| 18
   |11/01/10 1745|        |        |     |    |   |     |     |   |   |   |   |   |        
 27|11/01/10 1954|        |        |     |    |   |     |     |   |   |   |   |   |        
   |11/01/10 2140|26 30.11|75 54.53| 4746|4733| 11|   -2| 4818| 24| 24| 24| 24| 16| 21
   |11/01/10 2356|        |        |     |    |   |     |     |   |   |   |   |   |        
 28|12/01/10 0211|        |        |     |    |   |     |     |   |   |   |   |   |        
   |12/01/10 0349|26 29.91|75 43.56| 4696|4684|  9|   -3| 4768| 23| 22| 22| 24|  3|  4
   |12/01/10 0553|        |        |     |    |   |     |     |   |   |   |   |   |        
 29|12/01/10 0756|        |        |     |    |   |     |     |   |   |   |   |   |        
   |12/01/10 0928|26 30.03|75 30.53| 4687|4677|  7|   -3| 4760| 22| 21| 21| 20| 16| 18
   |12/01/10 1136|        |        |     |    |   |     |     |   |   |   |   |   |        
 30|12/01/10 1326|        |        |     |    |   |     |     |   |   |   |   |   |        
   |12/01/10 1501|26 29.81|75 18.72| 4642|4631|  9|   -3| 4713| 23| 23| 23| 22| 15| 19
   |12/01/10 1713|        |        |     |    |   |     |     |   |   |   |   |   |        
 31|12/01/10 1912|        |        |     |    |   |     |     |   |   |   |   |   |        
   |12/01/10 2042|26 30.19|75 04.38| 4605|4594|  9|   -2| 4675| 23| 23| 24| 24|  2|  5
   |12/01/10 2252|        |        |     |    |   |     |     |   |   |   |   |   |        
 32|13/01/10 0051|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/01/10 0224|26 29.80|74 48.25| 4538|4526| 10|   -2| 4605| 23| 23| 24| 23| 16| 18
   |13/01/10 0437|        |        |     |    |   |     |     |   |   |   |   |   |        
 33|13/01/10 0637|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/01/10 0805|26 29.88|74 31.01| 4496|4484|  9|   -2| 4562| 24| 23| 23| 23| 16| 19
   |13/01/10 1010|        |        |     |    |   |     |     |   |   |   |   |   |        
 34|13/01/10 1217|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/01/10 1342|26 29.88|74 14.52| 4542|4530| 10|   -2| 4609| 22| 21| 21| 21|  0|  1
   |13/01/10 1546|        |        |     |    |   |     |     |   |   |   |   |   |       
 35|13/01/10 1801|        |        |     |    |   |     |     |   |   |   |   |   |       
   |13/01/10 1935|26 30.98|73 35.14| 4918|4901| 12|   -4| 4991| 23| 21| 21| 21| 16| 19
   |13/01/10 2148|        |        |     |    |   |     |     |   |   |   |   |   |       



   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
 36|14/01/10 0023|        |        |     |    |   |     |     |   |   |   |              
   |14/01/10 0203|26 30.98|73 35.14| 4918|4901| 12|   -4| 4991| 23| 23| 23| 23| 16| 18
   |14/01/10 0414|        |        |     |    |   |     |     |   |   |   |   |   |     
 37|14/01/10 0700|        |        |     |    |   |     |     |   |   |   |   |   |     
   |14/01/10 0832|26 30.61|73 12.33| 5043|5031| 10|   -2| 5125| 23| 22| 21| 23|  0|  6
   |14/01/10 1046|        |        |     |    |   |     |     |   |   |   |   |   |     
 38|14/01/10 1320|        |        |     |    |   |     |     |   |   |   |   |   |     
   |14/01/10 1501|26 30.35|72 50.49| 5132|5123|  7|   -1| 5220| 23| 23| 23| 0 | 17| 19
   |14/01/10 1718|        |        |     |    |   |     |     |   |   |   |   |   |     
 39|14/01/10 2004|        |        |     |    |   |     |     |   |   |   |   |   |     
   |14/01/10 2145|26 30.46|72 27.83| 5140|5130|  8|   -2| 5227| 23| 22| 22| 22| 15| 17
   |15/01/10 0009|        |        |     |    |   |     |     |   |   |   |   |   |     
 40|15/01/10 0246|        |        |     |    |   |     |     |   |   |   |   |   |     
   |15/01/10 0430|26 30.81|72 06.40| 5269|5256| 11|   -2| 5356| 23| 23| 22| 22|  0|  0
   |15/01/10 0651|        |        |     |    |   |     |     |   |   |   |   |   |     
 41|15/01/10 0936|        |        |     |    |   |     |     |   |   |   |   |   |     
   |15/01/10 1117|26 30.82|71 43.13| 5378|5364| 11|   -3| 5468| 24| 24| 24| 24| 16| 16
   |15/01/10 1415|        |        |     |    |   |     |     |   |   |   |   |   |     
 42|15/01/10 1639|        |        |     |    |   |     |     |   |   |   |   |   |     
   |15/01/10 1818|26 29.75|71 21.69| 5481|5471|  8|   -1| 5579| 23| 23| 24| 24| 16| 20
   |15/01/10 2043|        |        |     |    |   |     |     |   |   |   |   |   |     
 43|15/01/10 2314|        |        |     |    |   |     |     |   |   |   |   |   |     
   |16/01/10 0115|26 28.54|71 00.25| 5489|5476| 11|   -2| 5584| 24| 20| 20| 20|  0|  5
   |16/01/10 0343|        |        |     |    |   |     |     |   |   |   |   |   |     
 44|16/01/10 0715|        |        |     |    |   |     |     |   |   |   |   |   |     
   |16/01/10 0856|26 06.16|70 38.03| 5503|5489| 12|   -3| 5597| 24| 24| 24| 24| 16| 19
   |16/01/10 1141|        |        |     |    |   |     |     |   |   |   |   |   |     
 45|16/01/10 1526|        |        |     |    |   |     |     |   |   |   |   |   |     
   |16/01/10 1710|25 41.94|70 15.94| 5513|5502|  9|   -2| 5610| 23| 21| 22| 21| 14| 20
   |16/01/10 1934|        |        |     |    |   |     |     |   |   |   |   |   |     
 46|16/01/10 2315|        |        |     |    |   |     |     |   |   |   |   |   |     
   |17/01/10 0101|25 18.31|69 54.16| 5501|5488| 10|   -3| 5595| 23| 23| 23| 23|  0| 10
   |17/01/10 0303|        |        |     |    |   |     |     |   |   |   |   |   |     
 47|17/01/10 0658|        |        |     |    |   |     |     |   |   |   |   |   |     
   |17/01/10 0842|24 54.27|69 32.15| 5593|5583|  9|   -2| 5693| 24| 24| 24| 24| 17| 18
   |17/01/10 1049|        |        |     |    |   |     |     |   |   |   |   |   |     
 48|17/01/10 1435|        |        |     |    |   |     |     |   |   |   |   |   |     
   |17/01/10 1615|24 30.30|69 09.17| 5637|5627|  9|   -1| 5738| 23| 23| 23| 22| 16| 19
   |17/01/10 1820|        |        |     |    |   |     |     |   |   |   |   |   |     
 49|17/01/10 2307|        |        |     |    |   |     |     |   |   |   |   |   |     
   |18/01/10 0055|24 30.56|68 24.43| 5711|5700|  9|   -2| 5815| 24| 24| 24| 24|  0|  0
   |18/01/10 0304|        |        |     |    |   |     |     |   |   |   |   |   |     
 50|18/01/10 0804|        |        |     |    |   |     |     |   |   |   |   |   |     
   |18/01/10 0946|24 30.50|67 40.20| 5716|5705|  9|   -2| 5819| 24| 23| 24| 23| 17| 19
   |18/01/10 1154|        |        |     |    |   |     |     |   |   |   |   |   |     
 51|18/01/10 1605|        |        |     |    |   |     |     |   |   |   |   |   |     
   |18/01/10 1754|24 29.99|66 56.35| 5699|5686| 10|   -3| 5800| 24| 24| 24| 24| 16| 21
   |18/01/10 2001|        |        |     |    |   |     |     |   |   |   |   |   |     
 52|19/01/10 0015|        |        |     |    |   |     |     |   |   |   |   |   |     
   |19/01/10 0147|24 29.94|66 12.63| 5135|5123| 11|   -2| 5218| 23| 23| 23| 24|  0|  8
   |19/01/10 0342|        |        |     |    |   |     |     |   |   |   |   |   |    
 53|19/01/10 0757|        |        |     |    |   |     |     |   |   |   |   |   |    
   |19/01/10 0958|24 30.10|65 29.36| -999|5436|  5| 6439| 5541| 23| 23| 23| 23| 16| 17
   |19/01/10 1204|        |        |     |    |   |     |     |   |   |   |   |   |    


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
 54|19/01/10 1643|        |        |     |    |   |     |     |   |   |   |   |   |      
   |19/01/10 1844|24 29.94|64 46.06| 5940|5925| 11|   -3| 6047| 24| 19| 23| 23| 16| 20
   |19/01/10 2102|        |        |     |    |   |     |     |   |   |   |   |   |    
 55|20/01/10 0150|        |        |     |    |   |     |     |   |   |   |   |   |    
   |20/01/10 0331|24 30.82|64 00.97| 5628|5615| 11|   -2| 5727| 24| 22| 22| 22|  0| 15
   |20/01/10 0533|        |        |     |    |   |     |     |   |   |   |   |   |    
 56|20/01/10 1006|        |        |     |    |   |     |     |   |   |   |   |   |    
   |20/01/10 1142|24 29.73|63 17.51| 5802|5789| 11|   -2| 5907| 24| 24| 24| 24| 17| 21
   |20/01/10 1341|        |        |     |    |   |     |     |   |   |   |   |   |    
 57|20/01/10 1806|        |        |     |    |   |     |     |   |   |   |   |   |    
   |20/01/10 1954|24 30.07|62 33.35| 5912|5901| 10|   -1| 6022| 24| 23| 23| 23| 16| 20
   |20/01/10 2210|        |        |     |    |   |     |     |   |   |   |   |   |    
 58|21/01/10 0246|        |        |     |    |   |     |     |   |   |   |   |   |    
   |21/01/10 0422|24 30.50|61 48.38| 5649|5639|  9|   -2| 5751| 24| 24| 24| 24|  0|  4
   |21/01/10 0623|        |        |     |    |   |     |     |   |   |   |   |   |    
 59|21/01/10 1024|        |        |     |    |   |     |     |   |   |   |   |   |    
   |21/01/10 1203|24 30.10|61 05.07| 5882|5871| 10|   -1| 5991| 24| 24| 24| 24| 16| 19
   |21/01/10 1407|        |        |     |    |   |     |     |   |   |   |   |   |    
 60|21/01/10 1817|        |        |     |    |   |     |     |   |   |   |   |   |    
   |21/01/10 2007|24 29.97|60 20.82| 5819|5806| 10|   -2| 5924| 24| 21| 21| 21| 14| 18
   |21/01/10 2227|        |        |     |    |   |     |     |   |   |   |   |   |    
 61|22/01/10 0245|        |        |     |    |   |     |     |   |   |   |   |   |    
   |22/01/10 0429|24 30.37|59 37.69| 5784|5773|  8|   -2| 5890| 24| 24| 24| 24|  2|  3
   |22/01/10 0635|        |        |     |    |   |     |     |   |   |   |   |   |    
 62|22/01/10 1959|        |        |     |    |   |     |     |   |   |   |   |   |    
   |22/01/10 2138|24 29.88|58 53.78| 5851|5839| 10|   -2| 5958| 24| 23| 22| 22| 17| 20
   |22/01/10 2341|        |        |     |    |   |     |     |   |   |   |   |   |    
 63|22/01/10 1959|        |        |     |    |   |     |     |   |   |   |   |   |    
   |22/01/10 2138|24 30.11|58 09.03| 5663|5653|  9|   -2| 5766| 24| 22| 21| 22| 15| 19
   |22/01/10 2341|        |        |     |    |   |     |     |   |   |   |   |   |     
 64|23/01/10 0434|        |        |     |    |   |     |     |   |   |   |   |   |     
   |23/01/10 0625|24 30.12|57 23.91| 6273|6265|  9|    1| 6399| 24| 24| 24| 24|  5|  1
   |23/01/10 0900|        |        |     |    |   |     |     |   |   |   |   |   |     
200|23/01/10 1120|        |        |     |    |   |     |     |   |   |   |   |   |     
   |23/01/10 1307|24 29.80|57 03.03| 6228|6218| 10|    0| 6350|  1| 24| 24|  0|  0|  0
   |23/01/10 1729|        |        |     |    |   |     |     |   |   |   |   |   |     
 65|23/01/10 1957|        |        |     |    |   |     |     |   |   |   |   |   |     
   |23/01/10 2148|24 29.35|56 41.38| 5840|5821| 15|   -3| 5940| 24| 24| 24| 24| 16| 20
   |24/01/10 0023|        |        |     |    |   |     |     |   |   |   |   |   |     
 66|24/01/10 0535|        |        |     |    |   |     |     |   |   |   |   |   |     
   |24/01/10 0742|24 28.79|55 56.62| 6461|6451| 11|    1| 6592| 24| 24| 24| 24| 17| 20
   |24/01/10 1051|        |        |     |    |   |     |     |   |   |   |   |   |     
 67|24/01/10 1834|        |        |     |    |   |     |     |   |   |   |   |   |     
   |24/01/10 2026|24 29.78|55 14.33| 6107|6097| 11|    1| 6225| 24| 24| 23| 24|  4|  7
   |24/01/10 2307|        |        |     |    |   |     |     |   |   |   |   |   |     
 68|25/01/10 0552|        |        |     |    |   |     |     |   |   |   |   |   |     
   |25/01/10 0830|24 30.58|54 27.17| 5292|5270| 21|    0| 5371| 23| 23| 22| 22| 17| 19
   |25/01/10 1047|        |        |     |    |   |     |     |   |   |   |   |   |     
 69|25/01/10 1508|        |        |     |    |   |     |     |   |   |   |   |   |     
   |25/01/10 1711|24 30.60|53 56.28| 6155|6147|  9|    1| 6277| 24| 24| 24| 24| 16| 21
   |25/01/10 1959|        |        |     |    |   |     |     |   |   |   |   |   |    
 70|26/01/10 0046|        |        |     |    |   |     |     |   |   |   |   |   |    
   |26/01/10 0251|24 50.35|53 23.96| 5931|5919| 12|    0| 6041| 24| 23| 23| 24|  3| 20  
   |26/01/10 0523|        |        |     |    |   |     |     |   |   |   |   |   |    
                                             


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
 71|26/01/10 0938|        |        |     |    |   |     |     |   |   |   |   |   |  
   |26/01/10 1143|25 06.65|52 50.43| 5859|5707| 18| -134| 5821| 24| 21| 20| 20| 15| 18
   |26/01/10 1406|        |        |     |    |   |     |     |   |   |   |   |   |
 72|26/01/10 1730|        |        |     |    |   |     |     |   |   |   |   |   |
   |26/01/10 1926|25 04.80|52 17.41| 5529|5517| 13|    0| 5625| 23| 20| 23| 22| 16| 19
   |26/01/10 2138|        |        |     |    |   |     |     |   |   |   |   |   |
 73|27/01/10 1218|        |        |     |    |   |     |     |   |   |   |   |   |
   |27/01/10 1410|25 01.33|51 45.19| 6038|6026| 10|   -1| 6152| 24| 24| 23| 24|  3|  0
   |27/01/10 1700|        |        |     |    |   |     |     |   |   |   |   |   |
 74|27/01/10 2032|        |        |     |    |   |     |     |   |   |   |   |   |
   |27/01/10 2212|24 56.24|51 11.11| 5784|5768| 14|   -2| 5885| 24| 23| 23| 23| 15| 20
   |28/01/10 0022|        |        |     |    |   |     |     |   |   |   |   |   |
 75|28/01/10 0337|        |        |     |    |   |     |     |   |   |   |   |   |
   |28/01/10 0515|24 47.90|50 37.92| 5138|5171| 13|    1| 5268| 23| 24| 24| 24| 18| 21
   |28/01/10 0718|        |        |     |    |   |     |     |   |   |   |   |   |
 76|28/01/10 1038|        |        |     |    |   |     |     |   |   |   |   |   |
   |28/01/10 1232|24 40.12|50 05.40| 5593|5581| 10|   -2| 5692| 23| 21| 21| 21|  1| 17
   |28/01/10 1450|        |        |     |    |   |     |     |   |   |   |   |   |  
 77|28/01/10 1816|        |        |     |    |   |     |     |   |   |   |   |   |  
   |28/01/10 2022|24 31.24|49 32.05| 5956|5944| 10|   -2| 6066| 24| 23| 23| 23| 16| 19
   |28/01/10 2300|        |        |     |    |   |     |     |   |   |   |   |   |  
 78|29/01/10 0226|        |        |     |    |   |     |     |   |   |   |   |   |  
   |29/01/10 0409|24 20.94|49 00.49| 5390|5380|  8|   -2| 5484| 24| 23| 23| 23| 17| 17
   |29/01/10 0612|        |        |     |    |   |     |     |   |   |   |   |   |  
 79|29/01/10 0937|        |        |     |    |   |     |     |   |   |   |   |   |  
   |29/01/10 1115|24 11.76|48 28.38| 5287|5274| 11|   -2| 5375| 24| 21| 22| 21|  2| 19
   |29/01/10 1312|        |        |     |    |   |     |     |   |   |   |   |   |  
 80|29/01/10 1630|        |        |     |    |   |     |     |   |   |   |   |   |  
   |29/01/10 1831|24 03.97|47 56.56| 5302|5290| 10|   -3| 5391| 24| 23| 23| 23| 16| 19
   |29/01/10 2032|        |        |     |    |   |     |     |   |   |   |   |   |  
 81|29/01/10 2357|        |        |     |    |   |     |     |   |   |   |   |   |
   |30/01/10 0122|23 58.53|47 24.52| 4564|4550| 99|   85| 4629| 23| 21| 21| 21|  0|  8
   |30/01/10 0343|        |        |     |    |   |     |     |   |   |   |   |   |
 82|30/01/10 0739|        |        |     |    |   |     |     |   |   |   |   |   |
   |30/01/10 0924|23 53.95|46 52.56| 4910|4853| 26|  -31| 4940| 23| 24| 24| 24| 16| 19
   |30/01/10 1139|        |        |     |    |   |     |     |   |   |   |   |   |
 83|30/01/10 1519|        |        |     |    |   |     |     |   |   |   |   |   |
   |30/01/10 1712|23 52.43|46 20.02| 5059|5064|  6|   12| 5158| 23| 21| 22| 22| 15| 19
   |30/01/10 1908|        |        |     |    |   |     |     |   |   |   |   |   |
 84|30/01/10 2251|        |        |     |    |   |     |     |   |   |   |   |   |
   |31/01/10 0020|23 46.02|45 48.12| 4529|4512| 15|   -2| 4590| 22| 24| 24| 24|  2| 13
   |31/01/10 0208|        |        |     |    |   |     |     |   |   |   |   |   |  
 85|31/01/10 0527|        |        |     |    |   |     |     |   |   |   |   |   |  
   |31/01/10 0654|23 43.95|45 16.20| 4469|4447| 21|   -1| 4523| 22| 22| 22| 21| 16| 15
   |31/01/10 0840|        |        |     |    |   |     |     |   |   |   |   |   |  
 86|31/01/10 1232|        |        |     |    |   |     |     |   |   |   |   |   |  
   |31/01/10 1401|23 38.13|44 44.12| 4419|4407| 13|    1| 4482| 21| 22| 23| 22| 15| 19
   |31/01/10 1545|        |        |     |    |   |     |     |   |   |   |   |   |  
 87|31/01/10 1919|        |        |     |    |   |     |     |   |   |   |   |   |  
   |31/01/10 2050|23 32.12|44 12.54| 4862|4842| 15|   -5| 4929| 24| 23| 23| 23|  2| 16
   |31/01/10 2246|        |        |     |    |   |     |     |   |   |   |   |   |  
 88|01/02/10 0218|        |        |     |    |   |     |     |   |   |   |   |   |  
   |01/02/10 0401|23 27.00|43 40.31| 4870|4854| 13|   -3| 4942| 22| 24| 24| 24| 17| 20
   |01/02/10 0554|        |        |     |    |   |     |     |   |   |   |   |   |   
                                      


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
 89|01/02/10 0921|        |        |     |    |   |     |     |   |   |   |   |   |    
   |01/02/10 1057|23 22.36|43 08.49| 4904|4892| 11|   -1| 4980| 22| 23| 23| 23| 16| 19
   |01/02/10 1255|        |        |     |    |   |     |     |   |   |   |   |   |    
 90|01/02/10 1618|        |        |     |    |   |     |     |   |   |   |   |   |    
   |01/02/10 1814|23 15.02|42 36.03| 5405|5391| 12|   -2| 5495| 23| 24| 24| 24|  3|  7
   |01/02/10 2031|        |        |     |    |   |     |     |   |   |   |   |   |    
 91|02/02/10 0144|        |        |     |    |   |     |     |   |   |   |   |   |    
   |02/02/10 0312|23 23.08|41 46.14| 4593|4518| 11|   -1| 4661| 22| 24| 23| 24| 15| 19
   |02/02/10 0504|        |        |     |    |   |     |     |   |   |   |   |   |    
 92|02/02/10 1005|        |        |     |    |   |     |     |   |   |   |   |   |    
   |02/02/10 1131|23 31.23|40 56.66| 4740|4729| 11|    0| 4813| 22| 24| 24| 24| 16| 20
   |02/02/10 1322|        |        |     |    |   |     |     |   |   |   |   |   |    
 93|02/02/10 1830|        |        |     |    |   |     |     |   |   |   |   |   |    
   |02/02/10 2017|23 40.03|40 06.50| 5421|5410|  6|   -5| 5514| 23| 21| 22| 24|  3| 10
   |02/02/10 2219|        |        |     |    |   |     |     |   |   |   |   |   |    
 94|03/02/10 0318|        |        |     |    |   |     |     |   |   |   |   |   |    
   |03/02/10 0457|23 47.96|39 15.73| 5444|5431| 10|   -3| 5536| 23| 24| 24| 24| 16| 20
   |03/02/10 0659|        |        |     |    |   |     |     |   |   |   |   |   |    
 95|03/02/10 1154|        |        |     |    |   |     |     |   |   |   |   |   |    
   |03/02/10 1335|23 56.09|38 25.99| 5728|5715| 10|   -3| 5829| 23| 24| 23| 24| 10| 18
   |03/02/10 1557|        |        |     |    |   |     |     |   |   |   |   |   |    
 96|03/02/10 2050|        |        |     |    |   |     |     |   |   |   |   |   |    
   |03/02/10 2235|24 05.37|37 36.66| 5238|5227| 13|    2| 5326| 22| 22| 22| 24|  3| 13
   |03/02/10 0030|        |        |     |    |   |     |     |   |   |   |   |   |    
 97|04/02/10 0531|        |        |     |    |   |     |     |   |   |   |   |   |    
   |04/02/10 0709|24 13.16|36 46.19| 5140|5127| 10|   -3| 5223| 23| 24| 24| 24| 16| 20
   |04/02/10 0911|        |        |     |    |   |     |     |   |   |   |   |   |    
 98|04/02/10 1354|        |        |     |    |   |     |     |   |   |   |   |   |    
   |04/02/10 1542|24 21.80|35 55.64| 5766|5753| 11|   -2| 5869| 22| 23| 23| 23| 16| 20
   |04/02/10 1755|        |        |     |    |   |     |     |   |   |   |   |   |    
 99|05/02/10 0052|        |        |     |    |   |     |     |   |   |   |   |   |    
   |05/02/10 0238|24 30.37|35 05.10| 5756|5746|  9|   -2| 5862| 24| 24| 23| 24|  2| 15
   |05/02/10 0448|        |        |     |    |   |     |     |   |   |   |   |   |    
100|05/20/10 0839|        |        |     |    |   |     |     |   |   |   |   |   |    
   |05/02/10 1028|24 29.73|34 25.00| 6096|6001| 76|  -19| 6125| 23| 22| 21| 23| 18| 20
   |05/02/10 1318|        |        |     |    |   |     |     |   |   |   |   |   |    
202|05/02/10 1534|        |        |     |    |   |     |     |   |   |   |   |   |    
   |05/02/10 1639|24 30.37|34 02.78| 5968|3500| 76| 2392| 3552|  1|  0| 24|  0|  0|  0
   |05/02/10 1738|        |        |     |    |   |     |     |   |   |   |   |   |    
101|05/02/10 1928|        |        |     |    |   |     |     |   |   |   |   |   |    
   |05/02/10 2106|24 29.77|33 43.71| 5350|5347|  4|    1| 5449| 24| 24| 24| 24| 15| 20
   |05/02/10 2311|        |        |     |    |   |     |     |   |   |   |   |   |    
102|06/02/10 0251|        |        |     |    |   |     |     |   |   |   |   |   |    
   |06/02/10 0435|24 30.01|33 02.69| 5732|5716| 13|   -2| 5831| 23| 24| 24| 24|  3|  8
   |06/02/10 0644|        |        |     |    |   |     |     |   |   |   |   |   |    
103|06/02/10 1035|        |        |     |    |   |     |     |   |   |   |   |   |    
   |06/02/10 1218|24 29.64|32 21.44| 5649|5632| 14|   -3| 5744| 23| 20| 20| 21| 14| 17
   |06/02/10 1425|        |        |     |    |   |     |     |   |   |   |   |   |    
104|06/02/10 1804|        |        |     |    |   |     |     |   |   |   |   |   |    
   |06/02/10 1957|24 29.86|31 40.85| 5674|5661| 11|   -3| 5774| 24| 24| 24| 24| 17| 21
   |06/02/10 2224|        |        |     |    |   |     |     |   |   |   |   |   |    
105|07/02/10 0221|        |        |     |    |   |     |     |   |   |   |   |   |    
   |07/02/10 0410|24 29.78|31 00.16| 5909|5892| 14|   -2| 6013| 24| 23| 23| 24|  3|  0
   |07/02/10 0630|        |        |     |    |   |     |     |   |   |   |   |   |    
                                           


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
106|07/02/10 1039|        |        |     |    |   |     |     |   |   |   |   |   |    
   |07/02/10 1229|24 29.52|30 19.29| 5409|5398| 10|   -2| 5502| 22| 22| 22| 24| 15| 19
   |07/02/10 1512|        |        |     |    |   |     |     |   |   |   |   |   |    
107|07/02/10 1930|        |        |     |    |   |     |     |   |   |   |   |   |    
   |07/02/10 2127|24 30.17|29 39.50| 5409|5399|  7|   -3| 5503| 24| 22| 22| 20| 15| 18
   |07/02/10 2350|        |        |     |    |   |     |     |   |   |   |   |   |    
108|08/02/10 0413|        |        |     |    |   |     |     |   |   |   |   |   |    
   |08/02/10 0618|24 30.05|28 57.65| 5674|5659| 12|   -3| 5772| 24| 24| 24| 24|  1|  6
   |08/02/10 0847|        |        |     |    |   |     |     |   |   |   |   |   |     
109|08/02/10 1303|        |        |     |    |   |     |     |   |   |   |   |   |     
   |08/02/10 1523|24 30.05|28 17.27| 5645|5633| 10|   -2| 5745| 24| 24| 24| 24| 13|  21
   |08/02/10 1750|        |        |     |    |   |     |     |   |   |   |   |   |     
110|08/02/10 2215|        |        |     |    |   |     |     |   |   |   |   |   |     
   |09/02/10 0001|24 29.50|27 35.96| 5577|5562| 13|   -2| 5671| 24| 23| 23| 24| 15|  19
   |09/02/10 0229|        |        |     |    |   |     |     |   |   |   |   |   |     
111|09/02/10 0637|        |        |     |    |   |     |     |   |   |   |   |   |     
   |09/02/10 0821|24 30.72|26 54.71| 5489|5479|  8|   -2| 5586| 24| 23| 23| 24|  1|  11
   |09/02/10 1049|        |        |     |    |   |     |     |   |   |   |   |   |     
112|09/02/10 1502|        |        |     |    |   |     |     |   |   |   |   |   |     
   |09/02/10 1643|24 30.60|26 13.50| 5390|5377| 11|   -2| 5480| 23| 23| 22| 24| 14|  19
   |09/02/10 1904|        |        |     |    |   |     |     |   |   |   |   |   |     
113|09/02/10 2328|        |        |     |    |   |     |     |   |   |   |   |   |     
   |10/02/10 0125|24 30.67|25 32.49| 5310|5297| 12|   -2| 5398| 23| 23| 24| 23| 14|  19
   |10/02/10 0343|        |        |     |    |   |     |     |   |   |   |   |   |     
114|10/02/10 0811|        |        |     |    |   |     |     |   |   |   |   |   |     
   |10/02/10 0950|24 30.85|24 50.82| 5226|5214| 10|   -2| 5312| 23| 23| 23| 23|  1|   0
   |10/02/10 1155|        |        |     |    |   |     |     |   |   |   |   |   |     
115|10/02/10 1558|        |        |     |    |   |     |     |   |   |   |   |   |     
   |10/02/10 1739|24 29.99|24 09.88| 5128|5117| 10|   -2| 5212| 23| 22| 22| 22| 11|  19
   |10/02/10 1940|        |        |     |    |   |     |     |   |   |   |   |   |     
116|10/02/10 2329|        |        |     |    |   |     |     |   |   |   |   |   |     
   |11/02/10 0102|24 29.65|23 30.06| 5013|5001| 10|   -2| 5093| 23| 22| 24| 20| 12|  16
   |11/02/10 0305|        |        |     |    |   |     |     |   |   |   |   |   |     
117|11/02/10 0651|        |        |     |    |   |     |     |   |   |   |   |   |      
   |11/02/10 0821|24 42.85|22 53.05| 4910|4899|  9|   -2| 4989| 23| 23| 23| 24|  1|  12
   |11/02/10 1024|        |        |     |    |   |     |     |   |   |   |   |   |     
118|11/02/10 1407|        |        |     |    |   |     |     |   |   |   |   |   |     
   |11/02/10 1537|24 55.12|22 15.94| 4767|4756|  9|   -2| 4841| 22| 23| 21| 23| 13|  18
   |11/02/10 1728|        |        |     |    |   |     |     |   |   |   |   |   |     
119|11/02/10 2109|        |        |     |    |   |     |     |   |   |   |   |   |     
   |11/02/10 2230|25 08.20|21 39.14| 4650|4638| 10|   -2| 4720| 23| 20| 22| 22| 14|  19
   |12/02/10 0016|        |        |     |    |   |     |     |   |   |   |   |   |     
120|12/02/10 0351|        |        |     |    |   |     |     |   |   |   |   |   |     
   |12/02/10 0512|25 20.08|21 01.82| 4457|4444|  9|   -4| 4520| 22| 21| 21| 20|  1|  13
   |12/02/10 0658|        |        |     |    |   |     |     |   |   |   |   |   |     
121|12/02/10 1032|        |        |     |    |   |     |     |   |   |   |   |   |     
   |12/02/10 1148|25 32.75|20 25.11| 4284|4271| 11|   -2| 4343| 21| 21| 22| 22| 13|  10
   |12/02/10 1334|        |        |     |    |   |     |     |   |   |   |   |   |     
122|12/02/10 1710|        |        |     |    |   |     |     |   |   |   |   |   |     
   |12/02/10 1824|25 44.55|19 47.81| 3922|3909| 10|   -2| 3971| 22| 21| 22| 21| 10|   0
   |12/02/10 2001|        |        |     |    |   |     |     |   |   |   |   |   |     
123|12/02/10 2339|        |        |     |    |   |     |     |   |   |   |   |   |     
   |13/02/10 0045|25 57.74|19 11.31| 3545|3532| 10|   -2| 3586| 21| 21| 20| 21|  1|   0
   |13/02/10 0212|        |        |     |    |   |     |     |   |   |   |   |   |     
                                           


   |             |        |        |     |    |Min|     |     |
   |             |        |        |Water|Max |Ht |Max  |Max  |
   |             |        |        |dep  |CTD |off|Wire-|CTD  |Number of Bottle Samples
   |             |        |        |corr |Dep |Bot|out  |Press|------------------------
Stn|  Date   Time|   Lat  |  Lon   |(m)  |(m) |(m)|(m)  |(db) |Dep|Sal|Oxy|Nut|CO2|CFC 
---|-------------|--------|--------|-----|----|---|-----|-----|---|---|---|---|---|----
124|13/02/10 0553|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/02/10 0658|26 10.06|18 34.43| 3442|3431|  9|   -1| 3482| 21| 23| 23| 23| 12|   1
   |13/02/10 0832|        |        |     |    |   |     |     |   |   |   |   |   |        
125|13/02/10 1212|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/02/10 1319|26 22.58|17 57.54| 3639|3628|  9|   -2| 3683| 22| 22| 22| 22|  6|   0
   |13/02/10 1458|        |        |     |    |   |     |     |   |   |   |   |   |        
126|13/02/10 1840|        |        |     |    |   |     |     |   |   |   |   |   |        
   |13/02/10 1949|26 34.58|17 20.06| 3628|3617|  9|   -1| 3673| 21| 24| 24| 24|  1|   0
   |13/02/10 2116|        |        |     |    |   |     |     |   |   |   |   |   |        
127|14/02/10 0105|        |        |     |    |   |     |     |   |   |   |   |   |        
   |14/02/10 0214|26 47.39|16 42.90| 3617|3608|  8|   -2| 3663| 22| 24| 24| 24|  5|   0
   |14/02/10 0349|        |        |     |    |   |     |     |   |   |   |   |   |        
128|14/02/10 0720|        |        |     |    |   |     |     |   |   |   |   |   |        
   |14/02/10 0826|26 59.31|16 05.81| 3481|3468| 10|   -3| 3520| 21| 23| 24| 24|  0|   0
   |14/02/10 0959|        |        |     |    |   |     |     |   |   |   |   |   |        
129|14/02/10 1338|        |        |     |    |   |     |     |   |   |   |   |   |        
   |14/02/10 1444|27 11.83|15 28.98| 3104|3092| 10|   -2| 3136| 22| 21| 22| 21|  1|   0
   |14/02/10 1611|        |        |     |    |   |     |     |   |   |   |   |   |        
130|14/02/10 1950|        |        |     |    |   |     |     |   |   |   |   |   |        
   |14/02/10 2047|27 24.87|14 52.12| 2605|2594|  9|   -2| 2628| 20| 24| 24| 24|  0|   0
   |14/02/10 2203|        |        |     |    |   |     |     |   |   |   |   |   |        
131|15/02/10 0149|        |        |     |    |   |     |     |   |   |   |   |   |        
   |15/02/10 0231|27 37.37|14 14.21| 2034|2023|  9|   -2| 2046| 18| 18| 24| 24|  0|   0
   |15/02/10 0332|        |        |     |    |   |     |     |   |   |   |   |   |        
132|15/02/10 0632|        |        |     |    |   |     |     |   |   |   |   |   |        
   |15/02/10 0704|27 47.37|13 46.63| 1446|1435|  9|   -2| 1449| 16| 14| 22| 22|  0|   0
   |15/02/10 0815|        |        |     |    |   |     |     |   |   |   |   |   |        
133|15/02/10 1015|        |        |     |    |   |     |     |   |   |   |   |   |        
   |15/02/10 1040|27 52.00|13 33.37| 1120|1107| 11|   -2| 1118| 14| 14| 22| 22|  0|   0
   |15/02/10 1122|        |        |     |    |   |     |     |   |   |   |   |   |        
134|15/02/10 1302|        |        |     |    |   |     |     |   |   |   |   |   |        
   |15/02/10 1320|27 54.68|13 24.61|  555|542 | 11|   -2|  546| 10| 10| 15| 20|  0|   0
   |15/02/10 1348|        |        |     |    |   |     |     |   |   |   |   |   |        
135|15/02/10 1525|        |        |     |    |   |     |     |   |   |   |   |   |        
   |15/02/10 1541|27 55.65|13 22.15|  356|343 | 11|   -2|  345|  8|  8| 15| 24|  0|   0
   |15/02/10 1601|        |        |     |    |   |     |     |   |   |   |   |   |        












CCHDO Data Processing Notes

Date        Contact        Data Type  Event           Summary
2010-02-21  King, Brian    CTD/BTL    submitted       format check, ctd public
            Brian King submitted these data 36 hours after making port.  
            Initial format checks passed, some expocode and filename 
            modification by S. Diggs.  CTD online, bottle data still 
            proprietary.

2012-03-21  Key, Bob       BTL        Submitted       NOT PUBLIC 
            So far as I know, all bottle data are still proprietary.
            Except for tco2 and alk (and their flags) data in this file is 
            identical to that downloaded from CCHDO on 8/3/2011 
            (a05_hy.csv.gz).  I received final carbon data from Ute Schuster 
            (Ollie Legge) on 3/16/2012. I merged new values then ran 1st QC. 
            Copy of this file sent to Brian King and Ute Schuster.  Since 
            there is no final cruise report yet, my file header is mostly 
            empty.

2012-09-20  Shen, Matthew  CTD        Website Update  NetCDF file online 
            2012-09-20
            A05 2010 ExpoCode 74DI20100106 conversion notes - Exchange to 
            netCDF
            M Shen

            Converted Exchange CTD file to netCDF using hydro.

            FORMATTED FILES
            * NetCDF CTD file created using hydro.
            * NetCDF file opened in JOA with no apparent problems

            Working directory:
            /data/co2clivar/atlantic/a05/a05_74DI20100106/original/20120919_ctd_nc_mys
  
2014-06-23  Kappa, Jerry   CrsRpt     Website Update  final pdf online
            I've placed a new PDF version of the cruise report: 
            a05_74DI20100106do.pdf
            into the  directory:      
            http://cchdo.ucsd.edu/data/co2clivar/atlantic/a05/a05_74DI20100106/.

            It includes all the reports provided by the cruise PIs, summary 
            pages and CCHDO data processing notes, as well as a linked Table 
            of Contents and links to figures, tables and appendices.

2014-06-26  Ute Schuster   TCO2/ALK   Data Status
            The tco2 and alk are free to be made public.  I cannot speak for 
            the other parameters.  The publication for the tco2 and alk data 
            is in ESSD now.  I will send published reference.

